Metabolic Modeling Tutorial
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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
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MetaCyc Gene-Ontology-Terms Class: GO:0005515 - protein binding

Synonyms: GO:0045308, protein amino acid binding

Definition: Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).

Parent Classes:
GO:0005488 - binding

Child Classes:
GO:0005102 - receptor binding (4) ,
GO:0005516 - calmodulin binding (1) ,
GO:0008013 - beta-catenin binding (1) ,
GO:0008134 - transcription factor binding (2) ,
GO:0019899 - enzyme binding (5) ,
GO:0030674 - protein binding, bridging (2) ,
GO:0031072 - heat shock protein binding (2) ,
GO:0032403 - protein complex binding (1) ,
GO:0032794 - GTPase activating protein binding (1) ,
GO:0042802 - identical protein binding (285) ,
GO:0044183 - protein binding involved in protein folding (2) ,
GO:0046983 - protein dimerization activity (133) ,
GO:0051082 - unfolded protein binding (8) ,
GO:0051087 - chaperone binding (3)

Term Members:
RelB-antitoxin and DNA-binding transcriptional repressor ,
PII (glnB) ,
biotin carboxyl carrier protein (accB) ,
thioredoxin 1 (trxA) ,
GlnK ,
reduced ferredoxin (fdx) ,
apo-[acyl carrier protein] (acpP) ,
RelB Qin prophage; antitoxin of the RelE-RelB toxin-antitoxin system and DNA binding transcriptional repressor ,
primosome factor N' (priA) ,
primosomal protein DnaT ,
aldehyde dehydrogenase, Fe-S subunit (yagT) ,
putative protein secretion protein for export (gspH) ,
EntB monomer ,
DNA polymerase III, χ subunit (holC) ,
putative protein secretion protein for export (gspE) ,
MalT transcriptional activator ,
iron-sulfur cluster scaffold protein (nfuA) ,
ATP synthase F1 complex - epsilon subunit (atpC) ,
PurR ,
predicted ring 1,2-epoxyphenylacetyl-CoA isomerase (oxepin-CoA forming) (paaG) ,
RNA polymerase, sigma 70 (sigma D) factor (rpoD) ,
PriB ,
DNA polymerase III, τ subunit (dnaX) ,
protein disulfide oxidoreductase - DsbBreduced ,
DNA polymerase III, θ subunit (holE) ,
CSD sulfur transfer protein (csdE) ,
serine/threonine kinase HipA ,
DnaN ,
aldehyde dehydrogenase: molybdenum cofactor-binding subunit (yagR) ,
DNA polymerase III, ψ subunit (holD) ,
ATP synthase F1 complex - gamma subunit (atpG) ,
co-chaperone for [Fe-S] cluster biosynthesis (hscB) ,
ATP synthase F1 complex - beta subunit (atpD) ,
DinJ antitoxin of YafQ-DinJ toxin-antitoxin system and DNA-binding transcriptional repressor ,
MqsA antitoxin of the MqsRA toxin-antitoxin system and DNA-binding transcriptional repressor ,
predicted 5-keto 4-deoxyuronate isomerase monomer (kduI) ,
scaffold protein for iron-sulfur cluster assembly (iscU) ,
RNA polymerase, sigma 24 (sigma E) factor (rpoE) ,
primosomal replication protein N'' (priC) ,
aldehyde dehydrogenase, FAD-binding subunit (yagS) ,
DNA polymerase III, δ prime subunit (holB) ,
iron-sulfur cluster assembly protein (iscA) ,
MazF toxin of the MazF-MazE toxin-antitoxin system that exhibits ribonuclease activity (chpA) ,
CP4-57 prophage; antitoxin of the RnlA-RnlB toxin-antitoxin system ,
accessory protein for nickel incorporation into hydrogenase 3 (hypA) ,
RNA polymerase, sigma 32 (sigma H) factor (rpoH) ,
50S ribosomal subunit protein L4 (rplD) ,
RhlB ,
RNA polymerase, sigma 28 (sigma F) factor (fliA) ,
acetohydroxy acid synthase I, small subunit (ilvN) ,
acetohydroxy acid synthase I, large subunit (ilvB) ,
UDP-glucose 4-epimerase monomer (galE) ,
mannose-6-phosphate isomerase (manA) ,
Ugd ,
LeuD ,
