GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Streptococcus oralis AZ_3a

Found 154 low-confidence and 27 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 ybhL: acetate uptake transporter YbhL H354_RS20720
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araE: L-arabinose:H+ symporter
arginine artP: L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA H354_RS12580 H354_RS14455
arginine bgtB: L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) H354_RS17525 H354_RS12575
arginine rocA: 1-pyrroline-5-carboxylate dehydrogenase H354_RS12390
arginine rocD: ornithine aminotransferase
arginine rocF: arginase
aspartate peb1C: aspartate ABC transporter, ATPase component Peb1C H354_RS15015 H354_RS14455
aspartate peb1D: aspartate ABC transporter, permease component 2 (Peb1D) H354_RS15030 H354_RS15025
cellobiose bgl: cellobiase H354_RS14630 H354_RS19235
citrate acn: aconitase
citrate icd: isocitrate dehydrogenase H354_RS12705
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component H354_RS12580 H354_RS14455
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 H354_RS17525 H354_RS14315
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 H354_RS12575 H354_RS20935
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline citrullinase: putative citrullinase
citrulline rocA: 1-pyrroline-5-carboxylate dehydrogenase H354_RS12390
citrulline rocD: ornithine aminotransferase
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase
D-lactate lctP: D-lactate:H+ symporter LctP or LidP
D-serine dsdA: D-serine ammonia-lyase H354_RS17545
deoxyribonate aacS: acetoacetyl-CoA synthetase
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase H354_RS15525 H354_RS19715
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
fucose fucA: L-fuculose-phosphate aldolase FucA
fucose fucI: L-fucose isomerase FucI
fucose fucK: L-fuculose kinase FucK
fucose fucO: L-lactaldehyde reductase H354_RS18645 H354_RS21725
fucose fucP: L-fucose:H+ symporter FucP
fucose fucU: L-fucose mutarotase FucU
fumarate dctA: fumarate:H+ symporter DctA
galactose ptcA: galactose PTS system, EIIA component H354_RS13805
galactose ptcB: galactose PTS system, EIIB component H354_RS13810
galactose ptcEIIC: galactose PTS system, EIIC component
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate kdgK: 2-keto-3-deoxygluconate kinase H354_RS19315
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 manX: glucosamine PTS system, EII-AB component ManX H354_RS20555 H354_RS13605
glucosamine manY: glucosamine PTS system, EII-C component ManY H354_RS13600 H354_RS20550
glucosamine manZ: glucosamine PTS system, EII-D component ManZ H354_RS13595 H354_RS20545
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate kdgK: 2-keto-3-deoxygluconate kinase H354_RS19315
glucuronate uxaC: D-glucuronate isomerase
glucuronate uxuA: D-mannonate dehydratase
glucuronate uxuB: D-mannonate dehydrogenase
glutamate gdhA: glutamate dehydrogenase, NAD-dependent H354_RS21230
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric)
glycerol glpK: glycerol kinase
histidine bgtA: L-histidine ABC transporter, ATPase component BgtA H354_RS12580 H354_RS14455
histidine bgtB: L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) H354_RS17525 H354_RS12575
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase H354_RS16270
isoleucine dddA: 3-hydroxypropionate dehydrogenase
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase H354_RS15555
isoleucine hpcD: 3-hydroxypropionyl-CoA dehydratase
isoleucine iolA: malonate semialdehyde dehydrogenase (CoA-acylating) H354_RS12390
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase H354_RS15525 H354_RS19325
isoleucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
L-malate sdlC: L-malate:Na+ symporter SdlC
leucine aacS: acetoacetyl-CoA synthetase
leucine liuA: isovaleryl-CoA dehydrogenase H354_RS16270
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit H354_RS15505
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) H354_RS12390
lysine bgtB: L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) H354_RS17525 H354_RS12575
lysine hglS: D-2-hydroxyglutarate synthase
lysine hisP: L-lysine ABC transporter, ATPase component HisP H354_RS12580 H354_RS14455
lysine lat: L-lysine 6-aminotransferase
lysine lysN: 2-aminoadipate transaminase H354_RS13005 H354_RS20095
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase
maltose susB: alpha-glucosidase (maltase) H354_RS17455
mannitol mt2d: mannitol 2-dehydrogenase H354_RS19325 H354_RS15525
mannitol PLT5: polyol transporter PLT5
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 H354_RS17560
myoinositol iolE: scyllo-inosose 2-dehydratase
myoinositol iolG: myo-inositol 2-dehydrogenase
myoinositol iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase H354_RS14790
myoinositol iolT: myo-inositol:H+ symporter
myoinositol mmsA: malonate-semialdehyde dehydrogenase H354_RS12390
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components H354_RS14510
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 H354_RS15555
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase H354_RS15525
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase H354_RS16260
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase H354_RS16260
phenylacetate paaK: phenylacetate-CoA ligase
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
phenylalanine aroP: L-phenylalanine:H+ symporter AroP H354_RS17125
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
phenylalanine QDPR: 6,7-dihydropteridine reductase
proline opuBA: proline ABC transporter, ATPase component OpuBA/BusAA H354_RS14020 H354_RS15150
proline put1: proline dehydrogenase
proline putA: L-glutamate 5-semialdeyde dehydrogenase H354_RS12390
propionate dddA: 3-hydroxypropionate dehydrogenase
propionate hpcD: 3-hydroxypropionyl-CoA dehydratase
propionate iolA: malonate semialdehyde dehydrogenase (CoA-acylating) H354_RS12390
propionate prpE: propionyl-CoA synthetase
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabD: succinate semialdehyde dehydrogenase H354_RS21725 H354_RS12390
putrescine gabT: gamma-aminobutyrate transaminase
putrescine patA: putrescine aminotransferase (PatA/SpuC)
putrescine patD: gamma-aminobutyraldehyde dehydrogenase H354_RS12390
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose fucO: L-lactaldehyde reductase H354_RS18645 H354_RS21725
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
sorbitol sdh: sorbitol dehydrogenase H354_RS19325 H354_RS15525
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
succinate sdc: succinate:Na+ symporter Sdc
threonine dddA: 3-hydroxypropionate dehydrogenase
threonine hpcD: 3-hydroxypropionyl-CoA dehydratase
threonine iolA: malonate semialdehyde dehydrogenase (CoA-acylating) H354_RS12390
thymidine nupG: thymidine permease NupG/XapB
trehalose treF: trehalase H354_RS17455
tryptophan tnaA: tryptophanase
tryptophan trpP: energy-coupling factor transporter, tryptophan-specific (S) component TrpP
tyrosine aacS: acetoacetyl-CoA synthetase
tyrosine aroP: L-tyrosine transporter (AroP/FywP) H354_RS17125
tyrosine fahA: fumarylacetoacetate hydrolase
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase
valine bch: 3-hydroxyisobutyryl-CoA hydrolase
valine dddA: 3-hydroxypropionate dehydrogenase
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase H354_RS15555
valine hpcD: 3-hydroxypropionyl-CoA dehydratase
valine iolA: malonate semialdehyde dehydrogenase (CoA-acylating) H354_RS12390
valine mmsA: methylmalonate-semialdehyde dehydrogenase H354_RS12390
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
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 Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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