EcoCyc Update History

This document summarizes the history of updates to EcoCyc.

**EcoCyc Knowledgebase Cumulative Statistics by Year**
	2025	2024	2023	2022	2021	2020	2019	2018	2017	2016	2015	2014	2013	2012	2011	2010	Description
Pathways	390	377	376	365	363	359	354	352	347	342	338	328	320	300	281	276	Metabolic plus signaling pathways. Excludes super-pathways.
Reactions	3325	3255	3226	3057	3017	2968	2911	2831	2728	2659	2478	2361	2284	2120	1991	1907	Includes metabolic reactions and transport reactions.
Enzymes	1744	1739	1734	1714	1703	1682	1641	1617	1593	1568	1555	1533	1505	1485	1470	1451	Number of enzymes that catalyze biochemical reactions.
Transporters	301	299	298	291	290	288	286	286	284	282	284	277	269	264	257	254	Number of transporters.
Gene product summaries	4168	4168	4170	4148	4129	4087	4070	4012	3940	3884	3852	3804	3751	3706	3710	3676	Number of gene products containing written summaries.
Genes	4541	4541	4557	4546	4545	4518	4534	4499	4496	4497	4500	4501	4501	4499	4503	4490	Number of genes, including some that have not been pinned to the DNA sequence.
Transcription Units	3767	3750	3718	3695	3697	3705	3597	3552	3555	3556	3549	3538	4510	4490	4463	3412	Number of transcription units -- includes operons and single-gene transcription-units.
Citations	45,372	44,733	44,142	42,700	41,490	39,865	37,929	36,151	34,421	32,534	30,224	27,887	25,406	23,909	22,039	20,890	Number of distinct references cited within EcoCyc.

The statistics for each year pertain to the last EcoCyc version released in that year.

These release notes omit the many small updates that occur in each release.

Release Notes for EcoCyc Version 29.1

Released on Sept 22, 2025.

**EcoCyc KB Statistics**
Pathways	390
Reactions	3,325
Enzymes	1,744
Transporters	301
Genes	4,541
Transcription Units	3,767
Citations	45,372

Improvements to the EcoCyc Database

Seven uncharacterized or partially characterized “y-genes” (ybiJ, ycfJ, ycgZ, ydgU, yhcN, yhdV and yjcB) were found to increase translation when exposed to low pH (pH 4.4) as measured by mRNA levels by RT-qPCR Schumacher et al. (2023).
A previously uncharacterized gene (yhiN) was characterized by Toubdji et al. (2024) as a ribosomal dihydrouridine synthase and renamed rdsA. Using a new method that blocks reverse transcriptase by labelling dihydrouridine with rhodoamine (called RhoRT-PCR), RdsA was found to carry out dihydrouridylation of uracil²⁴⁴⁹ in the 23S rRNA positioned at the peptidyl transferase site of the ribosome. A new reaction for 23S rRNA dihydrouridylation has been added.
We have also significantly updated the summaries of three tRNA dihydrouridine synthases, DusA, DusB, and DusC, with respect to their relative roles in tRNA dihydrouridylation.
We imported datasets of lysine lactylation sites in E. coli proteins (Dong et al. 2022) carried out by YiaC, which can lactylate lysine residues as well as acetylate lysine residues, though not always the same ones. We also found that EcoCyc was missing the lysine succinylation and associated acetylation sites from (Weinert et al. 2013) – thanks to the user who pointed this out to us! These lysine succinylation sites have also been imported. Posttranslational modifications of amino acids can be found by clicking on the Protein Features tab on protein information pages in EcoCyc.
We have also curated aspects of a large protein-protein interaction (PPI) study by Chowdhury et al. (2024) that identified interactions related to glycolysis. Several partially and uncharacterized genes were found to be involved in glycolytic enzyme interactions, such as YdiL interacting with both Eno and GapA, YjhP interacting with GpmI, and YodC interacting with PykA. Three protein-enzyme interactions (PEIs) (RpsB-AdhE, DcyD-NanE and MinE-Yccx), previously not known to regulate metabolism, were identified. A follow-up study of PEIs, defined as the connection between PPI and metabolomic networks, found three previously unknown PEI pairs are likely involved in regulation of carbohydrate metabolism (Chowdhury et al. 2025).
Ten CRISPR repeat regions were entered for MG1655 based on Brouns et al. 2008; these can be visualized within the Genome Browser as Extragenic Sites (see Legend panel popup) between genes iap and cas2
A minor project to audit and update our representation of iron-sulfur (Fe-S) cofactors was completed and a further 22 proteins are now correctly represented as Fe-S cluster binding, based on the experimental literature.
Data from Abdullah et al. (2025) reporting the experimental determination of cellular copy number for ABC transporter proteins has been added to the database.
New transport reactions have been added to the database for the import of copper mediated by the CopD-family protein copper transporter YebZ (Palmer et al. (2025)) and for the import of glutathione disulfide mediated by the ABC-family transporter complex GsiABCD (Knoke et al. 2025).
We incorporated evidence and references from RNA-seq and ChIP-exo experiments reported in Jang et al. (2024), supporting the association between 56 promoters and the sigma factor RpoS that activates them.

Release Notes for EcoCyc Version 29.0

Released on April 10, 2025.

**EcoCyc KB Statistics**
Pathways	378
Reactions	3,272
Enzymes	1,742
Transporters	299
Genes	4,541
Transcription Units	3,766
Citations	44,974

EcoCyc Curation Highlights

New functions have been determined for several genes, including five y-genes with previously unknown or putative functions:

The structure and function of the EF-P paralog YeiP, now called EfpL, has been characterized and found to be involved in translational stress response through rescuing ribosome stalling at polyproline (XP(P)X)-containing proteins as well as acting as a sensor for the metabolic state of the cell via lysine acylation (Sieber et al).
YoaC, YfeS, and YlaC were curated for their resistance to boric acid exposure based on mutational and complementation assays (Çöl et al).
YgaV’s regulatory interactions and role in iron uptake in response to intracellular H₂S have been determined, confirming its role as a transcription factor. As a result, its name has been changed from 'putative DNA-binding transcriptional regulator YgaV' to 'DNA-binding transcriptional regulator YgaV' (Nonoyama et al).
New oxidative and high heat stress-related tRNA^Tyr methylation capability has been determined for RsmF, which previously was only known to carry out m⁵C modification of the 16S ribosomal RNA (Valesyan et al).
Using single-cell RNA-seq analysis Yan et al discovered that PdeI functions as a cyclic di-GMP synthase rather than a phosphodiesterase.
Rex et al was able to rescue the ΔplsX ΔplsY synthetic lethality phenotype and determine that together these two proteins play a role in the fine-tuned regulation of lipid production and homeostasis of the cell envelope.

Three new reactions have been added to the important DNA repair enzyme, UvrABC excision nuclease, significantly improving the representation of its activity.

Regulation-related curation:

In addition to our ongoing curation of transcriptional regulation and regulation of small RNAs, we added five regulatory interactions involving the protein CsrA, which regulates the translation of a variety of genes, including many related to carbohydrate metabolism (Gorelik et al).
We also added further details to the RNA regulatory factors that control expression of the TonB-dependent BtuB membrane transporter responsible for the import of corrinoids such as vitamin B₁₂. Bastet et al have furthered our understanding of the regulation of btuB translation by two small RNAs and a riboswitch. A SmartTable listing all 11 riboswitches currently represented in EcoCyc can be easily accessed on the website under the Tools → SmartTables → Special SmartTables menu.
Additionally, a new mechanism of regulation between the transcription factors (TFs) ZntR and Zur has been described in their corresponding summaries. It is noted that non-metallated ZntR (ZntR_apo) enhances the dissociation of Zur from DNA (Chakraborty et al).
We have added information about a new conformation for the TF H-NS that occurs when the metabolite 2-C-methyl-D-erythritol-2,4-cyclodiphosphate (MEcPP) binds to H-NS when it is not bound to DNA, thus preventing the binding and repression of the fimE promoter by this TF (Guo et al). This is the first histone-like TF in EcoCyc for which the binding of a metabolite has been reported.
We have also curated the regulatory interactions of the transcription factor Nac, based on RNA-seq and ChIP-exo experiments reported in Park et al.

Release Notes for EcoCyc Version 28.5

Released on December 11, 2024.

**EcoCyc KB Statistics**
Pathways	377
Reactions	3,255
Enzymes	1,739
Transporters	299
Genes	4,541
Transcription Units	3,750
Citations	44,733

Improvements to the EcoCyc Database

We have added a dataset on E. coli protein turnover rates from Gupta et al (2024) to EcoCyc. Data are present on gene pages in the Summary tab under the heading Gene Product Active Half Life.

We have added links from EcoCyc gene pages to FoldSeek, which performs structure-similarity searches against the AlphaFold structural database and can find distant homology relationships that may provide clues regarding the function of a protein. From gene pages, see the right-sidebar Operations menu, and click on "Search the sequence in FoldSeek". Once the FoldSeek page appears, click Search on the bottom left.

We are now providing in the Unification Links panel on gene information pages links to the SHIGEN National BioResource Project for genes that have knockout mutant strains in the KEIO and/or ASKA collections.

Whole-Cell Model (WCM) Summary Page: A new page was added to EcoCyc, which provides a global overview of the computed data sets that result from the collaboration with Standford's Whole-Cell Model effort. This summary can be found in the Tools menu under "Analysis". For four object types, convenient buttons are provided for creating SmartTables that are populated with the datapoints from the model under a given growth condition. This simplifies projecting the data points onto our Omics displays.

EcoCyc Curation Highlights

The riboswitch-controlled transporter Alx has been characterized by Sharma et al. (2024) as a "low-activity" manganese ion exporter with a role in Mn²⁺ homeostasis at alkaline pH.

The function of an uncharacterized gene, ycgM, was determined to be a metabolite repair enzyme with oxaloacetate (OAA) tautomerase activity that removes the enol-OAA inhibition of succinate:quinone oxidoreductase (SDH) within the TCA cycle I (Zmuda et al. 2024).

We have modified and created new E. coli tRNA processing pathways, such as the polycistronic tRNA processing III and IV pathways, and superpathways of both polycistronic and monocistronic tRNA processes.

Bacterial AsmA-like proteins are structurally similar to a recently described family of eukaryotic bridge-like lipid transfer proteins. E. coli K-12 contains 6 AsmA-like paralogs including: the membrane-anchored protein YdbH now annotated as a putative intermembrane phospholipid transport protein based on a recent report by Kumar et al. (2024) providing evidence that YdbH and lipoprotein YnbE interact to form a bridge connecting the inner and outer membrane of the cell.

The kdpD-encoded histidine kinase has been reannotated as a serine histidine kinase. KdpD's atypical serine kinase activity mediates post-translational inhibition of the high-affinity K⁺-transporting P-type ATPase via phosphorylation of the KdpB subunit.

Regulatory interactions (RIs) of DNA-binding transcriptional dual regulator NtrC were annotated based on RNA-seq and ChIP-exo experiments reported in Park et al. (2023).

Release Notes for EcoCyc Version 28.1

Released on August 12, 2024.

**EcoCyc KB Statistics**
Pathways	375
Reactions	3,238
Enzymes	1,736
Transporters	298
Genes	4,557
Transcription Units	3,748
Citations	44,535

Improvements to the EcoCyc Database

EcoCyc now captures the level of functional characterization for each gene within Escherichia coli K-12 substr. MG1655 (excluding pseudogenes and phantom genes). Gene characterization levels can be found on gene information pages near the bottom of the summary tab with the prefix "Characterization". Characterizations are searchable in Tools → Search → Search Genes, Proteins, or RNAs. Characterization levels will be updated as new experimental evidence is curated, and can provide important information for planning new research directions.

Genes are assigned one of three characterization categories:

Well-Characterized for genes with extensive experimental characterization that provided detailed knowledge of both its molecular function and its mechanism for affecting cell phenotype, i.e., the biological process in which the gene product is involved. For example, glucose-6-phosphate dehydrogenase (G6PDH), encoded by zwf, is the first enzyme of the pentose phosphate pathway and is known to provide a large fraction of the NADPH needed for anabolism.

Uncharacterized genes are those for which little or no functional information is known, either experimentally or through sequence analysis. For example, their cellular location may have been determined, such as the DUF1656 domain-containing protein AaeX that resides in the inner membrane, but little else is known.

Partial characterization level is assigned to genes that fall in between well-characterized and partial. We may have experimental knowledge of either their molecular function or of the cellular process in which a gene is involved, but not both. A gene could also be assigned to the Partial category if it exhibits sequence similarity to a well-characterized or partially characterized protein, or a Pfam hit to a domain associated with a known function. An example of a gene within this category is the putative oxidoreductase, Fe-S subunit YgfK with experimental evidence for its NADPH:O₂ oxidoreductase activity but without knowledge as to which cellular process it contributes.

As part of implementing these new characterization-level categories, we manually made significant updates to well over 100 Gene Ontology (GO) term annotations and added evidence codes for dozens of pathways, such as L-ascorbate degradation II (bacterial, aerobic) pathway.

Curation Highlights to EcoCyc for This Release

New information from Huang et al. 2023 has been curated on the mRNA degrading RNase YicC based on crystallographic and mutant studies indicating its inverted funnel-shaped dimer of trimer structure and identification of its active site region, catalytic residue, RNA-binding groove residues and its RNA cleavage consensus motif.

The minimally characterized CP4-57 prophage YpjF-YfjZ toxin-antitoxin (TA) system was shown in a single-cell transcriptomic study to be transcribed as part of the lfgABCDE operon under H₂O₂ oxidative, acidic and heat stress conditions. However, the transcription was repressed by the MqsA antitoxin of the MqsRA TA system which also funcations as a DNA-binding transcriptional repressor, but the effect occurred to only a subset of cells within the entire population (Fernández-García et al. 2024).

Regulatory interactions for a variety of transcription factors were annotated:

YegW and YdaT, which were previously considered putative.
Fur based on RNA-seq and ChIP-seq experiments reported in Hou et al. 2023 and RNA-seq and ChIP-exo experiments reported in Seo et al. 2014.
Cra from ChIP-exo and RNA-seq analyses reported in Kim et al. 2018.
KdpE, ZraR, and CpxR from RNA-seq and ChIP-exo experiments reported in Choudhary et al. 2020.

Some of these regulatory interactions were further supported by identifying sequences similar to the consensus DNA binding site for each transcription factor.

Release Notes for EcoCyc Version 28.0

Released on April 02, 2024.

EcoCyc Modeling Tab Contains Reaction Flux Predictions from E. coli Whole Cell Model

This version of EcoCyc contains additional predictions of reaction fluxes from computer simulations of an E. coli cell from the E. coli whole-cell modeling project. While the Modeling Tab was first introduced for gene/protein pages for version 26.0, now additional reaction flux predictions are shown on reaction pages. For this, we added a Tab structure to the reaction pages.

Highlights of EcoCyc Database Improvements

EcoCyc contains the equivalent of 4,029 textbook-pages of mini-review summaries.

Information from more than 200 publications have been added for this release, which included improvements to various transcription units. Some examples of improvements include:

The mRNA-degrading endoribonuclease YicC had a structure published that identified the RNA cleavage consensus sequence as GUG and that it exists as a funnel-shaped hexamer (Huang et al. 2023).
Lee et al. report further characterization of the SoxR-reducing system, suggesting that RsxABCDGE, RseC, and ApbE form a complex that uses NAD(P)H to reduce the SoxR iron-sulfur cluster and a new reaction reflecting this activity has been added to the database.
We modified 12 terminators from Rho-independent to Rho-dependent based on the publication by Dar and Sorek, 2018.
We added 22 new Transcription Units (TUs) for small protein coding genes based on their genomic location; they were located on the opposite chromosome strand from the flanking genes or operons. Examples include: yecV, yfiS, yqfH, and ysdE. Furthermore, we included 13 new genes in existing transcription units because they are situated between the genes of the previously annotated TUs.

Release Notes for EcoCyc Version 27.5

Released on December 08, 2023.

**EcoCyc KB Statistics**
Pathways	376
Reactions	3226
Enzymes	1734
Transporters	298
Genes	4557
Transcription Units	3718
Citations	44,142

Improvements to the EcoCyc Database

EcoCyc contains the equivalent of 4,012 textbook-pages of mini-review summaries.

For this release of the EcoCyc database, we have curated new pathways and reactions, new functions for existing proteins and small RNAs, and new regulatory interactions:

In order to better represent the various ways that tRNAs undergo nuclease-based processing, we have created 3 new pathways: monocistronic tRNA processing I, II, and III. The new pathways represent how monocistronic tRNA genes are processed differently from each other and from polycistronic tRNA genes for how the ribonuclease enzymes cleave the 5’ and 3’ extensions to yield the uncharged tRNA ready for addition of its cognate amino acid.

Yang et al. have characterized LptM (formerly YifL) as a new player in the lipopolysaccharide transport (Lpt) pathway; LptM interacts physically with the outer membrane LPS translocon and promotes its assembly by the BAM complex.

A new transport function has been added to ThrP (formerly YifK), characterized by Khozov et al. as a PMF-dependent L-threonine and L-serine transporter.

The function of ABC transporter CydDC has long been debated. Using a combination of biochemical, structural and computational methods Wu et al. have now confirmed its role as a heme transporter that is required for maturation of cytochromes bd-I and bd-II.

We curated a publication of an integrative study reporting data from ChIP-exo and RNA-seq methodologies for the transcription factor Fur (Gao et al.): 56 new regulatory interactions for Fur were added and 67 were updated. Most of the regulatory interactions from this publication have been annotated, and the remaining ones that require further analysis will be available in the next release.

Additional curation resulted in summary updates for 33 transcription factors, 3 sigma factors (RpoS, RpoH, and RpoD) and 4 small regulatory RNAs (DsrA, RyhB, and OxyS).

Release Notes for EcoCyc Version 27.1

Released on August 28, 2023.

**EcoCyc KB Statistics**
Pathways	372
Reactions	3212
Enzymes	1732
Transporters	297
Genes	4557
Transcription Units	3705
Citations	43,542

Improvements to the EcoCyc Database

Several new pathways and reactions were added:

Misacylated tRNA editing pathway: Aminoacyl-tRNA synthetases (AARS) join amino acids with their cognate tRNAs in high fidelity reactions that define the genetic code. Most of these enzymes are specific for a particular amino acid. The reaction starts by activation of the amino acid in the AARS active site to an adenylated form before being transferred to the 2' or 3' hydroxyl group of the terminal ribose of the tRNA. The fidelity required to ensure proper protein biosynthesis is estimated to be 1 in 3300. However, 10 of the 24 AARS families cannot achieve the tolerable level of fidelity. To ensure proper protein synthesis, two "editing" mechanisms by different AARSs exist, such as:
- a pre-transfer editing reaction
- a post-transfer editing reaction
All of the aminoacyl-tRNA synthetases that have editing capabilities and the mischarged aminoacyl-tRNA deacylase (YeaK) reactions were added as well as text to their summaries to describe their editing activities.
A new pathway (poly-β-1,6-N-acetyl-D-glucosamine (PNAG) biosynthesis) describes the biosynthesis of PNAG, an exopolysaccharide that is a key component of the biofilm matrix of many pathogenic bacteria.
The new glycine degradation pathway describes how bacteria can convert glycine to pyruvate and ammonium, satisfying the need for both carbon and nitrogen.
The thiamine diphosphate salvage V pathway describes the conversion of 5-(2-hydroxyethyl)-4-methyl-1,3-thiazole-2-carboxylate, a degradation product of an intermediate in thiamine diphosphate biosynthesis, back to thiamine diphosphate.

Significant upgrades to major nucleotide binding and cell division proteins:

The RNA-binding protein Hfq is a major global regulator of cell physiology. With the addition of information from 88 publications we have updated the summary to include descriptions of its many functions within the cell. The regulatory aspects of Hfq have expanded beyond its role as a post-transcriptional regulatory factor of small RNAs and their mRNA targets to include roles in ribosome biogenesis, tRNA processing and possibly regulation of DNA replication and compaction. Additional protein-protein and protein-lipid interactions of Hfq also have been documented.
The bacterial condensin protein complex, MukBEF, an ATPase-powered molecular machine, is involved with the global organization of E. coli’s chromosome and its segregation during cell division. The summaries of this complex and its different subunits have also been upgraded with information from 24 publications to highlight their distinct roles in the function of chromosome organization.
The cell division protein FtsZ is a highly conserved protein essential to forming the Z-ring site where cell division will occur. Addition of information from 23 publications rounds out the information about this important “wrangler” of proteins.
Another important wrangler of proteins involved in assembling the divisome is FtsA, which had experimental information from 17 articles added to its summary.

Additional upgrades of note include:

Modification of the DNA binding consensus sequence of the FlhDC DNA-binding transcriptional dual regulator: two conserved motifs that were previously considered independent sites are now part of a single site.
Extensive editing of the Suf system components, particularly L-cysteine desulfurase SufS, which went from 4 wrong reactions to two correct ones.
Clarifying that each of the following small Long Direct Repeat (LDR) toxic polypeptides (LdrA, B, C, and D) are part of their own toxin-antitoxin pair.
Significant changes were made to the commentary of two fatty acid beta-oxidation complexes (aerobic FAO complex and anaerobic fatty acid β-oxidation complex), and reactions were assigned.
Extensive editing was done on the carbon-phosphorus lyase system, the transcription termination factor Rho and L-cysteine desulfidase.

Release Notes for EcoCyc Version 27.0

Released on April 12, 2023.

**EcoCyc KB Statistics**
Pathways	367
Reactions	3073
Enzymes	1717
Transporters	292
Genes	4556
Transcription Units	3305
Citations	42,963

Highlights of EcoCyc Database Improvements

Multiple new genes, including two new proteins and several small RNAs, and new functions for existing proteins have been added and curated with summaries for each new gene product and regulatory interactions for the small RNAs with functions identified.

New genes:

The new small protein, XtpA, is a putative transcription regulator of genes involved in aminoglycoside antibiotic resistance through regulation of the small regulatory RNA GcvB.
Another new small protein, SpfP, was characterized and found to tightly bind and regulate the CRP-cAMP transcription factor. It is encoded by the same transcriptional unit as spf which codes the small regulatory RNA Spot 42.

New small RNAs added to Ecocyc:

FimR2, reported by Raad et al. to be a significant regulator of gene expression in stationary phase.
GlnZ was found to modulate a variety of genes under low nitrogen conditions.
aMEF stimulates expression of the type II mazEF toxin-antitoxin system.
StfZ represses the transcriptional regulator FtsZ affecting other genes involved in cell division.
AsflhD represses the transcriptional regulator FlhD affecting mobility.
three small antisense RNAs were identified but no function assigned: (AsCRP, AsompR, AsphoP).

New gene functions curated:

the 5′-3′ exoribonuclease RNase AM encoded by rnmhas been found to have FAD-capped RNA decapping (deFADding) and degradation functions.
A new NAD(P)H oxidation reaction that produces hydrogen peroxide and superoxide radical under aerobic conditions was ascribed for SthA.
a new function added to the outer membrane protein PqqU (formerly yncD), characterized by Hantke et al. as a TonB-dependent transporter of the redox cofactor pyrroloquinoline quinone.
the function of YdiJ has been characterized as a D-2-hydroxyglutarate dehydrogenase (D2HGDH) than can metabolize the D-2-hydroxyglutarate (D-2-HGA) produced by SerA.
a new function for ZapG (also called LapD) indicates it plays a role in cell envelope homeostasis by possibly regulating LpxC levels and aiding in MsbA-mediated LPS translocation.
the iron-sulfur cluster repair protein YtfE has a new function as a nitric oxide (NO)-generating nitrite reductase.