LeuC ,
LysA ,
HisB ,
geranyl diphosphate synthase / farnesyl diphosphate synthase (ispA) ,
octaprenyl diphosphate synthase (ispB) ,
glutamate synthase, small subunit (gltD) ,
glutamate synthase, large subunit (gltB) ,
carbamoyl phosphate synthetase, α chain (carA) ,
carbamoyl phosphate synthetase, β chain ,
aspartate carbamoyltransferase, PyrI subunit ,
aspartate carbamoyltransferase, PyrB subunit ,
PyrF ,
N-acetylmuramic acid 6-phosphate etherase (murQ) ,
2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinone hydroxylase (ubiF) ,
UbiG ,
fructoselysine 6-kinase (frlD) ,
GlmS ,
glycerol-3-phosphate acyltransferase (plsB) ,
LpxB ,
3-deoxy-D-manno-octulosonate cytidylyltransferase (kdsB) ,
AccC ,
acetyl-CoA carboxyltransferase, α subunit (accA) ,
acetyl-CoA carboxyltransferase, β subunit (accD) ,
ScpA ,
PhnG subunit of methylphosphonate degradation complex ,
acetaldehyde dehydrogenase 2 (mhpF) ,
dihydroxyacetone kinase subunit L (dhaL) ,
dihydroxyacetone kinase subunit K (dhaK) ,
anaerobic glycerol-3-phosphate dehydrogenase subunit A (glpA) ,
MenB ,
ribonucleoside hydrolase 1 (pyrimidine-specific) (rihA) ,
molybdopterin synthase large subunit (moaE) ,
molybdopterin synthase small subunit (moaD) ,
molybdopterin molybdenumtransferase (moeA) ,
molybdenum cofactor guanylyltransferase (mobA) ,
methionine adenosyltransferase (metK) ,
molybdenum cofactor cytidylyltransferase (mocA) ,
guanosine 3'-diphosphate 5'-triphosphate 3'-diphosphatase [multifunctional] (spoT) ,
α-galactosidase monomer (melA) ,
pyridine nucleotide transhydrogenase, α subunit (pntA) ,
pyridine nucleotide transhydrogenase, β subunit (pntB) ,
glutamate-1-semialdehyde aminotransferase (hemL) ,
HemA ,
acetyl-CoA:acetoacetyl-CoA transferase, β subunit (atoA) ,
GlpK ,
CadA ,
LdcC ,
cobalamin-independent homocysteine transmethylase (metE) ,
AspA ,
7-cyano-7-deazaguanine synthase (queC) ,
Gsk ,
PurA ,
adenylate kinase (adk) ,
ThiS adenylyltransferase (thiF) ,
tyrosine lyase (thiH) ,
ThiG ,
citrate synthase monomer (gltA) ,
bifunctional aconitate hydratase 2 and 2-methylisocitrate dehydratase (acnB) ,
succinyl-CoA synthetase, β subunit ,
succinyl-CoA synthetase, α subunit (sucD) ,
succinate:quinone oxidoreductase, iron-sulfur cluster binding protein (sdhB) ,
succinate:quinone oxidoreductase, FAD binding protein (sdhA) ,
sulfate adenylyltransferase, CysN subunit ,
sulfate adenylyltransferase, CysD subunit ,
Pta ,
4-hydroxy-2-ketovalerate aldolase (mhpE) ,
phosphoribosylglycinamide formyltransferase 2 (purT) ,
threonyl-tRNA synthetase (thrS) ,
phenylalanyl-tRNA synthetase β-chain (pheT) ,
phenylalanyl-tRNA synthetase α-chain (pheS) ,
methionyl-tRNA synthetase (metG) ,
glycyl-tRNA synthetase, α subunit (glyQ) ,
glycyl-tRNA synthetase, β subunit (glyS) ,
biosynthetic peptidoglycan transglycosylase (mtgA) ,
essential cell division protein FtsI; penicillin-binding protein 3 ,
peptidoglycan synthetase; penicillin-binding protein 1A (mrcA) ,
MrcB ,
UDP-N-acetylmuramate-alanine ligase (murC) ,
ribulose-5-phosphate 3-epimerase (rpe) ,
pyruvate kinase II monomer (pykA) ,
triose phosphate isomerase monomer (tpiA) ,
3-dehydroquinate synthase (aroB) ,
AroH ,
biotin synthase monomer (bioB) ,
dihydrofolate reductase ,
ring 1,2-phenylacetyl-CoA epoxidase, structural subunit (paaC) ,
3-phenylpropionate dioxygenase, predicted ferredoxin reductase subunit (hcaD) ,
NAD(P)H-dependent FMN reductase (ssuE) ,
5-formyltetrahydrofolate cyclo-ligase (fau) ,
pantothenate synthetase monomer (panC) ,
