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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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