GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Roseburia faecis M72

Found 164 low-confidence and 38 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 adh: acetaldehyde dehydrogenase (not acylating)
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 araVsh: L-arabinose ABC transporter, ATPase component AraV(Sh) M72_RS00735 M72_RS03760
arabinose araWsh: L-arabinose ABC transporter, permease component 1 AraW(Sh) M72_RS00730
arabinose araZsh: L-arabinose ABC transporter, permease component 2 AraZ(Sh) M72_RS00725
arginine arcA: arginine deiminase
arginine putA: L-glutamate 5-semialdeyde dehydrogenase
arginine rocD: ornithine aminotransferase M72_RS12800
arginine rocE: L-arginine permease
asparagine ans: asparaginase
aspartate glt: aspartate:proton symporter Glt
cellobiose mglB: glucose ABC transporter, substrate-binding component M72_RS03785
cellobiose mglC: glucose ABC transporter, permease component (MglC) M72_RS03765
citrate acn: aconitase M72_RS07580
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component M72_RS07610 M72_RS01610
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 M72_RS01615
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline putA: L-glutamate 5-semialdeyde dehydrogenase
citrulline rocD: ornithine aminotransferase M72_RS12800
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase M72_RS11705
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 M72_RS12545
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating)
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate aacS: acetoacetyl-CoA synthetase
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)
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
ethanol adh: acetaldehyde dehydrogenase (not acylating)
fucose fucA: L-fuculose-phosphate aldolase FucA
fucose fucI: L-fucose isomerase FucI
fucose fucK: L-fuculose kinase FucK
fucose fucO: L-lactaldehyde reductase M72_RS11935 M72_RS00605
fucose fucP: L-fucose:H+ symporter FucP
fucose fucU: L-fucose mutarotase FucU
fumarate dctA: fumarate:H+ symporter DctA
galactose mglB: galactose ABC transporter, substrate-binding component MglB M72_RS03785
galactose mglC: galactose ABC transporter, permease component MglC M72_RS03765
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 SLC2A2: glucosamine transporter SLC2A2
glucose mglB: glucose ABC transporter, substrate-binding component M72_RS03785
glucose mglC: glucose ABC transporter, permease component (MglC) M72_RS03765
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 M72_RS14525
glucuronate garR: tartronate semialdehyde reductase
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate udh: D-glucuronate dehydrogenase
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric)
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 M72_RS02625
isoleucine Bap2: L-isoleucine permease Bap2
isoleucine dddA: 3-hydroxypropionate dehydrogenase
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase M72_RS04305
isoleucine hpcD: 3-hydroxypropionyl-CoA dehydratase M72_RS04305
isoleucine iolA: malonate semialdehyde dehydrogenase (CoA-acylating)
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase M72_RS11610 M72_RS02545
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
lactose lacE: lactose ABC transporter, substrate-binding component M72_RS06485
lactose lacK: lactose ABC transporter, ATPase component M72_RS12660 M72_RS03885
leucine aacS: acetoacetyl-CoA synthetase
leucine leuT: L-leucine:Na+ symporter LeuT M72_RS15420
leucine liuA: isovaleryl-CoA dehydrogenase M72_RS02625
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit
leucine liuC: 3-methylglutaconyl-CoA hydratase M72_RS04305
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 M72_RS12800
lysine lysN: 2-aminoadipate transaminase M72_RS04030 M72_RS12800
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase
maltose malE_Aa: maltose ABC transporter, substrate-binding component M72_RS05545
maltose malK_Aa: maltose ABC transporter, ATPase component M72_RS12660 M72_RS07435
mannitol mt2d: mannitol 2-dehydrogenase M72_RS01595 M72_RS11610
mannitol PLT5: polyol transporter PLT5
mannose manP: mannose PTS system, EII-CBA components M72_RS00360
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 M72_RS00795
myoinositol iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase M72_RS02035
myoinositol iolT: myo-inositol:H+ symporter
myoinositol mmsA: malonate-semialdehyde dehydrogenase
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 M72_RS04305
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase M72_RS04305
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase M72_RS02635
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase M72_RS02635
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
phenylalanine iorAB: phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB
phenylalanine paaA: phenylacetyl-CoA 1,2-epoxidase, subunit A
phenylalanine paaB: phenylacetyl-CoA 1,2-epoxidase, subunit B
phenylalanine paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C
phenylalanine paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E
phenylalanine paaF: 2,3-dehydroadipyl-CoA hydratase M72_RS04305
phenylalanine paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase M72_RS04305
phenylalanine paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase M72_RS02635
phenylalanine paaJ2: 3-oxoadipyl-CoA thiolase M72_RS02635
phenylalanine paaZ1: oxepin-CoA hydrolase
phenylalanine paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
proline putA: L-glutamate 5-semialdeyde dehydrogenase
propionate dddA: 3-hydroxypropionate dehydrogenase
propionate hpcD: 3-hydroxypropionyl-CoA dehydratase M72_RS04305
propionate iolA: malonate semialdehyde dehydrogenase (CoA-acylating)
propionate prpE: propionyl-CoA synthetase
propionate putP: propionate transporter; proline:Na+ symporter M72_RS11845
putrescine gabD: succinate semialdehyde dehydrogenase
putrescine gabT: gamma-aminobutyrate transaminase M72_RS12800 M72_RS13930
putrescine patA: putrescine aminotransferase (PatA/SpuC) M72_RS12800
putrescine patD: gamma-aminobutyraldehyde dehydrogenase
putrescine potB: putrescine ABC transporter, permease component 1 (PotB/PotH) M72_RS07430
putrescine potC: putrescine ABC transporter, permease component 2 (PotC/PotI) M72_RS07425
putrescine potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) M72_RS07420
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose fucO: L-lactaldehyde reductase M72_RS11935 M72_RS00605
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 serP: L-serine permease SerP
sorbitol sdh: sorbitol dehydrogenase M72_RS01595 M72_RS01845
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 M72_RS04305
threonine iolA: malonate semialdehyde dehydrogenase (CoA-acylating)
threonine tdcB: L-threonine dehydratase M72_RS12545
threonine tdcC: L-threonine:H+ symporter TdcC
thymidine adh: acetaldehyde dehydrogenase (not acylating)
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
trehalose malK: trehalose ABC transporter, ATPase component MalK M72_RS12660 M72_RS07435
trehalose malX: trehalose ABC transporter, substrate-binding component MalX
trehalose PsTP: trehalose phosphorylase
tryptophan ecfA1: energy-coupling factor transporter, ATPase 1 (A1) component M72_RS04040 M72_RS04045
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)
tyrosine fahA: fumarylacetoacetate hydrolase
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase M72_RS02625
valine Bap2: L-valine permease Bap2
valine bch: 3-hydroxyisobutyryl-CoA hydrolase
valine dddA: 3-hydroxypropionate dehydrogenase
valine hpcD: 3-hydroxypropionyl-CoA dehydratase M72_RS04305
valine iolA: malonate semialdehyde dehydrogenase (CoA-acylating)
valine mmsA: methylmalonate-semialdehyde dehydrogenase
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase M72_RS01845 M72_RS01595
xylose xylA: xylose isomerase
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