GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Snodgrassella alvi wkB2

Found 176 low-confidence and 26 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate kgtP: 2-oxoglutarate:H+ symporter KgtP SALWKB2_RS01745 SALWKB2_RS02065
4-hydroxybenzoate adh: acetaldehyde dehydrogenase (not acylating) SALWKB2_RS03665 SALWKB2_RS09970
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK
4-hydroxybenzoate pobA: 4-hydroxybenzoate 3-monooxygenase
4-hydroxybenzoate praA: protocatechuate 2,3-dioxygenase
4-hydroxybenzoate xylF: 2-hydroxymuconate semialdehyde hydrolase
acetate dctA: organic acid/proton symporter DctA SALWKB2_RS09015 SALWKB2_RS03180
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter
arginine odc: L-ornithine decarboxylase
arginine puuB: gamma-glutamylputrescine oxidase SALWKB2_RS08220
arginine puuC: gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase SALWKB2_RS03665 SALWKB2_RS05850
arginine rocE: L-arginine permease SALWKB2_RS09620 SALWKB2_RS03650
arginine rocF: arginase
asparagine ans: asparaginase SALWKB2_RS03690
cellobiose bgl: cellobiase
cellobiose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
citrate citA: citrate:H+ symporter CitA SALWKB2_RS01745 SALWKB2_RS02065
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component SALWKB2_RS01045 SALWKB2_RS00760
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 SALWKB2_RS01040
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 SALWKB2_RS01040 SALWKB2_RS02765
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline arcC: carbamate kinase
citrulline odc: L-ornithine decarboxylase
citrulline puuB: gamma-glutamylputrescine oxidase SALWKB2_RS08220
citrulline puuC: gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase SALWKB2_RS03665 SALWKB2_RS05850
D-lactate D-LDH: D-lactate dehydrogenase SALWKB2_RS07940 SALWKB2_RS00060
D-serine dsdA: D-serine ammonia-lyase SALWKB2_RS04155
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) SALWKB2_RS03665 SALWKB2_RS09970
deoxyinosine deoB: phosphopentomutase SALWKB2_RS08270
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose adh: acetaldehyde dehydrogenase (not acylating) SALWKB2_RS03665 SALWKB2_RS09970
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
ethanol adh: acetaldehyde dehydrogenase (not acylating) SALWKB2_RS03665 SALWKB2_RS09970
fructose 1pfk: 1-phosphofructokinase
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
fucose aldA: lactaldehyde dehydrogenase SALWKB2_RS03665 SALWKB2_RS03375
fucose fucA: L-fuculose-phosphate aldolase FucA
fucose fucI: L-fucose isomerase FucI
fucose fucK: L-fuculose kinase FucK
fucose fucP: L-fucose:H+ symporter FucP
fucose fucU: L-fucose mutarotase FucU
galactose galK: galactokinase (-1-phosphate forming)
galactose galP: galactose:H+ symporter GalP
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galacturonate eda: 2-keto-3-deoxygluconate 6-phosphate aldolase
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate kdgK: 2-keto-3-deoxygluconate kinase
galacturonate uxaA: D-altronate dehydratase
galacturonate uxaB: tagaturonate reductase
galacturonate uxaC: D-galacturonate isomerase
gluconate gnd: 6-phosphogluconate dehydrogenase, decarboxylating
gluconate gntK: D-gluconate kinase
gluconate gntT: gluconate:H+ symporter GntT
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE)
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) SALWKB2_RS09925
glucose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate garL: 5-dehydro-4-deoxy-D-glucarate aldolase SALWKB2_RS04305
glucuronate garR: tartronate semialdehyde reductase
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate udh: D-glucuronate dehydrogenase
glutamate aspA: L-aspartate ammonia-lyase SALWKB2_RS04415
glycerol dhaD: glycerol dehydrogenase SALWKB2_RS08960
glycerol glpF: glycerol facilitator glpF
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
histidine PA5503: L-histidine ABC transporter, ATPase component SALWKB2_RS05440 SALWKB2_RS00760
histidine PA5504: L-histidine ABC transporter, permease component SALWKB2_RS05445
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase
isoleucine Bap2: L-isoleucine permease Bap2 SALWKB2_RS09620 SALWKB2_RS03650
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase SALWKB2_RS08960 SALWKB2_RS02250
isoleucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
isoleucine prpB: 2-methylisocitrate lyase
isoleucine prpC: 2-methylcitrate synthase SALWKB2_RS06570
isoleucine prpD: 2-methylcitrate dehydratase
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose glk: glucokinase
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
leucine leuT: L-leucine:Na+ symporter LeuT
leucine liuA: isovaleryl-CoA dehydrogenase
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit SALWKB2_RS08160
leucine liuC: 3-methylglutaconyl-CoA hydratase
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
lysine amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) SALWKB2_RS03665
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase SALWKB2_RS03670 SALWKB2_RS00840
