GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Oleispira antarctica RB-8

Found 158 low-confidence and 32 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate kgtP: 2-oxoglutarate:H+ symporter KgtP
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 actP: cation/acetate symporter ActP OLEAN_RS19290
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter
arginine rocD: ornithine aminotransferase OLEAN_RS03755 OLEAN_RS06405
arginine rocE: L-arginine permease
cellobiose bgl: cellobiase
cellobiose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component OLEAN_RS14330 OLEAN_RS18015
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline rocD: ornithine aminotransferase OLEAN_RS03755 OLEAN_RS06405
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase OLEAN_RS18180 OLEAN_RS18185
D-lactate lctP: D-lactate:H+ symporter LctP or LidP
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase OLEAN_RS17970
deoxyinosine deoB: phosphopentomutase
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase OLEAN_RS08615
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate aacS: acetoacetyl-CoA synthetase OLEAN_RS13935 OLEAN_RS10585
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase OLEAN_RS05785 OLEAN_RS03865
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate garK: glycerate 2-kinase
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
fructose 1pfk: 1-phosphofructokinase
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
fucose aldA: lactaldehyde dehydrogenase OLEAN_RS18035 OLEAN_RS01640
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 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 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) OLEAN_RS19710
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 kdgK: 2-keto-3-deoxygluconate kinase
glucuronate uxaC: D-glucuronate isomerase
glucuronate uxuA: D-mannonate dehydratase
glucuronate uxuB: D-mannonate dehydrogenase
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) OLEAN_RS08485
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 permease: L-histidine permease
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase OLEAN_RS16500 OLEAN_RS16525
isoleucine Bap2: L-isoleucine permease Bap2
isoleucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit OLEAN_RS02940 OLEAN_RS07665
isoleucine pccB: propionyl-CoA carboxylase, beta subunit OLEAN_RS02925 OLEAN_RS05310
L-lactate lctO: L-lactate oxidase or 2-monooxygenase
L-lactate Shew_2731: L-lactate:Na+ symporter, large component OLEAN_RS19290
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 aacS: acetoacetyl-CoA synthetase OLEAN_RS13935 OLEAN_RS10585
leucine leuT: L-leucine:Na+ symporter LeuT
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit OLEAN_RS02940 OLEAN_RS07665
leucine liuC: 3-methylglutaconyl-CoA hydratase OLEAN_RS02935 OLEAN_RS13050
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit OLEAN_RS02925
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
lysine amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) OLEAN_RS17490
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase OLEAN_RS06405 OLEAN_RS03755
lysine lysN: 2-aminoadipate transaminase OLEAN_RS07170 OLEAN_RS06405
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase OLEAN_RS18180
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 OLEAN_RS09855
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 OLEAN_RS00575
myoinositol iolT: myo-inositol:H+ symporter
myoinositol mmsA: malonate-semialdehyde dehydrogenase OLEAN_RS18035
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) OLEAN_RS19710
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components
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 OLEAN_RS08010 OLEAN_RS02935
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase OLEAN_RS08010 OLEAN_RS13050
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase OLEAN_RS17915 OLEAN_RS07255
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase OLEAN_RS17915 OLEAN_RS07255
phenylacetate paaK: phenylacetate-CoA ligase OLEAN_RS10585 OLEAN_RS13935
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aacS: acetoacetyl-CoA synthetase OLEAN_RS13935 OLEAN_RS10585
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine fahA: fumarylacetoacetate hydrolase
phenylalanine hmgA: homogentisate dioxygenase
phenylalanine HPD: 4-hydroxyphenylpyruvate dioxygenase
phenylalanine maiA: maleylacetoacetate isomerase
phenylalanine PAH: phenylalanine 4-monooxygenase
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase OLEAN_RS02570
propionate pccA: propionyl-CoA carboxylase, alpha subunit OLEAN_RS02940 OLEAN_RS07665
propionate pccB: propionyl-CoA carboxylase, beta subunit OLEAN_RS02925 OLEAN_RS05310
propionate putP: propionate transporter; proline:Na+ symporter OLEAN_RS17495
putrescine gabD: succinate semialdehyde dehydrogenase OLEAN_RS05680 OLEAN_RS18035
putrescine gabT: gamma-aminobutyrate transaminase OLEAN_RS06405 OLEAN_RS06545
putrescine patA: putrescine aminotransferase (PatA/SpuC) OLEAN_RS06405 OLEAN_RS06545
putrescine patD: gamma-aminobutyraldehyde dehydrogenase OLEAN_RS18035 OLEAN_RS05680
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate yjcH: putative small subunit of pyruvate transporter (yjcH-like) OLEAN_RS19285
rhamnose aldA: lactaldehyde dehydrogenase OLEAN_RS18035 OLEAN_RS01640
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 OLEAN_RS17970
serine serP: L-serine permease SerP
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase OLEAN_RS03865 OLEAN_RS15340
sucrose scrK: fructokinase
sucrose SUS: sucrose synthase
sucrose sut: sucrose:proton symporter SUT/SUC
threonine ltaE: L-threonine aldolase OLEAN_RS17405
threonine tdcC: L-threonine:H+ symporter TdcC
thymidine deoA: thymidine phosphorylase DeoA OLEAN_RS05365
thymidine deoB: phosphopentomutase
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 aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aacS: acetoacetyl-CoA synthetase OLEAN_RS13935 OLEAN_RS10585
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine fahA: fumarylacetoacetate hydrolase
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase OLEAN_RS16500 OLEAN_RS16525
valine Bap2: L-valine permease Bap2
valine bch: 3-hydroxyisobutyryl-CoA hydrolase OLEAN_RS07355 OLEAN_RS07250
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase OLEAN_RS07250 OLEAN_RS13050
valine mmsA: methylmalonate-semialdehyde dehydrogenase OLEAN_RS18035 OLEAN_RS05680
valine mmsB: 3-hydroxyisobutyrate dehydrogenase OLEAN_RS15505
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
valine pccA: propionyl-CoA carboxylase, alpha subunit OLEAN_RS02940 OLEAN_RS07665
valine pccB: propionyl-CoA carboxylase, beta subunit OLEAN_RS02925 OLEAN_RS05310
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase
xylose xylA: xylose isomerase
xylose xylB: xylulokinase
xylose xylT: D-xylose transporter

Confidence: high confidence medium confidence low confidence

This GapMind analysis is from Apr 09 2024. 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