Other updates include:

Confirmation that FimZ is a transcription factor by Ogawa et al., and four regulatory interactions were annotated for it.
60 new regulatory interactions of the transcription factor CpxR as a result of qRT-PCR, cpxR knockout mutant, DNA binding analysis and computational predictions; see Zhao et al.
4 new inactive conformations of the transcription factor AcrR were included.
changes to evidence codes and the evidence ontology resulting in 14 new evidence codes and 6 reclassified ones that are now used in curation. These evidence codes refer to specific experimental methodologies, both classical and high throughput methods.

Release Notes for EcoCyc Version 26.5

Released on December 13, 2022.

**EcoCyc KB Statistics**
Pathways	365
Reactions	3057
Enzymes	1714
Transporters	291
Genes	4546
Transcription Units	3695
Citations	42,700

Highlights of EcoCyc Database Improvements

We have curated the previously uncharacterized protein, YmdF, based on recent work by Kaleta et al. 2022, which indicates this protein is likely involved in motility, biofilm formation and susceptibility to a variety of antimicrobial agents.
We also curated regulatory interactions for YiaU and YgfI confirming their role as transcription factors, and their regulation of specific processes was described in the summaries.
In this release summaries were added for 58 putative transcription factors that include properties such as their protein family, the domain for DNA binding, some putative processes that they regulate, and how they are regulated (Duarte-Velázquez et al. 2022).
We included five new inactive conformations of transcription factors: AcrR-3,6-diaminoacridine (proflavin), AcrR-rhodamine 6G (RDG), Cbl-thiosulfate, MurR-N-acetyl-D-glucosamine-6-phosphate and AraC-D-fucose.
New DNA-binding consensus sequences for five sigma factors were added.
New structural insights into several proteins involved in cell division were curated, including FtsQBL and FtsA-FtsZ, as well as additional structural characterizations for PsuK, IaaA, and GyrA.

Release Notes for EcoCyc Version 26.1

Released on August 24, 2022.

**EcoCyc KB Statistics**
Pathways	365
Reactions	3055
Enzymes	1714
Transporters	291
Genes	4546
Transcription Units	3694
Citations	42,357

Highlights of EcoCyc Database Improvements

We have updated curation of a formerly uncharacterized protein and functional RNA, respectively:
- SmrB, based on a report by Saito et al who have shown that it is a ribosome rescue factor which cleaves mRNAs upstream of stalled ribosomes and triggers tmRNA-mediated ribosome rescue.
- Raina et al have characterized the dual-function RNA, AzuCR, which is implicated in the modulation of carbon utilization. AzuCR acts as a base-pairing regulatory RNA and encodes the 28 amino acid small membrane protein, AzuC.
We have added
- A new transport reaction for the divalent metal ion transporter ZupT based on recent characterization of its asymmetric binuclear metal center by Roberts et al.
- The consensus sequences of 125 transcription factors, which were determined in Baumgart et al. We also added to the database the first regulatory interactions for the transcription factors YieP, YeiE, and YafC, which were determined by Gao et al.

Release Notes for EcoCyc Version 26.0

Released on April 13, 2022.

**EcoCyc KB Statistics**
Pathways	364
Reactions	3052
Enzymes	1713
Transporters	291
Genes	4545
Transcription Units	3696
Citations	41,925

EcoCyc Modeling Tab Contains Predictions from E. coli Whole Cell Model

This version of EcoCyc contains predictions from computer simulations of an E. coli cell from the E. coli whole-cell modeling project. The aim of the project is to build a computational representation of an E. coli cell that fully captures the dynamics of every known molecule within an E. coli cell, using a heterogeneous set of parameters that are curated from decades of research conducted on this model microbe. The model ties together multiple submodels that each represent a particular domain of an E. coli cell, using the mathematical framework that is most appropriate for the given domain. Macklin et al., 2020 provides more details on how the model was constructed and how its outputs were validated.

The predictions are present on the new Modeling tab on EcoCyc gene pages (example). The Modeling tab contains predictions of the cellular copy numbers for the mRNA and protein product of that gene under three conditions of E. coli growth: aerobic and anaerobic growth under M9 medium with 0.4% glucose, and aerobic growth under M9-derived rich medium. The presented data were calculated by running a batch of computer simulations of an E. coli cell.

Through a collaborative effort between the EcoCyc team and the whole-cell modeling project team, we have built a pipeline that allows the whole-cell model to import a subset of the required input parameters, which includes genome annotations, RNA/protein sequences, metabolic reaction networks, transcription factor networks, and reaction stoichiometries, directly from the latest release of the EcoCyc database. With each updated release of EcoCyc, a new batch of simulations is initialized with the newly imported parameters from EcoCyc, and the outputs from the updated simulations are reported on the modeling tabs for EcoCyc gene pages.

The whole-cell model simulates the dynamics of individual cells, which allows it to capture how stochastic processes can lead to heterogeneity between cells that are grown under the same conditions. Thus, in addition to the mean values that are taken from the average of all simulated cells, we are also able to report the standard deviations of each value between the simulated cells, which are presented as error terms in the provided data.

The latest released version of the model code can be accessed for a closer look into the inner workings of the whole-cell model. Please note that the Modeling tab data were generated from the latest working version of the model that contains further updates that may lead to output values that are different from the released version.

Highlights of EcoCyc Database Improvements

We have expanded the corpus of E. coli literature available for searching within EcoCyc to 48,189 abstracts plus 38,269 full-text articles (see Tools → Search → Search Full Text Articles).
We have added one new pathway: NiFe(CO)(CN)₂ cofactor biosynthesis
Sellner et al. and Junkermeier et al. have described the production of a novel surface-associated polysaccharide that is exploited as a phage receptor in both pathogenic and non-pathogenic E. coli. The inner membrane cyclic di-3',5'-guanylate-activated glycosyltransferase NfrB, the outer membrane protein NfrA, and a periplasmic protein YbcH are all implicated as components of a secretion system responsible for biosynthesis and export of the uncharacterized sugar.
The first regulatory interactions for the transcription factors YfeC, YidZ, YciT and YgbI were annotated in EcoCyc. These interaction were determined by Gao et al. using RNAseq and ChIP-exo analysis.
The alternative sigma factor RpoN was described by Shimada et al. as a transcriptional repressor of Sigma70 promoters in the absence of enhancers.

Release Notes for EcoCyc Version 25.5

Released on December 15, 2021.

**EcoCyc KB Statistics**
Pathways	363
Reactions	3017
Enzymes	1703
Transporters	290
Genes	4545
Transcription Units	3697
Citations	41,490

Highlights of EcoCyc Database Improvements

Kim et al. provide evidence that fdrA encodes the orphan enzyme oxamate carbamoyltransferase in anaerobic allantoin degradation.
Rodionova et al. report that PunC (formerly YdhC) is a purine nucleoside transporter which can support growth under nitrogen-limiting conditions.
The first experimental evidence for the function of the transcription factors AaeR and PunR (formerly named YdhB) was published by Shimada et al. and Rodionova et al., respectively.
Based on data by Pietrzyk-Brzezinska and Cociurovscaia, we added the homodimer form as well as the inactive ligand-bound forms of the transcription factor RcdA to EcoCyc.

Release Notes for EcoCyc Version 25.1

Released on August 5, 2021.

**EcoCyc KB Statistics**
Pathways	362
Reactions	3010
Enzymes	1701
Transporters	290
Genes	4523
Transcription Units	3697
Citations	41,037

Highlights of EcoCyc Database Improvements

We have added two new pathways:
- L-aspartate degradation II (aerobic)
- L-aspartate degradation II (anaerobic)
Three existing metabolic pathways were modified based on new information in the literature:
The summaries for 29 transcription factors and 6 sigma factors were updated.

Release Notes for EcoCyc Version 25.0

Released on May 20, 2021.

**EcoCyc KB Statistics**
Pathways	360
Reactions	2995
Enzymes	1692
Transporters	288
Genes	4523
Transcription Units	3697
Citations	40,472

Highlights of EcoCyc Database Improvements

Enzyme I (EI) of the bacterial phosphotransferase system is known to form clusters that localize to the cell poles. Szoke et al. now report that EI is recruited to the poles by a formerly uncharacterized protein, TmaR. Polar localization of both proteins is dependent on tyrosine phosphorylation and TmaR-mediated polar sequestration, and release of EI serves to regulate sugar metabolism.
We added new conformations for some transcription factors, including dimers for the transcriptions factors FrlR (Graf von Armansperg et al.) and DgoR (Arya et al.) as well as the new inactive conformations FrlR-fructoselysine-6-phosphate (Graf von Armansperg et al.) and MprA-salicylate (Arshad et al.).
Summaries for four sigma factors and 29 transcription factors were updated.

Release Notes for EcoCyc Version 24.5

Released on January 7, 2021.

**EcoCyc KB Statistics**
Pathways	359
Reactions	2968
Enzymes	1682
Transporters	288
Genes	4518
Transcription Units	3705
Citations	39,865

Highlights of EcoCyc Database Improvements

New players in cell division continue to be discovered. Yahashiri et al. characterized the function of YedR, a non-essential cell division protein that localizes to the septal ring, and renamed it DrpB.
Based on a list of small RNAs published with a recent review by Hör et al., we have updated the summaries and regulatory interactions of most small RNAs encoded by E. coli K-12.
Galego et al. showed that the phosphorylated form of the transcription factor BolA is essential for its activity. All of the previous regulatory interactions of BolA are now linked to the active BolA-phosphate form.

Release Notes for EcoCyc Version 24.1

Released on September 8, 2020.

**EcoCyc KB Statistics**
Pathways	359
Reactions	2965
Enzymes	1681
Transporters	287
Genes	4539
Transcription Units	3716
Citations	39,572

Highlights of EcoCyc Database Improvements

To improve the other E. coli PGDBs in BioCyc (meaning those PGDBs describing strains other than K-12 MG1655), we propagated gene and protein annotations from EcoCyc to the 480 other E. coli PGDBs in BioCyc. On average, each of those PGDBs received updates to 2535 gene or proteins. The information we propagated included gene and protein names, protein complex assignments, and the reactions assigned to each protein. Propagation was performed from a gene or protein in EcoCyc only if it had experimental support, and only if the existing annotations for the target gene or protein did not have experimental evidence. The target gene/protein is a computed ortholog of the source gene/protein. The propagation event was recorded in a "history entry" for the target gene/protein that is displayed on the gene/protein page and explains what information was propagated.

The following improvements were made to EcoCyc itself.

New functions were added to the membrane proteins YihG, characterized as a lysophosphatidic acid acyltransferase which affects swimming motility, and DigH (formerly YddW), a glycosyl hydrolase that cleaves denuded peptidoglycan during cell division.
Bradley et al. have reported that YcaQ is an alkylpurine DNA glycosylase involved in the repair of interstrand DNA crosslinks.
Kentache et al. and Bell et al. (and references therein) have elucidated the function of NanY in E. coli. The enzyme is involved in the utilization of dehydrated forms of N-acetylneuraminate as a source of carbon and energy. The gut bacterium Ruminococcus gnavus is able to convert host-derived mucins to 2,7-anhydro-α-N-acetylneuraminate, which appears to be imported and utilized by E. coli.
A total of 1009 new regulatory interactions from high throughput experiments have been uploaded for the following transcription factors:
- ArcA from Federowicz et al.
- ArgR from Caldara et al. and Cho et al.
- CsiR from Aquino et al.
- FNR from Federowicz et al.
- Lrp from Cho et al. and Kroner et al.
- Nac from Aquino et al.
- OmpR from Shimada et al.
Promoters were modified to be consistent with the definition in Mejia-Almonte et al.. When RNA polymerase initiates transcription using a different sigma factor, even if using the same transcription start site (TSS), we now consider it a different promoter. As a consequence, we generated new promoters (and consequently new transcription units), each with a different sigma factor, that share the same TSS.

Release Notes for EcoCyc Version 24.0

Released on May 14, 2020.

**EcoCyc KB Statistics**
Pathways	355
Reactions	2934
Enzymes	1655
Transporters	286
Genes	4534
Transcription Units	3599
Citations	38,924

Highlights of EcoCyc Database Improvements

Bulk Import of Acetylation Data: We have loaded five new acetylome datasets into EcoCyc, which indicate specific lysine positions in proteins that have been subject to acetylation. Acetylation of lysines is implicated in various types of regulation.
These new data are recorded and displayed as EcoCyc protein features. When visiting a protein page, clicking on the tab "Protein Features" will show the amino acid sequence and a table of annotations, which indicate specific sites or regions, that have evidence for a variety of functional properties. The newly added data have comments starting with "N6-acetyllysine site ...". One example can be found here.
Prof. Alan Wolfe (Loyola University Chicago) has guided us in integrating these data, expanding the lysine acetylation to include studies by Kuhn et al., 2014; Schilling et al., 2015; and Christensen et al., 2018. Some of the acetylations are enhanced during growth in excess carbon or mutants that accumulate acetyl phosphate, supporting the hypothesis that they are primarily due to acetyl phosphate-dependent non-enzymatic acetylation. Other acetylations are enhanced by overexpression of five lysine acetyltransferases (YjaB, YiaC, RimI, PhnO, and YfiQ [also known as Pka or PatZ]).
In summary, 914 proteins were updated by data showing at least one lysine that can be acetylated. The total count of distinct lysine positions in the proteome for which acetylation data was added is 2065.
In the 1970's, an enzyme that catalyzed the transfer of the aminocarboxypropyl group from S-adenosylmethionine to the N3 position of uridine within tRNAs was identified. However, the identity of the gene encoding this enzyme remained unknown. Recently, Takakura et al. and Meyer et al. both identified tapT (formerly known as yfiP) as the responsible gene.
We have updated curation of the AlkB nucleic acid repair protein following a study by Reichle et al. identifying 2-thiocytidine-modified tRNA as a target of methylation damage and demonstrating AlkB-mediated repair.
The representation of cytochrome bd-1 oxidase has been updated to include a previously unknown accessory subunit, CydH, identified in the cryo-EM structure reported by Safarian et al..
Data from four high-throughput analyses, including RNA quadruplex structures (Shao et al.), RNA polymerase-binding RNA aptamers affecting gene expression (Magan et al.), the kinetics of gene expression after σ^E induction (Lacoux et al.), and the location of mRNAs inside the cell (Kannaiah et al.) has been incorporated into summaries.

Highlights of Website Improvements

Improvements have been made to pathway layouts and depiction of pathways spanning multiple cellular compartments, as well as to display of chemical structures.
The organism selector has new options for filtering the set of organisms displayed, such as to see genomes from the NCBI representative genomes set.

Release Notes for EcoCyc Version 23.5

Released on December 18, 2019.

**EcoCyc KB Statistics**
Pathways	354
Reactions	2911
Enzymes	1641
Transporters	286
Genes	4534
Transcription Units	3597
Citations	37,929

Highlights of EcoCyc Database Improvements

Three groups, Mohni et al., Thompson et al. and Wang et al., have identified and characterized YedK as a genome maintenance protein which forms covalent cross-links to abasic (apurinic/apyrimidinic) (AP) sites in ssDNA. YedK is proposed to sense and bind to AP sites at stalled replication forks, forming a stable structure that shields these lesions from endonucleases and error-prone polymerases.
The new complex CRP-Sxy, which regulates some genes related to DNA uptake (natural competence), was added to the database. According to Søndberg et al., the CRP-Sxy complex recognizes a DNA-binding site that has an asymmetric organization: it has two distinct half-sites, one of which is similar to the canonical CRP-cAMP DNA-binding site, whereas the other half-site is less conserved.
Turnbull and Gerdes have identified the HicB protein, known as the antitoxin of the HicA-HicB toxin-antitoxin system, as a transcription factor that autoregulates the transcription of the hicAB operon.

Highlights of Website Improvements

BLAST search: We made several improvements to BLAST searches including adding the ability within the BLAST search page to select a different PGDB for searching other than the current PGDB.
Favorites SmartTable A "Favorites" SmartTable is now defined for each user. It is accessible through the "Add to SmartTable" button near the top of many pages.

Release Notes for EcoCyc Version 23.1

Released on September 19, 2019.

**EcoCyc KB Statistics**
Pathways	354
Reactions	2896
Enzymes	1641
Transporters	286
Genes	4540
Transcription Units	3595
Citations	37,630

We propagated extensive information from EcoCyc to the BioCyc database for E. coli CFT073. For more details see the BioCyc release notes.

Highlights of EcoCyc Database Improvements

A new pathway, D-gulosides conversion to D-glucosides, was discovered by Mukherjee et al..
Ubiquinol biosynthesis has been the focus of several discoveries. Hajj Chehade et al. have shown that enzymes and accessory factors of the aerobic ubiquinol-8 biosynthesis pathway form a soluble metabolon that protects the hydrophobic polyisoprenyl tail of the pathway intermediate from the aqueous environment of the cytoplasm. Pelosi et al. have discovered an oxygen-independent pathway of ubiquinol biosynthesis that requires UbiT, UbiU, and UbiV.
A new function has been added to the periplasmic protein MepK (formerly YcbK), characterized by Chodisetti et al. as an L,D-endopeptidase which cleaves the cross-bridge between meso-diaminopimelic acid residues (mDAP-mDAP or 3-3 cross-links) in peptidoglycan.
The function of DgoT, a predicted D-galactonate transporter, has been confirmed. Leano et al. have shown that DgoT is an electrogenic galactonate:proton symporter which mediates uptake of the sugar to support growth.
Sakai et al. and Lauhon have identified new proteins — TrhO, TrhP, and YfhL — that are required for generating chemical modifications in the wobble position of certain tRNAs.
The PyrR transcription factor is the response regulator component of the PyrSR Two-Component Signal Transduction System. Miyake et al. showed that PyrSR regulates at least eight novel targets, including yjhX, in the presence of a high concentration of pyruvate.
The summary for ppGpp was significantly extended, based on results obtained by Sanchez-Vazquez et al.. Those authors found that ppGpp alters expression of more than 750 transcripts, most of which had not been identified as regulated by ppGpp in previous studies. Sequence features of ppGpp-regulated promoters were also identified. Roghanian et al. showed that ppGpp coordinates cell growth in response to imbalances in outer membrane biogenesis and adenosine ribonucleotide synthesis. However, Gray showed that DksA regulates the production of inorganic polyphosphate (polyP) without the help of ppGpp.

Release Notes for EcoCyc Version 23.0

Released on April 29, 2019.

**EcoCyc KB Statistics**
Pathways	352
Reactions	2852
Enzymes	1619
Transporters	286
Genes	4501
Transcription Units	3553
Citations	36,585

Highlights of EcoCyc Database Improvements

The L-lysine degradation I pathway was significantly updated and extended. Knorr et al. elucidated the functions of several new enzymes in the pathway and showed that the pathway is utilized as an adaptation to stationary phase growth conditions.
A new pathway, cadaverine biosynthesis, now shows the use of lysine decarboxylation to cadaverine as a mediator of acid resistance (AR4).
Singh et al. have investigated the transcriptional regulator DgoR. The amino acid residues within DgoR that are important for recognizing the inverted repeat binding sites were identified. The effector D-galactonate was shown to induce a conformational change in DgoR, resulting in derepression of the dgoRKADT operon.
We added 129 regulatory interactions from high-throughput analysis by Aquino et al. for the Nac transcriptional dual regulator.

Highlights of Website Improvements

A new metabolomics data analysis tool called "pathway covering" computes a minimal set of metabolic pathways that "cover" (explain) a provided set of metabolites. See Analysis → Metabolomics Pathway Coverage.

Highlights of Desktop Software Improvements

The desktop version of Pathway Tools now enables users to issue queries across multiple organism databases in one operation. For example, a user could create organism databases for a set of microbiome organisms, and then issue queries to find what genes, pathways, or metabolites exist across that set of organisms.
The EcoCyc metabolic model now supports Flux Variability Analysis, which computes the minimum and maximum fluxes that each reaction can take on.

Release Notes for EcoCyc Version 22.6

Released on December 12, 2018.

**EcoCyc KB Statistics**
Pathways	352
Reactions	2831
Enzymes	1617
Transporters	286
Genes	4499
Transcription Units	3552
Citations	36,151

Highlights of EcoCyc Database Improvements

We have added two new pathways to EcoCyc:
- periplasmic disulfide bond formation
- periplasmic disulfide bond reduction
Lundgren et al. have reported that cytochrome b561 is a superoxide:ubiquinone oxidoreductase whose primary function may be to quench the membrane-proximal superoxide produced by respiratory chain enzymes.
We have updated curation of enterobacterial common antigen (ECA) following a report by Mitchell et al. implicating a protein of unknown function – YhdP – and the cyclic form of ECA in maintaining outer membrane integrity. The database now represents all three forms of ECA synthesized by E. coli: cyclic ECA, ECA-lipopolysaccharide, and ECA-phosphatidylglycerol.
Until recently, only one protein-lysine acetyltransferase was known in E. coli. Christensen et al. have now identified four additional enzymes that catalyze lysine acetylation of distinct sets of target proteins:

Release Notes for EcoCyc Version 22.5

Released on September 25, 2018.

**EcoCyc KB Statistics**
Pathways	350
Reactions	2817
Enzymes	1611
Transporters	285
Genes	4500
Transcription Units	3550
Citations	35,788

New GenBank File for Escherichia coli K-12 MG1655 Released!

A new GenBank file of the E. coli K-12 MG1655 genome and annotation (U00096.3) was released on September 24, 2018. The updated genome annotation in this file was directly generated from EcoCyc Version 22.5 in a collaboration with Guy Plunkett III (University of Wisconsin), Andrea Auchincloss (UniProt/Swiss-Prot), and NCBI.

The most recent prior update to U00096.3 was released on August 1, 2014. The version suffix is changed only when the nucleotide sequence has changed -- thus the version number remains the same for this new release because no changes have been made to the nucleotide sequence. This new update does contain a large number of other changes based on publications in the past four years. The most significant updates include:

Newly discovered gene functions, including gene and product name changes
Newly discovered genes and gene products
Updated gene product names to conform to UniProt and NCBI guidelines

Highlights of EcoCyc Database Improvements

We have added gene and protein objects for 32 new small proteins recently identified by VanOrsdel et al.
We have updated the drug efflux proteins represented in EcoCyc. Text summaries for 11 complexes and 40 proteins have been revised and/or updated; 19 new transport reactions, 30 compounds (antibiotics, dyes and other toxins) and just under 200 literature references were added to the database as part of this project. Click here for a SmartTable of all E. coli transporters of known function. A new function was also added to the small multidrug resistance (SMR) family transporter, Gdx (formerly SugE) - characterized by Kermani et al. as a proton-coupled guanidinium exporter.
Fitzgerald et al. showed that binding sites for the alternative sigma factor FliA represent active promoters that transcribe highly unstable RNAs.
Insertion sequences and prophages are now represented as database objects within EcoCyc, enabling their inclusion in the generated Genbank file.
A number of crystal and solution structures for the transcription machinery and transcriptional regulators have been published, including
- RNA polymerase by Molodtsov et al. and Narayanan et al.
- RcsB by Filippova et al.
- CpxA/ CpxR by Mechaly et al.
- PhoB by Kou et al.
We have added one new pathway to EcoCyc: prenylated FMNH₂ biosynthesis

Highlights of Website Improvements

New Search Commands: The following new search commands have been added:
- Search for cryptic prophages via Search → Search DNA or RNA sites → Search by site type → Cryptic Prophages
- Search for pseudogenes via Search → Search genes, proteins, or RNAs → Search/filter by type/subunits → Pseudogenes only
Performance Enhancements: We have engineered a number of performance enhancements, particularly to decrease the time to generate gene pages.

