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 (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