Potential Gaps in catabolism of small carbon sources in Rhodanobacter denitrificans 2APBS1
Found 105 low-confidence and 32 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | R2APBS1_RS00080 | R2APBS1_RS10450 |
| 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 | | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | R2APBS1_RS15115 | |
| arginine | rocE: L-arginine permease | R2APBS1_RS05445 | R2APBS1_RS12170 |
| asparagine | glt: aspartate:proton symporter Glt | R2APBS1_RS07595 | |
| aspartate | glt: aspartate:proton symporter Glt | R2APBS1_RS07595 | |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | R2APBS1_RS13010 | R2APBS1_RS12060 |
| 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 | citrullinase: putative citrullinase | R2APBS1_RS08030 | |
| D-lactate | D-LDH: D-lactate dehydrogenase | R2APBS1_RS05170 | R2APBS1_RS15935 |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
| D-serine | dsdA: D-serine ammonia-lyase | R2APBS1_RS17865 | R2APBS1_RS17775 |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | R2APBS1_RS18280 | R2APBS1_RS13540 |
| 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 | deoP: deoxyribose transporter | R2APBS1_RS03315 | |
| fucose | aldA: lactaldehyde dehydrogenase | R2APBS1_RS10710 | R2APBS1_RS05730 |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | | |
| fucose | fucI: L-fucose isomerase FucI | | |
| fucose | fucK: L-fuculose kinase FucK | | |
| fucose | fucP: L-fucose:H+ symporter FucP | R2APBS1_RS03315 | |
| fucose | fucU: L-fucose mutarotase FucU | | |
| fumarate | dctA: fumarate:H+ symporter DctA | | |
| galactose | galE: UDP-glucose 4-epimerase | R2APBS1_RS10505 | R2APBS1_RS17980 |
| galactose | galK: galactokinase (-1-phosphate forming) | | |
| galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | kdgK: 2-keto-3-deoxygluconate kinase | R2APBS1_RS03310 | |
| galacturonate | uxaA: D-altronate dehydratase | | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | | |
| gluconate | gntK: D-gluconate kinase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | nagX: transmembrane glucosamine N-acetyltransferase NagX | R2APBS1_RS00810 | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | kdgK: 2-keto-3-deoxygluconate kinase | R2APBS1_RS03310 | |
| glucuronate | uxaC: D-glucuronate isomerase | | |
| glucuronate | uxuA: D-mannonate dehydratase | | |
| glucuronate | uxuB: D-mannonate dehydrogenase | | |
| glutamate | gltP: L-glutamate:cation symporter GltP/GltT | R2APBS1_RS07595 | R2APBS1_RS16535 |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | R2APBS1_RS12360 | |
| glycerol | glpF: glycerol facilitator glpF | R2APBS1_RS10455 | |
| histidine | hutH: histidine ammonia-lyase | R2APBS1_RS07010 | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | R2APBS1_RS06205 | R2APBS1_RS12095 |
| isoleucine | Bap2: L-isoleucine permease Bap2 | R2APBS1_RS12170 | |
| isoleucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| L-lactate | lctO: L-lactate oxidase or 2-monooxygenase | | |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| L-malate | sdlC: L-malate:Na+ symporter SdlC | | |
| lactose | galE: UDP-glucose 4-epimerase | R2APBS1_RS10505 | R2APBS1_RS17980 |
| lactose | galK: galactokinase (-1-phosphate forming) | | |
| lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | R2APBS1_RS19040 | R2APBS1_RS00825 |
| leucine | leuT: L-leucine:Na+ symporter LeuT | | |
| leucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| lysine | hglS: D-2-hydroxyglutarate synthase | | |
| lysine | lysN: 2-aminoadipate transaminase | R2APBS1_RS07570 | R2APBS1_RS03870 |
| lysine | lysP: L-lysine:H+ symporter LysP | R2APBS1_RS05445 | R2APBS1_RS12170 |
| lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | R2APBS1_RS05170 | R2APBS1_RS15935 |
| maltose | susB: alpha-glucosidase (maltase) | R2APBS1_RS15035 | R2APBS1_RS15060 |
| mannitol | mt2d: mannitol 2-dehydrogenase | R2APBS1_RS07650 | R2APBS1_RS12930 |
| mannitol | PLT5: polyol transporter PLT5 | | |
| mannose | gluP: mannose:Na+ symporter | R2APBS1_RS03315 | R2APBS1_RS00790 |
| myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | | |
| myoinositol | iolC: 5-dehydro-2-deoxy-D-gluconate kinase | | |
| myoinositol | iolD: 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase | | |
| myoinositol | iolE: scyllo-inosose 2-dehydratase | | |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | | |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | | |
| myoinositol | iolT: myo-inositol:H+ symporter | R2APBS1_RS15115 | |
| myoinositol | mmsA: malonate-semialdehyde dehydrogenase | R2APBS1_RS05730 | R2APBS1_RS00470 |
| phenylacetate | H281DRAFT_04042: phenylacetate:H+ symporter | R2APBS1_RS05445 | R2APBS1_RS12170 |
| 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 | R2APBS1_RS12580 | R2APBS1_RS06035 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | R2APBS1_RS12580 | R2APBS1_RS06035 |
| phenylacetate | paaK: phenylacetate-CoA ligase | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | R2APBS1_RS06035 | R2APBS1_RS12580 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | R2APBS1_RS05445 | R2APBS1_RS12170 |
| phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | R2APBS1_RS08985 | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | | |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | gabD: succinate semialdehyde dehydrogenase | R2APBS1_RS05730 | R2APBS1_RS00470 |
| putrescine | gabT: gamma-aminobutyrate transaminase | R2APBS1_RS03870 | R2APBS1_RS04240 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | R2APBS1_RS03870 | R2APBS1_RS04240 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | R2APBS1_RS05730 | R2APBS1_RS00470 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| rhamnose | aldA: lactaldehyde dehydrogenase | R2APBS1_RS10710 | R2APBS1_RS05730 |
| rhamnose | rhaA: L-rhamnose isomerase | | |
| rhamnose | rhaB: L-rhamnulokinase | | |
| rhamnose | rhaD: rhamnulose 1-phosphate aldolase | | |
| rhamnose | rhaM: L-rhamnose mutarotase | | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | serP: L-serine permease SerP | R2APBS1_RS12170 | R2APBS1_RS05445 |
| sorbitol | sdh: sorbitol dehydrogenase | R2APBS1_RS16990 | R2APBS1_RS11655 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | R2APBS1_RS15115 | |
| succinate | sdc: succinate:Na+ symporter Sdc | | |
| sucrose | ams: sucrose hydrolase (invertase) | R2APBS1_RS15035 | R2APBS1_RS15050 |
| threonine | serP1: L-threonine uptake transporter SerP1 | R2APBS1_RS12170 | R2APBS1_RS05445 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | R2APBS1_RS05445 | R2APBS1_RS12170 |
| tryptophan | kynB: kynurenine formamidase | | |
| tryptophan | mhpD: 2-hydroxypentadienoate hydratase | | |
| tryptophan | mhpE: 4-hydroxy-2-oxovalerate aldolase | | |
| tryptophan | nbaE: 2-aminomuconate 6-semialdehyde dehydrogenase | R2APBS1_RS05730 | R2APBS1_RS00470 |
| tryptophan | nbaF: 2-aminomuconate deaminase | R2APBS1_RS05720 | R2APBS1_RS02860 |
| tryptophan | nbaG: 2-oxo-3-hexenedioate decarboxylase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | R2APBS1_RS05445 | R2APBS1_RS12170 |
| valine | acdH: isobutyryl-CoA dehydrogenase | R2APBS1_RS06205 | R2APBS1_RS12095 |
| valine | Bap2: L-valine permease Bap2 | R2APBS1_RS12170 | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | R2APBS1_RS12580 | |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | R2APBS1_RS12580 | R2APBS1_RS10950 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | R2APBS1_RS05730 | R2APBS1_RS00470 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | R2APBS1_RS13060 | |
| valine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | R2APBS1_RS07650 | R2APBS1_RS18135 |
| xylose | xylA: xylose isomerase | | |
| xylose | xylB: xylulokinase | | |
| xylose | xylT: D-xylose transporter | R2APBS1_RS15115 | |
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:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
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:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
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:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
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