Release Notes for EcoCyc Version 22.0

Released on April 24, 2018.

**EcoCyc KB Statistics**
Pathways	349
Reactions	2777
Enzymes	1599
Transporters	284
Genes	4501
Transcription Units	3560
Citations	35,024

Highlights of EcoCyc Database Improvements

Protein copy number data based on genome-wide ribosome profiling experiments for three different growth media were imported from Li et al. Copy-number data are found within the Summary tab for gene pages.
Kimura et al. have identified RlhA as the enzyme responsible for generating the 5-hydroxycytidine modification at the C2501 position (ho⁵C2501) of the 23S rRNA.
New functions have been added to the inner membrane protein BtsT (formerly YjiY) characterised by Kristoficova et al. as a pyruvate:proton symporter mediating pyruvate uptake under nutrient-limiting conditions, and to ZntB (formerly YdaN) characterized by Gati et al. as a zinc importer driven by the proton gradient.
Using the SELEX screening system, Shimada et al. identified XynR as a regulator of xylonate catabolism; it regulates expression of the divergent transcripts yagA and yagEF.
Davis et al. showed that acetylation of lysine (K100) residue of CRP is a mechanism by which the cell downregulates CRP-dependent class II promoter activity while elevating CRP steady-state levels, thus indirectly increasing class I promoter activity.
We have added the ATP biosynthesis pathway to EcoCyc.

Highlights of Website Improvements

Pathway regulation: Pathway diagrams can now include detailed regulatory information for each step that are taken from the extensive EcoCyc compendium of regulatory data. From any pathway page, such as L-homoserine biosynthesis, click on the "Show Regulation Details" button above the pathway diagram to see transcriptional, translational and substrate-level regulators included in the diagram. This button will only be present if there is regulation data available for the pathway, and if the pathway is displayed at a detail level that shows enzyme names. Mouse over any regulator icon for more information. Mouse over regulation arrows to identify which ligands influence specific isozymes.
Cellular Overview reborn: The EcoCyc cellular overview (metabolic map) diagram has been re-engineered to use modern web graphics. See Metabolism → Cellular Overview. The graphics now look sharper, and you can zoom the diagram quickly using your mouse wheel (the +/- bar at the upper left provides finer zoom control). When using the diagram in its Omics Viewer mode to display transcriptomics or metabolomics data, the sliders at the top of the diagram enable you to control the thicknesses of all edges in the diagram, and of the highlighted edges in the diagram. Additional sliders in the omics dialog enable thresholding of what omics data are visible.
Metabolic Model Fluxes on Dashboard: A new method is available for viewing the fluxes computed by running the EcoCyc metabolic model. Previously, after running a metabolic model (command Metabolism → Run Metabolic Model), the user could display the computed fluxes on the Cellular Overview diagram. Now, a new button "Show Fluxes on Dashboard" enables the user to display the fluxes on the Omics Dashboard tool. This tool enables the user to both view aggregate reaction fluxes (e.g., for all amino acid biosynthetic reactions), and to drill down to see fluxes for individual pathways and reactions.

Release Notes for EcoCyc Version 21.5

Released on Nov 28, 2017.

**EcoCyc KB Statistics**
Pathways	347
Reactions	2728
Enzymes	1593
Transporters	284
Genes	4496
Transcription Units	3555
Citations	34,421

Highlights of EcoCyc Database Improvements

EcoCyc contains the equivalent of 3,000 textbook-pages of mini-review summaries.

A new electron transport reaction has been added and assigned to the periplasmic protein Ccp (formerly YhjA), characterized by Kademian et al. as a cytochrome c peroxidase which uses membrane quinones for the reduction of hydrogen peroxide.
Two new pathways have been added to EcoCyc to reflect Ccp's role in anaerobic respiration:
- NADH to hydrogen peroxide electron transfer
- glycerol-3-phosphate to hydrogen peroxide electron transport
The curation of exodeoxyribonuclease V (RecBCD), rhomboid protease (GlpG) and K⁺-transporting P-type ATPase (KdpFABC) has been revised and updated for this release. Reactions catalysed by ExoV and GlpG are now more accurately represented, and literature coverage has been extended significantly for all three.
5-Oxo-L-proline is a cyclic metabolite that is deleterious to the cell. An ATP-dependent 5-oxoprolinase was recently discovered by Niehaus et al..

Highlights of Website Improvements

Dashboard: Many improvements have been made to the Omics Dashboard.
Improved Graphics and Fonts: We have upgraded many additional Web visualizations produced by Pathway Tools in its web server mode to use modern graphics and fonts, including the genome browser; genome overview; transport reactions; operon diagrams; transcription-unit diagrams; functionally-linked gene cluster diagrams; gene-neighbor diagrams; mapped-genes diagram; protein features; and sequence diagrams for promoters, binding-sites, and attenuators.
Full Pathway Tools release notes: http://brg.ai.sri.com/ptools/release-notes.html

Release Notes for EcoCyc Version 21.1

Released on Aug 15, 2017.

**EcoCyc KB Statistics**
Pathways	345
Reactions	2715
Enzymes	1585
Transporters	284
Genes	4489
Transcription Units	3555
Citations	33,843

Highlights of EcoCyc Database Improvements

Three new pathways have been added to EcoCyc:
New information has been added for several membrane proteins including YhhQ - implicated in the uptake of queuosine precursors for salvage; MgtS (formerly YneM) - required for accumulation of the magnesium transporter MgtA under magnesium limiting conditions, and YbaT - which, along with glutaminase I, functions to overcome disrupted glutamate synthesis under copper stress conditions.
The curation of DNA repair proteins AlkB and Endonuclease VIII has been revised and updated for this release; reactions catalyzed by these enzymes are now accurately represented and literature coverage has been extended significantly.

Release Notes for EcoCyc Version 21.0

Released on April 27, 2017.

**EcoCyc KB Statistics**
Pathways	343
Reactions	2686
Enzymes	1572
Transporters	283
Genes	4497
Transcription Units	3556
Citations	33,232

Highlights of EcoCyc Database Improvements

A new pathway, the HprSR two-component signal transduction pathway, implicated in the stress response to hydrogen peroxide, has been added.
The curation of proteins belonging to the ABC family of transporters has been updated. Text summaries for 59 complexes and 209 proteins have been revised and/or updated, stoichiometries of complexes have been corrected, and protein features (eg. ATP binding motifs and ligand binding residues) have been added. Just over 300 references have been added to EcoCyc as part of this project.
A new protein, the CopA(Z) copper chaperone, has been added. As reported by Meydan et al., CopA(Z) is generated by -1 programmed ribosomal frameshifting (-1PRF) of full length copA mRNA. The copA gene in E. coli K-12 thus generates two products, a copper-exporting P-type ATPase and a small cytoplasmic copper chaperone.
YhaJ was identified by Palevski et al. as a new transcriptional regulator controlling genes involved in a variety of processes. It had previously been identified as a member of the LysR family associated with regulation of virulence in an enterohemorrhagic Escherichia coli (EHEC) strain by Connolly et al.
Denby et al. showed that FrmR, a transcriptional regulator, senses the toxic chemical formaldehyde directly, with no metal dependence. The crystal structure of the protein isolated from E. coli O157:H7 was solved at 2.7 Å resolution.
Kingston et al. report progress in identifying a function for the previously uncharacterized transposase_31 family of proteins. Three of the five members of this family in E. coli, RpnA, RphB, and RpnC, function as recombination-promoting nucleases.

Highlights of Website Improvements

Omics Dashboard: The Omics Dashboard is an interactive tool for exploration and analysis of gene-expression and metabolomics datasets. The Dashboard is organized as a hierarchy of cellular systems. At its highest level the Dashboard contains panels for cellular systems such as biosynthesis, energy metabolism, and non-metabolic functions. Each of those panels contains a series of X-Y plots depicting the expression levels of genes within subsystems of that panel, e.g., subsystems within "Non-Metabolic Functions" include Central Dogma, Virulence, Development, and Sigma Factors. The Dashboard facilitates a rapid user survey of how all cellular systems are responding to a given stimulus, and enables the user to quickly find and understand the response of genes within one or more specific systems of interest. See the Dashboard Help document and an example of the Omics Dashboard.

Release Notes for EcoCyc Version 20.5

Released on December 17, 2016.

**EcoCyc KB Statistics**
Pathways	342
Reactions	2659
Enzymes	1568
Transporters	282
Genes	4497
Transcription Units	3556
Citations	32,534

Highlights of EcoCyc Database Improvements

EcoCyc currently represents 59 transport complexes (including 10 putative complexes) which belong to the ATP-binding cassette (ABC) superfamily. We have begun a project to update the curation of this large and important family of transporters in the database.
A recent paper by Cho et al. provides evidence that subcomplexes of class B penicillin binding proteins (PBP2 and PBP3) with SEDS-family proteins (FtsW and MrdB) are the primary peptidoglycan synthases during cell elongation and division, a role previously ascribed to the Class A PBPs (PBP1A, PBP1B and PBP1C).
The E. coli chromosome is organized into several macrodomains. The region surrounding the origin of replication is known as the Ori macrodomain. Valens et al. recently showed that the MaoP protein organizes and constrains the mobility of the Ori macrodomain.
Klein et al. identified several promoters and transcription factors that control rpoE-rseABC operon expression under different growth conditions.
PdeL is a bifunctional protein. In addition to its enzymatic activity as a phosphodiesterase, Reinders et al. identified it as a transcriptional regulator due its capability to bind to its own promoter region and stimulate its expression in response to c-di-GMP.
The HigBA toxin-antitoxin (TA) complex and HigA antitoxin were also identified as transcriptional repressors of their own expression. The crystal structure of the TA HigBA complex was solved and displays a hetero-tetramer, (HigBA)₂, comprised of two HigB and two HigA subunits (Yang et al.).

Highlights of Website Improvements

Receive Notification of Database Updates -- This new facility allows scientists to sign up to be notified of curation of new information in their research interest area(s). Sign up via the Update Notifications Page (available through Analysis → Update Notifications) to be notified when new curation (which indicates new published experimental findings) occurs for specific genes or metabolic pathways. You can also sign up for notifications in interest areas specified by Gene Ontology terms, such as cell motility or cell division -- you will then be notified whenever new curation occurs in genes involved in those biological processes. Notifications will be sent by email in conjunction with BioCyc releases.
Revised Protein Feature Coloring: We have revised the coloring scheme within the protein-feature display to assign a fixed set of colors to different feature types. For example, all enzyme active site features will be colored purple.

Release Notes for EcoCyc Version 20.1

Released on September 29, 2016.

**EcoCyc KB Statistics**
Pathways	341
Reactions	2653
Enzymes	1567
Transporters	282
Genes	4505
Transcription Units	3553
Citations	31,999

Highlights of EcoCyc Database Improvements

We have added two new pathways to EcoCyc:
- aminomethylphosphonate degradation
- N-end rule pathway I (prokaryotic)
The curation of several periplasmic proteins (Skp, multicopper oxidase and γ-glutamyltranspeptidase) has been revised and updated for this release.
Ashraf et al. found that Kbp is a potassium-binding protein that is required for normal growth in the presence of high external concentrations of potassium and under salt-induced osmotic stress conditions. Potassium binding by Kbp results in compaction of its tertiary structure.
Two new transcription factors have been identified:
- CecR (Cefoperazone and chloramphenicol Regulator of sensitivity) belongs to the TetR family of transcriptional regulators and was found by Yamanaka et al. to be involved in the control of sensitivity to cefoperazone and chloramphenicol. The the ABC transporter regulated by CecR, YbhFSR, was characterized as a drug exporter.
- DecR was identified by Shimada et al. as a new transcriptional regulator involved in cysteine detoxification.

Release Notes for EcoCyc Version 20.0

Released on May 6, 2016.

**EcoCyc KB Statistics**
Pathways	339
Reactions	2614
Enzymes	1564
Transporters	281
Genes	4506
Transcription Units	3547
Citations	31,054

EcoCyc now uses the updated U00096.3 sequence

Through release 19.5, EcoCyc used the U00096.2 version of the E. coli K-12 MG1655 genome sequence. We have now upgraded the sequence to version U00096.3. The nucleotide coordinates of genes and other features differ between U00096.2 and U00096.3. We are offering a coordinate mapping service as part of this new release, which is available here. This service will translate data files containing the old coordinates to contain new mapped coordinates.

Highlights of EcoCyc Database Improvements

Sulfoquinovose is one of the most common organo-sulfur compounds in nature. Speciale et al. have now identified the YihQ protein as a sulfoquinovosidase which catalyzes the hydrolysis of terminal sulfoquinovosyl diacylglycerides and sulfoquinovosyl glycerol. The released sulfoquinovose can then serve as a source of carbon and energy via the sulfoquinovose degradation I pathway.
Two new electron transport reactions have been added and assigned to the MsrPQ complex, characterised by Gennaris et al. as a periplasmic protein L-methionine sulfoxide reducing system; MsrPQ uses electrons from the membrane quinone pool to provide reducing power for protein quality control in the periplasm.
A new function was added for the inner membrane protein MltG reported by Yunck et al. to have endolytic murein transglycosylase activity -- the authors suggest MltG may act during processing of nascent peptidoglycan to terminate strand synthesis.
New properties of several transcription factors were identified:
- Katsir et al. showed that the NarL receptor domain is able to stimulate gene transcription in a nitrate-responsive manner.
- Gunasekara et al. showed that the Thr¹²⁷ and Ser¹²⁸ residues of CRP provide high cAMP affinity and play a key role in stabilization of the CRP inactive form.
- The response regulators KdpE and RcsB are capable of driving gene expression (Narayanan et al.) and form complexes with other proteins in a unphosphorylated manner (Pannen et al.).
- Beauchene et al. showed that under anaerobic and iron-dependent conditions, Fur binds to more sites across the genome, increasing the number of target genes.

Highlights of Website Improvements

Execute metabolic models via the EcoCyc website. The metabolic model derived from EcoCyc can now be executed via the EcoCyc website. Several variations of the model are available whereby the model can be run with different nutrients and secreted compounds. You can directly execute the model variations listed on the following page; to run the model on different nutrients, make your own copy of a model, modify its nutrients, and execute the new model.
- Click here to access the EcoCyc metabolic model
The new command Search → Search DNA or mRNA sites enables searching for sites such as attenuators, promoters, riboswitches, and terminators that meet specified criteria.
Re-design of compound pages
Protein feature coloring
Computed Pfam features are now present within the Protein Features tabs of many EcoCyc gene pages.
The option to generate a table of pathways overlaid with omics data now ranks pathways by Pathway Perturbation Score, a new score that attempts to measure the overall average degree to which the reactions in a pathway are perturbed over the course of an omics experiment. From the Metabolism → Cellular Overview page, select Upload Data from File and ask to show the data as a table of pathway diagrams.

Release Notes for EcoCyc Version 19.5

Released on November 13, 2015.

**EcoCyc KB Statistics**
Pathways	338
Reactions	2478
Enzymes	1555
Transporters	284
Genes	4500
Transcription Units	3549
Citations	30,224

Highlights of EcoCyc Database Improvements

We have added two new pathways to EcoCyc:
- N⁶-L-threonylcarbamoyladenosine³⁷-modified tRNA biosynthesis
- citrate degradation
Curation updates have been made for the inner membrane protein YjeH, recently characterised as an L-methionine / branched chain amino acid transporter, for the protein complex OsmF YehYXW, reported by Lang et al. to catalyse the uptake of glycine betaine, and for the periplasmic protein CpoB (formerly YbgF), whose role in coordinating the interaction between peptidoglycan synthases and the energy transducing Tol system during cell division has been described by Gray et al..

Highlights of Website Improvements

Redesigned gene pages: We have redesigned the Web gene pages for a more modern look and to make information easier to find. Gene pages now contain a series of tabs; clicking on a given tab shows a specific type of information, such as the reactions catalyzed by a gene product, the GO terms assigned to the gene, or the features defined for the gene product. Note that the set of tabs present varies depending on the type of the gene product and the information available. The "Show All" tab combines all information in one page for easier searching.
New pathway collage feature: A pathway collage is a diagram depicting a set of connected metabolic pathways, possibly with omics data superimposed (example here). You can now interactively create a pathway collage in Pathway Tools desktop and Web modes. To create a pathway collage in Web mode:
- (Optional) Load a gene expression or metabolomics data file if you want to include such data within your collage, by bringing up the cellular overview (Metabolism → Cellular Overview) and then running Right-Sidebar Menu → Overlay Experimental Data (Omics Viewer) → Upload Data from File.
- Specify the pathways to include in the collage in one of two ways:
  - Go to any pathway page and then invoke Right-Sidebar Menu → Generate Pathway Collage.
  - Create a SmartTable containing the pathways to include in the collage and then invoke Right-Sidebar Menu → Export → Export Pathways to Pathway Collage.
- The collage will be created in your web browser, where you will be able to reposition the pathways interactively, add additional pathways to the collage, add connections between metabolites, change various display styles, and view omics data, to create your desired diagram. Export the diagram to a file for inclusion in a publication. For more details see the Website User's Guide.

Release Notes for EcoCyc Version 19.1

Released on June 25, 2015.

**EcoCyc KB Statistics**
Pathways	337
Reactions	2418
Enzymes	1545
Transporters	282
Genes	4500
Transcription Units	3543
Citations	29,227

Highlights of EcoCyc Database Improvements

We have added eight new pathways to EcoCyc:
New functions have been added for a number of inner membrane proteins. NimT (formerly YeaN) was characterized as a 2-nitroimidazole efflux transporter, and LysO (formerly YbjE) was characterized as an L-lysine efflux transporter. OrtT (formerly YdcX) was reported to be an orphan protein toxin that may be activated during the stringent response.
Two enzymes have been newly implicated in RNA metabolism: The NADH pyrophosphatase NudC is able to de-cap RNA molecules that have been capped with an NAD modification at the 5' end, and the YeaK protein has aminoacyl-tRNA editing activity for certain mischarged tRNAs.
Ogasawara et al. showed that the transcriptional repressor NimR (formerly YeaM) regulates resistance to 2-nitroimidazole, an antibacterial and antifungal agent, by regulating the divergent transcription of the nimT and nimR genes.

Release Notes for EcoCyc Version 19.0

Released on March 20, 2015.

**EcoCyc KB Statistics**
Pathways	329
Reactions	2384
Enzymes	1538
Transporters	279
Genes	4501
Transcription Units	3541
Citations	28,535

Highlights of Website Improvements

Genome browser: The BioCyc genome browser now depicts transcription factor binding sites and attenuators, and will display the nucleotide sequence at high magnification levels.
Sequence variant data analysis: Web SmartTables support a new analysis operation for sequence variant data. The user can define a SmartTable of replicon regions and associated sequence variants via a file import operation. Then, the SmartTables transformation "Sequence -- nearest gene to DNA region" adds additional columns to the SmartTable showing the nearest gene to each region, and the amino-acid change caused by each sequence substitution.

Highlights of EcoCyc Database Improvements

A significant advance in our understanding of cytochrome c maturation has been achieved by San Francisco et al. who have demonstrated experimentally that CcmFH is the cytochrome c synthetase responsible for the covalent attachment of heme to apocytochromes c in the periplasm of E. coli K-12.
We have added two new pathways to EcoCyc:
- autoinducer AI-2 degradation
- nitrate reduction VIIIb (dissimilatory)
SutR (formerly YdcN) was identified as a transcriptional dual regulator of genes involved in sulfur metabolism by Yamamoto et al..
New transport reactions have been added for cysteine uptake and export following reports that fliY, yecS and yecC encode an L-cysteine/L-cystine ABC transporter and yijE encodes an L-cystine efflux protein.

Release Notes for EcoCyc Version 18.5

Released on November 7, 2014.

**EcoCyc KB Statistics**
Pathways	328
Reactions	2361
Enzymes	1533
Transporters	277
Genes	4501
Transcription Units	3538
Citations	27,887

Highlights of Website Improvements
- Functionally Linked Gene Clusters (FunGCs): Discover novel pathways and obtain insights on gene functions using the new EcoCyc FunGCs. FunGCs are constructed using genome-context methods, which are computational comparative-genomics methods that search for patterns of gene occurrence across 1800 reference genomes in BioCyc. These methods identify both pairwise functional linkages among genes, and larger clusters of genes that are likely to belong to a common pathway or process. EcoCyc FunGC predictions are available here.
- Metabolomics Operations: Muliple new metabolomics operations are available including displaying metabolomics data on pathway diagrams (e.g., with metabolomics data shown as bar charts arranged on pathway diagrams), searching for metabolites by multiple criteria (see table of search operations), and translating among metabolite identifiers from multiple databases. Many of these operations are available both in the desktop software and as customizable URLs. Examples:
  - Metabolomics data displayed as bar charts on the E. coli chorismate biosynthesis pathway:
    http://biocyc.org/ECOLI/new-image?type=PATHWAY&object=ARO-PWY&url=http://bioinformatics.ai.sri.com/ptools/ECOLI-Compounds-ALL.txt&expressiontype=relative&datacolumns=1,3,5&log=on&class=compound&color=rbg&omicsPopups=on
  - Metabolomics data displayed as X-Y plots on the E. coli valine biosynthesis pathway:
    http://biocyc.org/ECOLI/new-image?type=PATHWAY&object=VALSYN-PWY&url=http://bioinformatics.ai.sri.com/ptools/ECOLI-Compounds-ALL.txt&expressiontype=relative&datacolumns=1,3,5&log=on&class=compound&omicsPopups=on&defaultPopup=plot
- Gene-Expression Operations: Similar new operations are available for painting gene-expression and proteomics data onto pathways, in both web and desktop versions. Web example:
  - Gene expression data displayed as heat maps on the E. coli TCA cycle
EcoCyc Database Improvements:
- The metabolic model derived from EcoCyc was published as Weaver et al., BMC Syst Biol. 2014. Version 18.0 of the model showed an accuracy of 95.2% in predicting the growth phenotype of experimental gene knockouts. The model was used to make nutrient utilization predictions for 431 different media conditions, for which an overall accuracy of 80.7% was achieved.
- We have embarked on a project to update the curation of respiratory electron transport pathways in EcoCyc. 7 pathways have been added taking the total number of electron transport pathways represented to 19. Curation of the individual respiratory enzymes has also been updated. 157 literature citations have been added to date. The added pathways are:
- YdcI was identified as a transcriptional repressor involved in the survival, stress response, and cell interactions in Salmonella enterica serovar Typhimurium by Solomon et al.. Based on N- and C-terminal exchange between the S. Typhimurium and Escherichia coli proteins, it was also possible to determine that YdcI is a transcriptional repressor in E. coli.
- Summaries for the OmpR, H-NS, CRP, IHF, and PhoB transcriptional regulators, and the specialized sigma factor in response in heat shock and misfolded proteins, σ^E, were updated.
Release Notes for EcoCyc Version 18.1

Released on June 23, 2014.

