GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Actinomyces timonensis 7400942

Found 154 low-confidence and 52 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate kgtP: 2-oxoglutarate:H+ symporter KgtP A1QA_RS0103835 A1QA_RS13180
4-hydroxybenzoate adh: acetaldehyde dehydrogenase (not acylating) A1QA_RS0101845 A1QA_RS0105610
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
arabinose araA: L-arabinose isomerase
arabinose araE: L-arabinose:H+ symporter A1QA_RS0100940 A1QA_RS0101825
arginine arcA: arginine deiminase A1QA_RS0111070
arginine put1: proline dehydrogenase A1QA_RS0108110
arginine putA: L-glutamate 5-semialdeyde dehydrogenase A1QA_RS0108110
arginine rocD: ornithine aminotransferase A1QA_RS0100050 A1QA_RS0104200
arginine rocE: L-arginine permease A1QA_RS0108530 A1QA_RS0103780
asparagine ans: asparaginase A1QA_RS0103785
aspartate glt: aspartate:proton symporter Glt
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component A1QA_RS0109835 A1QA_RS0100120
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 A1QA_RS0109830
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline put1: proline dehydrogenase A1QA_RS0108110
citrulline putA: L-glutamate 5-semialdeyde dehydrogenase A1QA_RS0108110
citrulline rocD: ornithine aminotransferase A1QA_RS0100050 A1QA_RS0104200
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase A1QA_RS0106295
D-lactate lctP: D-lactate:H+ symporter LctP or LidP A1QA_RS0102775
D-serine dsdA: D-serine ammonia-lyase A1QA_RS0110680
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) A1QA_RS0101845 A1QA_RS0105610
deoxyinosine deoB: phosphopentomutase A1QA_RS0101465
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine nupC: deoxyinosine:H+ symporter NupC A1QA_RS0105745
deoxyribonate aacS: acetoacetyl-CoA synthetase
deoxyribonate atoB: acetyl-CoA C-acetyltransferase
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase A1QA_RS0109325
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) A1QA_RS0101845 A1QA_RS0105610
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoP: deoxyribose transporter
ethanol adh: acetaldehyde dehydrogenase (not acylating) A1QA_RS0101845 A1QA_RS0105610
fructose 1pfk: 1-phosphofructokinase A1QA_RS0103345
fucose aldA: lactaldehyde dehydrogenase A1QA_RS0101845 A1QA_RS0108110
fucose fucA: L-fuculose-phosphate aldolase FucA A1QA_RS0100680
fucose fucI: L-fucose isomerase FucI
fucose fucK: L-fuculose kinase FucK A1QA_RS0101080
fucose fucP: L-fucose:H+ symporter FucP
fucose fucU: L-fucose mutarotase FucU
fumarate dctA: fumarate:H+ symporter DctA
galactose galE: UDP-glucose 4-epimerase A1QA_RS0111350 A1QA_RS0106535
galactose galP: galactose:H+ symporter GalP A1QA_RS0100940 A1QA_RS0101950
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 A1QA_RS0102635 A1QA_RS0105755
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 nagA: N-acetylglucosamine 6-phosphate deacetylase A1QA_RS0101615
glucosamine nagX: transmembrane glucosamine N-acetyltransferase NagX
glucose gtsA: glucose ABC transporter, substrate-binding component (GtsA) A1QA_RS0101255
glucose gtsB: glucose ABC transporter, permease component 1 (GtsB) A1QA_RS0101250 A1QA_RS0107465
glucose gtsD: glucose ABC transporter, ATPase component (GtsD) A1QA_RS0106175 A1QA_RS0104755
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter A1QA_RS0108025
glucuronate eda: 2-keto-3-deoxygluconate 6-phosphate aldolase
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate kdgK: 2-keto-3-deoxygluconate kinase A1QA_RS0102635 A1QA_RS0105755
glucuronate uxaC: D-glucuronate isomerase
glucuronate uxuA: D-mannonate dehydratase
glucuronate uxuB: D-mannonate dehydrogenase A1QA_RS0102810
glutamate glnP: L-glutamate ABC transporter, fused permease and substrate-binding components GlnP
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) A1QA_RS0102750
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 A1QA_RS0105780 A1QA_RS0100120
histidine PA5505: L-histidine ABC transporter, substrate-binding component A1QA_RS0105790
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase A1QA_RS0109970
isoleucine brnQ: L-isoleucine:cation symporter BrnQ/BraZ/BraB A1QA_RS0107505
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase A1QA_RS0109335 A1QA_RS0111065
isoleucine fadA: 2-methylacetoacetyl-CoA thiolase
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase A1QA_RS0109325
isoleucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
isoleucine prpB: 2-methylisocitrate lyase
isoleucine prpC: 2-methylcitrate synthase A1QA_RS14515
isoleucine prpD: 2-methylcitrate dehydratase
L-lactate lctP: L-lactate:H+ symporter LctP or LidP A1QA_RS0102775
L-malate sdlC: L-malate:Na+ symporter SdlC
lactose galE: UDP-glucose 4-epimerase A1QA_RS0111350 A1QA_RS0106535
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric) A1QA_RS0105715 A1QA_RS0108845
leucine aacS: acetoacetyl-CoA synthetase
leucine atoB: acetyl-CoA C-acetyltransferase
leucine brnQ: L-leucine:Na+ symporter BrnQ/BraB A1QA_RS0107505
leucine liuA: isovaleryl-CoA dehydrogenase
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit A1QA_RS0109210
leucine liuC: 3-methylglutaconyl-CoA hydratase
