GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Dyella japonica UNC79MFTsu3.2

Found 84 low-confidence and 39 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 N515DRAFT_0574
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
arabinose araVsh: L-arabinose ABC transporter, ATPase component AraV(Sh) N515DRAFT_2413 N515DRAFT_3232
arginine rocD: ornithine aminotransferase N515DRAFT_3630 N515DRAFT_3308
arginine rocE: L-arginine permease N515DRAFT_2630 N515DRAFT_3653
citrate SLC13A5: citrate:Na+ symporter
citrulline citrullinase: putative citrullinase N515DRAFT_1536
citrulline PS417_17590: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline PS417_17595: ABC transporter for L-Citrulline, permease component 1
citrulline PS417_17600: ABC transporter for L-Citrulline, permease component 2
citrulline PS417_17605: ABC transporter for L-Citrulline, ATPase component N515DRAFT_1085 N515DRAFT_2216
citrulline rocD: ornithine aminotransferase N515DRAFT_3630 N515DRAFT_3308
D-alanine dadA: D-alanine dehydrogenase N515DRAFT_3723
D-lactate D-LDH: D-lactate dehydrogenase N515DRAFT_3582 N515DRAFT_1999
D-lactate lctP: D-lactate:H+ symporter LctP or LidP
D-serine cycA: D-serine:H+ symporter CycA N515DRAFT_2630 N515DRAFT_3653
D-serine dsdA: D-serine ammonia-lyase N515DRAFT_0537 N515DRAFT_0565
deoxyinosine deoB: phosphopentomutase N515DRAFT_1372
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase N515DRAFT_0396
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase N515DRAFT_1253 N515DRAFT_0334
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter N515DRAFT_2085
deoxyribonate garK: glycerate 2-kinase
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoP: deoxyribose transporter N515DRAFT_1222 N515DRAFT_1918
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate uxaA: D-altronate dehydratase
galacturonate uxaB: tagaturonate reductase
galacturonate uxaC: D-galacturonate isomerase
glucosamine nagX: transmembrane glucosamine N-acetyltransferase NagX N515DRAFT_0596 N515DRAFT_4388
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate uxaC: D-glucuronate isomerase
glucuronate uxuA: D-mannonate dehydratase N515DRAFT_1231
glucuronate uxuB: D-mannonate dehydrogenase
glycerol glpF: glycerol facilitator glpF N515DRAFT_3908 N515DRAFT_1366
histidine hutH: histidine ammonia-lyase N515DRAFT_2941
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase N515DRAFT_0492 N515DRAFT_0941
isoleucine Bap2: L-isoleucine permease Bap2 N515DRAFT_2630 N515DRAFT_3653
isoleucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit N515DRAFT_0356
isoleucine bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit N515DRAFT_0355 N515DRAFT_0481
isoleucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component N515DRAFT_2156 N515DRAFT_0354
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
lactose lacP: lactose permease LacP
leucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit N515DRAFT_0356
leucine bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit N515DRAFT_0355 N515DRAFT_0481
leucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component N515DRAFT_2156 N515DRAFT_0354
leucine leuT: L-leucine:Na+ symporter LeuT
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase N515DRAFT_3630 N515DRAFT_3308
lysine lysN: 2-aminoadipate transaminase N515DRAFT_0006 N515DRAFT_3308
lysine lysP: L-lysine:H+ symporter LysP N515DRAFT_2630 N515DRAFT_3653
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase N515DRAFT_3582 N515DRAFT_1999
maltose susB: alpha-glucosidase (maltase) N515DRAFT_3393 N515DRAFT_3389
mannitol mt2d: mannitol 2-dehydrogenase N515DRAFT_0039 N515DRAFT_1104
mannitol PLT5: polyol transporter PLT5 N515DRAFT_1228 N515DRAFT_0382
mannose gluP: mannose:Na+ symporter N515DRAFT_1918 N515DRAFT_1222
myoinositol iolG: myo-inositol 2-dehydrogenase