EcoCyc KB Statistics
Pathways 323

Reactions 2342

Enzymes 1524

Transporters 277

Genes 4501

Transcription Units 3528

Citations 26,870
- A new two component signal transduction pathway, YehUT, has been added. YehUT is involved in a carbon control network that functions when nutrients are limited.
- Although the chemistry of DNA charge transfer has been well described, the role it plays within the cell (if any) has remained enigmatic. A recent report (Grodick et al.) suggests that the DNA repair proteins DinG and Endonuclease III use DNA charge transfer to communicate over distance and redistribute to sites of DNA damage.
- New functions have been described for the inner membrane proteins LapA and LapB (formerly YciS and YciM) characterised by Klein et al. as heat shock proteins with a role in lipopolysaccharide assembly, and for CysZ, reported to be a sulfate:proton symporter with a role during cysteine synthesis.
- MraZ was identified by Eraso et al. as a transcriptional repressor involved in the control of cell division and cell wall genes. It binds to a region of DNA containing three successive TGGGN direct repeats that are separated by two consecutive 5-nt spacers close to the mraZp promoter.
Release Notes for EcoCyc Version 18.0

Released on March 24, 2014.

EcoCyc KB Statistics
Pathways 322

Reactions 2318

Enzymes 1518

Transporters 273

Genes 4499

Transcription Units 4522

Citations 26,275
- Highlights of Website Improvements
  - RouteSearch: Search for lowest-cost paths through the metabolic network of the selected organism. Or, design lowest-cost pathways to novel compounds by adding reactions from MetaCyc.
  - Sequence pattern searches: You can now search a genome for exact or degenerate short patterns of nucleotides or amino acids.
  - You can now obtain multiple sequence alignments among E. coli genes and proteins, and to other genes/proteins in BioCyc
  - Groups have been renamed to SmartTables
  - Full Pathway Tools release notes: http://brg.ai.sri.com/ptools/release-notes.html
- EcoCyc Database Improvements:
  - We have added one new metabolic pathway, sulfoglycolysis. Denger et al. describe the degradation of sulfoquinovose, which is a major component of organo-sulfur compounds in nature and can be utilized as the sole source of carbon and energy by E. coli K-12.
  - Curation of transport proteins includes the addition of 5 new functions. The 3 inner membrane proteins GhxP, GhxQ and AdeQ (formerly YjcD, YgfQ and YicO) have been characterised by Papakostas et al. as purine transporters: GhxP and GhxQ are high affinity permeases specific for guanine and hypoxanthine while AdeQ and the previously characterised PurP transporter are specific for adenine. New transport functions were added for the inner membrane proteins SatP (formerly YaaH) reported by Sa-Pessoa et al. to be an acetate:proton symporter active at the exponential growth stage and YihO which was implicated in the transport of sulfoquinovose.
  - The characterisation of an E. coli inner membrane glycolipid with enzyme-like activity that is essential for membrane protein integration was first reported by Nishiyama et al. in 2012. More recently Moser et al. have shown that this membrane protein integrase (MPIase) is a novel chaperone that drives protein integration into membranes by modulating the dimer orientation of SecYEG translocase.
  - E. coli K-12 contains eight members of the highly conserved DedA family of membrane proteins which are collectively essential but whose function remains obscure. A recent report by Kumar and Doerrler suggests that two of these proteins (YghB and YqjA) are membrane transporters required for PMF-dependent drug efflux in E. coli K-12.
  - RclR (formerly YkgD) has been experimentally determined to be a redox-sensitive transcriptional activator of essential genes for survival under reactive chlorine stress by Parker et al..
  - Park et al. showed that ArcA utilizes its diverse binding site architecture for global control of carbon oxidation pathways.
Release Notes for EcoCyc Version 17.5

Released on October 11, 2013.

EcoCyc KB Statistics
Pathways 320

Reactions 2284

Enzymes 1505

Transporters 269

Genes 4501

Transcription Units 4510

Citations 25,406
- Highlights of Website Improvements
  - New Right-Sidebar Menu: The previous object-specific menus have been replaced by a right-sidebar menu of operations that changes depending on what type of page the user is visiting. For example, the menu of operations differs for pathway pages versus metabolite pages. Some operations previously accessible by buttons (e.g., retrieving a protein sequence) are now accessible through this new right menu in gene pages. If you do not see the menu, please reload the page in your web browser while holding down the "Shift" key.
  - Web Cellular Overview and Omics Viewer: This tool has undergone a major overhaul including
    - It runs much faster and many bug fixes have been made
    - Gene expression data to be displayed on the Cellular Overview can now be retrieved from PortEco, from GEO, and from Web Groups
    - Pop-up improvements
    - Many new search commands are available
    - Labels for pathway groups are now included in the diagram
  - Groups Enhancements: A number of enhancements have been made to both Web Groups including:
    - Groups can now be published. Once published a group is publically readable, and the group cannot be deleted, even by its owner. The idea is to encourage scientists to refer to published groups in their scientific publications.
    - Users can now create temporary groups without creating a BioCyc account to facilitate experimentation with Groups.
    - Database identifiers in database links can be added as groups columns, e.g., KEGG IDs for BioCyc compounds.
    - A group of objects can be created via text entry.
    - New row selection operations are available.
    - The star in the heading of the first column allows the user to toggle between viewing object names and object identifiers.
  - Full Pathway Tools release notes: http://brg.ai.sri.com/ptools/release-notes.html
- EcoCyc Database Improvements:
  - We have added three new metabolic pathways:
    - 5-(carboxymethoxy)uridine biosynthesis describes the formation of a posttranscriptionally modified nucleotide in tRNAs
    - hydroxymethylpyrimidine salvage
    - thiamin salvage II
    In addition, the colanic acid building blocks biosynthesis pathway has been turned into a superpathway consisting of five component pathways.
  - New transport reactions have been added for pyruvate uptake and export. Although specific transport protein(s) have not been identified, experimental work by Kreth et al. suggests that E. coli K-12 contains both inducible and constitutive systems for the import of pyruvate plus an additional system for pyruvate efflux.
  - A new function has been added to the multidrug resistance protein MdtM, which was reported to be a low-affinity cation:H+ antiporter with a role in alkaline pH homeostasis.
  - VanOrsdel et al. have reported that the small membrane protein CydX (formerly YbgT) is a subunit of cytochrome bd-1 and is required for terminal oxidase activity.
  - We have added the tetrameric conformation for the transcriptional regulator LsrR. Wu et al. reported that in the presence of phosphorylated autoinducer 2 (AI-2), the tetramer dissociates into dimers, and the interaction of LsrR with DNA is greatly reduced. Therefore, we also added its inactive conformation, LsrR-AI-2.
  - Two new conformations, MetJ-MTA and MetJ-adenine for the protein MetJ were recently added. Marti-Arbona et al. reported that the metabolites 5´-deoxy-5´-(methylthio) adenosine (MTA) and adenine (Ade) bind with high affinity to MetJ, but the biological effects of this binding are not known.
Release Notes for EcoCyc Version 17.1

Released on June 11, 2013.

EcoCyc KB Statistics
Pathways 314

Reactions 2232

Enzymes 1500

Transporters 268

Genes 4501

Transcription Units 4509

Citations 24,870
- 1,4-dihydroxy-2-naphthoyl-CoA thioesterase, EC 3.1.2.28, is an enzyme of the menaquinone biosynthesis pathway. It had long been an orphan activity: the gene encoding the enzyme had been unknown. Recently, Chen et al. showed that ydiI encodes this enzyme and renamed the gene menI.
- New functions have been added to three membrane proteins. DauA was reported to be an aerobic succinate transporter active at acidic pH by Karinou et al.. WaaH and EptC were shown by Klein et al. to catalyse glucuronic acid and phosphoethanolamine modification to E. coli LPS under low phosphate conditions.
- Curation of the nitrogen phosphoenolpyruvate-dependent phosphotransferase system (PTSNtr), consisting of the three cytoplasmic proteins PtsP, PtsO and PtsN, has been updated for this release.
- As part of our curation on transcriptional regulation, we have added literature references to the experimental evidence codes for 225 promoters in which they were missing.
- We have corrected and relocated the transcription factor binding sites of PuuR. The binding sites of PuuR identified by Nemoto et al. consist of 15 nucleotides, with the following recognition sequence: AAAATATAATGAACA (Nemoto et al. (2012)). Analysis done by the curator on the experimental assays and the sequences identified by Nemoto et al. showed that the binding sites of PuuR may have a length of 20 nucleotides with an inverted repeat symmetry: ATGGaCAATATATTGaCCAT (The consensus sequence identified by Nemoto et al. is included in this proposed consensus sequence, and the nucleotides conserved between the two sequences are underlined.)
- We have made several revisions to improve agreement between Biolog Phenotype MicroArray activity and flux-balance analysis (FBA) predictions, including fixes to incorrectly reversible reactions and addition of new transport reactions.
Release Notes for EcoCyc Version 17.0

Released on March 28, 2013.

EcoCyc KB Statistics
Pathways 312

Reactions 2175

Enzymes 1497

Transporters 268

Genes 4499

Transcription Units 4506

Citations 24,391
- We have added a new signaling pathway and two new metabolic pathways to EcoCyc:
  - YpdAB Two-Component Signal Transduction System: This pathway acts to stimulate nutrient scavenging as a result of carbon starvation and thus plays a role in the carbon control network of E. coli K-12.
  - cardiolipin biosynthesis III
  - muropeptide degradation
  In addition, pyrimidine nucleotide biosynthesis pathways have been extensively rearranged, resulting in smaller base pathways and new superpathways.
- Curation of the lipopolysaccharide transport system, comprising seven Lpt proteins in E. coli K-12, has been updated for this release.
- New functions have been added for the membrane proteins Spr, YdhO and YebA recently characterised by Singh et al. as murein hydrolases. The three D-D endopeptidases are redundantly essential for peptidoglycan incorporation and cell growth.
- The role of the inner membrane proteins PgaC and PgaD in biofilm formation has been further described and a novel mechanism of cyclic-di-GMP mediated exopolysaccharide control elucidated. Steiner et al. have shown that the second messenger molecule c-di-GMP binds specifically to a PgaCD complex, mediating a productive interaction that results in the formation of an active glycosyltransferase complex.
- Three newly identified transcription factors have been curated:
  - PgrR is a repressor of the expression of genes related to peptidoglycan degradation (Shimada et al. (2013)).
  - RcdA is involved in the regulation of a number of stress response genes, biofilm formation and of transcription regulator genes (Shimada et al. (2012)).
  - YdfH belongs to the GntR transcription factor family and is a repressor of the rspAB operon (Sakihama et al. (2012)).
Release Notes for EcoCyc Version 16.5

Released on Nov 14, 2012.

EcoCyc KB Statistics
Pathways 300

Reactions 2120

Enzymes 1485

Transporters 264

Genes 4499

Transcription Units 4490

Citations 23,909
- We have added a new electron transport pathway to EcoCyc:
  - proline to cytochrome bo oxidase electron transfer
  In addition, a number of pathways have been added to EcoCyc based on information in MetaCyc:
- With the discovery of RlmJ as the enzyme responsible for methylation of A2030 in 23S ribosomal RNA by Golovina et al., the set of methyltransferases that modify E. coli ribosomal RNAs is now complete.
- New functions have been added for the inner membrane protein UacT (formerly YgfU), characterized as a urate transporter in E. coli K-12, and the outer membrane protein LoiP (formerly YggG) reported to be a metalloprotease.
- Selkrig et al. have reported the characterization of a novel "translocation and assembly module" that spans the inner and outer membranes of E. coli K-12 and is responsible for the efficient secretion of adhesin protein. This newly described complex comprises the inner membrane protein TamB (YtfO) and the outer membrane protein TamA (YtfM).
- The release of solutes through mechanosensitive ion channels functions to protect bacterial cells against hypo-osmotic shock. Edwards et al. have recently reported experimental characterization of two mechanosensitive channels encoded by the genes ynaI and ybiO. This latest report brings the total number of known mechanosensitive channels in E. coli K-12 to seven, experimental evidence from Edwards et al. suggests that this represents the full complement.
- EcoCyc now includes consensus sequences of binding sites for 130 transcription factors (TFs). 70% of the sites have inverted repeat symmetry, 22% are asymmetric binding sites, and 8% have direct repeat symmetry. 49 regulators are local transcription factors that have three or less binding sites and 81 regulators have four or more binding sites in the database.
- We have also annotated 35 predictions for TF binding sites of 13 regulators. The matrices used for these predictions were constructed by the RegulonDB database (Medina-Rivera et al. (2010)). Four TFs (ArgR, AscG, Cra, and Rob) have regulatory interactions with weak evidence and interactions for eight regulators (CRP, EvgA, ExuR, FIS, LexA, NtrC, PhoP, TorR, and UxuR) have strong evidence.
- We have completed adding references and evidence codes to 85 transcriptional regulatory interactions. Now every manually curated regulatory interaction has a reference and an evidence code associated with it.
- We have added a fifth dataset measuring respiration under aerobic conditions using the Biolog platform to our growth media page. This data was published by Yoon et al..
- The all-growth-media page has been enhanced to enable better visualization and comparison between the five datasets. Some disagreements between the datasets have been resolved by a curator using data from the experimental literature, or by disregarding single outlier results.
- Previously, there were three different (and on occasion inconsistent) ways to represent protein cellular location: via GO terms, via MultiFun terms, and via our own cellular component ontology. We have combined the data from all three representations, and resolved the inconsistencies. We now store only GO terms, and compute the value of the protein location field from the stored GO terms. We have eliminated the use of MultiFun terms to represent cellular location.
Release Notes for EcoCyc Version 16.1

Released on July 05, 2012.

EcoCyc KB Statistics
Pathways 293

Reactions 2074

Enzymes 1474

Transporters 258

Genes 4500

Transcription Units 4477

Citations 23,382
- We have reviewed and standardised the naming of membrane transport proteins within EcoCyc. Our aim was to use names that are indicative of both transporter substrate and energetics (e.g. "serine/threonine:Na+ symporter" replaces "SssT DAACS transporter") and to ensure that this was extended to include the individual subunits of transport protein complexes, which until now have often been identified by gene name alone (e.g. "arabinose ABC transporter - ATP binding subunit" replaces "AraG"). Approximately 450 proteins were renamed as part of this project.
- We have added more Phenotype Microarray (PM) growth data to EcoCyc. Data are available from four PM studies under aerobic conditions, and from one PM study under anaerobic conditions. Significant differences were found. Growth data can be accessed from the All Growth Media page. For details on how to access these data, see the "Conditions of E. coli Growth and Non-Growth" section of the Guide to EcoCyc.
- For information about the four existing large-scale gene essentiality datasets within EcoCyc, see the "Essential Gene Information" section of the Guide to EcoCyc.
- Two groups, Thomason et al. and Jørgensen et al., independently discovered that the small RNA McaS regulates the expression of curli as well as flagellar motility and biofilm formation.
- FliZ is a repressor that contains an α-helix which is similar to helix 3.0 of σ^S and that represses genes involved in the regulation of motility system and curli expression. Pesavento et al. 2012 determined that this regulator binds to σ^S-dependent promoters, can recognize alternative σ^S promoter-like sequences and can also discriminate vegetative promoters.
- Two new transcription factors have been identified, MatA and YjiE.
  - MatA is a transcriptional dual regulator in the meningitis isolate strain IHE 3034 and it interferes with bacterial motility and flagellar synthesis in E. coli K-12 (Lehti et al. 2012). Given the high similarity between the two strains, we have added this information to E. coli K-12.
  - The YjiE transcription factor regulates genes involved in cysteine, methionine biosynthesis, sulfur metabolism, iron acquisition and homeostasis (Gebendorfer et al. 2012). It was formerly named "QseD", but it does not appear to be directly involved in quorum sensing and was thus renamed to its original name.
- A new function was identified for OxyR, controlling genes under nitrosative stress during anaerobic respiration (Seth et al. 2012).
- We have included new consensus binding sequences for 17 transcription factors: AgaR, AraC, ArcA, AscG, CaiF, DnaA, FhlDC, IclR, KdpE, LeuO, MalT, MelR, NanR, PrpR, PutA, RhaS, XylR.
Release Notes for EcoCyc Version 16.0

Released on February 17, 2012.

EcoCyc KB Statistics
Pathways 293

Reactions 2037

Enzymes 1475

Transporters 259

Genes 4502

Transcription Units 4472

Citations 22,895
- We have added a number of new metabolic pathways to EcoCyc. Three new pathways show reactions in the biosynthesis of molybdenum cofactors:
  Other pathways have been recently described in the literature, including:
  - methylphosphonate degradation
  - hydrogen sulfide biosynthesis
- Additional knock-out datasets are available in this release of EcoCyc. To list all growth media and their associated knock-outs use command Tools → Summary Statistics, then click on "Growth Media" at the bottom of the table. Knock-out data are also available in a table on most gene pages.
- A new function was assigned to the inner membrane protein MntP (formerly YebN), characterized by Waters et al. as a manganese transporter.
- The long running controversy over the structure of the multidrug transporter EmrE may be drawing to a close with a report in the journal Nature providing further evidence for the asymmetric, antiparallel arrangement of monomers within the dimer.
- Curation of cytochrome bdII oxidase has been updated to include the report by Borisov et al. who have shown that this terminal oxidase does contribute to the generation of proton motive force in E. coli K-12.
- We have reviewed the reactions included in the new E. coli metabolic model of Orth et al. and updated EcoCyc if necessary.
- We continue with the effort to update and assign the correct lengths and positions of transcription factor (TF) binding sites. In this release, we added consensus sequences, lengths, and binding site symmetries for 10 TFs. We updated the binding sites for four TFs that belong to the LysR family (ArgP, IlvY, MetR, and NhaR) and three two-component system response regulators (BaeR, CitB, and CpxR), as well as DinJ (part of a toxin/antitoxin system), PurR (regulates genes involved in purine/pyrimidine biosynthesis), and PdhR (involved in central metabolic fluxes, the utilization of glycolate, and cell division).
  In these cases we used different strategies to identify the characteristics of the TFBSs. We performed alignments of the sequences upstream of genes regulated by these proteins and compared orthologous intergenic regions, and we also used other databases, such as RegPrecise (Novichkov et al. 2010). In addition, the binding sites of the regulator MetR were corrected based on comparisons with homologous sequences reported for Salmonella typhimurium. In all cases we also analyzed the available experimental evidence that corresponded to each regulatory interaction.
- We are continuing to annotate allosteric regulation of RNA polymerase by ppGpp and DksA. In this sense we have expanded the summaries for GreB, GreA and DksA and for transcriptions factors including AidB, ArgP, AtoC, DcuS, DpiB, Fur, HNS, LacI, MalT, MntR, PaaX, PhoB, PutA and SoxS.
Release Notes for EcoCyc Version 15.5

Released on October 21, 2011.

EcoCyc KB Statistics
Pathways 281

Reactions 1991

Enzymes 1470

Transporters 257

Genes 4503

Transcription Units 4463

Citations 22,039
- All articles from the EcoSal collection are now available for full-text searching from the EcoCyc website (see Search → Search Full-text Articles). Those 131 EcoSal articles are part of a collection of 40,000 indexed articles at EcoCyc; for 27,000 of those articles, the full text is searchable. Note you must have a subscription from EcoSal and other content providers to view many of the full articles.
- We have begun a new effort to capture conditions of E. coli growth and non-growth within EcoCyc. EcoCyc now contains 406 such growth conditions. You can access information on growth conditions in two ways through the EcoCyc website:
  - To find growth media according to criteria such as name and components of the media, use command Search → Growth Media
  - To list all growth media use command Tools → Summary Statistics, then click on "Growth Media" at the bottom of the table
  Example growth medium page: MOPS medium with 0.4% glucose
  To suggest additional growth media for inclusion, please contact .
- We have begun a new effort to capture E. coli essential gene information within EcoCyc. When conditions of gene essentiality or non-essentiality for gene G are known, that information will be presented within a table within the gene page for G, located just below the table of Gene Ontology terms.
  Example gene page with essentiality data: fbaA
- BioCyc.org now contains 130 E. coli genomes. To access them, click "select organism database" under the quick-search box at the top-right of EcoCyc web pages, and select the genome you wish to explore.
- EcoCyc now includes a functional steady-state metabolic flux model for E. coli produced using the method of flux-balance analysis. Data files describing the model and its computed fluxes can be accessed in the fba subdirectory of the EcoCyc datafile distribution. You can run the model using the downloadable version of EcoCyc plus the Pathway Tools software to explore growth predictions under different nutrient conditions and under different gene and reaction knock-outs.
- The function of the inner membrane protein RseP has been expanded. Formerly characterised for its role in the activation of the sigmaE stress response, Saito et al. have reported that it is also involved in the degradation of remnant signal proteins left in the inner membrane (a function previously ascribed to the SppA protein of E. coli).
- New functions have been added to the periplasmic protein RcnB (formerly YohN) - implicated in the maintenance of intracellular levels of nickel and cobalt, and the membrane-associated protein YidD - required for the efficient insertion and maturation of YidC-dependent inner membrane proteins.
- The curation of a number of inner membrane proteins in EcoCyc has been updated for this release. Updated text summaries for the inner membrane proteins D-lactate dehydrogenase, HPr, PtsI and the protein complexes PntAB and RuvABC have resulted in the addition of 94 new literature citations to EcoCyc.
- We have curated mechanisms of regulation affecting allosterically the RNA polymerase at transcription initiation. ppGpp is a nucleotide that binds the RNA polymerase alone or forming a complex with DksA, affecting transcription in either a positive or negative manner. Genes involved in response to nutrient limitation as well as amino acid biosynthesis were positively affected by ppGpp and DksA. On the other hand, genes related to rRNA promoters and to the stringent response were negatively controlled by both regulators. Currently, 67 promoter interactions regulated by ppGpp, as well as some of them including regulation by DksA were curated.
Release Notes for EcoCyc Version 15.1

Released on June 8, 2011.

EcoCyc KB Statistics
Pathways 281

Reactions 1945

Enzymes 1467

Transporters 258

Genes 4490

Transcription Units 3433

Citations 21,448
- We have added three new metabolic pathways to EcoCyc:
- New functions have been added for three previously uncharacterized inner membrane proteins. PlaP (formerly YeeF) was reported to be a low affinity putrescine symporter; AlaE (formerly YgaW) was characterized as an inducible L-alanine exporter and YjbB was reported to be involved in the export of inorganic phosphate.
- Biochemical characterization and a crystal structure of the periplasmic protein, Spy, has been recently reported by Quan et al.. Spy is a periplasmic chaperone with a unique cradle structure and it is strongly induced by conditions that induce protein unfolding. Spy acts to prevent protein aggregation; it also supports protein refolding in the absence of an energy cofactor - exactly how this is achieved remains a question for further research.
- We have analyzed consensus binding sequences for 20 transcription factors (TFs) and as a result we have corrected and generated new regulatory interactions, updated their consensus sequences, length and symmetry of the transcription factor binding sites (TFBSs).
- We corrected and relocated the TFBSs of seven response regulators of the two component systems: DcuR, EvgA, NtrC, OmpR, PhoB, PhoP and RstA. We have updated the sites of 5 TFs involved in the Acid Resistance System: BglJ, GadE, GadX, GadW, RcsB. We added new consensus sequences for four local transcription factors: SoxR, YqhC, YqjI and CspA.
- The experimentally characterized TFBSs for the transcriptional regulator components of the HipBA, MqsAR, RelBE and YefM-YoeB toxin/antitoxin systems have been updated.
Release Notes for EcoCyc Version 15.0

Released on March 18, 2011.

