GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Pedobacter arcticus A12

Found 123 low-confidence and 45 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 mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase B176_RS0114765
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 dctA: organic acid/proton symporter DctA B176_RS0112665
alanine alsT: L-alanine symporter AlsT/DagA B176_RS0111760
arabinose araA: L-arabinose isomerase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose Echvi_1880: L-arabinose:Na+ symporter B176_RS0111735
arginine rocD: ornithine aminotransferase B176_RS0112620 B176_RS0113865
arginine rocE: L-arginine permease
arginine rocF: arginase
cellobiose glk: glucokinase B176_RS0112945 B176_RS0113790
citrate SLC13A5: citrate:Na+ symporter B176_RS0115730
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component B176_RS0101905 B176_RS0104595
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 B176_RS0112620 B176_RS0113865
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
deoxyinosine deoB: phosphopentomutase B176_RS0104620
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyribonate aacS: acetoacetyl-CoA synthetase
deoxyribonate atoB: acetyl-CoA C-acetyltransferase B176_RS0105415
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase
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 B176_RS0101140 B176_RS0101105
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) B176_RS0100410 B176_RS0105305
fructose 1pfk: 1-phosphofructokinase
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
fucose fucD: L-fuconate dehydratase B176_RS0116770 B176_RS0101115
fucose fuconolactonase: L-fucono-1,5-lactonase B176_RS0116755 B176_RS0101130
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galacturonate uxaB: tagaturonate reductase
gluconate gntK: D-gluconate kinase
gluconate gntT: gluconate:H+ symporter GntT
glucose glk: glucokinase B176_RS0112945 B176_RS0113790
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter B176_RS0105180
glucuronate exuT: D-glucuronate:H+ symporter ExuT B176_RS0116825 B176_RS0104380
glucuronate uxuB: D-mannonate dehydrogenase
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) B176_RS0105165
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 B176_RS0118105 B176_RS0105420
isoleucine Bap2: L-isoleucine permease Bap2
isoleucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit B176_RS0116080
isoleucine bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit B176_RS0103030 B176_RS0114965
isoleucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component B176_RS0111930 B176_RS0116160
isoleucine dddA: 3-hydroxypropionate dehydrogenase
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase B176_RS0103535 B176_RS0105405
isoleucine hpcD: 3-hydroxypropionyl-CoA dehydratase B176_RS0103535
isoleucine iolA: malonate semialdehyde dehydrogenase (CoA-acylating) B176_RS0102530 B176_RS0110040
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase B176_RS0105290 B176_RS0116765
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
L-lactate lldG: L-lactate dehydrogenase, LldG subunit B176_RS0105015 B176_RS0116735
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose glk: glucokinase B176_RS0112945 B176_RS0113790
lactose lacP: lactose permease LacP
leucine aacS: acetoacetyl-CoA synthetase
leucine atoB: acetyl-CoA C-acetyltransferase B176_RS0105415
leucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit B176_RS0116080
leucine bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit B176_RS0103030 B176_RS0114965
leucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component B176_RS0111930 B176_RS0116160
leucine leuT: L-leucine:Na+ symporter LeuT
leucine liuA: isovaleryl-CoA dehydrogenase B176_RS0118105 B176_RS0105420
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit B176_RS0100605
leucine liuC: 3-methylglutaconyl-CoA hydratase B176_RS0103535
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit
leucine liuE: hydroxymethylglutaryl-CoA lyase
lysine hglS: D-2-hydroxyglutarate synthase
lysine lysN: 2-aminoadipate transaminase B176_RS0111710 B176_RS0113865
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase B176_RS0102395
maltose glk: glucokinase B176_RS0112945 B176_RS0113790
mannitol mtlA: mannitol phosphotransferase system, EII-CBA components
mannitol mtlD: mannitol-1-phosphate 5-dehydrogenase
mannose gluP: mannose:Na+ symporter B176_RS0102425 B176_RS0116780
mannose manA: mannose-6-phosphate isomerase B176_RS0114095 B176_RS0110120
mannose mannokinase: D-mannose kinase B176_RS0112945 B176_RS19335
myoinositol iolG: myo-inositol 2-dehydrogenase B176_RS0117140
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
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
phenylacetate paaF: 2,3-dehydroadipyl-CoA hydratase B176_RS0103535
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase B176_RS0103535
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase B176_RS0105415
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase B176_RS0105415
phenylacetate paaK: phenylacetate-CoA ligase
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase B176_RS0103535
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aacS: acetoacetyl-CoA synthetase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine atoB: acetyl-CoA C-acetyltransferase B176_RS0105415
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 B176_RS0112735
phenylalanine QDPR: 6,7-dihydropteridine reductase B176_RS0103950
proline N515DRAFT_2924: proline transporter B176_RS19350 B176_RS0116065
propionate dddA: 3-hydroxypropionate dehydrogenase
propionate hpcD: 3-hydroxypropionyl-CoA dehydratase B176_RS0103535
propionate iolA: malonate semialdehyde dehydrogenase (CoA-acylating) B176_RS0102530 B176_RS0110040
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabT: gamma-aminobutyrate transaminase B176_RS0112620 B176_RS0113865
putrescine patA: putrescine aminotransferase (PatA/SpuC) B176_RS0113865 B176_RS0116205
putrescine patD: gamma-aminobutyraldehyde dehydrogenase B176_RS0110040 B176_RS0102530
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose rhaM: L-rhamnose mutarotase
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 B176_RS0105290 B176_RS0101135
sucrose ams: sucrose hydrolase (invertase)
sucrose glk: glucokinase B176_RS0112945 B176_RS0113790
threonine tdcC: L-threonine:H+ symporter TdcC
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase B176_RS0104620
thymidine deoC: deoxyribose-5-phosphate aldolase
trehalose glk: glucokinase B176_RS0112945 B176_RS0113790
trehalose treF: trehalase B176_RS0103940
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aacS: acetoacetyl-CoA synthetase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine atoB: acetyl-CoA C-acetyltransferase B176_RS0105415
tyrosine fahA: fumarylacetoacetate hydrolase
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase B176_RS0118105 B176_RS0105420
valine Bap2: L-valine permease Bap2
valine bch: 3-hydroxyisobutyryl-CoA hydrolase B176_RS0103535
valine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit B176_RS0116080
valine bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit B176_RS0103030 B176_RS0114965
valine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component B176_RS0111930 B176_RS0116160
valine dddA: 3-hydroxypropionate dehydrogenase
valine hpcD: 3-hydroxypropionyl-CoA dehydratase B176_RS0103535
valine iolA: malonate semialdehyde dehydrogenase (CoA-acylating) B176_RS0102530 B176_RS0110040
valine mmsA: methylmalonate-semialdehyde dehydrogenase B176_RS0102530 B176_RS0110040
valine mmsB: 3-hydroxyisobutyrate dehydrogenase B176_RS0111490
xylitol PLT5: xylitol:H+ symporter PLT5
xylitol xdhA: xylitol dehydrogenase B176_RS0116765 B176_RS0101120

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