1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase (ispG) ,
fructose bisphosphate aldolase monomer (fbaA) ,
glutamate decarboxylase A subunit (gadA) ,
E3 monomer (lpd) ,
SucB ,
subunit of E1(0) component of 2-oxoglutarate dehydrogenase (sucA) ,
AceF ,
subunit of E1p component of pyruvate dehydrogenase complex (aceE) ,
ADP-L-glycero-D-mannoheptose-6-epimerase (rfaD) ,
PflB ,
fumarate reductase ,
fumarate reductase iron-sulfur protein (frdB) ,
fumarate reductase flavoprotein (frdA) ,
thioredoxin reductase monomer (trxB) ,
cytochrome bo terminal oxidase subunit III (cyoC) ,
cytochrome bo terminal oxidase subunit I (cyoB) ,
cytochrome bo terminal oxidase subunit IV (cyoD) ,
formate dehydrogenase N, α subunit (fdnG) ,
formate dehydrogenase-O, α subunit (fdoG) ,
trimethylamine N-oxide reductase, catalytic subunit (torA) ,
TorC trimethylamine N-oxide reductase, cytochrome c-type subunit ,
dimethyl sulfoxide reductase, chain A (dmsA) ,
NADH:ubiquinone oxidoreductase, chain CD (nuoC) ,
NADH:ubiquinone oxidoreductase, chain E (nuoE) ,
NADH:ubiquinone oxidoreductase, chain G (nuoG) ,
NADH:ubiquinone oxidoreductase, membrane subunit K (nuoK) ,
cytochrome bd-I terminal oxidase subunit II (cydB) ,
cytochrome bd-I terminal oxidase subunit I (cydA) ,
succinylglutamate desuccinylase (astE) ,
tryptophanase (tnaA) ,
bifunctional β-cystathionase, PLP-dependent and regulator of maltose regulon (malY) ,
O-acetylserine sulfhydrylase A (cysK) ,
L-serine deaminase I (sdaA) ,
GTP cyclohydrolase II (ribA) ,
glyoxalase I (gloA) ,
glyoxalase III, Hsp31 molecular chaperone (hchA) ,
carnitine-CoA ligase (caiC) ,
FabF ,
DegP ,
rep ,
ATP-dependent DNA helicase (recQ) ,
acetyl esterase (aes) ,
aminopeptidase (ypdF) ,
Mlc titration factor (mtfA) ,
ClpA ,
regulatory ATPase (ravA) ,
sulfite reductase, flavoprotein subunit (cysJ) ,
NADPH nitroreductase (nfsA) ,
DNA polymerase IV (Y-family DNA polymerase; translesion DNA synthesis) (dinB) ,
SOS mutagenesis; error-prone repair; processed to UmuD'; forms complex with UmuC ,
SOS mutagenesis and repair (umuC) ,
PepP ,
tRNA threonylcarbamoyladenosine dehydratase (tcdA) ,
MutH ,
MutL ,
meso-diaminopimelic acid-D-alanyl endopeptidase / D-alanyl-D-alanine carboxypeptidase (dacB) ,
nucleoside triphosphate pyrophosphohydrolase (mazG) ,
AidB ,
DNA polymerase III, ε subunit (dnaQ) ,
DNA polymerase III, α subunit (dnaE) ,
mRNA interferase, toxin of the MqsR-MqsA toxin-antitoxin system ,
CP4-57 prophage; RNase LS, toxin of the RnlAB toxin-antitoxin system ,
DNA gyrase, subunit B (gyrB) ,
DNA gyrase, subunit A ,
toxin of the YafQ-DinJ toxin-antitoxin system ,
Qin prophage; toxin of the RelE-RelB toxin-antitoxin system and cofactor to enhance the repressor activity of RelB ,
protein involved in modification of U34 in tRNA (mnmG) ,
GTPase, involved in modification of U34 in tRNA (mnmE) ,
cysteine sulfinate desulfinase (csdA) ,
23S rRNA pseudouridine synthase (rluD) ,
Lon ,
nitrate reductase A, β subunit (narH) ,
nitrate reductase A, α subunit (narG) ,
nitrate reductase Z, α subunit (narZ) ,
nitrate reductase Z, β subunit (narY) ,
methionine-oxo-acid transaminase, PLP-dependent (ybdL) ,
HflK-HflC complex; regulator of FtsH protease ,
regulator of FtsH protease (hflK) ,
regulator of FtsH protease (hflC) ,
ssDNA and dsDNA binding, ATP binding (recF) ,
DNA-cytosine methyltransferase (dcm) ,
branch migration of Holliday structures; repair helicase (ruvB) ,
Holliday junction nuclease; resolution of structures; repair (ruvC) ,
peptidase T ,
crRNA endonuclease (casE) ,
Cascade subunit D (casD) ,