EcoCyc KB Statistics
Pathways 277

Reactions 1922

Enzymes 1458

Transporters 254

Genes 4489

Transcription Units 3422

Citations 21,110
- We have added one new metabolic pathway to EcoCyc:
  - cinnamate and 3-hydroxycinnamate degradation to 2-oxopent-4-enoate
- The curation of all the histidine kinase proteins involved in two-component regulatory systems has been updated. EcoCyc includes information on 27 experimentally characterized histidine kinases plus 3 proteins (YedV, YedU and YpdA) with predicted histidine kinase function.
- The set of full-text E. coli scientific articles available for searching has been updated; 29,000 articles are available for searching, and an additional 7,000 abstracts are available for searching. See website command Search → Search Full-text Articles.
- As the target of the β-lactam class of antibiotics, the peptidoglycan synthesizing enzymes are always of great interest. Two groups of researchers recently reported the characterization of the outer membrane lipoproteins LpoA (formerly YraM) and LpoB (formerly YcfM), showing that they form complexes with and regulate the activity of, the peptidoglycan synthetases, PBP1A and PBP1B.
- A new function was added to the inner membrane protein PgpC, characterized by Lu et al. as a phosphatidylglycerophosphatase with a role in phospholipid biosynthesis.
- A new transcription factor, YqjI, has been identified. The local regulator YqjI was reported to act as a repressor of the synthesis of an NADPH-dependent ferric reductase and its autorepression. Wang et al. determined that this regulator maintains iron homeostasis during high levels of nickel.
- We have included new consensus sequences for 45 local transcription factors that have three or less binding sites in the database. In these cases we performed alignments of the sequences upstream of genes regulated by these proteins and evaluated the lengths and symmetries of the consensus sequences. Most of these regulators bind to small sequence motifs (11 to 24 nucleotides) with different symmetries and these are arranged as inverted repeats (39), direct repeats (2) or asymmetrical sequences (4). In general, the sequences of unique binding sites are highly conserved and their length and symmetry are evident.
  - Transcription Factors with inverted repeat symmetry: AcrR, AllR, ArsR, AtoC, BaeR, BirA, BetI, CueR, CusR, EnvR, FabR, GlrR, HcaR, HyfR, KdgR IdnR, ilvY, LacI, LldR, MalI, MarR, MhpR, MntR, MurR, NadR, NemR, NikR, NorR, PrpR, RbsR, RcnR, TdcA, TreR, UhpA, UidR, YiaJ, YoeB-YefM, ZntR, Zur.
  - Transcription Factors with direct repeat symmetry: CreB, MngR.
  - Transcription Factors with asymmetric binding sites: ChbR, RhaR, XapR, ZraR.
Release Notes for EcoCyc Version 14.6

Released on December 3, 2010.

EcoCyc KB Statistics
Pathways 276

Reactions 1907

Enzymes 1451

Transporters 254

Genes 4490

Transcription Units 3412

Citations 20,890
- We have added one new metabolic pathway and one new signalling pathway to EcoCyc:
  - sedoheptulose bisphosphate bypass
  - Aerotactic Two-Component Signal Transduction System
  In addition, several purine nucleoside/nucleotide degradation and salvage pathways have been re-arranged into smaller component pathways.
- All two-component signal transduction pathways in EcoCyc have now been updated. A new aerotactic signalling pathway was added, thus bringing the total number of two-component pathways represented in EcoCyc to 27.
- A new function was assigned to the periplasmic PliG protein (formerly YcgK), recently reported to be an inhibitor of g-type lysozyme activity.
- The crystal structures of several transport proteins have been recently solved. EcoCyc provides links to the new Protein Data Bank entries for the membrane transporters CaiT, CusA and FucP and the periplasmic binding protein XylF.
- Curation of transcription factors (TFs) included updates to the summaries for MalT, UlaR, ArgR, MlrA, McbR, TreR, and YqhC. In addition, GO terms were updated for different TFs. The names of TFs were revised, adding "DNA-binding".
Release Notes for EcoCyc Version 14.5

Released on October 1, 2010.

EcoCyc KB Statistics
Pathways 260

Reactions 1884

Enzymes 1450

Transporters 252

Genes 4489

Transcription Units 3409

Citations 20,284
- New Regulation Summary Diagram: Gene pages now contain a diagram that summarizes all regulatory influences on the gene as described in the PGDB. For example, the EcoCyc gene page for bglG shows the influences of transcription factors, attenuation, and post-translational modification of the gene product.
- New Web Services: EcoCyc now supports an array of Web services that enable Web-based retrieval of EcoCyc data such as data for a gene or pathway. [Details]
- New Monoisotopic Mass Search to Support Metabolomics: The Search → Compounds page now contains a filter for searching for compounds by monoisotopic molecular weight, which is useful for analyzing mass spectroscopy data.
- Faster Web Cellular Overview: The recent re-implementation of the Web Cellular Overview has been reworked to significantly increase its speed. The Cellular Omics Viewer speed has been increased, and the dialog for invoking the Omics Viewer has been simplified. Tooltips for this diagram have been improved -- these pop-up windows can be moved, and kept, and multiple such windows can be opened simultaneously.
- Omics Viewer available for Web Regulatory Overview: The Omics viewer is now available for the Web Regulatory Overview, and the speed of the Web Regulatory Overview has been increased significantly.
- We have added three new metabolic pathways to EcoCyc:
- Updates have been made to 21 of the 26 two-component pathways currently included in EcoCyc. The pathways now show correct localisation of components plus an intuitive depiction of the phosphotransfer (including multistep phosphorelay) reactions. Text summaries have also been added. Some examples of updated pathways include:
- Many RNases have been updated so that their associated reactions are more accurate and more comprehensible. EcoCyc also features a new tRNA processing pathway that captures the complex interplay of ribonucleolytic reactions that converts tRNA precursors into the final tRNA that is ready for modification and charging with an amino acid.
- New functions were assigned for the inner membrane proteins YfgF, reported to be a cyclic di-GMP phosphodiesterase and YbdG, characterised as a low abundance mechanosensitive channel of miniconductance.
- We are continuing the analysis of binding sites of different transcription factors, resulting in corrected and relocated binding sites for FhlA, YiaJ, NhaR, Ada, and CaiF. This work is based on evidence supporting the identification of overrepresented motifs in the regulatory regions analyzed, using computational tools and the expertise of the curators.
  Initially, the FhlA-binding sites were represented by large regions of 40 bp, but in 2000 Leonhartsberger et al. proposed that FhlA binds to inverted repeat sequences of 16 bp (CATTTCGTACGAAATG) (Leonhartsberger et al. (2000)). However, sequence alignments showed that this sequence is less conserved in the upstream regulated regions. We showed a new overrepresented sequence (TGTCGnnnnTGACA) that overlaps with the sequence proposed by Leonhartsberger and colleagues. We have therefore relocated, reassigned, and corrected all FhlA binding sites in EcoCyc. In addition, the binding sites of the regulators YiaJ and NhaR were corrected, based on comparisons with homologous sequences reported for Klebsiella pneumoniae (Campos et al. (2008)) and in the RegPrecise database (Novichkov et al. (2010)), respectively. We also have corrected the binding sites of two other transcription factors, Ada and CaiF.
Release Notes for EcoCyc Version 14.1

Released on June 16, 2010.

EcoCyc KB Statistics
Pathways 253

Reactions 1829

Enzymes 1445

Transporters 252

Genes 4490

Transcription Units 3397

Citations 20,123
- We have added three new metabolic pathways and two new signal transduction pathways to EcoCyc:
  - D-malate degradation
  - trehalose degradation VI (periplasmic)
  - uracil degradation III -- We would like to thank Dr. Sydney Kustu for reviewing this pathway.
  - DcuSR two-component signal transduction system
  - QseBC two-component signal transduction system
- The characterisation of several chaperone-usher fimbrial operons (sfmACDHF, ycbQRSTUVF, yraHIJK, yadCKLMhtrEecpDyadN, yehABCD, and yfcOPQRSTUV) in E.coli K-12 was recently reported by Korea et al. (PMID 20345943). These operons are cryptic under normal laboratory conditions, but induced expression in strains lacking the normal type I fimbrial genes resulted in phenotypes that included biofilm formation, adhesion to eukaryotic epithelial cells and microscopically observable pili.
- A new function was assigned to the ChiP protein - reported to be an outer membrane porin for chitooligosaccharides. ChiP expression is controlled by a novel mechanism of gene regulation in E. coli K-12, whereby the induction of an mRNA 'trap' leads to selective degradation of a small regulatory RNA molecule. In this particular case the chitobiose operon (chb) mRNA 'traps' and degrades the constitutively expressed regulatory RNA MicM, resulting in the induction of chiP mRNA translation and ultimately transport of chitooligosaccharides.
- The motif obtained from aligning OxyR binding sites is highly variable due to the length of sequences, even though, through manipulation of the alignment it is possible to detect four conserved regions. For this reason we have relocated, reassigned, and corrected binding sites of the OxyR regulon, corresponding to 19 transcription units. Toledano et al. (1994) showed that OxyR binds in tandem to four ATAG elements and defines a consensus motif, ATAGntnnnanCTATnnnnnnnATAGntnnnanCTAT covering around 40 bp. We now propose a new consensus sequence, GATAGGTTnAACCTATCnnnnnGATAGGTTnAACCTATC, which contains two inverted repeat motifs, GATAGGTTnAACCTATC, of 17 bp separated by 5 bp. This sequence consensus is based on agreement of alignments realized by the curator of these upstream regions and on the corresponding evidence, obtained in the bibliography for every operon, including the similarity to the consensus sequence, data from footprinting assays, computational analysis of these sequences, and profiling of OxyR-dependent gene expression. In the database the OxyR-binding sites are represented by an inverted repeat motif of 17 bp.
- During this last period, we have updated curation on transcription initiation including publications until end of April, 2010.
Release Notes for EcoCyc Version 14.0

Released on March 18, 2010.

EcoCyc KB Statistics
Pathways 248

Reactions 1815

Enzymes 1430

Transporters 249

Genes 4497

Transcription Units 3386

Citations 19,563
- We have added one new metabolic pathway and one new signal transduction pathway to EcoCyc:
  - tetrahydromonapterin biosynthesis
  - GlrKR two-component signal transduction system
    This pathway describes the regulatory system that controls expression of the GlmY small RNA which is itself a regulator of amino sugar metabolism in E. coli.
- Crystal structures of a number of proteins that are thought to form a carboxysome-like proteinaceous microcompartment that functions in ethanolamine utilization were recently reported by Tanaka et al. (PMID 20044574). The structures of EutS, EutL, EutK and EutM are suggestive of their functions, and we are looking forward to their functional characterization in E. coli.
- Curation of transport proteins has included the newly charcterised YtfQ galactofuranose binding protein - the periplasmic component of a predicted ABC type transporter (YtfQRT/YjfF).
- Summaries relating to the cytochrome c biogenesis proteins (CcmA-H) have been updated based on a recent study which sought to purify and characterise the various complexes in order to elucidate the mechanism of haem binding and trafficking.
- We have corrected and relocated the binding sites of the CytR transcription factor. This regulator negatively controls the expression of genes that encode the proteins required for transport and utilization of ribonunucleosides and deoxyribonucleosides. The CytR binding sites were previously represented as long regions which were determined by footprinting of several promoter sequences.
  Computational analysis of these sequences showed that the optimal CytR binding site consists of two octamer repeats, GTTGCATT, in direct o invert orientation and preferably separated by 2 bp. Experimental support of this consensus sequence was obtained from footprinting, site-directed mutagenesis experiments and gene expression. (Pedersen et al. (1997), Jorgensen et al. (1998))
- We have updated curation on transcription initiation including publications until end of December, 2009.
Release Notes for EcoCyc Version 13.6

Released on November 21, 2009.

EcoCyc KB Statistics
Pathways 246

Reactions 1800

Enzymes 1425

Transporters 247

Genes 4495

Transcription Units 3370

Citations 19,156
- We have made many smaller updates to protein summaries to reflect information from recent publications. Updated proteins include HscA, a chaperone required for the assembly of iron-sulfur clusters, and SufA, a protein that transports iron-sulfur clusters during cluster assembly.
- Curation of membrane proteins has included the recent experimental confirmation of YjdL as a dipeptide transporter, while the function of the ChaA protein as a calcium ion transporter was disputed.
- The cytoplasmic protein UspC was reported to act as a scaffolding protein of the KdpD/KdpE two component signal cascade. Under conditions of salt stress the KdpD/KdpE system acts to increase intracellular K+ levels. The stabilizing effect of UspC on the KdpD/KdpE/DNA complex is thought to attenuate the inhibiting effect of increasing intracellular K+ on the kinase activity of KdpD.
- OmpA was reported to influence cellulose production and biofilm formation though the CpxR/CpxA two-component signaling pathway.
Release Notes for EcoCyc Version 13.5

Released on October 7, 2009.

EcoCyc KB Statistics
Pathways 246

Reactions 1805

Enzymes 1422

Transporters 246

Genes 4495

Transcription Units 3369

Citations 18,969

Data Content Improvements
- We have added two new metabolic pathways and one new signal transduction pathway to EcoCyc:
- The DpiAB Two-Component Signal Transduction System was added to the database. This pathway describes the regulatory system that activates the set of genes involved in citrate fermentation in E. coli.
- Curation of transport proteins has included two recently described members of the ATP binding cassette (ABC) family of transporters - the MlaBCDEF transporter, an inner membrane phospholipid transporter involved in the trafficking system that maintains outer membrane organisation in E. coli, and LptABCFG, a lipopolysaccharide transporter.
- New functions were assigned for the membrane protein complexes YnfEFGH - reported to be a selenate reductase - and YagTSR - an aldehyde ferredoxin oxidoreductase with a role in the detoxification of aromatic aldehydes in E. coli.
- Our curation update project for transcriptional regulation is progressing; we have substantially curated published information on regulation of transcription initiation up to the end of June 2009.
- FASTA files in the exported flatfiles: protseq.fasta was renamed to protseq.fsa, and contains the amino acid sequences for all protein-coding genes in EcoCyc. The new file dnaseq.fsa was added, containing the nucleotide sequences for every gene in EcoCyc.
Improvements to EcoCyc Web Site and Desktop EcoCyc
- Genome browser tracks improvements:When displaying external data tracks, a new bar graph mode was added, which fills the rectangular area between the horizontal line and the baseline (corresponding to the score zero) with a solid color. This mode is useful for features that are very narrow, which might otherwise be hard to see. In the graph modes, a single color is assigned to each track. The color can be chosen by adding a special header comment into the GFF file, to allow users to follow their own color conventions. Many common colors can be specified, using this syntax (without quotes): "##color green" . The original graph mode was changed to show scores as horizontal lines spanning the length of the features, instead of showing a dot in the center. On the desktop version, the ordering of the tracks can be changed. In the graph modes, score values that fall outside the selected range are visually indicated. Error reporting of syntactic problems in the GFF files has been improved.
EcoCyc Web Site Improvements
- Web Regulatory Overview: The Regulatory Overview diagram that depicts the transcriptional regulatory network of an organism is now available through the Web. Try toolbar command Tools → Regulatory Overview.
- Quick search enhancements: Make your quick searches more precise as follows. By default a quick search for a term such as "argA" returns a list of all genes, proteins, pathways, compounds, etc that contain that string as a substring. By including additional qualifiers in the search, you can further constrain the search to go directly to the information page you want. For example, by searching for "argA type:gene" you will go directly to the gene page. If you prefer an exact search to a substring search, add the qualifier search:exact. Example: "argA search:exact". The search and type qualifiers can be combined in one search.
- Find Current Object in Other Database: From a protein page, new toolbar commands are available that allow you to display the equivalent protein(s) from one or more other databases in this Web site (such as other E. coli strains). Similar functionality is available for genes, pathways, reactions, and compounds. See these toolbar commands:
  - Protein → Show This Protein in Another Database (equivalent object found based on orthology and name search)
  - Protein → Show This Protein in All Databases (orthology and name search)
  - Gene → Show This Gene in Another Database (orthology and name search)
  - Gene → Show This Gene in All Databases (orthology and name search)
  - Pathway → Show This Pathway in Another Database (frame-id search)
  - Pathway → Show This Pathway in All Databases (frame-id search)
  - Peaction → Show This Reaction in Another Database (frame-id search)
  - Reaction → Show This Reaction in All Databases (frame-id search)
  - Compound → Show This Compound in Another Database (frame-id search)
  - Compound → Show This Compound in All Databases (frame-id search)
EcoCyc Desktop Software Improvements
- Manipulation of Object Groups for Omics Data Analysis: A new facility is available for manipulating groups of objects, such as a group of genes that are up-regulated in a gene expression experiment, or a group of metabolites that are up-regulated in a metabolomics experiment. The facility allows users to:
  - Define and store a group of objects
  - Transform the group into another group (such as to transform a gene list into a list of pathways containing those genes, or into an expanded list of genes that includes all genes in the same operon as the original genes)
  - Perform over-representation analysis on a group, such as asking if the group is statistically enriched for genes in one or more metabolic pathways, for genes in a Gene Ontology biological process, or for genes controlled by a given regulator.
  See the Groups menu and Section 3.8.13 of the Pathway Tools User's Guide.
- Omics data graphing capabilities: The Omics Viewers now have the capability to show a graph of the set of data values (such as for a time series experiment) for a given object or set of objects (such as all the genes in a pathway) in a small popup overlay that the user can drag to reposition as desired. The graph can be customized to display either as a heat map, a bar graph or a plot. In addition, the software remembers the most recently loaded omics dataset so that these graphs can be added to any object display (such as for genes in an individual pathway display). To show the omics graph popup, right click on any object (such as a gene or reaction in any of the Omics Viewers, or a reaction in a pathway display). If there is omics data associated with that object, the menu will include the command "Show Omics Data in Popup". In the Cellular Overview, this command will also appear in the Pathway submenu, which shows the graph for all the objects in the pathway. Right-clicking on any omics graph popup allows you to change the display preferences.
- 13 Additional E. coli and Shigella genomes available: You can download a configuration of the EcoCyc software that contains 13 E. coli and Shigella genomes in addition to EcoCyc.
Release Notes for EcoCyc Version 13.1

Released on June 19, 2009.

EcoCyc KB Statistics
Pathways 242

Reactions 1784

Enzymes 1415

Transporters 244

Genes 4496

Transcription Units 3356

Citations 18,469
- We have added four new metabolic pathways to EcoCyc:
- A number of membrane and transporter proteins have been updated, including the PuuP protein recently confirmed as a putrescine importer and DtpB, a peptide transporter.
- 18 newly identified small proteins (16-50 amino acids) reported by Hemm et al. (PMID 19121005) were added to the database, reflecting an increased recognition of the significance of such proteins in cellular processes.
- We have now completed summaries for all 170 Transcription Factors (TFs) that have at least one experimentally characterized binding site or interaction. These regulators represent 33 families of TFs, and the summaries describe relevant characteristics of each regulatory protein. A list of TFs within EcoCyc, organized by the Gene Ontology, is available here. A summary of the functions of these 170 TFs is the following:
  - Seven TFs are considered to be global regulators and are involved in regulating multiple operons and genes of different functional classes or gene ontologies, including DNA architecture, such as: anaerobiosis (ArcA and FNR), carbon source (CRP), factor for inversion stimulation (FIS), organization, maintenance of nucleoid, as well as other cellular processes (HNS, Lrp, and IHF).
  - Additionally, 21 response regulators belong to two-component systems, 42 TFs are included in the carbon sources system, 17 TFs are related to processes such as transport, biosynthesis and catabolism of the amino acids, 13 TFs are involved in the transport and metabolism of different nitrogen sources, and 8 TFs are classified as metallo-regulators. Note that the TFs can be involved in more than one function.
  - The rest of the TFs are considered to be local regulators that control the genetic transcription of different cellular processes and functional classes, for instance, flagellar and chemotaxis systems, metabolism of nucleosides, transport and synthesis of fatty acids, DNA replication, quorum sensing, toxin-antitoxin systems, adaptation and resistance to different conditions of stress, among others.
- We have completed adding references and evidence codes to 210 promoters. Now every manually curated promoter has a reference and an evidence code associated with it.
Release Notes for EcoCyc Version 13.0

Released on March 9, 2009.

EcoCyc KB Statistics
Pathways 237

Reactions 1751

Enzymes 1409

Transporters 243

Genes 4477

Transcription Units 3375

Citations 17,842
- The EcoCyc Web site has been redesigned to provide a new toolbar and new search commands. For quick instructions on how to use it, click here, or watch the webinar on how to use the new site.
- EcoCyc now provides full-text searches of an E. coli literature corpus of 24,000 articles and 6,000 abstracts. It is available from the new search toolbar at Search → Textpresso. We are grateful to the EcoliHub project for providing the E. coli literature corpus.
- Curation of peptidoglycan metabolizing enzymes has incorporated recent discoveries such as the identification of RodZ filaments that form within the E. coli cell to direct the peptidoglycan synthesis machinery to maintain the cell's rod shape. Also, the MurJ flippase has been identified as being responsible for moving lipid II molecules synthesized on the inner face of the inner membrane to the outer face where they can act as substrates for peptidoglycan biosynthesis enzymes. The identification of this transporter at last makes the connection between peptidoglycan precursor molecule synthesis and polymerization.
- Our curation update project is progressing; we have substantially curated information on regulation of transcription initiation up to the end of Nov 2008.
- We have imported many protein features from UniProt. EcoCyc now contains more than 18,500 protein features such as phosphorylation sites, enzyme active sites, and transmembrane regions. More than half of these features are supported by experimental evidence. Features are highlighted as regions on the protein sequence, at the bottom of protein pages, directly above the References section.
- We updated our GO term assignments by re-importing term assignments from UniProt, as of December 2008. More than 10,000 new annotations were added. The total number of GO term assignments in EcoCyc increased from 33,259 (in version 12.5) to 41,541.
  - Note that the GOAFF file deposited with the Gene Ontology Consortium now carries the more specific taxon ID 511145 (for strain E. coli K-12 MG1655) rather than the more generic taxon ID 83333 (for the group of E. coli K-12 strains).
- To aid the development of flux-balance models of E. coli metabolism, we have calculated and stored the predicted protonation state at pH 7.3 of all chemical compounds in EcoCyc, and we subsequently computationally proton-balanced all EcoCyc reactions.
- A large number of chemicals referred to in enzymatic reactions have been converted to database objects. Chemical structures were added if possible.
Release Notes for EcoCyc Version 12.5

Released on October 15, 2008.

EcoCyc KB Statistics
Pathways 237

Reactions 1714

Enzymes 1397

Transporters 241

Genes 4472

Transcription Units 3359

Citations 17,258
- EcoCyc can now display electron transfer pathways with the correct localization of the component reactions, as well as proton transport across the membrane. Eleven new pathways were created:
- We have added two new metabolic pathways to EcoCyc:
  - biosynthesis of L-Ara4N-modified lipid A
  - oleate β-oxidation
  In addition, the pathway of initiation of fatty acid biosynthesis was reorganized into three component pathways.
- ErfK, YcfS, YbiS, YcbB, and YnhG, the recently identified L,D-transpeptidases involved in peptidoglycan structure and anchoring to the outer membrane, along with a number of other enzymes important for maintaining the rod-shaped structure of E. coli through growth and cell division, have been curated.
- We are now beginning to curate new types of E. coli regulatory processes in EcoCyc in addition to regulation of transcription initiation. Look for information about regulation by attenuation, and regulation by small RNAs, which appears in the transcription unit diagrams present on gene pages, RNA pages, and transcription unit pages.
  Examples:
  - Trp operon page depicts attenuation
  - GlmZ small RNA page lists all transcription units regulated by GlmZ, and depicts its binding sites
  Click below to generate lists of all:
  - Small-RNA mediated regulatory events
  - Attenuation regulation events
- Our general curation update project is progressing; this version contains curated information on regulation of transcription initiation up to end of May 2008.
- Regulatory Overview (desktop EcoCyc): This tool for viewing and exploring the complete E. coli transcriptional regulatory network has been modified so that the inner ring of genes now contains master regulators (defined as the top 15% of regulatory genes based on the number of genes regulated, plus all sigma factors). Mousing over a regulatory arrow pops up a tooltip displaying the name of the regulatory gene and the list of the genes that it regulates, organized by operon. There is a new command in the right-click highlighting menu on a gene: This command shows regulatory arrows for the direct regulatees of the gene, and for all direct regulators of those regulatees.
- Graph tracks for ChIP-chip data: The genome browser graph-track capability was designed for analysis of ChIP-chip datasets. It plots protein binding strength from ChIP-chip datasets as a function of genome position. First released in version 12.0 of Pathway Tools for Web mode only, this capability is now available in desktop mode in addition to Web mode.
  For more information, go to the genome browser and click on the green "?" to the right of the navigation control, and read Section "View Positional Data with External Tracks."
- Many improvements have been made to the Structured Advanced Query Form, which allows you to execute complex queries against EcoCyc through the Web.
- A new reference list at the bottom of each pathway page includes all references cited in the pathway, and in all enzymes belonging to the pathway.
Release Notes for EcoCyc Version 12.1

Released on June 27, 2008.

