Potential Gaps in catabolism of small carbon sources in Gallaecimonas xiamenensis 3-C-1
Found 83 low-confidence and 46 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | Psest_0084: 2-oxoglutarate TRAP transporter, fused 4TM/12TM components | B3C1_RS04150 | |
| 2-oxoglutarate | Psest_0085: 2-oxoglutarate TRAP transporter, solute receptor component | B3C1_RS04155 | |
| 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 | | |
| arginine | rocE: L-arginine permease | | |
| cellobiose | bgl: cellobiase | | |
| citrate | tctB: citrate/Na+ symporter, small transmembrane component TctB | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | B3C1_RS12960 | B3C1_RS03530 |
| 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 | B3C1_RS06770 | |
| citrulline | aruF: ornithine/arginine N-succinyltransferase subunit AruAI (AruF) | B3C1_RS02880 | |
| citrulline | aruG: ornithine/arginine N-succinyltransferase subunit AruAII (AruG) | B3C1_RS02880 | |
| citrulline | citrullinase: putative citrullinase | B3C1_RS08705 | B3C1_RS12980 |
| 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 | B3C1_RS00900 | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | B3C1_RS11290 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | B3C1_RS17540 | B3C1_RS16220 |
| 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 | deoK: deoxyribokinase | B3C1_RS12760 | B3C1_RS16155 |
| deoxyribose | deoP: deoxyribose transporter | | |
| fructose | fruP: fructose porter FruP | B3C1_RS00395 | B3C1_RS00390 |
| fructose | scrK: fructokinase | B3C1_RS06795 | B3C1_RS01960 |
| fucose | aldA: lactaldehyde dehydrogenase | B3C1_RS03260 | B3C1_RS02820 |
| 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 | B3C1_RS00395 | B3C1_RS00390 |
| fucose | fucU: L-fucose mutarotase FucU | | |
| galactose | dgoD: D-galactonate dehydratase | B3C1_RS10895 | |
| galactose | dgoK: 2-dehydro-3-deoxygalactonokinase | B3C1_RS16155 | |
| galactose | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | B3C1_RS10855 | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | B3C1_RS16170 | |
| gluconate | gntK: D-gluconate kinase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | dctP: D-glucuronate TRAP transporter, solute receptor component | B3C1_RS16210 | |
| glucuronate | dctQ: D-glucuronate TRAP transporter, small permease component | | |
| glucuronate | uxaC: D-glucuronate isomerase | B3C1_RS16170 | |
| glucuronate | uxuA: D-mannonate dehydratase | | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | B3C1_RS15255 | |
| glycerol | glpF: glycerol facilitator glpF | | |
| glycerol | glpK: glycerol kinase | | |
| histidine | permease: L-histidine permease | | |
| isoleucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | B3C1_RS00795 | |
| isoleucine | bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | B3C1_RS00800 | |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | B3C1_RS12365 | B3C1_RS12800 |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| lactose | dgoD: D-galactonate dehydratase | B3C1_RS10895 | |
| lactose | dgoK: 2-dehydro-3-deoxygalactonokinase | B3C1_RS16155 | |
| lactose | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | B3C1_RS10855 | |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | | |
| leucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | B3C1_RS00795 | |
| leucine | bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | B3C1_RS00800 | |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | B3C1_RS12365 | B3C1_RS12800 |
| lysine | davA: 5-aminovaleramidase | B3C1_RS00580 | B3C1_RS12980 |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | davT: 5-aminovalerate aminotransferase | B3C1_RS02875 | B3C1_RS09655 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| maltose | susB: alpha-glucosidase (maltase) | B3C1_RS03095 | B3C1_RS09360 |
| mannitol | mt2d: mannitol 2-dehydrogenase | B3C1_RS16165 | B3C1_RS01685 |
| mannitol | PLT5: polyol transporter PLT5 | | |
| mannitol | scrK: fructokinase | B3C1_RS06795 | B3C1_RS01960 |
| mannose | gluP: mannose:Na+ symporter | B3C1_RS00395 | B3C1_RS00390 |
| mannose | manA: mannose-6-phosphate isomerase | B3C1_RS09430 | |
| mannose | mannokinase: D-mannose kinase | B3C1_RS06795 | B3C1_RS01960 |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | B3C1_RS00525 | |
| 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 | uxuA: D-mannonate dehydratase | | |
| 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 | B3C1_RS04935 | B3C1_RS13490 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | B3C1_RS10040 | B3C1_RS13490 |
| phenylacetate | paaK: phenylacetate-CoA ligase | B3C1_RS15765 | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | B3C1_RS13490 | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylacetate | ppa: phenylacetate permease ppa | B3C1_RS04235 | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| propionate | putP: propionate transporter; proline:Na+ symporter | B3C1_RS13470 | |
| putrescine | gabT: gamma-aminobutyrate transaminase | B3C1_RS02875 | B3C1_RS11725 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | B3C1_RS02875 | B3C1_RS09655 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | B3C1_RS03260 | B3C1_RS02820 |
| rhamnose | aldA: lactaldehyde dehydrogenase | B3C1_RS03260 | B3C1_RS02820 |
| 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 | rbsK: ribokinase | B3C1_RS12760 | B3C1_RS16155 |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | snatA: L-serine transporter | B3C1_RS13330 | B3C1_RS04095 |
| sorbitol | mtlA: PTS system for polyols, EII-CBA components | | |
| sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | B3C1_RS13475 | B3C1_RS04105 |
| sucrose | ams: sucrose hydrolase (invertase) | B3C1_RS03095 | |
| threonine | snatA: L-threonine transporter snatA | B3C1_RS13330 | B3C1_RS04095 |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | treF: trehalase | B3C1_RS03095 | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | B3C1_RS13495 | B3C1_RS13525 |
| valine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | B3C1_RS00795 | |
| valine | bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | B3C1_RS00800 | |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | B3C1_RS12365 | B3C1_RS12800 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | B3C1_RS13480 | B3C1_RS13240 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | B3C1_RS01685 | |
| xylose | kdaD: 2-keto-3-deoxy-D-arabinonate dehydratase | | |
| xylose | xad: D-xylonate dehydratase | B3C1_RS10895 | B3C1_RS00895 |
| xylose | xdh: D-xylose dehydrogenase | B3C1_RS10890 | B3C1_RS00525 |
| xylose | xylC: xylonolactonase | | |
| xylose | xylT: D-xylose transporter | | |
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