GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Streptococcus anginosus CCUG 39159

Found 145 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 HMPREF1043_RS10845
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araE: L-arabinose:H+ symporter
arginine rocA: 1-pyrroline-5-carboxylate dehydrogenase
arginine rocD: ornithine aminotransferase
arginine rocE: L-arginine permease HMPREF1043_RS06195
aspartate glt: aspartate:proton symporter Glt
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component HMPREF1043_RS04910 HMPREF1043_RS06115
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 HMPREF1043_RS06175 HMPREF1043_RS09470
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 HMPREF1043_RS04915 HMPREF1043_RS09470
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component HMPREF1043_RS06120
citrulline rocA: 1-pyrroline-5-carboxylate dehydrogenase
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
deoxyinosine deoB: phosphopentomutase HMPREF1043_RS00680 HMPREF1043_RS09265
deoxyribonate atoA: acetoacetyl-CoA transferase, A subunit HMPREF1043_RS02735
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase HMPREF1043_RS01020
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 aldA: lactaldehyde dehydrogenase
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
fumarate dctA: fumarate:H+ symporter DctA
galactose galP: galactose:H+ symporter GalP
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate kdgK: 2-keto-3-deoxygluconate kinase HMPREF1043_RS04815
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 HMPREF1043_RS01080
glucosamine manY: glucosamine PTS system, EII-C component ManY HMPREF1043_RS01075
glucosamine manZ: glucosamine PTS system, EII-D component ManZ HMPREF1043_RS01070 HMPREF1043_RS04285
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate kdgK: 2-keto-3-deoxygluconate kinase HMPREF1043_RS04815
glucuronate uxaC: D-glucuronate isomerase
glucuronate uxuA: D-mannonate dehydratase
glucuronate uxuB: D-mannonate dehydrogenase
glutamate gdhA: glutamate dehydrogenase, NAD-dependent HMPREF1043_RS11435
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
histidine permease: L-histidine permease HMPREF1043_RS06195
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase HMPREF1043_RS02740 HMPREF1043_RS00990
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase HMPREF1043_RS01020 HMPREF1043_RS04805
isoleucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
isoleucine prpB: 2-methylisocitrate lyase
isoleucine prpC: 2-methylcitrate synthase HMPREF1043_RS01885
isoleucine prpD: 2-methylcitrate dehydratase
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
L-malate sdlC: L-malate:Na+ symporter SdlC
lactose lacC: D-tagatose-6-phosphate kinase HMPREF1043_RS09455 HMPREF1043_RS09285
leucine atoA: acetoacetyl-CoA transferase, A subunit HMPREF1043_RS02735
leucine liuA: isovaleryl-CoA dehydrogenase
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit HMPREF1043_RS01040
leucine liuC: 3-methylglutaconyl-CoA hydratase HMPREF1043_RS02740
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)
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase
lysine lysN: 2-aminoadipate transaminase HMPREF1043_RS06940 HMPREF1043_RS07850
lysine lysP: L-lysine:H+ symporter LysP HMPREF1043_RS06195
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase
maltose susB: alpha-glucosidase (maltase) HMPREF1043_RS01460
mannitol mt2d: mannitol 2-dehydrogenase HMPREF1043_RS04805 HMPREF1043_RS01020
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
myoinositol iolE: scyllo-inosose 2-dehydratase
myoinositol iolG: myo-inositol 2-dehydrogenase
myoinositol iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase HMPREF1043_RS01265
myoinositol iolT: myo-inositol:H+ symporter
myoinositol mmsA: malonate-semialdehyde dehydrogenase
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components HMPREF1043_RS10725 HMPREF1043_RS03220
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 HMPREF1043_RS02740
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase HMPREF1043_RS00990 HMPREF1043_RS02740
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase HMPREF1043_RS01020
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase HMPREF1043_RS06760
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase HMPREF1043_RS06760
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 aroP: L-phenylalanine:H+ symporter AroP HMPREF1043_RS06195
phenylalanine atoA: acetoacetyl-CoA transferase, A subunit HMPREF1043_RS02735
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 HMPREF1043_RS05655 HMPREF1043_RS03925
proline opuBB: proline ABC transporter, fused permease and substrate-binding components OpuBB/BusAB HMPREF1043_RS05650
proline put1: proline dehydrogenase
proline putA: L-glutamate 5-semialdeyde dehydrogenase
propionate prpB: 2-methylisocitrate lyase
propionate prpC: 2-methylcitrate synthase HMPREF1043_RS01885
propionate prpD: 2-methylcitrate dehydratase
propionate prpE: propionyl-CoA synthetase
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabD: succinate semialdehyde dehydrogenase HMPREF1043_RS07640
putrescine gabT: gamma-aminobutyrate transaminase
putrescine patA: putrescine aminotransferase (PatA/SpuC)
putrescine patD: gamma-aminobutyraldehyde dehydrogenase
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose aldA: lactaldehyde dehydrogenase
rhamnose rhaA: L-rhamnose isomerase
rhamnose rhaB: L-rhamnulokinase
rhamnose rhaD: rhamnulose 1-phosphate aldolase HMPREF1043_RS00410
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 HMPREF1043_RS04805 HMPREF1043_RS02635
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
succinate sdc: succinate:Na+ symporter Sdc
threonine prpB: 2-methylisocitrate lyase
threonine prpC: 2-methylcitrate synthase HMPREF1043_RS01885
threonine prpD: 2-methylcitrate dehydratase
threonine tdcB: L-threonine dehydratase
thymidine deoB: phosphopentomutase HMPREF1043_RS00680 HMPREF1043_RS09265
thymidine nupG: thymidine permease NupG/XapB
trehalose treEIIA: N-acetylglucosamine phosphotransferase system, EII-A component (Crr/PtsG/YpqE/GamP) HMPREF1043_RS10725 HMPREF1043_RS11355
tryptophan tnaA: tryptophanase
tryptophan trpP: energy-coupling factor transporter, tryptophan-specific (S) component TrpP
tyrosine aroP: L-tyrosine transporter (AroP/FywP) HMPREF1043_RS06195
tyrosine atoA: acetoacetyl-CoA transferase, A subunit HMPREF1043_RS02735
tyrosine fahA: fumarylacetoacetate hydrolase
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase HMPREF1043_RS06770
valine bch: 3-hydroxyisobutyryl-CoA hydrolase HMPREF1043_RS02740
valine mmsA: methylmalonate-semialdehyde dehydrogenase
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
valine prpB: 2-methylisocitrate lyase
valine prpC: 2-methylcitrate synthase HMPREF1043_RS01885
valine prpD: 2-methylcitrate dehydratase
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.

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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