GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Alistipes indistinctus YIT 12060

Found 141 low-confidence and 35 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) HMPREF9450_RS09195
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
alanine cycA: L-alanine symporter CycA
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter HMPREF9450_RS06450
arginine rocA: 1-pyrroline-5-carboxylate dehydrogenase
arginine rocD: ornithine aminotransferase HMPREF9450_RS06615 HMPREF9450_RS00480
arginine rocE: L-arginine permease
arginine rocF: arginase HMPREF9450_RS02355
aspartate glt: aspartate:proton symporter Glt
cellobiose MFS-glucose: glucose transporter, MFS superfamily HMPREF9450_RS06450 HMPREF9450_RS05320
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component HMPREF9450_RS07385 HMPREF9450_RS03600
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 arcC: carbamate kinase
citrulline rocA: 1-pyrroline-5-carboxylate dehydrogenase
citrulline rocD: ornithine aminotransferase HMPREF9450_RS06615 HMPREF9450_RS00480
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase HMPREF9450_RS03705 HMPREF9450_RS10830
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
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) HMPREF9450_RS09195
deoxyinosine deoB: phosphopentomutase HMPREF9450_RS10990
deoxyinosine nupC: deoxyinosine:H+ symporter NupC HMPREF9450_RS08165
deoxyribonate atoB: acetyl-CoA C-acetyltransferase
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase HMPREF9450_RS09570 HMPREF9450_RS11305
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 adh: acetaldehyde dehydrogenase (not acylating) HMPREF9450_RS09195
deoxyribose deoP: deoxyribose transporter HMPREF9450_RS06960
ethanol adh: acetaldehyde dehydrogenase (not acylating) HMPREF9450_RS09195
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) HMPREF9450_RS07615 HMPREF9450_RS07620
fucose fucA: L-fuculose-phosphate aldolase FucA HMPREF9450_RS06355
fumarate dctA: fumarate:H+ symporter DctA
galactose galP: galactose:H+ symporter GalP HMPREF9450_RS06450
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galacturonate uxaA: D-altronate dehydratase
galacturonate uxaB: tagaturonate reductase
gluconate gntK: D-gluconate kinase
gluconate gntT: gluconate:H+ symporter GntT
glucosamine nagP: N-acetylglucosamine transporter NagP HMPREF9450_RS05320
glucosamine nagX: transmembrane glucosamine N-acetyltransferase NagX
glucose MFS-glucose: glucose transporter, MFS superfamily HMPREF9450_RS06450 HMPREF9450_RS05320
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter HMPREF9450_RS11745
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate uxuB: D-mannonate dehydrogenase
glutamate gltS: L-glutamate:Na+ symporter GltS
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) HMPREF9450_RS11760
glycerol glpF: glycerol facilitator glpF
glycerol glpK: glycerol kinase
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 HMPREF9450_RS05640
isoleucine Bap2: L-isoleucine permease Bap2
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase
isoleucine fadA: 2-methylacetoacetyl-CoA thiolase
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase HMPREF9450_RS09570 HMPREF9450_RS00875
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit HMPREF9450_RS11730
isoleucine vorA: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA HMPREF9450_RS10810 with HMPREF9450_RS10805
isoleucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC HMPREF9450_RS10820
L-lactate lctO: L-lactate oxidase or 2-monooxygenase
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
L-malate sdlC: L-malate:Na+ symporter SdlC
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric) HMPREF9450_RS06460 HMPREF9450_RS09575
leucine atoB: acetyl-CoA C-acetyltransferase
leucine leuT: L-leucine:Na+ symporter LeuT HMPREF9450_RS07340 HMPREF9450_RS00940
leucine liuA: isovaleryl-CoA dehydrogenase HMPREF9450_RS05640
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit HMPREF9450_RS11730
leucine liuC: 3-methylglutaconyl-CoA hydratase