Cascade subunit C ,
Cascade subunit B (casB) ,
Cascade subunit A (casA) ,
hydrogenase 2, small subunit (hybO) ,
hydrogenase 1, large subunit (hyaB) ,
dTDP-4-dehydrorhamnose 3,5-epimerase (rfbC) ,
toxin of the YoeB-YefM toxin-antitoxin pair ,
oxidoreductase subunit (ynfF) ,
oxidoreductase subunit (ynfE) ,
large subunit of periplasmic nitrate reductase, molybdoprotein (napA) ,
peptide deformylase ,
adenylate cyclase (cyaA) ,
protein-lysine deacetylase and desuccinylase (cobB) ,
chaperone for [Fe-S] cluster biosynthesis (hscA) ,
16S rRNA pseudouridine 516 synthase (rsuA) ,
glutathione S-transferase B (gstB) ,
RNase R (rnr) ,
L-cysteine desulfurase (sufS) ,
DNA primase (dnaG) ,
DnaB ,
23S rRNA pseudouridine 2605 synthase (rluB) ,
protein disulfide oxidoreductase - DsbAreduced ,
Gss ,
cysteine desulfurase monomer (iscS) ,
serine hydroxymethyltransferase (glyA) ,
ribosomal protein-arginine oxygenase (roxA) ,
uracil-DNA glycosylase (ung) ,
endonuclease III; specific for apurinic and/or apyrimidinic sites (nth) ,
lipid hydroperoxide peroxidase (tpx) ,
ribonuclease II (rnb) ,
proofreading thioesterase in enterobactin biosynthesis (entH) ,
RecB ,
RecC ,
Ada DNA-binding transcriptional dual regulator ,
2-keto-3-deoxy-L-rhamnonate aldolase (yfaU) ,
methyltransferase for 50S ribosomal subunit protein L11 (prmA) ,
NrdF ,
[protein-PII] uridylyltransferase (glnD) ,
excision nuclease subunit A (uvrA) ,
DNA repair; excision nuclease subunit B (uvrB) ,
alkyl hydroperoxide reductase, AhpC component ,
RNA polymerase, α subunit (rpoA) ,
RNA polymerase, β' subunit (rpoC) ,
RNA polymerase, β subunit (rpoB) ,
isopentenyl-adenosine A37 tRNA methylthiolase (miaB) ,
hydrogenase 3 and formate hydrogenlyase complex, HycG subunit ,
hydrogenase 3, large subunit (hycE) ,
lipid kinase (yegS) ,
GuaC ,
Eno ,
polynucleotide phosphorylase monomer (pnp) ,
RNase E (rne) ,
Ppk ,
L-tartrate dehydratase, α subunit (ttdA) ,
fused 23S rRNA m2G2445 methyltransferase and 23S rRNA m7G2069 methyltransferase (rlmL) ,
23S rRNA m2A2503 methyltransferase and tRNA m2A37 methyltransferase (rlmN) ,
8-oxo-dGTP diphosphatase (mutT) ,
alkanesulfonate monooxygenase, FMNH2-dependent (ssuD) ,
GTPase that interacts with methylmalonyl-CoA mutase (argK) ,
ribosome small subunit-dependent GTPase A (rsgA) ,
accessory protein for nickel incorporation into hydrogenase isoenzymes (hypB) ,
FKBP-type peptidyl prolyl cis-trans isomerase (slyD) ,
peptidyl-prolyl cis-trans isomerase B (rotamase B) (ppiB) ,
peptidyl-prolyl cis-trans isomerase C (rotamase C) (ppiC) ,
peptidyl-prolyl cis-trans isomerase (fkpB) ,
peptidyl-prolyl cis-trans isomerase (PPIase) (surA) ,
chaperone protein Tig; trigger factor ,
NADH-dependent dihydropyrimidine dehydrogenase subunit (preA) ,
NADH-dependent dihydropyrimidine dehydrogenase subunit (preT) ,
Ppa ,
cyclic di-GMP phosphodiesterase (gmr) ,
exonuclease VII, small subunit (xseB) ,
exonuclease VII, large subunit (xseA) ,
diguanylate cyclase (dosC) ,
c-di-GMP phosphodiesterase, heme-regulated (dosP) ,
diguanylate cyclase (ydaM) ,
PhoA ,
Ndk ,
MalX PTS permease ,
poly-β-1,6-N-acetyl-D-glucosamine synthase - PgaC subunit ,
poly-β-1,6-N-acetyl-D-glucosamine synthase - PgaD subunit ,
essential cell division protein FtsW; lipid II flippase ,
LptA ,
LptC ,
outer membrane lipopolysaccharide transport and assembly complex - LptD subunit ,
outer membrane lipopolysaccharide transport and assembly complex - LptE subunit ,
chitobiose PTS permease - ChbB subunit ,
chitobiose PTS permease - ChbA subunit ,