lysine lysN: 2-aminoadipate transaminase SALWKB2_RS03670 SALWKB2_RS01365
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase SALWKB2_RS07940
maltose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
maltose susB: alpha-glucosidase (maltase)
mannitol mtlA: mannitol phosphotransferase system, EII-CBA components
mannitol mtlD: mannitol-1-phosphate 5-dehydrogenase
mannose manA: mannose-6-phosphate isomerase
mannose manP: mannose PTS system, EII-CBA components
myoinositol iolB: 5-deoxy-D-glucuronate isomerase
myoinositol iolC: 5-dehydro-2-deoxy-D-gluconate kinase
myoinositol iolD: 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase
myoinositol iolE: scyllo-inosose 2-dehydratase
myoinositol iolG: myo-inositol 2-dehydrogenase
myoinositol iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase SALWKB2_RS09870
myoinositol iolT: myo-inositol:H+ symporter
myoinositol mmsA: malonate-semialdehyde dehydrogenase SALWKB2_RS03665 SALWKB2_RS05850
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) SALWKB2_RS09925
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components
phenylacetate H281DRAFT_04042: phenylacetate:H+ symporter SALWKB2_RS09620 SALWKB2_RS10300
phenylacetate paaA: phenylacetyl-CoA 1,2-epoxidase, subunit A
phenylacetate paaB: phenylacetyl-CoA 1,2-epoxidase, subunit B
phenylacetate paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C
phenylacetate paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E
phenylacetate paaF: 2,3-dehydroadipyl-CoA hydratase
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase SALWKB2_RS08835 SALWKB2_RS01790
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase SALWKB2_RS01790 SALWKB2_RS08835
phenylacetate paaK: phenylacetate-CoA ligase
phenylacetate paaZ1: oxepin-CoA hydrolase
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP SALWKB2_RS10300 SALWKB2_RS03660
phenylalanine fahA: fumarylacetoacetate hydrolase
phenylalanine hmgA: homogentisate dioxygenase
phenylalanine HPD: 4-hydroxyphenylpyruvate dioxygenase
phenylalanine maiA: maleylacetoacetate isomerase SALWKB2_RS07550 SALWKB2_RS06450
phenylalanine PAH: phenylalanine 4-monooxygenase
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase
phenylalanine QDPR: 6,7-dihydropteridine reductase SALWKB2_RS06765 SALWKB2_RS00180
proline put1: proline dehydrogenase
proline putA: L-glutamate 5-semialdeyde dehydrogenase SALWKB2_RS03665 SALWKB2_RS09970
propionate prpB: 2-methylisocitrate lyase
propionate prpC: 2-methylcitrate synthase SALWKB2_RS06570
propionate prpD: 2-methylcitrate dehydratase
propionate prpE: propionyl-CoA synthetase
putrescine potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) SALWKB2_RS03250 SALWKB2_RS03050
putrescine puuB: gamma-glutamylputrescine oxidase SALWKB2_RS08220
putrescine puuC: gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase SALWKB2_RS03665 SALWKB2_RS05850
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose aldA: lactaldehyde dehydrogenase SALWKB2_RS03665 SALWKB2_RS03375
rhamnose rhaA: L-rhamnose isomerase
rhamnose rhaB: L-rhamnulokinase
rhamnose rhaD: rhamnulose 1-phosphate aldolase
rhamnose rhaM: L-rhamnose mutarotase
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsK: ribokinase
ribose rbsU: probable D-ribose transporter RbsU
serine sdaB: L-serine ammonia-lyase SALWKB2_RS04155
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase SALWKB2_RS08960
sucrose scrK: fructokinase
sucrose SUS: sucrose synthase
sucrose sut: sucrose:proton symporter SUT/SUC
threonine adh: acetaldehyde dehydrogenase (not acylating) SALWKB2_RS03665 SALWKB2_RS09970
threonine gcvH: glycine cleavage system, H component (lipoyl protein)
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase)
threonine gcvT: glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase)
thymidine adh: acetaldehyde dehydrogenase (not acylating) SALWKB2_RS03665 SALWKB2_RS09970
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase SALWKB2_RS08270
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
trehalose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
trehalose treF: trehalase
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP) SALWKB2_RS10300 SALWKB2_RS03660
tyrosine fahA: fumarylacetoacetate hydrolase
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase SALWKB2_RS07550 SALWKB2_RS06450
valine acdH: isobutyryl-CoA dehydrogenase
valine Bap2: L-valine permease Bap2 SALWKB2_RS09620 SALWKB2_RS03650
valine bch: 3-hydroxyisobutyryl-CoA hydrolase
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase
valine mmsA: methylmalonate-semialdehyde dehydrogenase SALWKB2_RS03665
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
valine prpB: 2-methylisocitrate lyase
valine prpC: 2-methylcitrate synthase SALWKB2_RS06570
valine prpD: 2-methylcitrate dehydratase
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase SALWKB2_RS10565
xylose xylA: xylose isomerase
xylose xylB: xylulokinase
xylose xylT: D-xylose transporter

Confidence: high confidence medium confidence low confidence

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory