GapMind for catabolism of small carbon sources


Potential Gaps in catabolism of small carbon sources in Pedobacter sp. GW460-11-11-14-LB5

Found 88 low-confidence and 44 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
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 CA265_RS12370
acetate deh: acetate/haloacid transporter CA265_RS19920 CA265_RS22390
alanine TRIC: TRIC-type L-alanine transporter CA265_RS15435
arginine rocD: ornithine aminotransferase CA265_RS15205 CA265_RS18530
arginine rocE: L-arginine permease
arginine rocF: arginase
cellobiose glk: glucokinase CA265_RS15640 CA265_RS11300
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component CA265_RS16020 CA265_RS04175
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 rocD: ornithine aminotransferase CA265_RS15205 CA265_RS18530
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
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 CA265_RS14425 CA265_RS15860
deoxyinosine deoB: phosphopentomutase CA265_RS09660
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase CA265_RS08355 CA265_RS04230
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 deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter CA265_RS04675 CA265_RS08575
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) CA265_RS12755 CA265_RS12005
fructose glcP: fructose:H+ symporter GlcP CA265_RS23325 CA265_RS01275
fructose scrK: fructokinase CA265_RS18205
fucose fucDH: 2-keto-3-deoxy-L-fuconate 4-dehydrogenase CA265_RS08355 CA265_RS13715
fucose fuconolactonase: L-fucono-1,5-lactonase CA265_RS08340
glucose glk: glucokinase CA265_RS15640 CA265_RS11300
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate uxuB: D-mannonate dehydrogenase
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) CA265_RS07875
histidine hutI: imidazole-5-propionate hydrolase
histidine LAT2: L-histidine transporter CA265_RS14990
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase CA265_RS22715 CA265_RS02820
isoleucine Bap2: L-isoleucine permease Bap2
isoleucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit CA265_RS18405 CA265_RS19580
isoleucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component CA265_RS09070 CA265_RS19585
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase CA265_RS20005 CA265_RS17590
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase CA265_RS15450 CA265_RS00760
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit CA265_RS02215 CA265_RS18365
L-lactate L-LDH: L-lactate dehydrogenase CA265_RS08335 CA265_RS03080
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
lactose glk: glucokinase CA265_RS15640 CA265_RS11300
leucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit CA265_RS18405 CA265_RS19580
leucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component CA265_RS09070 CA265_RS19585
leucine leuT: L-leucine:Na+ symporter LeuT
leucine liuA: isovaleryl-CoA dehydrogenase CA265_RS02820 CA265_RS22715
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit CA265_RS02215 CA265_RS18365
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit CA265_RS10640 CA265_RS16635
lysine davD: glutarate semialdehyde dehydrogenase CA265_RS14635 CA265_RS24850
lysine davT: 5-aminovalerate aminotransferase CA265_RS18530 CA265_RS15205
lysine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase CA265_RS20005 CA265_RS09125
lysine gcdG: succinyl-CoA:glutarate CoA-transferase CA265_RS08550
lysine lysP: L-lysine:H+ symporter LysP
lysine patD: 5-aminopentanal dehydrogenase CA265_RS14635 CA265_RS24850
maltose glk: glucokinase CA265_RS15640 CA265_RS11300
mannitol mtlA: mannitol phosphotransferase system, EII-CBA components
mannitol mtlD: mannitol-1-phosphate 5-dehydrogenase
mannose gluP: mannose:Na+ symporter CA265_RS04675 CA265_RS08575
mannose man-isomerase: D-mannose isomerase
mannose scrK: fructokinase CA265_RS18205
myoinositol iolG: myo-inositol 2-dehydrogenase CA265_RS23295
myoinositol iolM: 2-inosose 4-dehydrogenase CA265_RS12005
myoinositol iolN: 2,4-diketo-inositol hydratase
myoinositol iolO: 5-dehydro-L-gluconate epimerase CA265_RS12255
myoinositol iolT: myo-inositol:H+ symporter CA265_RS01275 CA265_RS23325
myoinositol uxaE: D-tagaturonate epimerase
myoinositol uxuB: D-mannonate dehydrogenase
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 CA265_RS25075
phenylacetate paaF: 2,3-dehydroadipyl-CoA hydratase CA265_RS20005 CA265_RS09125
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase CA265_RS17585 CA265_RS06590
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase CA265_RS17585 CA265_RS06590
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 fahA: fumarylacetoacetate hydrolase
phenylalanine maiA: maleylacetoacetate isomerase
phenylalanine PAH: phenylalanine 4-monooxygenase
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase
phenylalanine QDPR: 6,7-dihydropteridine reductase
propionate pccA: propionyl-CoA carboxylase, alpha subunit CA265_RS02215 CA265_RS18365
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabD: succinate semialdehyde dehydrogenase CA265_RS24850 CA265_RS01080
putrescine gabT: gamma-aminobutyrate transaminase CA265_RS14455 CA265_RS18530
putrescine patD: gamma-aminobutyraldehyde dehydrogenase CA265_RS14635 CA265_RS24850
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose rhaT: L-rhamnose:H+ symporter RhaT CA265_RS02625
ribose rbsK: ribokinase
ribose rbsU: probable D-ribose transporter RbsU
serine serP: L-serine permease SerP
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase CA265_RS08605 CA265_RS08355
sucrose ams: sucrose hydrolase (invertase) CA265_RS18440
sucrose glk: glucokinase CA265_RS15640 CA265_RS11300
threonine tdcC: L-threonine:H+ symporter TdcC
thymidine deoB: phosphopentomutase CA265_RS09660
thymidine deoC: deoxyribose-5-phosphate aldolase
trehalose glk: glucokinase CA265_RS15640 CA265_RS11300
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine fahA: fumarylacetoacetate hydrolase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase CA265_RS22715 CA265_RS02820
valine Bap2: L-valine permease Bap2
valine bch: 3-hydroxyisobutyryl-CoA hydrolase CA265_RS20005
valine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit CA265_RS18405 CA265_RS19580
valine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component CA265_RS09070 CA265_RS19585
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase CA265_RS20005 CA265_RS09125
valine mmsA: methylmalonate-semialdehyde dehydrogenase CA265_RS14635 CA265_RS19780
valine mmsB: 3-hydroxyisobutyrate dehydrogenase CA265_RS01080
valine pccA: propionyl-CoA carboxylase, alpha subunit CA265_RS02215 CA265_RS18365
xylitol PLT5: xylitol:H+ symporter PLT5 CA265_RS23325 CA265_RS01275
xylitol xdhA: xylitol dehydrogenase CA265_RS08610 CA265_RS12005

Confidence: high confidence medium confidence low confidence

This GapMind analysis is from Sep 17 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