EcoCyc KB Statistics
Pathways 230

Reactions 1676

Enzymes 1374

Transporters 229

Genes 4472

Transcription Units 3356

Citations 16,909
- A number of DNA repair enzymes, transporters, and other membrane proteins have been updated including the recent identification of LpxT as the protein responsible for attaching phosphate groups to lipopolysaccharide, the identification of MltF as a new lytic transglycosylase involved in peptidoglycan metabolism, and the identification of YgaZ/YgaH as a valine exporter.
- This release includes a collection of 259 new transcription start sites that have been experimentally determined in a high throughput experimental modified RACE approach (with the corresponding new evidence code: EV-EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP). The experiments were performed in the laboratory of Dr. Enrique Morett, Institute of Biotechnology, in collaboration with the laboratory of Dr. Julio Collado-Vides, both at UNAM. This mapping has been supported by NIGMS grant RO1-GM71962.
- This version contains curated information on regulation of transcription initiation up to end of March, 2008.
Release Notes for EcoCyc Version 12.0

Released on April 1, 2008.

EcoCyc KB Statistics
Pathways 224

Reactions 1658

Enzymes 1361

Transporters 227

Genes 4472

Transcription Units 3277

Citations 16,297
- We have greatly expanded EcoCyc assignments to Gene Ontology terms by importing term assignments from UniProt. Previously, EcoCyc contained nearly 4000 GO term assignments covering approximately half of the gene products of E. coli; about one third of those GO terms had an experimental evidence code associated with them. We added more than 1000 GO term assignments with experimental evidence codes and approximately 30,000 GO term assignments with computational evidence codes from UniProt, now covering more than 80% of the gene products of E. coli. Note that GO term assignments in EcoCyc are made to gene products (monomers and multimeric complexes, depending on their function) to optimize the accuracy of annotation. GO term assignments will be updated on an ongoing basis by the EcoCyc curators.
- Updates were made to approximately 40 membrane, transporter, and membrane structure-related proteins. Included are the recent assignments of MdtJI as a sperimidine exporter and YddG as an aromatic amino acid exporter.
- We are currently updating our curation related to transcriptional regulation in E. coli, including the recent literature. In this release we have initiated the annotation of some promoters and DNA binding sites from computational predictions and from high-throughput experiments such as microarrays and ChIP-chip experiments. Only promoters or DNA binding sites that have evidence from at least two of these three types of experiments have been added to EcoCyc. Some examples are: Fur DNA binding sites identified by computational prediction and binding of purified protein in Chen et al. (2007), Sigma32 promoters identified by ChIP-chip, microarray analysis and in vitro transcription assays in Wade et al. (2006), and Sigma32 promoters identified by microarray analysis, transcription initiation mapping and in vitro transcription assays in Nonaka et al. (2006). Promoters identified by libraries of fluorescent transcriptional fusions (Zaslaver et al. (2006)) are also included in this release.
Release Notes for EcoCyc Version 11.6

Released on December 5, 2007.

EcoCyc KB Statistics
Pathways 225

Reactions 1661

Enzymes 1357

Transporters 226

Genes 4470

Transcription Units 3199

Citations 15,883
- We have added two new pathways to EcoCyc:
  - 2-ketoglutarate dehydrogenase complex
  - fructose degradation
  In addition, a number of pathways were re-organized into superpathways with shorter component pathways.
- Data on the regulation of transcription initiation is now up-to-date. EcoCyc contains all promoters, transcription units, regulatory interactions, transcription factors and terminators that were published up to approximately four months before the release date. To achieve this goal, we have used four main strategies: curation by publication year, by regulon, by sigmulon and by biological systems. Note that our current curation does not include plausible interactions derived from high-throughput experiments, such as ChIP-chip and microarrays.
- Updates were made to 28 transporters and 13 membrane and transport-related proteins.
- Using the EC-to-GO mappings of enzymes to the Gene Ontology, we have added GO molecular function terms to every protein that catalyzes a reaction with a full EC number. All terms that were added were assigned computational evidence codes, although experimental evidence exists for the majority of the assignments. As part of our ongoing curation efforts, we will update the evidence codes to the proper experimental evidence codes when appropriate.
Release Notes for EcoCyc Version 11.5

Released on August 15, 2007.

EcoCyc KB Statistics
Pathways 224

Reactions 1615

Enzymes 1342

Transporters 224

Genes 4471

Transcription Units 3187

Citations 16,154
- We have added one pathway to EcoCyc:
  - chitobiose degradation
- In addition to adding new pathways, we have begun to systematically update pathways that were entered into EcoCyc in the early years of the project. All enzymes participating in a pathway are re-curated, and the pathway summary is updated and expanded. Recently updated pathways include the methylerythritol phosphate pathway for the biosynthesis of isoprene units, serine biosynthesis, and glycine biosynthesis.
- We have corrected and relocated the binding sites of the ArcA response regulator. ArcA is considered to be a global regulator and is involved in respiratory metabolism and controlling the expression of about 60 transcription units. The ArcA binding sites were previously represented as long regions of 60 bp, which were determined by foot printing of several promoter sequences. Computational analysis of these sequences showed a shorter 15 bp site, GTTAnnnnnnnGTTA, consisting of two direct repeats of 4 bp separated by 7 bp. Experimental support of this consensus sequence was obtained from foot printing, site-directed mutagenesis experiments and profiling ArcA-P dependent gene expression.
- A number of newly predicted genes were recently added to the E. coli K-12 MG1655 GenBank and RefSeq sequence annotation files. These genes have been added to EcoCyc.
Release Notes for EcoCyc Version 11.1

Released on May 25, 2007.

EcoCyc KB Statistics
Pathways 223

Reactions 5220

Enzymes 1338

Transporters 223

Genes 4436

Transcription Units 3156

Citations 15,953
- We have added six pathways to EcoCyc:
- In an ongoing effort, we are updating the curation of metabolic pathways and enzymes that were initially added to EcoCyc more than ten years ago.
- Acid resistance mechanisms have been curated, including updates to twelve acid resistance proteins, the addition of arginine and glutamate dependent acid resistance pathways (see above), and an update of the lysine degradation I pathway.
- Updates were made to 43 membrane and transport related proteins.
- The annotation of transcriptional promoters regulated by the sigma factors sigma19 (FecI), sigma28 (FliA), and sigma54 (RpoN) has been reviewed and updated. These factors are required for the transcription of specific sets of genes involved in the iron stress response, the flagellar system, and in nitrogen metabolism, respectively. Where experimental data was available, appropriate literature citations and notes were added.
- The TyrR, TrpR and Lrp regulons have been updated. These regulons are related to processes such as transport, biosynthesis and catabolism of the amino acids tyrosine, phenylalanine, and tryptophan (aromatic), and also serine, glycine, glutamate, leucine, isoleucine, valine and threonine. The Lrp regulon is also important for the assimilation of ammonia in poor nitrogen conditions.
- All transcription factors have now been assigned Gene Ontology and MultiFun terms.
Release Notes for EcoCyc Version 11.0

Released on March 16, 2007.
EcoCyc KB Statistics
Pathways 215

Reactions 5003

Enzymes 1323

Transporters 214

Genes 4461

Transcription Units 3063

Citations 15,335
- We have significantly revised a number of pathways in EcoCyc:
  - The "threonine degradation I" pathway was divided into four individual pathways; an overview of all threonine metabolism pathways is represented in the superpathway of threonine metabolism. In addition, aminopropanol biosynthesis was made into a separate pathway.
  - The "methylglyoxal pathway I" was divided into four individual pathways; an overview of all methylglyoxal degradation pathways is represented in the superpathway of methylglyoxal degradation.
  - The "(deoxy)ribose phosphate degradation" pathway was divided into four individual pathways:
  - Glycolysis I was significantly revised to include the enzymes catalyzing the two reactions which allow the pathway to run in the reverse direction, fructose 1,6-bisphosphatase and phosphoenolpyruvate synthase.
- We updated a number of protein function annotations with predictions from an updated annotation of the E. coli genome performed by the Paulsen group at TIGR.
- We finished curation of information about transcriptional regulation of genes involved in the transport and metabolism of different nitrogen sources (including the preferred source, ammonia). This curation included the annotation of sigma54 promoters and nine trancription factors and their regulons, involved in nitrogen metabolism: NtrC, FlhA, NorR, PspF, PspR, HyfR, NacC, ZraR and RtcR.
Release Notes for EcoCyc Version 10.6

Released on January 10, 2007.
EcoCyc KB Statistics
Pathways 205

Reactions 4956

Enzymes 1307

Transporters 211

Genes 4465

Transcription Units 3133

Citations 14,951
- We have updated evidence codes for a large number of proteins that were lacking this information.
- Curation of flagellar proteins has been updated to include information regarding structure and function of several sub-complexes of the flagellum.
- Approximately thirty transporters and other membrane proteins have been curated.
- Notes for 30 regulatory proteins have been expanded and now include short summaries about the evolutionary family to which they belong, their domain composition, and the cellular processes in which the regulated genes are involved. When available, an indication of the active conformation of a complex (dimer, tetramer...) is given. Relevant physiological data about the effectors of transcription factors is also covered, with the aim of helping the understanding of regulation physiology. These summaries also have descriptive information about binding site features (size, consensus sequence, relative position to the transcription start, spatial arrangement of the site sequences).
- We have computationally predicted transcription units for all E. coli genes that were not part of an existing transcription unit. Please be aware of the evidence codes on the right side of many pages that indicate what information was derived from experiments versus from computational predictions. Click on the evidence-code icons (such as the flask) for more information, and citations. Also be aware of the graphical conventions for distinguishing computationally predicted promoters and transcription factor binding sites in operon displays.
Release Notes for EcoCyc Version 10.5

Released on September 8, 2006.
EcoCyc KB Statistics
Pathways 197

Reactions 4854

Enzymes 1276

Transporters 211

Genes 4516

Transcription Units 1662

Citations 14,269
- EcoCyc has reached a major curation milestone: the EcoCyc team has manually curated all E. coli gene products. For many years our curation staff has been performing literature searches for E. coli genes, and writing mini-review summaries describing the gene products for which we found published experimental information. We have completed our first pass of literature searches, resulting in summaries covering 3257 E. coli gene products in EcoCyc. The summaries are present in EcoCyc protein and RNA pages. For the remaining genes, no information was found in the literature.
- We have added two new pathways to EcoCyc:
  - Lipid A-core biosynthesis
  - lipoate biosynthesis and incorporation II
  In addition, a small number of pathways have been reorganized and split into two or more separate pathways.
- We finished curating information on the transcriptional regulation of genes involved in both flagellar and chemotaxis systems; eight new promoters and five new transcription units as well as 21 new DNA-binding sites for the transcriptional regulator FlhDC were added.
- We have completed the curation of 364 transcription units based on single-gene directons. A directon is one or a set of genes transcribed in the same direction, organized into one or several transcription units and operons (Salgado et al. (2000)). In other words, these 364 genes are surrounded by genes that are transcribed in a different direction, and therefore they must be transcribed in isolation.
- Several transporters, DNA metabolism enzymes, proteins involved in peptidoglycan metabolism, lipopolysaccharide and colanic acid biosynthesis enzymes, and other membrane proteins have been curated.
- We have curated the individual ribosomal subunit polypeptides.
- The key players in transcription have been curated, including the core RNA polymerase, Sigma70, Sigma54 and the transcriptional regulators NusA, NusB, NusG and Rho.
- We have updated links to the Swiss-Model and Modbase databases and removed links that were not connected to a model in these databases.
Release Notes for EcoCyc Version 10.1

Released on May 19, 2006.
EcoCyc KB Statistics
Pathways 190

Reactions 4469

Enzymes 1257

Transporters 209

Genes 4517

Transcription Units 1304

Citations 13,274
- We have added one new pathway to EcoCyc:
  - formaldehyde oxidation II (glutathione-dependent)
  In addition, a small number of pathways have been reorganized and split into two separate pathways.
- We have added or updated links to several databases:
  - Links from EcoCyc proteins to UniProt were updated.
  - Links were added from EcoCyc proteins to MODBASE and Swiss-Model. Please note that for many E. coli proteins, protein structure models are not yet available.
- Our general curation update project is progressing. Of the 4517 gene products within EcoCyc, 4349 now have comments or citations or are components of a complex that has a comment or citations. The database now contains 13274 literature citations. Specific areas that were updated include:
  - All 82 tRNAs are now curated
  - Leader peptides of various operons that are regulated by attenuation
  - Proteins involved in transcriptional regulation, including histidine kinases of two-component systems and several transcription factors
  - More than 30 membrane proteins, transporters, and DNA repair enzymes
  - Curation of Escherichia coli strain EDL933, serotype O157:H7 continues, with updates from the literature for approximately 20 proteins.
Release Notes for EcoCyc Version 10.0

Released on March 13, 2006.
EcoCyc KB Statistics
Pathways 187

Reactions 4308

Enzymes 1232

Transporters 208

Genes 4521

Transcription Units 1261

Citations 12,489
- EcoCyc has been updated to reflect many aspects of the revised E. coli genome annotation published in Riley et al. (2006). Specific updates include:
  - 31 genes were deleted from the genome annotation. They have moved to the class "Phantom-Genes" in EcoCyc -- the class of entities previously thought to be genes, but no longer believed to be genes.
  - Approximately 60 new genes were created in EcoCyc to reflect newly discovered genes in the genome.
  - Start and end positions of EcoCyc genes were adjusted where necessary to make them the same as in the revised genome annotation.
  No sequence changes were made as part of the revised genome annotation.
- We have added or updated links to several databases:
  - Links from EcoCyc proteins to PDB were updated.
  - Links were added from EcoCyc proteins to Pfam.
  - Links were added from EcoCyc genes to EchoBASE.
  - Links from EcoCyc to EcoGene now use the new EcoGene web site.
- EcoCyc and RegulonDB have recently been updated with additional regulatory information and represent the largest comprehensive and constantly curated regulatory network of E. coli K-12. A report on our progress has been published in Salgado et al. (2006).
- Our general curation update project is progressing. Of the 4480 polypeptides within EcoCyc, 3848 now have comments or citations or are components of a complex that has a comment or citations. The database now contains 12489 citations. Specific areas that were updated include:
  - More than 60 membrane proteins, transporters, flagellar proteins, and DNA repair enzymes
  - Expansion of coverage of DNA replication to include additional helicases, DNA polymerase I, DNA gyrase and DNA ligase
  - Curation of Escherichia coli strain EDL933, serotype O157:H7 is underway, with updates from the literature for 82 proteins.
- Regulation of degradation pathways: We expanded a project to curate within EcoCyc information about transcriptional regulation of gene expression for genes involved in the degradation of carbon sources, including the catabolism of sugars, polysaccharides and sugar derivatives. Pathways whose gene regulation has been curated are:
  - Methylcitrate cycle
  - Methylmalonyl pathway
  - Conversion of succinate to propionate
  - Acetate utilization
  - Glycolate degradation I
  - Glyoxylate degradation
  - L-ascorbate degradation
  - Glycerol degradation I
  - Glycerol degradation II
  - Superpathway of glycol metabolism and degradation
  - 3-phenylpropionate and 3-(3-hydroxyphenyl)propionate degradation
Release Notes for EcoCyc Version 9.6

Released on December 15, 2005.
EcoCyc KB Statistics
Pathways 187

Reactions 4260

Enzymes 1222

Transporters 206

Genes 4480

Transcription Units 1232

Citations 12,026
- We have added two new pathways to EcoCyc:
  - 1,6-anhydro-N-acetylmuramic acid recycling
  - ADP-L-glycero-β-D-manno-heptose biosynthesis
- We have added Gene Ontology (GO) classifications to our gene pages. GO terms were added automatically based on the existing MultiFun terms and the mapping provided at the GO site. Both GO and MultiFun provide a classification scheme for attributes such as molecular function and biological process. We are planning to curate genes and proteins according to both classification schemes for a period of time.
- Annotations of more than 70 membrane proteins, transporters, and flagellar proteins have been updated and expanded. Annotation of membrane proteins of E. coli strain CFT073 is underway.
- We have curated RNA degradation and processing, including fourteen RNases and related proteins and the degradosome.
- Twenty-four DNA replication genes have been curated, including most of the DNA polymerases, the DNA polymerase III holoenzyme complex and the primosome.
- We have curated within EcoCyc gene regulatory interactions identified in datasets from Ma et al. (2004) and Shen-Orr et al. (2002) that were not present in EcoCyc.
- Regulation of respiration pathways: We completed a project to curate within EcoCyc information about transcriptional regulation of gene expression for genes involved in respiration pathways in E. coli, which include aerobic and anaerobic phases, as well as those for electron transfer, electron donors and electron acceptors. Specific attention involved modifying all NarL binding sites with new central positions resulting from a consensus sequence of the site now defined by 7 nucleotides. Pathways whose gene regulation has been curated are:
  - Aerobic electron transfer
  - Aerobic respiration (electron donors reaction list)
  - Electron transfer (anaerobic)
  - Respiration (anaerobic)
  - Respiration (anaerobic)-electron acceptors reaction list
  - Respiration (anaerobic)-electron donors reaction list
- Regulation of degradation pathways: We completed a project to curate within EcoCyc information about transcriptional regulation of gene expression for genes involved in the degradation of carbon sources, including the catabolism of sugars, polysaccharides and sugar derivatives. Regulation of operons encoding enzymes of glycolysis, the pentose phosphate pathway, the TCA cycle, and the Entner-Doudoroff pathway were also curated in this phase. Pathways whose gene regulation has been curated are:
  - Lactose degradation III
  - D-allose degradation
  - D-arabinose degradation
  - Fucose degradation
  - Galactose degradation I
  - Glucose and glucose-1-phosphate degradation
  - Glycogen degradation
  - L-arabinose degradation
  - L-xylose degradation
  - Mannose degradation
  - Rhamnose degradation
  - Ribose degradation
  - Trehalose biosynthesis and degradation-low osmolarity
  - Xylose degradation
  - beta-D-glucuronide degradation
  - D-galactarate degradation
  - D-galacturonate degradation
  - D-glucarate degradation
  - Galactonate degradation
  - Ketogluconate metabolism
  - L-idonate degradation
  - Galactitol degradation
  - Mannitol degradation
  - Sorbitol degradation
  - Superpathway of hexitol degradation
  - Fructoselysine degradation
  - Glucosamine degradation
  - Glucosamine degradation
  - N-acetylglucosamine
  - N-acetylmannosamine
  - N-acetylneuraminic acid dissimilation
  - Glycolysis I
  - Methylglyoxal pathway
  - Non-oxidative branch of the pentose phosphate pathway
  - Oxidative branch of the pentose phosphate pathway
  - TCA cycle
  - Glyoxylate cycle
  - Pyruvate dehydrogenase
  - Pyruvate oxidation pathway
  - Entner-Doudoroff pathway I
- Our general curation update project is progressing. Of the 4471 polypeptides within EcoCyc, 3758 now have comments or citations or are components of a complex that has a comment or citations. The database now contains 12026 citations.
Release Notes for EcoCyc Version 9.5

Released on September 30th, 2005.
EcoCyc KB Statistics
Pathways 184

Reactions 3939

Enzymes 1198

Transporters 198

Genes 4481

Transcription Units 1127

Citations 11,079
- There have been many enhancements to the Pathway Tools software used to query EcoCyc. Please see the Pathway Tools Release Notes for more details. Highlights include:
  - Many improvements to the Cellular Overview and Omics Viewer, including abilities to magnify the display of a pathway within the Overview and Omics Viewer, and the ability to generate a table of omics-colored pathway drawings for all pathways whose omics values exceed some threshold.
  - A new suite of comparative genomics tools allows you to perform global comparisons among the 170 BioCyc DBs including EcoCyc. See the new Comparative Analysis section in the BioCyc Query Page.
  - A new comparative genome browser allows you to visualize chromosomal regions containing orthologous genes from EcoCyc and the other 170 BioCyc databases.
- We have added one new pathway to EcoCyc:
  - putrescine degradation II
- Annotations of 57 transcriptional regulators have been updated and checked. Where experimental data was available, appropriate literature citations were added. In addition, annotations of membrane proteins have been updated and expanded, and we have added significant curation of proteins involved in RNA degradation and processing.
- In an ongoing effort to eliminate duplicate information, we have combined the display of polypeptides and their homomultimers. Due to this update, the reported number of proteins that have comments in EcoCyc has declined since version 9.1.
Release Notes for EcoCyc Version 9.1
Released on May 23, 2005.

EcoCyc KB Statistics
Pathways 183

Reactions 3873

Enzymes 1186

Transporters 197

Genes 4477

Transcription Units 1113

Citations 10,747
- EcoCyc has passed the 10,000 citation milestone!
  The information in EcoCyc has been derived from 10,747 peer-reviewed publications which are cited in the database. EcoCyc curators integrate information from many biomedical publications. They produce mini reviews of protein and RNA gene products that are stored as comments within those database objects. Of the 4465 polypeptides within EcoCyc, 3722 now have comments or citations or are components of a complex that has a comment or citations.
- We have curated protein degradation and processing, including twenty-eight proteases and peptidases and a number of functionally related proteins.
- We have added one new pathway to EcoCyc:
  - trehalose degradation II (high osmolarity)
- We have analyzed the E. coli regulatory network in RegulonDB and EcoCyc in detail. Differences between the two databases were mentioned in Ma HW, et al., 2004, Nucleic Acids Res. 2004 32(22):6643-9. We have identified all differences and have generated a unified description of the regulatory network in terms of regulatory and regulated genes and proteins.
- Annotations of transcriptional regulators have been updated and expanded.
Release Notes for EcoCyc Version 9.0
Released on February 25, 2005.

