Database Authors
Pallavi Subhraveti1, Peter Midford, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 15-Feb-2019 from the annotated genome of Vibrio cholerae HE-16, as obtained from RefSeq (see the RefSeq entry for the authors of the original genome sequence). The PGDB was created computationally by the PathoLogic component of the Pathway Tools software (version 23.0) [Karp16, Karp11] using MetaCyc version 23.0 [Caspi18]. It has not undergone any manual curation or review, and may contain errors. Development of this PGDB was supported by grant GM080746 from the National Institutess of Health.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_JH9414428307722731903,352RefSeq:NZ_JH941442
NZ_JH941438495472221556,801RefSeq:NZ_JH941438
NZ_JH941440443423317496,876RefSeq:NZ_JH941440
NZ_JH941441300286014347,858RefSeq:NZ_JH941441
NZ_JH941432302280175329,517RefSeq:NZ_JH941432
NZ_JH94144325224417254,216RefSeq:NZ_JH941443
NZ_JH94143913512726143,218RefSeq:NZ_JH941439
NZ_JH94142011310814111,938RefSeq:NZ_JH941420
NZ_JH9414331049815110,537RefSeq:NZ_JH941433
NZ_JH94142178686485,688RefSeq:NZ_JH941421
NZ_JH94143579751379,773RefSeq:NZ_JH941435
NZ_JH94141578760274,548RefSeq:NZ_JH941415
NZ_JH94155353511160,783RefSeq:NZ_JH941553
NZ_JH94142435330237,006RefSeq:NZ_JH941424
NZ_JH94142528240432,317RefSeq:NZ_JH941425
NZ_JH94142922192125,706RefSeq:NZ_JH941429
NZ_JH94143024194119,733RefSeq:NZ_JH941430
NZ_JH94143122220018,721RefSeq:NZ_JH941431
218 Undisplayed Contigs/Replicons26025013109222,798
Total:3,7653,447812373,911,386
Ortholog data available?Yes
Database Contents
Genes3,762
Pathways277
Enzymatic Reactions1,415
Transport Reactions173
Polypeptides3,478
Protein Complexes58
Enzymes771
Transporters376
Compounds1,099
Transcription Units2,601
tRNAs72
GO Terms420
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Vibrionales
Vibrionaceae
Vibrio
Vibrio cholerae
Vibrio cholerae HE-16
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00622032
NCBI BioProjectPRJNA224116
NCBI-Taxonomy991999
EnvironmentGray Water, External Clinic
Geographic LocationHaiti
Collection Date2010
HostHomo sapiens
Annotation ProviderNCBI
Annotation Date2017-03-23
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.1
Annotation CommentBest-placed reference protein set; GeneMarkS+

References

Caspi18: Caspi R, Billington R, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Midford PE, Ong Q, Ong WK, Paley S, Subhraveti P, Karp PD (2018). "The MetaCyc database of metabolic pathways and enzymes." Nucleic Acids Res 46(D1);D633-D639. PMID: 29059334

Karp11: Karp PD, Latendresse M, Caspi R (2011). "The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592

Karp16: Karp PD, Latendresse M, Paley SM, Krummenacker M, Ong QD, Billington R, Kothari A, Weaver D, Lee T, Subhraveti P, Spaulding A, Fulcher C, Keseler IM, Caspi R (2016). "Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology." Brief Bioinform 17(5);877-90. PMID: 26454094

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