GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Echinicola vietnamensis KMM 6221, DSM 17526

Found 78 low-confidence and 54 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
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 Echvi_1267
arginine rocE: L-arginine permease
arginine rocF: arginase Echvi_2468
cellobiose glk: glucokinase Echvi_3894 Echvi_3892
citrate SLC13A5: citrate:Na+ symporter Echvi_4197 Echvi_3555
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component Echvi_2204 Echvi_4044
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
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate larD: D,L-lactic acid transporter Echvi_1769
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase Echvi_1189 Echvi_0643
deoxyinosine deoB: phosphopentomutase Echvi_2982
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase Echvi_3364 Echvi_4610
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate garK: glycerate 2-kinase Echvi_4031
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter Echvi_0508
fucose fucDH: 2-keto-3-deoxy-L-fuconate 4-dehydrogenase Echvi_2940 Echvi_4610
fucose fuconolactonase: L-fucono-1,5-lactonase Echvi_2938 Echvi_1688
galacturonate exuT: D-galacturonate transporter ExuT Echvi_3106
galacturonate kdgK: 2-keto-3-deoxygluconate kinase Echvi_3631
glucosamine nagA: N-acetylglucosamine 6-phosphate deacetylase Echvi_4311
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) Echvi_0158 Echvi_4314
glucosamine nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components
glucose glk: glucokinase Echvi_3894 Echvi_3892
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate dctP: D-glucuronate TRAP transporter, solute receptor component Echvi_3629
glucuronate dctQ: D-glucuronate TRAP transporter, small permease component
glucuronate kdgK: 2-keto-3-deoxygluconate kinase Echvi_3631
glucuronate uxuB: D-mannonate dehydrogenase
glutamate gdhA: glutamate dehydrogenase, NAD-dependent Echvi_1535
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) Echvi_1771
histidine hutG: N-formiminoglutamate formiminohydrolase Echvi_3131
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
histidine permease: L-histidine permease
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase Echvi_1212 Echvi_1473
isoleucine Bap2: L-isoleucine permease Bap2
isoleucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit Echvi_1750 Echvi_1221
isoleucine bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit Echvi_3823 Echvi_1750
isoleucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component Echvi_2446 Echvi_0772
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase Echvi_4069 Echvi_1069
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase Echvi_4610 Echvi_1862
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit Echvi_3962 Echvi_0191
lactose glk: glucokinase Echvi_3894 Echvi_3892
leucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit Echvi_1750 Echvi_1221
leucine bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit Echvi_3823 Echvi_1750
leucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component Echvi_2446 Echvi_0772
leucine leuT: L-leucine:Na+ symporter LeuT
leucine liuA: isovaleryl-CoA dehydrogenase Echvi_1473 Echvi_1212
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit Echvi_3962 Echvi_0191
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit Echvi_0113 Echvi_0160
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase Echvi_2919 Echvi_0150
lysine lysN: 2-aminoadipate transaminase Echvi_0675 Echvi_3848
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase Echvi_3865
maltose glk: glucokinase Echvi_3894 Echvi_3892
mannitol mt2d: mannitol 2-dehydrogenase Echvi_4610 Echvi_2940
mannitol PLT5: polyol transporter PLT5
mannose gluP: mannose:Na+ symporter Echvi_3909 Echvi_0508
mannose man-isomerase: D-mannose isomerase
myoinositol iolG: myo-inositol 2-dehydrogenase Echvi_3375
myoinositol iolM: 2-inosose 4-dehydrogenase Echvi_0507 Echvi_3219
myoinositol iolN: 2,4-diketo-inositol hydratase
myoinositol iolO: 5-dehydro-L-gluconate epimerase
myoinositol iolT: myo-inositol:H+ symporter Echvi_2805 Echvi_2810
myoinositol kdgK: 2-keto-3-deoxygluconate kinase Echvi_3631
myoinositol uxaE: D-tagaturonate epimerase
myoinositol uxuB: D-mannonate dehydrogenase
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase Echvi_4311
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) Echvi_0158 Echvi_4314
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 Echvi_0363
phenylacetate paaF: 2,3-dehydroadipyl-CoA hydratase Echvi_4069 Echvi_0343
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase Echvi_0069
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase Echvi_1071 Echvi_3705
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase Echvi_1071 Echvi_3705
phenylacetate paaK: phenylacetate-CoA ligase Echvi_2567
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 maiA: maleylacetoacetate isomerase
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase Echvi_0850
phenylalanine QDPR: 6,7-dihydropteridine reductase Echvi_4494 Echvi_0893
proline ectP: proline transporter EctP Echvi_0794
propionate pccA: propionyl-CoA carboxylase, alpha subunit Echvi_3962 Echvi_0191
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabT: gamma-aminobutyrate transaminase Echvi_2919 Echvi_2790
putrescine patA: putrescine aminotransferase (PatA/SpuC) Echvi_2919 Echvi_0577
putrescine patD: gamma-aminobutyraldehyde dehydrogenase Echvi_0481 Echvi_3822
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate actP: large subunit of pyruvate transporter (actP-like) Echvi_1267
pyruvate yjcH: putative small subunit of pyruvate transporter (yjcH-like) Echvi_1266
ribose rbsK: ribokinase
serine serP: L-serine permease SerP
sorbitol sdh: sorbitol dehydrogenase Echvi_3928 Echvi_3219
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2 Echvi_2805
threonine tdcC: L-threonine:H+ symporter TdcC
thymidine deoA: thymidine phosphorylase DeoA Echvi_1798 Echvi_3166
thymidine deoB: phosphopentomutase Echvi_2982
trehalose glk: glucokinase Echvi_3894 Echvi_3892
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase Echvi_1212 Echvi_1473
valine Bap2: L-valine permease Bap2
valine bch: 3-hydroxyisobutyryl-CoA hydrolase Echvi_4069
valine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit Echvi_1750 Echvi_1221
valine bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit Echvi_3823 Echvi_1750
valine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component Echvi_2446 Echvi_0772
valine mmsA: methylmalonate-semialdehyde dehydrogenase Echvi_0481
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine pccA: propionyl-CoA carboxylase, alpha subunit Echvi_3962 Echvi_0191
xylitol PLT5: xylitol:H+ symporter PLT5 Echvi_2810
xylitol xdhA: xylitol dehydrogenase Echvi_3219 Echvi_3928

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