EcoCyc KB Statistics
Pathways 183

Reactions 3634

Enzymes 1148

Transporters 196

Genes 4476

Transcription Units 983

Citations 9873
- EcoCyc's coverage of complex cellular systems has grown. We have recently entered or updated comments on essential and non-essential cell division proteins in E. coli. This curation was performed under the guidance of Dr. William Margolin at the University of Texas, Houston. In addition, we have curated a number of flagellar proteins and membrane lipoproteins.
- Our general curation update project is progressing. Of the 4463 polypeptides within EcoCyc, 3609 now have comments or citations or are components of a complex that has a comment or citations. The database now contains 9873 citations.
- We have added one new pathway to EcoCyc:
  - folate polyglutamylation I
- Due to our ongoing effort to eliminate duplicate binding sites of transcriptional regulatory proteins in the promoter regions of divergently transcribed genes and operons, the number of reactions reported in EcoCyc has declined.
- We have substantially reorganized and expanded our display of genes and transcription units on the gene pages. In addition to the gene and operon, we now display information on the surrounding genes and their regulatory sites. This allows visualization of potentially overlapping regulatory regions, and thus the formulation of new hypotheses concerning transcriptional regulation. For example, see ybjC.
- A new genome browser with expanded features implemented in the more common horizontal display format is available. For example, see the browser centered around dnaA. Some of the key features are:
  - At the top of the page, the full chromosome is shown at low resolution. A selected region of the chromosome is displayed at higher magnification in the lower part of the screen.
  - The full chromosome view at the very top indicates the magnified region by means of a red, rectangular cursor.
  - Magnified regions are wrapped over several lines, thus showing more context.
  - Several levels of semantic zooming show increasing detail upon increased magnification.
  - Protein ORFs are visually distinguished from RNA genes, and genes belonging to the same operon are assigned the same color.
  - An improved navigation interface offers a panel of control arrows that allow movement and zooming. Additionally, base-pair positions or a gene name can be manually entered into text entry boxes to position the browser.
  - Mouse-over of genes shows gene names and intergenic distances to the neighbors in base pairs. Mouse-over of promoters shows the activating and inhibiting transcription factors.
Release Notes for EcoCyc Version 8.6
Released on November 8, 2004.

EcoCyc KB Statistics
Pathways 182

Reactions 3676

Enzymes 1144

Transporters 197

Genes 4476

Transcription Units 977

Citations 9305
- This EcoCyc release includes updates derived from the revised 2004 E. coli K-12 GenBank entry U00096.2, which supersedes the GenBank entry U00096.1 deposited by the Blattner laboratory in 1997. A summary of the updates to EcoCyc is listed below. Please note that due to changes in U00096.1, the genes encoded by successive b-numbers above b4409 are not necessarily adjacent on the chromosome.
- Our curation update project is progressing. Of the 4458 polypeptides within EcoCyc, 3503 now have comments or citations or are components of a complex that has a comment or citations. The database now contains 9305 citations.
- We have reorganized and added comments to three pathways in EcoCyc:
- Summary of the EcoCyc updates performed as a result of incorporating GenBank entry U00096.2:
  - The nucleotide sequence has been revised in 254 locations. The revisions include insertions, deletions, and substitutions. The Blattner laboratory provides a full list of sequence updates at URL http://www.genome.wisc.edu/sequencing/MG1655_update.xls.
  - Those sequence revisions necessitated updating all sequence features in EcoCyc including the locations of genes, transcription start sites, terminators, and transcription factor binding sites. We are grateful to Tatiana Tatusov and James Ostell of NCBI for assistance in computing the new coordinates of these sequence features. All EcoCyc version 8.6 gene sequence coordinates were obtained directly from U00096.2, with the exception that in approximately 25 cases, the EcoCyc project has modified the extents of the genes based on information from the experimental literature. However, coordinates of transcription start sites, terminators, and transcription factor binding sites in EcoCyc version 8.6 were derived from the EcoCyc version 8.5 coordinates, transformed to reflect the nucleotide sequence insertions and deletions.
  - U00096.2 modifies the E. coli gene list with deletions, additions, merges, and splits, and those modifications have been imported into EcoCyc as follows. Please note that gene names and product names were not imported from U00096.2 into EcoCyc on a large scale because of the careful curation of these fields that has occurred in EcoCyc for many years. However, for the genes below we did review all gene names and product names from U00096.2 and import them into EcoCyc when appropriate (e.g., for the created genes listed below).
    - The following genes were deleted: b0302 b0322 b0332 b0395 b0663 b0667 b0669 b0671 b1017 b1030 b1031 b2391 b3122 b3837
    - The following genes were created: b4409 b4411 b4412 b4415 b4419 b4420 b4421 b4422 b4423 b4424 b4425 b4428 b4429 b4447 b4455
    - The following genes were merged:
      - b2612 and b2613 were merged and became b4461
      - b1898 and b1899 were merged and became b4460
      - b2655 and b2656 were merged and became b4462
      - b2772 and b2773 were merged and became b4463
      - b2884 and b2885 were merged and became b4464
      - b2931 and b2932 were merged and became b4465
      - b2973 and b2974 were merged and became b4466
      - b3015 and b3016 were merged and became b4469
      - b3108 and b3109 were merged and became b4470
      - b3111 and b3112 were merged and became b4471
      - b3245 and b3246 were merged and became b4472
      - b3285 and b3286 were merged and became b4473
      - b3372 and b3373 were merged and became b4474
      - b3419 and b3420 were merged and became b4475
      - b3435 and b3436 were merged and became b4476
      - b3694 and b3695 were merged and became b4479
      - b3762 and b3763 were merged and became b4480
      - b3814 and b3815 were merged and became b4482
      - b3840 and b3841 were merged and became b4483
      - b3913 and b3914 were merged and became b4484
      - b4228 and b4229 were merged and became b4485
      - b4343 and b4344 were merged and became b4486
      - b4404 and b4405 were merged and became b4481
      - b3948 was merged into b3947
    - The following genes were split:
      - b2978 was split into b4467 and b4468
      - b3692 was split into b4477 and b4478
    - The following genes changed b-numbers. Many of these genes are interrupted genes that contain distinct IDs within EcoCyc, but are assigned a single b-number in U00096.2.
      - b3767 and b3768 became b4488
      - b1016 became b4490
      - b1169 and b1170 became b4491
      - b1401 and b1405 became b4492
      - b1416 and b1417 became b4493
      - b1720 and b1721 became b4494
      - b1933 and b1934 became b4495
      - b1964, b1965 and b1966 became b4496
      - b1979 and b1980 became b4497
      - b2087 and b2090 became b4498
      - b2115, b2116 and b2117 became b4499
      - b2227 and b2228 became b4500
      - b4091 became b4487
Release Notes for EcoCyc Version 8.5
Released on Sept. 17, 2004.

EcoCyc KB Statistics
Pathways 182

Reactions 3629

Enzymes 1133

Transporters 197

Genes 4497

Transcription Units 956

Citations 8862
- Our curation update project is progressing. Of the 4478 polypeptides within EcoCyc, 3461 now have comments or citations or are components of a complex that has a comment or citations. The database now contains 8862 citations.
- Coverage of regulation of transcription initiation has grown. EcoCyc now describes 2393 specific interactions of transcription initiation (promoters and binding sites for regulators), including more than 1000 mapped transcription initiation sites with nearly 1400 binding sites for specific transcriptional regulatory factors (TFs). Furthermore, the names of TFs have been standardized, describing whether a TF acts as a repressor, activator, or has a dual effect. Comments on regulatory proteins have been expanded and updated. Annotations include the active conformation of TFs with the associated signal metabolites, the evolutionary family to which they belong, and whether they are auto regulated.
- The EcoCyc Cellular Overview diagram has been re-organized. Metabolic pathways within the Overview are now grouped by classes, for example, all amino-acid biosynthetic pathways are grouped together on the diagram. Mousing-over a shaded background region of the Overview will identify the class of pathways in that region.
- Please note that EcoCyc has not yet been modified to include the recent update to the E. coli genome sequence deposited in Genbank. We plan to include the updated E. coli sequence in our November 2004 release.
- EcoCyc is now an open database, meaning it is free to all users, and that it can be redistributed, with or without modifications. See the license agreement that you click through on the way to the data files for more details. EcoCyc continues to be available in the following forms:
  - Bundled with the Pathway Tools software in a form that you can run on a PC/Windows, PC/Linux, or SUN computer as a desktop application, or that you can run as a local EcoCyc Web server on your intranet
  - As a set of flat files you can load into your local database, or query using Perl scripts
Release Notes for EcoCyc Version 8.1
Released on June 23, 2004.

EcoCyc KB Statistics
Pathways 182

Reactions 3547

Enzymes 1132

Transporters 197

Genes 4491

Transcription Units 931

Citations 8696
- Our curation update project is progressing. Of the 4479 polypeptides within EcoCyc, 3395 now have comments or citations or are components of a complex that has a comment or citations. The database now contains 8696 citations.
- We have added five new pathways to EcoCyc:
- We have completed curation of DNA repair enzymes in E. coli. In E. coli, there are a wide range of DNA repair systems. These systems include those for the direct reversal of DNA damage (photo reactivation, alkyl transfer) as well as indirect repair through the excision of damaged bases/sections of DNA and subsequent re-synthesis using the intact strand as template (base excision repair, nucleotide excision repair, mismatch repair) and homologous recombination. This curation work was performed at TIGR under the guidance of Dr. Jonathan Eisen.
- EcoCyc is now an open database, meaning it is free to all users, and that it can be redistributed, with or without modifications. See the license agreement that you click through on the way to the data files for more details. EcoCyc continues to be available in the following forms:
  - Bundled with the Pathway Tools software in a form that you can run on a PC/Windows, PC/Linux, or SUN computer as a desktop application, or that you can run as a local EcoCyc Web server on your intranet
  - As a set of flat files you can load into your proprietary database
- A Web page generated at each EcoCyc release contains a list of unsequenced enzymes of E. coli. These are enzymes that have been characterized biochemically and reported in the experimental literature, but whose gene has not been identified in the E. coli genome. Identification of these genes represents a challenge to the experimental community. A link to this page can be found under Information on the right menu on the EcoCyc.org page. A commentary on the larger topic of enzyme activities for which no sequence is known has been published by P. Karp in Genome Biology.
- Conferences of interest to the E. coli community are now tabulated on our Web site. See the Conferences link under Services on the right menu on the EcoCyc.org page, or click here.
- EcoCyc gene pages now contain links to corresponding pages in the EcoGene database.
Release Notes for EcoCyc Version 8.0
Released on March 12, 2004.

EcoCyc KB Statistics
Pathways 178

Reactions 3331

Enzymes 1043

Transporters 183

Genes 4479

Transcription Units 858

Citations 8014
- Our curation update project is progressing. Of the 4474 polypeptides within EcoCyc, 2595 now have comments or citations or are components of a complex that has a comment or citations. The database now contains 8014 citations.
- The reactions contained within the superpathway of arginine degradation have been organized into separate subpathways:
  - arginine degradation XII, which includes the reactions from arginine to putrescine
  - putrescine degradation, which includes the reactions from putrescine to 4-aminobutyrate
  - 4-aminobutyrate degradation, which includes the reactions from 4-aminobutyrate to succinate
- We have made extensive updates to the database links within EcoCyc. The links from EcoCyc to Swiss-Prot were previously incomplete; we have added links to virtually all EcoCyc polypeptides, so that 99% of EcoCyc entries now contain links to Swiss-Prot. We have also added links from most EcoCyc polypeptides to RefSeq. The preceding links are all displayed under the heading "Unification Links," meaning links to information about the same biological object in a different database.
Release Notes for EcoCyc Version 7.6
Released on November 4, 2003.

EcoCyc KB Statistics
Pathways 176

Reactions 3177

Enzymes 992

Transporters 169

Genes 4477

Transcription Units 828

Citations 6223
- Our curation update project is progressing. Of the 4474 polypeptides within EcoCyc, 1925 now have comments or citations or are components of a complex that has a comment or citations. The database now contains 6223 citations.
- We have added information about untranslated RNA species to EcoCyc. Information about the following RNAs has been curated: csrB, csrC, dicF, dsrA, ffs, gcvB, micF, oxyS, rdlD, rnpB, rprA, rybA, rybB, rydB, ryeA, ryeB, ryeC, ryeD, ryeE, ryfA, rygB, rygC, spf, sraA, sraB, sraD, sraE, sraF, sraG, sraH, sraI, sraJ, sraL, ssrA, ssrS, C0067, C0293, C0299, C0343, C0362, C0465, C0614, C0664, C0719, C0730, IS061, IS092, IS102, IS128, IS183, T44, tke1, tke8, tp2, tpke11, and tpke70.
- Since February, we have added 129 new regulatory interactions, 57 promoters, 48 transcription units, 5 protein complexes of transcriptional regulators, 9 terminators, and corrected 3 genes. These updates are supported by 323 references to the literature.
- Transcriptional regulator names have been updated to be more descriptive.
- The following pathways have been updated:
  - The PPRP biosynthesis I and PPRP biosynthesis II pathways have been added.
  - The pantothenate and coenzyme A biosynthesis pathway has been split into two distinct pathways, pantothenate biosynthesis and coenzyme A biosynthesis.
  - The glutamate biosynthesis pathway has also been divided into two distinct pathways, glutamate biosynthesis I and glutamate biosynthesis III.
- Many other miscellaneous corrections and updates have been applied.
Release Notes for EcoCyc Version 7.5
Released on August 29, 2003.

EcoCyc KB Statistics
Pathways 173

Reactions 3090

Enzymes 975

Transporters 168

Genes 4399

Transcription Units 810

Citations 4710
- We are currently updating and expanding our curation of all E. coli gene products. As part of this expansion, we are authoring extended comments and curating updated reference lists. This information is typically found in the display windows for gene products in EcoCyc (rather than in the gene windows). Of the 4468 polypeptides within EcoCyc, 1600 now have comments or citations or are components of a complex that has a comment or citation. Our goal is to complete this expansion within the next few years.
- EcoCyc database windows now feature full lists of references in addition to the links to abstracts that have been supplied previously. The list of references associated with each database object (e.g., polypeptide, pathway, transcription unit, etc.) is located at the bottom of the display window.
- The pathway class hierarchy within EcoCyc has been updated and improved to facilitate browsing of metabolic pathways within the BioCyc databases. The pathway hierarchy may be viewed here.
- The Pathway Tools software now supports association of evidence codes with information in the database. Currently, EcoCyc uses these codes most frequently for transcription units and promoters to indicate the type of evidence for the existence of these entities (for example, was a promoter predicted computationally or elucidated experimentally?). In subsequent releases, more evidence information will be available. The presence of a computer icon or a flask icon, respectively, indicate computational versus experimental evidence for an entity. Click on those icons to obtain more details about the evidence for an entity.
- Many other miscellaneous corrections and updates have been applied.
Release Notes for EcoCyc Version 7.1
Released on May 20, 2003.

EcoCyc KB Statistics
Pathways 173

Reactions 3001

Enzymes 944

Transporters 168

Genes 4396

Transcription Units 777

Citations 4406
- We are pleased to announce that new releases of EcoCyc at the BioCyc web site now occur quarterly, rather than twice a year. Newly updated EcoCyc flat files are also released quarterly. (The downloadable executable Pathway Tools containing EcoCyc is still released twice per year.)
- The following pathways have been added to EcoCyc:
  - cyclopropane fatty acid (CFA) biosynthesis
  - fructoselysine degradation
  - lipoate biosynthesis and modification
  - lipoate salvage and modification
- The y-gene names created by Dr. K. Rudd have been added to all ORFs within EcoCyc to enable searching for E. coli genes by those names. For example, the gene b1806 is now named yeaY.
- Many other miscellaneous corrections and updates have been applied.
Release Notes for EcoCyc Version 7.0
Released on February 28, 2003.

EcoCyc KB Statistics
Pathways 169

Reactions 2909

Enzymes 930

Transporters 169

Genes 4392

Transcription Units 747

Citations 3780
- In 2001, Serres et al. (Genome Biol 2(9)RESEARCH0035) published an update to the annotation of the E. coli genome in which new functions for unidentified E. coli ORFs were listed, based on experimental reports in the literature, and based on sequence analysis. We have loaded an even newer version of the annotation updates by Riley's group (from Riley's GenProtEC database) into EcoCyc. These updates involved changes to the function of ORFs only, and not to other genes with functions already assigned. In many cases, the new functional information was partial, such as indicating only that a protein is a putative membrane protein.
- The pathways describing synthesis of nucleotides have been updated and divided into de novo and salvage synthesis pathways. The salvage synthesis pathways have been moved within the pathway hierarchy from the Network of nucleotide interconversions class (a subclass of Central intermediary metabolism) to the Nucleotides class (a subclass of Biosynthesis). The pathway objects replaced by these new updated pathways have been removed from EcoCyc.
  - The pathway de novo biosynthesis of pyrimidine ribonucleotides replaces and extends the former pyrimidine biosynthesis pathway. The pyrimidine biosynthesis pathway ended with the synthesis of UMP; the new de novo biosynthesis of pyrimidine ribonucleotides pathway extends to UDP, UTP, CDP, and CTP.
  - The new salvage pathways of pyrimidine ribonucleotides replace the former pyrimidine ribonucleotide/ribonucleoside metabolism pathway.
  - The pathways de novo biosynthesis of pyrimidine deoxyribonucleotides and salvage pathways of pyrimidine deoxyribonucleotides replace the former deoxypyrimidine nucleotide/side metabolism. The pathway de novo biosynthesis of pyrimidine deoxyribonucleotides includes the reduction of the nucleoside di- and tri-phosphates to the corresponding deoxyribonucleotides, which was not depicted within deoxypyrimidine nucleotide/side metabolism.
  - The pathway de novo biosynthesis of purine nucleotides replaces and extends the former purine biosynthesis pathway to include the reductions of the nucleoside di- and triphosphates to the corresponding deoxyribonucleotides.
  - Two salvage pathways of purine nucleoside biosynthesis have been added, salvage pathways of adenine, hypoxanthine, and their nucleosides and salvage pathways of guanine, xanthine, and their nucleosides, which replace the former purine ribonucleotide/ribonucleoside metabolism pathway.
  - Because the reduction of each ribonucleotide to the corresponding deoxyribonucleotide has been added to the pathways describing the de novo biosyntheses, the pathway that formerly comprised this group of reactions (entitled deoxyribonucleotide metabolism) has been removed.
- The following other pathways have been added:
  - phenylacetate degradation, aerobic
  - L-ascorbate degradation
- We have added 17 new promoters, 25 new DNA-binding sites for specific transcriptional regulators and 23 new transcription units. As a result of identifying the promoter, we verified and modified the precise position of the initiation of 21 genes (aldB, aspA, focA, gntK, livJ, slp, tdcR, caiF, upp, fixA, aroK, tauA, gcvR,nmpC, zraP, phoA, rbsD, ilvI, csiD, sugE, fxsA), whose initiation was overlapping transcription initiation.
- Many other miscellaneous corrections and updates have been applied.
Release Notes for EcoCyc Version 6.5
Released on August 30, 2002.

EcoCyc KB Statistics
Pathways 164

Reactions 2862

Enzymes 918

Transporters 168

Genes 4393

Transcription Units 724

Citations 3701
- Note that the reaction count includes metabolic reactions, transport reactions, and reactions related to transcriptional control of gene expression
- Approximately 40 new transcription units have been added to EcoCyc since the last release. We have currently gathered information for 110 transcriptional regulators, 956 associated operator sites and interactions, and 812 mapped promoters. We estimate that these numbers correspond to approximately 25% of the interactions and knowledge necessary to describe the regulatory network of E. coli. Some general properties of this fraction of the network are the following. Around 80% of all transcription units are composed of one to three genes. These genes are mostly transcribed by a single promoter (80% of the cases) with few genes having two to six different promoters. We estimate that more than 85% of these are of the type recognized by sigma 70 RNA polymerase. More than 90% of genes are regulated by at most 3 different regulatory proteins. This significant fraction of the regulatory network in E. coli is a powerful resource for analysis of global experimental studies of transription and proteome, as well as in studies of properties of regulatory networks.
Release Notes for EcoCyc Version 6.0
Released on February 15, 2002.

EcoCyc KB Statistics
Pathways 164

Reactions 2760

Enzymes 914

Transporters 164

Genes 4393

Transcription Units 684

Citations 3636
- Note that the reaction count includes metabolic reactions, transport reactions, and reactions related to transcriptional control of gene expression
- EcoCyc contains many updates to the descriptions of E. coli genes, enzymes, pathways, and transporters
- Approximately 50 new transcription units have been added to EcoCyc since the last release
Release Notes for EcoCyc Version 5.6
Released on June 15, 2001.

EcoCyc KB Statistics
Pathways 165

Reactions 2604

Enzymes 905

Transporters 162

Genes 4393

Transcription Units 629

Citations 3508
- EcoCyc contains many updates to the descriptions of E. coli genes, enzymes, and transporters
- Over 100 new E. coli transcription units have been added since the last version
- EcoCyc proteins now contain WWW links to the PIR database
- The following pathways were added to EcoCyc since the last release:
  - threonine biosynthesis from homoserine
  - alkanesulfonate monooxygenase two-component system
  - conversion of succinate to propionate
  - propionate metabolism, methylcitrate cycle
  - allantoin assimilation
  - D-allose catabolism
  - ketogluconate metabolism
  - tRNA charging reactions
  - biosynthesis of 2'-(5"-triphosphoribosyl)-3'-dephospho-CoA
  - BarA-UvrY Two-Component Signal Transduction System
Release Notes for EcoCyc Version 5.4
Released on Sept 1, 2000.

EcoCyc KB Statistics
Pathways 165

Reactions 2115

Enzymes 884

Transporters 158

Genes 4393

Chemical Compounds 773

Citations 3208
- Dr. Julio Collado's RegulonDB database has been integrated with EcoCyc. EcoCyc therefore contains descriptions of many transcription units, where a transcription unit is defined as a promoter, its associated regulatory elements, and its downstream genes. EcoCyc also contains descriptions of many transcription factors, and their interactions with the transcription units they control.
  This information may be accessed within EcoCyc in several ways. Gene-display windows now show schematic diagrams of known transcription units for the gene. Within that transcription unit:
  - Clicking on the transcription unit as a whole will produce a new type of window that displays information about the transcription unit and all of its internal regulatory sites.
  - Clicking on a transcription-factor binding site within the transcription unit will produce a display window for the transcription factor that lists all transcription units that it controls.
  - Clicking on the promoter ...
  - Clicking on a gene within the transcription unit will display a window for that gene.
- Because MetaCyc is now meant as our general-purpose metabolic-pathway database, we have removed non-E. coli specific metabolic information from EcoCyc, such as metabolic reactions and compounds that do not occur in E. coli. That data had previously been present in EcoCyc for general reference purposes.
- A new version of Dr. Monica Riley's classification system for E. coli genes has been added to EcoCyc.
- An assignment of E. coli genes to paralogous groups by Dr. Riley and Dr. Bernard Labedan has been added to EcoCyc. When a gene is a member of a paralogous group, the name of the group will be displayed in the EcoCyc gene window. Clicking on the group name will display a list of all genes within the group. See: Labedan, B and M. Riley. (1999) Genetic inventory: Escherichia coli as a window on ancestral proteins .In Organization of the Prokaryotic Genome (Robert Charlebois, editor) Chapter 17, pages 311-329, ASM Press, Washington, D.C.
- Many revisions to E. coli gene names and to the functions of E. coli gene products have been incorporated in EcoCyc.
Release Notes for EcoCyc Version 5.0

Released on June 16, 1999.

EcoCyc KB Statistics
Pathways 159

Reactions 946

Enzymes 629

Transporters 13

Genes 4390

Chemical Compounds 1868

Citations 1944

Notes: "Pathways" includes both pathways of small-molecule metabolism and signalling pathways. "Reactions" includes enzymatic and transport reactions.