mannose PTS permease - ManX subunit ,
K+ transporting ATPase - KdpC subunit ,
K+ transporting ATPase - ATP binding subunit (kdpB) ,
glycine betaine / proline ABC transporter - periplasmic binding protein (proX) ,
glycine betaine / proline ABC transporter - membrane subunit (proW) ,
glycine betaine / proline ABC transporter - ATP binding subunit (proV) ,
protoheme IX ABC transporter - ATP binding subunit (ccmA) ,
protoheme IX ABC transporter - membrane subunit CcmB ,
protoheme IX ABC transporter - membrane subunit CcmD ,
membrane anchored periplasmic heme chaperone CcmE ,
protoheme IX ABC transporter - membrane subunit CcmC ,
ribose ABC transporter - putative periplasmic binding protein (rbsB) ,
ribose ABC transporter - putative ATP binding subunit (rbsA) ,
galactose ABC transporter - periplasmic binding protein (mglB) ,
maltose ABC transporter - periplasmic binding protein (malE) ,
maltose ABC transporter - membrane subunit (malF) ,
L-methionine / D-methionine ABC transporter - membrane subunit (metI) ,
L-methionine / D-methionine ABC transporter - ATP binding subunit (metN) ,
KefC ,
TatC ,
TatB ,
copper / silver efflux system - membrane subunit (cusA) ,
copper / silver efflux system - periplasmic binding protein and metallochaperone (cusF) ,
copper / silver efflux system - membrane fusion protein (cusB) ,
copper / silver efflux system - outer membrane porin (cusC) ,
branched chain amino acid transporter BrnQ ,
vitamin B12 ABC transporter - ATP binding subunit (btuD) ,
vitamin B12 ABC transporter - membrane subunit (btuC) ,
ferric enterobactin / colicin B / colicin D outer membrane porin FepA ,
tonB energy transducing system - ExbD subunit ,
TonB energy transducing system - ExbB subunit ,
TonB energy transducing system - TonB subunit ,
OmpC ,
LamB ,
AqpZ ,
50S ribosomal subunit protein L11 (rplK) ,
50S ribosomal subunit protein L14 (rplN) ,
30S ribosomal subunit protein S5 (rpsE) ,
50S ribosomal subunit protein L22 (rplV) ,
50S ribosomal subunit protein L1 (rplA) ,
periplasmic chaperone (skp) ,
chaperone protein DnaK ,
30S ribosomal subunit protein S18 (rpsR) ,
30S ribosomal subunit protein S2 (rpsB) ,
50S ribosomal subunit protein L15 (rplO) ,
30S ribosomal subunit protein S12 (rpsL) ,
MazE antitoxin of the MazF-MazE toxin-antitoxin system (chpR) ,
30S ribosomal subunit protein S6 (rpsF) ,
50S ribosomal subunit protein L23 (rplW) ,
50S ribosomal subunit protein L2 (rplB) ,
50S ribosomal subunit protein L27 (rpmA) ,
DNA polymerase III, δ subunit (holA) ,
30S ribosomal subunit protein S10 (rpsJ) ,
30S ribosomal subunit protein S7 (rpsG) ,
30S ribosomal subunit protein S4 (rpsD) ,
chaperone protein DnaJ ,
sulfite reductase, hemoprotein subunit (cysI) ,
TolB ,
ATP synthase F1 complex - alpha subunit (atpA) ,
pyridoxal phosphate phosphatase (PHOSPHO2) ,
prostaglandin E synthase 3 (PTGES3) ,
GAP-like protein that activates GTPase activity of Der ,
sulfur acceptor that activates SufS cysteine desulfurase ,
Src proto-oncogene tyrosine-protein kinase ,
pyruvate dehydrogenase protein E3 component, mitochondrial (PDHX) ,
pyruvate dehydrogenase E2 component (DLAT) ,
N-formyl-4-amino-5-aminomethyl-2- methylpyrimidine deformylase (thiQ) ,
retinoid isomerohydrolase (RPE65) ,
50S ribosomal subunit protein L3 (rplC) ,
50S ribosomal subunit protein L28 (rpmB) ,
50S ribosomal subunit protein L32 (rpmF)

Unification Links: GO:0005515


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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Fri Dec 19, 2014, biocyc12.