myoinositol iolM: 2-inosose 4-dehydrogenase N515DRAFT_0211
myoinositol iolN: 2,4-diketo-inositol hydratase
myoinositol iolO: 5-dehydro-L-gluconate epimerase
myoinositol iolT: myo-inositol:H+ symporter N515DRAFT_1228 N515DRAFT_0382
myoinositol uxaE: D-tagaturonate epimerase
myoinositol uxuA: D-mannonate dehydratase N515DRAFT_1231
myoinositol uxuB: D-mannonate dehydrogenase
phenylacetate H281DRAFT_04042: phenylacetate:H+ symporter N515DRAFT_2630 N515DRAFT_3653
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 N515DRAFT_1164 N515DRAFT_0930
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase N515DRAFT_1164 N515DRAFT_0930
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase N515DRAFT_2688 N515DRAFT_0938
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase N515DRAFT_2688 N515DRAFT_0938
phenylacetate paaK: phenylacetate-CoA ligase N515DRAFT_1417
phenylacetate paaZ1: oxepin-CoA hydrolase N515DRAFT_1164
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP N515DRAFT_3653 N515DRAFT_2630
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase N515DRAFT_1530
phenylalanine QDPR: 6,7-dihydropteridine reductase
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabT: gamma-aminobutyrate transaminase N515DRAFT_3308 N515DRAFT_1751
putrescine patA: putrescine aminotransferase (PatA/SpuC) N515DRAFT_3308 N515DRAFT_1751
putrescine patD: gamma-aminobutyraldehyde dehydrogenase N515DRAFT_3729 N515DRAFT_2488
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
rhamnose LRA1: L-rhamnofuranose dehydrogenase N515DRAFT_1006 N515DRAFT_1583
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase N515DRAFT_1231
rhamnose LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase N515DRAFT_2873 N515DRAFT_1253
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsU: probable D-ribose transporter RbsU
serine serP: L-serine permease SerP N515DRAFT_2630 N515DRAFT_3653
sorbitol sdh: sorbitol dehydrogenase N515DRAFT_0461 N515DRAFT_1253
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2 N515DRAFT_1228 N515DRAFT_0382
sucrose ams: sucrose hydrolase (invertase) N515DRAFT_3393 N515DRAFT_3391
threonine RR42_RS28305: L-threonine:H+ symporter N515DRAFT_2630 N515DRAFT_3653
thymidine deoB: phosphopentomutase N515DRAFT_1372
thymidine deoC: deoxyribose-5-phosphate aldolase
trehalose treF: trehalase N515DRAFT_3393 N515DRAFT_1888
tryptophan aroP: tryptophan:H+ symporter AroP N515DRAFT_3653 N515DRAFT_2630
tryptophan kynB: kynurenine formamidase
tryptophan mhpD: 2-hydroxypentadienoate hydratase
tryptophan mhpE: 4-hydroxy-2-oxovalerate aldolase N515DRAFT_0574
tryptophan nbaE: 2-aminomuconate 6-semialdehyde dehydrogenase N515DRAFT_3729 N515DRAFT_0379
tryptophan nbaF: 2-aminomuconate deaminase N515DRAFT_3727 N515DRAFT_4323
tryptophan nbaG: 2-oxo-3-hexenedioate decarboxylase
tyrosine aroP: L-tyrosine transporter (AroP/FywP) N515DRAFT_2630 N515DRAFT_3653
valine acdH: isobutyryl-CoA dehydrogenase N515DRAFT_0492 N515DRAFT_0941
valine Bap2: L-valine permease Bap2 N515DRAFT_2630 N515DRAFT_3653
valine bch: 3-hydroxyisobutyryl-CoA hydrolase N515DRAFT_1164
valine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit N515DRAFT_0356
valine bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit N515DRAFT_0355 N515DRAFT_0481
valine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component N515DRAFT_2156 N515DRAFT_0354
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase N515DRAFT_1164 N515DRAFT_0416
valine mmsA: methylmalonate-semialdehyde dehydrogenase N515DRAFT_3729 N515DRAFT_0379
valine mmsB: 3-hydroxyisobutyrate dehydrogenase N515DRAFT_1074 N515DRAFT_2996
xylitol PLT5: xylitol:H+ symporter PLT5 N515DRAFT_1228 N515DRAFT_0382
xylitol xdhA: xylitol dehydrogenase N515DRAFT_0039 N515DRAFT_1006

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, 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