Changes to the EcoCyc Data
- Drs. Ian Paulsen and Milton Saier of UC San Diego have recently joined the EcoCyc collaboration. Their group will be annotating the transport proteins of E. coli using the same detailed, literature-based approach as used for E. coli enzymes and pathways. Version 5.0 of EcoCyc contains all of the E. coli phosphotransferase system (PTS) transporters. Subsequent versions of Ecocyc will include detailed descriptions of the primary and secondary transporters and channel proteins present in E. coli.
  The PTS functions by transporting and concomitantly phosphorylating their sugar substrates using phosphoenolpyruvate as a phosphate donor. Each PTS transporter characteristically consists of a sugar-specific multidomain Enzyme II complex with between one and four protein subunits and two general energy coupling proteins, Enzyme I and Hpr. The Version 5.0 release describes each of the 20 Enzyme II complexes and the two general energy coupling proteins of the PTS.
- New pathways in this version are:
  - isopentenyl diphosphate biosynthesis, mevalonate-independent
  - acetate utilization
  - dissimilation of N-acetylglucosamine, N-acetylmannosamine and N-acetylneuraminic acid
  - ammonia assimilation cycle
  - L-idonate catabolism
  - arginine catabolism
- A variety of miscellaneous updates have been applied to EcoCyc genes and enzymes.
Modifications to the Pathway/Genome Navigator Interface
- You must now use Netscape 4.0 or Internet Explorer 4.0 (or higher) to access EcoCyc because older versions of these programs do not have proper support for Javascript.
- The EcoCyc web site has been upgraded and reorganized. Although the location of the EcoCyc home page has not changed, the URL of the main EcoCyc query page has changed to [old URL removed]. Please update any bookmarks you may have to the old server page.
- Users may now issue structured queries to the EcoCyc database using an HTML query form that is available at [old URL removed].
- X-Windows version: In Overview mode, the menu that appears when the user right clicks on a compound or reaction in the Overview has been reorganized and has additional functionality. A new function is the ability to show all connections from one occurrence of a compound in the Overview to all other occurrences of that compound.
- X-windows version: A new user preference allows the Overview diagram to be scaled as desired.
- X-windows version: The user can now print the contents of the Answer List and the History List using commands under the Special menu.
- X-Windows version: Users can now control the font size using a newly defined user preference
Release Notes for EcoCyc Version 4.5

Released September 4, 1998.
The most significant changes are marked with a "*".
Changes to the EcoCyc Data
- The gene descriptions within EcoCyc have undergone extensive curation to update gene name and synonym information, as well as product descriptions for all E. coli genes.
- EcoCyc is very careful to distinguish genes whose functions have been determined experimentally, from those whose functions have been determined through sequence analysis. The names of gene products whose functions have been determined through sequence analysis always contain the word "putative" and, very occasionally for a high certainty hit, "probable." The level of assurance for each functional assignment is given in the following way. If an orf sequence shows similarity to a number of hydrolases, all of which act on on sugars, the orf is identified as, for instance, a "putative sugar hydrolase" . In other cases an assignment may be "putative amidotransferase" or "putative aminotransferase" or "putative formyl acetyltransferase". More often a degree of uncertainty is signified by by confining the assignment to a general class such as "putative transferase" or sometimes only as an "enzyme" if the orf can be identified as an enzyme, but not what kind of enzyme. the same gradations are used throughout for all types of gene products such as regulators, transport components, rnas.
Modifications to the EcoCyc Graphical User Interface (GUI)
- *EcoCyc pathway diagrams now include arrows showing regulatory interactions between small molecules and enzymes of a pathway. Each arrow portraying feedback inhibition or activation leads from a small molecule in the pathway to a "+" or "-" sign adjacent to the enzyme whose activity it moderates. The presence of the "+" or "-" indicates whether activators, inhibitors, or both, are known for a given enzyme.
- The Overview diagram now uses different icons for different classes of compounds:
  square = carbohydrate
  triangle = amino acid
  diamond = lipid
  horiz elipse = purine
  vert elipse = pyrimidine
  hexagon = protein
  circle = all other compound types
  Solid icons mean the compound is phosphorylated
- *EcoCyc now generates automatic layouts of signal-transduction pathways, and the Overview diagram now includes signal-transduction pathways. For example, query the proteins PhoB or NarQ, and you will see links to their pathways, which can be displayed.
X-Windows EcoCyc GUI Modifications
- *The Highlighting menu for Overview mode has been redesigned and has a number of additional features and query operations, including the ability to paint expression data on the Overview diagram.
- A new user preference controls whether the "Next Answer" command retrieves only one answer per click, or N answers, when there are N display panes active.
- The main menu now includes commands called Fix and Unfix, which allow the user to fix a display pane, thus preventing additional object displays from replacing the object shown in that pane. Fix a pane if you wish to see the same object across a number of queries. If all panes are fixed and the user displays an additional object, it will be displayed in a pop-up window (an existing window will be reused; otherwise a new window will be created).
Current knowledge base size:
```
   :::: Ecocyc KB statistics on Fri Sep 4, 1998 ::::

Reactions: 4607 total
  180 have no EC#
  904 occur in E. coli

Polypeptides: 1265
Protein complexes: 576
Enzymes: 802
Two-component sig trans: 45

Pathways:
  Small-molecule metabolism: 131
  Signaling: 20
  Superpathways: 34

Compounds: 1308   (975 have structures)

Genes:  4391 
  1400 ORFs

tRNAs: 79
```
Release Notes for EcoCyc Version 4.0

Released April 15, 1998.
The most significant changes are marked with a "*".
Changes to the EcoCyc Data
- EcoCyc describes all published pathways of E. coli metabolism. The following pathways were added since version 3.7:
- *EcoCyc now describes E. coli two-component signal transduction proteins.
- EcoCyc now describes E. coli tRNAs.
- *Data from the full E. coli nucleotide sequence determined by the Blattner laboratory (Science 277:1453 1997) are now included within EcoCyc. The included data were obtained from the Genbank entry submitted by the Blattner laboratory.
- Many more citations are now linked to PubMed.
Modifications to the EcoCyc Graphical User Interface (GUI)
- The display of chemical structures within compound windows now uses a concept called superatoms, which is a hierarchical structuring of chemical structures. For example, when displaying the structure for succinyl-CoA, the structure is initially displayed with the word "CoA" in place of the structure of the CoA moiety. If the user clicks on the word CoA, however, the full structure of that moiety will be displayed (clicking on the name to expand works only in the X-windows version).
- Pathway displays now include a small circular genome map, marked with the positions of all genes that encode the enzymes within the current pathway. Moving the mouse over the mark for a given gene flashes the gene name at the bottom of the screen, and also (X-Windows version only) highlights the arrows within the pathway for the reaction(s) catalyzed by the gene product. Clicking on a gene navigates to the gene display.
- Circular pathways are now drawn with curved reaction arrows.
- *EcoCyc uses a new scheme for displaying iterative pathways of synthesis or degradation of polymeric compounds. For each iteration the polymer increases or decreases a fixed number of monomers. The repeating iterations are indicated with a dashed line.
- Displays for gene classes now show gene name and gene product (where known) rather than just gene name.
- In the display of compounds and proteins, the presentation of the reactions in which a compound or protein is a substrate has been reorganized. Each reaction is listed under the pathway(s) (if any) in which it occurs.
Modifications Specific to the X-windows GUI
- *Overview Mode is now available for the first time in the X-windows Ecocyc. This mode displays the full metabolic map of E. coli. A number of queries are supported including highlighting reactions within the map according to EC number, enzyme name, gene name, and according to activation or inhibition of an enzyme by a specified compound.
- Enzyme command mode has been renamed Protein Mode because it can be used to query and display other types of proteins in addition to enzymes.
- A new command called Get Rxn by Substrates allows you to query all reactions that contain a specified set of reactants and/or products.
- EcoCyc uses a dedicated Netscape window for looking up citations.
- Cloned windows now have forward and back buttons.
- Hard copy printing of Greek letters now works, and some lines that previously were drawn with an extremely thin width are now drawn wider.
- Short comments are now displayed in the pointer documentation window when the mouse is passed over them. (Longer comments still need to be displayed in a pop-up window)
- The EcoCyc history list now stores the window scrolling position within the history, so that when the user moves forward and backward in the history, the scrolled position is remembered.
Modifications Specific to the World-Wide Web GUI
- We are now using client-side image maps, rather than server-side image maps, with imbedded javascript to show object names/descriptions instead of URLs.
Current knowledge base size:
```
   :::: Ecocyc KB statistics on Fri Dec 12, 1997 ::::

Reactions: 4412 total;  988 occur in ECOLI;  166 have no EC#

Polypeptides: 1196;  Protein complexes: 563; Enzymes: 804

Genes: 4909   (4357 have assigned map positions)

Base pathways: 123;  Superpathways: 34

Compounds: 1303   (977 have structures)
```
EcoCyc Version 3.7, released March 7, 1997
Changes introduced in this version include:
- An Overview diagram of the entire E. coli metabolic map is now available
- We believe that EcoCyc now describes all published pathways of E. coli metabolism. The following pathways were added since version 3.1:
  - trehalose biosynthesis
  - NAD phosphorylation and dephosphorylation
  - betaine biosynthetic pathway
  - mannose and GDP-mannose metabolism
  - formylTHF biosynthesis
  - methylglyoxal metabolism
  - nucleotide metabolism
  - arginine utilization
  - L-serine degradation
  - glutamine utilization
  - glutamate utilization
  - L-cysteine catabolism
  - tryptophan utilization
  - ornithine degradation
  - putrescine degradation
  - D-galactarate catabolism
  - galactitol catabolism pathway
  - mannitol degradation
  - sorbitol degradation
  - trehalose degradation, low osmolarity
  - D-glucarate catabolism
  - cobalamin biosynthesis
  - glutathione-glutaredoxin redox reactions
  - anaerobic respiration, electron acceptors reaction list
  - aerobic electron transfer
  - aerobic respiration, electron donors reaction list
  - anaerobic respiration, electron donors reaction list
  - anaerobic respiration
  - anaerobic electron transfer
- Compound displays now sort the set of reactions that contain the compound according to the pathways that contain the reactions.
- The X-window version of EcoCyc now displays links to other databases; if you click on a link then EcoCyc will invoke Netscape to query the linked object via the WWW.
- In the X-window version, most modes that allow you to query objects by their exact name allow you to enter in several names within one pop-up window, separated by commas, e.g., "Find Gene by Name" allows you to enter "hisA, hisB, hisC." The exception is compound mode, because many compounds have commas within their names.
- Links have been added from EcoCyc to the Swiss-Model database (thanks to Manuel Peitsch for assistance).
- A second gene-classification system has been added to EcoCyc. This second system, also developed by Riley, is much simpler than the first system, and classifies genes according to the type of their product, e.g., enzyme, regulator, transport protein.
- EcoCyc executables are now available for Solaris but are no longer available for SunOS.
- EcoCyc does not yet contain the full annotation of the E. coli genome; that task is next on our list. Thus, the data in slots centisome-position, left-end-position, and right-end-position, are all derived from EcoGene7.
Current knowledge base size:
```
    :::: Ecocyc KB statistics on Thu Feb 20, 1997 ::::

Reactions: 3241 total;  736 occur in ECOLI;  165 have no EC#

Polypeptides: 1029;  Protein complexes: 419; Enzymes: 731

Genes: 3025   (2571 are mapped)

Base pathways: 131;  Superpathways: 26

Compounds: 1294   (964 have structures)
```
EcoCyc Version 3.1, released July 17, 1996
Improvements introduced in this version include:
- EcoCyc executables are now available for Solaris in addition to SunOS.
- This version contains detailed descriptions of pathways that were only superficially encoded in the previous version, including detailed information on 125 new enzymes. It also contains a number of new reactions that connect to many pathways, and hence are not recorded as being part of specific pathway.
- Many data corrections and additions have been made.
- The following pathways were added since version 2.7:
  - lactose degradation
  - (deoxy)ribose phosphate metabolism
  - riboflavin, FMN and FAD biosynthesis
  - pyridoxal 5'-phosphate biosynthesis
  - menaquinone biosynthesis
  - biosynthesis of proto- and siroheme
- EcoCyc now displays superscripts, subscripts, and Greek characters in appropriate places.
- Database links -- EcoCyc is now linked to the CGSC in addition to SwissProt and PDB.
- The Clone Window command in the X-window EcoCyc allows a display of any object to be cloned in a separate window. Replaces the Fix-Item and Unfix-Item commands.
- The EcoCyc class hierarchy can now be queried through the WWW interface, and users can navigate the hierarchy within individual object displays by following the Superclass, Subclass, and Instance links.
- EcoCyc genes are now classified according to two hierarchies developed by Riley: one hierarchy considers the physiological role of the gene product, the other hierarchy considers the type of the product (enzyme, regulator, etc)
- The WWW map browser now allows the user to expand the map to show a gene that is specified by the user
- The representation of cofactors and coenzymes in EcoCyc has been revised.
- The X-window version of EcoCyc now queries Medline and Entrez using Netscape, which must be installed on your system for these queries to work
- For the bracketed numbers that refer to citations and comments in EcoCyc displays, such as [1], if the number is italicized it is a comment, otherwise it is a citation.
Current knowledge base size:
```
Reactions: 2965 total;  690 occur in ECOLI;  87 have no EC#

Polypeptides: 598;  Protein complexes: 312; Enzymes: 523

Genes: 2957   (2571 are mapped)

Base pathways: 101;  Superpathways: 26

Compounds: 1274

Publications: 765
```
EcoCyc Version 2.7, released Feb 19, 1996
Improvements introduced in this version include:
- A number of minor programming enhancements
- The following pathways were added since version 2.4:
  - methyl-donor molecule biosynthesis
  - propionate metabolism, methylmalonyl pathway
  - UDP-N-acetylglucosamine biosynthesis
  - peptidoglycan precursor and lipid a precursor biosynthesis
  - ppGpp metabolism
  - glycolate metabolism
  - glucosamine catabolism
  - pyrimidine ribonucleotide/ribonucleoside metabolism
  - glycine biosynthesis
  - asparagine biosynthesis
  - glycogen biosynthesis
  - peptidoglycan precursor biosynthesis
  - peptidoglycan biosynthesis
  - dTDP-rhamnose biosynthesis
  - KDO biosynthesis
  - lipid-A-precursor biosynthesis
  - degradation of short-chain fatty acids
  - galactose, galactoside and glucose catabolism
  - glyoxylate degradation
  - rhamnose catabolism
Current knowledge base size:
```
    Reactions: 2929 total;  627 occur in E. coli;  87 have no EC#
    
    Polypeptides: 523;  Protein complexes: 264
    
    Enzymes: 397
    
    Genes: 2956   (2571 are mapped)
    
    Total Pathways: 94;  Superpathways: 11
    
    Compounds: 1253
    
    Publications: 565
```
EcoCyc Version 2.6, released Dec 11, 1995
(This version was released on our WWW server only.)
Improvements introduced in this version include:
- New gene data -- EcoCyc now contains Rudd's EcoGene.7, which describes 1000 more mapped E. coli genes than EcoGene.6
- Database links -- EcoCyc is now linked to SwissProt and PDB
- Gene-Reaction schematics summarize gene/enzyme/reaction relationships
- Several new pathways have been added
- Pathway windows now contain commands called More Detail / Less Detail, which apply different levels of information filtering to pathway displays
Knowledge base size:
```
    Reactions: 2910 total;  598 in E. coli;  87 w/ no EC#
    
    Polypeptides: 491;  Protein complexes: 250
    
    Enzymes: 348
    
    Genes: 2962   (2577 are mapped)
    
    Total Pathways: 97;  Superpathways: 11
    
    Compounds: 1241
    
    Publications: 470
```
EcoCyc Version 2.4, released Oct 4, 1995
Improvements introduced in this version include:
- More data -- EcoCyc now contains 100 metabolic pathways
- The circular genomic-map viewer is introduced (see Gene Map Mode command)
- Any EcoCyc window can be saved to a postscript file for printing (see Print To File command)
- All reactions known to occur in E. coli are now marked as such, even if EcoCyc does not yet describe the corresponding enzyme
- Many citations were added to the KB
- A new user preference controls whether reactions are drawn in the systematic direction defined by Enzyme Nomenclature, or in the direction they proceed in the context of a pathway
- Different enzyme names can now be explicitly associated with the different activities of an enzyme
- Citations and Genbank sequences can be saved to a file
- Relationships among components of an enzyme complex are displayed more accurately, and reactions catalyzed by the components are shown
- The curved arcs adjacent to side compounds are now drawn in pathway displays

Pathways	323
Reactions	2342
Enzymes	1524
Transporters	277
Genes	4501
Transcription Units	3528
Citations	26,870

Pathways	322
Reactions	2318
Enzymes	1518
Transporters	273
Genes	4499
Transcription Units	4522
Citations	26,275

Pathways	314
Reactions	2232
Enzymes	1500
Transporters	268
Genes	4501
Transcription Units	4509
Citations	24,870

Pathways	312
Reactions	2175
Enzymes	1497
Transporters	268
Genes	4499
Transcription Units	4506
Citations	24,391

Pathways	293
Reactions	2074
Enzymes	1474
Transporters	258
Genes	4500
Transcription Units	4477
Citations	23,382

Pathways	293
Reactions	2037
Enzymes	1475
Transporters	259
Genes	4502
Transcription Units	4472
Citations	22,895

Pathways	281
Reactions	1945
Enzymes	1467
Transporters	258
Genes	4490
Transcription Units	3433
Citations	21,448

Pathways	277
Reactions	1922
Enzymes	1458
Transporters	254
Genes	4489
Transcription Units	3422
Citations	21,110

Pathways	260
Reactions	1884
Enzymes	1450
Transporters	252
Genes	4489
Transcription Units	3409
Citations	20,284

Pathways	253
Reactions	1829
Enzymes	1445
Transporters	252
Genes	4490
Transcription Units	3397
Citations	20,123

Pathways	248
Reactions	1815
Enzymes	1430
Transporters	249
Genes	4497
Transcription Units	3386
Citations	19,563

Pathways	246
Reactions	1800
Enzymes	1425
Transporters	247
Genes	4495
Transcription Units	3370
Citations	19,156

Pathways	246
Reactions	1805
Enzymes	1422
Transporters	246
Genes	4495
Transcription Units	3369
Citations	18,969

Pathways	242
Reactions	1784
Enzymes	1415
Transporters	244
Genes	4496
Transcription Units	3356
Citations	18,469

Pathways	237
Reactions	1751
Enzymes	1409
Transporters	243
Genes	4477
Transcription Units	3375
Citations	17,842

Pathways	230
Reactions	1676
Enzymes	1374
Transporters	229
Genes	4472
Transcription Units	3356
Citations	16,909

Pathways	224
Reactions	1658
Enzymes	1361
Transporters	227
Genes	4472
Transcription Units	3277
Citations	16,297

Pathways	225
Reactions	1661
Enzymes	1357
Transporters	226
Genes	4470
Transcription Units	3199
Citations	15,883

Pathways	224
Reactions	1615
Enzymes	1342
Transporters	224
Genes	4471
Transcription Units	3187
Citations	16,154

Pathways	223
Reactions	5220
Enzymes	1338
Transporters	223
Genes	4436
Transcription Units	3156
Citations	15,953

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Analysis

EcoCyc Update History

Release Notes for EcoCyc Version 29.1

Improvements to the EcoCyc Database

Release Notes for EcoCyc Version 29.0

EcoCyc Curation Highlights

Release Notes for EcoCyc Version 28.5

Improvements to the EcoCyc Database

EcoCyc Curation Highlights

Release Notes for EcoCyc Version 28.1

Improvements to the EcoCyc Database

Curation Highlights to EcoCyc for This Release

Release Notes for EcoCyc Version 28.0

EcoCyc Modeling Tab Contains Reaction Flux Predictions from E. coli Whole Cell Model

Highlights of EcoCyc Database Improvements

Release Notes for EcoCyc Version 27.5

Improvements to the EcoCyc Database

Release Notes for EcoCyc Version 27.1

Improvements to the EcoCyc Database

Release Notes for EcoCyc Version 27.0

Highlights of EcoCyc Database Improvements

New genes:

New small RNAs added to Ecocyc:

New gene functions curated:

Other updates include:

Release Notes for EcoCyc Version 26.5

Highlights of EcoCyc Database Improvements

Release Notes for EcoCyc Version 26.1

Highlights of EcoCyc Database Improvements

Release Notes for EcoCyc Version 26.0

EcoCyc Modeling Tab Contains Predictions from E. coli Whole Cell Model

Highlights of EcoCyc Database Improvements

Release Notes for EcoCyc Version 25.5

Highlights of EcoCyc Database Improvements

Release Notes for EcoCyc Version 25.1

Highlights of EcoCyc Database Improvements

Release Notes for EcoCyc Version 25.0

Highlights of EcoCyc Database Improvements

Release Notes for EcoCyc Version 24.5

Highlights of EcoCyc Database Improvements

Release Notes for EcoCyc Version 24.1

Highlights of EcoCyc Database Improvements

Release Notes for EcoCyc Version 24.0

Highlights of EcoCyc Database Improvements

Highlights of Website Improvements

Release Notes for EcoCyc Version 23.5

Highlights of EcoCyc Database Improvements

Highlights of Website Improvements

Release Notes for EcoCyc Version 23.1

Highlights of EcoCyc Database Improvements

Release Notes for EcoCyc Version 23.0

Highlights of EcoCyc Database Improvements

Highlights of Website Improvements

Highlights of Desktop Software Improvements

Release Notes for EcoCyc Version 22.6

Highlights of EcoCyc Database Improvements

Release Notes for EcoCyc Version 22.5

New GenBank File for Escherichia coli K-12 MG1655 Released!

Highlights of EcoCyc Database Improvements

Highlights of Website Improvements

Release Notes for EcoCyc Version 22.0

Highlights of EcoCyc Database Improvements

Highlights of Website Improvements

Release Notes for EcoCyc Version 21.5

Highlights of EcoCyc Database Improvements

Highlights of Website Improvements

Release Notes for EcoCyc Version 21.1

Highlights of EcoCyc Database Improvements

Release Notes for EcoCyc Version 21.0

Highlights of EcoCyc Database Improvements

Highlights of Website Improvements

Release Notes for EcoCyc Version 20.5

Highlights of EcoCyc Database Improvements

Highlights of Website Improvements

Release Notes for EcoCyc Version 20.1

Highlights of EcoCyc Database Improvements

Pathways	215
Reactions	5003
Enzymes	1323
Transporters	214
Genes	4461
Transcription Units	3063
Citations	15,335

Pathways	205
Reactions	4956
Enzymes	1307
Transporters	211
Genes	4465
Transcription Units	3133
Citations	14,951

Pathways	197
Reactions	4854
Enzymes	1276
Transporters	211
Genes	4516
Transcription Units	1662
Citations	14,269

Pathways	190
Reactions	4469
Enzymes	1257
Transporters	209
Genes	4517
Transcription Units	1304
Citations	13,274

Pathways	187
Reactions	4308
Enzymes	1232
Transporters	208
Genes	4521
Transcription Units	1261
Citations	12,489

Pathways	187
Reactions	4260
Enzymes	1222
Transporters	206
Genes	4480
Transcription Units	1232
Citations	12,026

Pathways	184
Reactions	3939
Enzymes	1198
Transporters	198
Genes	4481
Transcription Units	1127
Citations	11,079

Pathways	183
Reactions	3873
Enzymes	1186
Transporters	197
Genes	4477
Transcription Units	1113
Citations	10,747

Pathways	183
Reactions	3634
Enzymes	1148
Transporters	196
Genes	4476
Transcription Units	983
Citations	9873

Pathways	182
Reactions	3629
Enzymes	1133
Transporters	197
Genes	4497
Transcription Units	956
Citations	8862