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit A1QA_RS0109205
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
lysine amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) A1QA_RS0108110
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase A1QA_RS0100050
lysine lysN: 2-aminoadipate transaminase A1QA_RS0102560 A1QA_RS0105170
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase
maltose gtsA: glucose ABC transporter, substrate-binding component (GtsA) A1QA_RS0101255
maltose gtsB: glucose ABC transporter, permease component 1 (GtsB) A1QA_RS0101250 A1QA_RS0107465
maltose gtsD: glucose ABC transporter, ATPase component (GtsD) A1QA_RS0106175 A1QA_RS0104755
mannitol PLT5: polyol transporter PLT5 A1QA_RS0100940
mannitol scrK: fructokinase A1QA_RS0110735 A1QA_RS0101865
mannose manX: mannose PTS system, EII-AB component ManX/ManL A1QA_RS0106055
mannose manY: mannose PTS system, EII-C component ManY/ManM A1QA_RS0106060
myoinositol iolB: 5-deoxy-D-glucuronate isomerase A1QA_RS0101855
myoinositol iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase A1QA_RS0101865
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase A1QA_RS0101615
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 A1QA_RS0109325
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase
phenylacetate paaK: phenylacetate-CoA ligase A1QA_RS12870
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 A1QA_RS0105330 A1QA_RS0108530
phenylalanine atoB: acetyl-CoA C-acetyltransferase
phenylalanine fahA: fumarylacetoacetate hydrolase A1QA_RS0107335
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 put1: proline dehydrogenase A1QA_RS0108110
proline putA: L-glutamate 5-semialdeyde dehydrogenase A1QA_RS0108110
propionate prpB: 2-methylisocitrate lyase
propionate prpC: 2-methylcitrate synthase A1QA_RS14515
propionate prpD: 2-methylcitrate dehydratase
propionate prpE: propionyl-CoA synthetase A1QA_RS12870
propionate putP: propionate transporter; proline:Na+ symporter A1QA_RS0109195
putrescine gabD: succinate semialdehyde dehydrogenase A1QA_RS0101845 A1QA_RS0108110
putrescine gabT: gamma-aminobutyrate transaminase A1QA_RS0100050 A1QA_RS0104200
putrescine patA: putrescine aminotransferase (PatA/SpuC) A1QA_RS0100050 A1QA_RS0104200
putrescine patD: gamma-aminobutyraldehyde dehydrogenase A1QA_RS0101845
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
rhamnose aldA: lactaldehyde dehydrogenase A1QA_RS0101845 A1QA_RS0108110
rhamnose rhaA: L-rhamnose isomerase
rhamnose rhaB: L-rhamnulokinase A1QA_RS0101080
rhamnose rhaD: rhamnulose 1-phosphate aldolase
rhamnose rhaM: L-rhamnose mutarotase
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsU: probable D-ribose transporter RbsU
serine serP: L-serine permease SerP A1QA_RS0105330 A1QA_RS0103780
sorbitol scrK: fructokinase A1QA_RS0110735 A1QA_RS0101865
sorbitol sdh: sorbitol dehydrogenase A1QA_RS0102810 A1QA_RS0100675
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2 A1QA_RS0100940
succinate sdc: succinate:Na+ symporter Sdc
sucrose 1pfk: 1-phosphofructokinase A1QA_RS0103345
sucrose ams: sucrose hydrolase (invertase) A1QA_RS0105555 A1QA_RS0112315
threonine prpB: 2-methylisocitrate lyase
threonine prpC: 2-methylcitrate synthase A1QA_RS14515
threonine prpD: 2-methylcitrate dehydratase
threonine serP1: L-threonine uptake transporter SerP1 A1QA_RS0105330 A1QA_RS0103780
thymidine adh: acetaldehyde dehydrogenase (not acylating) A1QA_RS0101845 A1QA_RS0105610
thymidine deoA: thymidine phosphorylase DeoA A1QA_RS0107830
thymidine deoB: phosphopentomutase A1QA_RS0101465
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
trehalose treB: trehalose PTS system, EII-BC components TreB A1QA_RS14145
trehalose treC: trehalose-6-phosphate hydrolase A1QA_RS0112315 A1QA_RS0105645
trehalose treEIIA: N-acetylglucosamine phosphotransferase system, EII-A component (Crr/PtsG/YpqE/GamP) A1QA_RS14145 A1QA_RS0108255
tryptophan aroP: tryptophan:H+ symporter AroP A1QA_RS0105330 A1QA_RS0103780
tryptophan tnaA: tryptophanase
tyrosine aacS: acetoacetyl-CoA synthetase
tyrosine aroP: L-tyrosine transporter (AroP/FywP) A1QA_RS0105330 A1QA_RS0103780
tyrosine atoB: acetyl-CoA C-acetyltransferase
tyrosine fahA: fumarylacetoacetate hydrolase A1QA_RS0107335
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase A1QA_RS0109970
valine bch: 3-hydroxyisobutyryl-CoA hydrolase
valine brnQ: L-valine:cation symporter BrnQ/BraZ/BraB A1QA_RS0107505
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase A1QA_RS0111065
valine mmsA: methylmalonate-semialdehyde dehydrogenase A1QA_RS0101845
valine mmsB: 3-hydroxyisobutyrate dehydrogenase A1QA_RS0100440
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
valine prpB: 2-methylisocitrate lyase
valine prpC: 2-methylcitrate synthase A1QA_RS14515
valine prpD: 2-methylcitrate dehydratase
xylitol fruI: xylitol PTS, enzyme IIABC (FruI) A1QA_RS0103340
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase
xylose xylA: xylose isomerase
xylose xylB: xylulokinase A1QA_RS0102615 A1QA_RS0100665
xylose xylT: D-xylose transporter A1QA_RS0100940 A1QA_RS0101825

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