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit HMPREF9450_RS08605 HMPREF9450_RS11720
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine vorA: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA HMPREF9450_RS10810 with HMPREF9450_RS10805
leucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC HMPREF9450_RS10820
lysine amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd)
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase HMPREF9450_RS00595
lysine lysN: 2-aminoadipate transaminase HMPREF9450_RS00595 HMPREF9450_RS06615
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase
maltose MFS-glucose: glucose transporter, MFS superfamily HMPREF9450_RS06450 HMPREF9450_RS05320
maltose susB: alpha-glucosidase (maltase)
mannitol mtlA: mannitol phosphotransferase system, EII-CBA components
mannose manA: mannose-6-phosphate isomerase HMPREF9450_RS04910 HMPREF9450_RS11515
mannose STP6: mannose:H+ symporter HMPREF9450_RS06450
myoinositol iolG: myo-inositol 2-dehydrogenase HMPREF9450_RS05355
myoinositol iolM: 2-inosose 4-dehydrogenase
myoinositol iolN: 2,4-diketo-inositol hydratase
myoinositol iolO: 5-dehydro-L-gluconate epimerase
myoinositol iolT: myo-inositol:H+ symporter HMPREF9450_RS06450
myoinositol uxaE: D-tagaturonate epimerase
myoinositol uxuB: D-mannonate dehydrogenase
NAG nagP: N-acetylglucosamine transporter NagP HMPREF9450_RS05320
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 HMPREF9450_RS09570 HMPREF9450_RS09660
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase
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 atoB: acetyl-CoA C-acetyltransferase
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 proY: proline:H+ symporter
proline put1: proline dehydrogenase
proline putA: L-glutamate 5-semialdeyde dehydrogenase
propionate pccA: propionyl-CoA carboxylase, alpha subunit HMPREF9450_RS11730
propionate prpE: propionyl-CoA synthetase
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabD: succinate semialdehyde dehydrogenase HMPREF9450_RS09195
putrescine gabT: gamma-aminobutyrate transaminase HMPREF9450_RS00480 HMPREF9450_RS00595
putrescine patA: putrescine aminotransferase (PatA/SpuC) HMPREF9450_RS00595 HMPREF9450_RS00480
putrescine patD: gamma-aminobutyraldehyde dehydrogenase HMPREF9450_RS09195
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose rhaD: rhamnulose 1-phosphate aldolase
serine serP: L-serine permease SerP
sorbitol sdh: sorbitol dehydrogenase HMPREF9450_RS06255 HMPREF9450_RS09570
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2 HMPREF9450_RS06450
succinate sdc: succinate:Na+ symporter Sdc
sucrose ams: sucrose hydrolase (invertase)
threonine adh: acetaldehyde dehydrogenase (not acylating) HMPREF9450_RS09195
threonine tdcC: L-threonine:H+ symporter TdcC
thymidine adh: acetaldehyde dehydrogenase (not acylating) HMPREF9450_RS09195
thymidine deoA: thymidine phosphorylase DeoA HMPREF9450_RS11510
thymidine deoB: phosphopentomutase HMPREF9450_RS10990
thymidine nupC: thymidine permease NupC HMPREF9450_RS08165
trehalose MFS-glucose: glucose transporter, MFS superfamily HMPREF9450_RS06450 HMPREF9450_RS05320
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase HMPREF9450_RS02265
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine atoB: acetyl-CoA C-acetyltransferase
tyrosine fahA: fumarylacetoacetate hydrolase
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase HMPREF9450_RS05640
valine Bap2: L-valine permease Bap2
valine bch: 3-hydroxyisobutyryl-CoA hydrolase
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase
valine mmsA: methylmalonate-semialdehyde dehydrogenase
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine pccA: propionyl-CoA carboxylase, alpha subunit HMPREF9450_RS11730
valine vorA: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA HMPREF9450_RS10810 with HMPREF9450_RS10805
valine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC HMPREF9450_RS10820
xylitol PLT5: xylitol:H+ symporter PLT5 HMPREF9450_RS06450
xylitol xdhA: xylitol dehydrogenase HMPREF9450_RS00875 HMPREF9450_RS09660

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