Potential Gaps in catabolism of small carbon sources in Limnohabitans curvus MWH-C5
Found 112 low-confidence and 49 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | B9Z44_RS05440 | |
| 4-hydroxybenzoate | ligU: 4-oxalomesaconate tautomerase | | |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| alanine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | B9Z44_RS00730 | |
| alanine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | B9Z44_RS04225 | B9Z44_RS05730 |
| alanine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | B9Z44_RS04220 | B9Z44_RS12865 |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arginine | braC: ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC | B9Z44_RS00730 | |
| arginine | braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) | B9Z44_RS04220 | B9Z44_RS12865 |
| arginine | braF: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) | B9Z44_RS05725 | B9Z44_RS04215 |
| arginine | braG: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) | B9Z44_RS05720 | B9Z44_RS04210 |
| arginine | rocA: 1-pyrroline-5-carboxylate dehydrogenase | B9Z44_RS11550 | B9Z44_RS07890 |
| arginine | rocD: ornithine aminotransferase | B9Z44_RS03080 | |
| arginine | rocF: arginase | | |
| asparagine | ans: asparaginase | B9Z44_RS00190 | |
| cellobiose | bgl: cellobiase | | |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | B9Z44_RS09155 | B9Z44_RS03630 |
| 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 | arcC: carbamate kinase | | |
| citrulline | rocA: 1-pyrroline-5-carboxylate dehydrogenase | B9Z44_RS11550 | B9Z44_RS07890 |
| citrulline | rocD: ornithine aminotransferase | B9Z44_RS03080 | |
| D-alanine | cycA: D-alanine:H+ symporter CycA | B9Z44_RS14795 | |
| D-serine | cycA: D-serine:H+ symporter CycA | B9Z44_RS14795 | |
| D-serine | dsdA: D-serine ammonia-lyase | B9Z44_RS09005 | B9Z44_RS09180 |
| deoxyinosine | adh: acetaldehyde dehydrogenase (not acylating) | B9Z44_RS11745 | B9Z44_RS11550 |
| deoxyinosine | deoB: phosphopentomutase | | |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | B9Z44_RS11555 | B9Z44_RS13785 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | B9Z44_RS11555 | B9Z44_RS13785 |
| deoxyribose | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribose | drdehyd-alpha: 2-deoxy-D-ribose dehydrogenase, alpha subunit | B9Z44_RS10955 | B9Z44_RS10265 |
| deoxyribose | drdehyd-beta: 2-deoxy-D-ribose dehydrogenase, beta subunit | B9Z44_RS10960 | |
| deoxyribose | drdehyd-cytc: 2-deoxyribose-D dehydrogenase, cytochrome c component | | |
| deoxyribose | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| ethanol | adh: acetaldehyde dehydrogenase (not acylating) | B9Z44_RS11745 | B9Z44_RS11550 |
| ethanol | etoh-dh-nad: ethanol dehydrogenase (NAD(P)) | B9Z44_RS05710 | B9Z44_RS01585 |
| fructose | scrK: fructokinase | B9Z44_RS13905 | |
| fucose | aldA: lactaldehyde dehydrogenase | B9Z44_RS11550 | B9Z44_RS11745 |
| 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 | | |
| fucose | fucU: L-fucose mutarotase FucU | B9Z44_RS13885 | |
| galactose | galE: UDP-glucose 4-epimerase | B9Z44_RS08620 | B9Z44_RS08720 |
| galactose | galK: galactokinase (-1-phosphate forming) | | |
| galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| galactose | PfGW456L13_1897: ABC transporter for D-Galactose and D-Glucose, ATPase component | B9Z44_RS13810 | B9Z44_RS03630 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | | |
| galacturonate | uxuL: D-galactaro-1,5-lactonase (UxuL or UxuF) | B9Z44_RS02155 | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | B9Z44_RS08880 | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | dctQ: D-glucuronate TRAP transporter, small permease component | | |
| glucuronate | garL: 5-dehydro-4-deoxy-D-glucarate aldolase | B9Z44_RS07610 | B9Z44_RS02170 |
| glucuronate | uxuL: D-glucaro-1,5-lactonase UxuL or UxuF | B9Z44_RS02155 | |
| glutamate | aspA: L-aspartate ammonia-lyase | B9Z44_RS12820 | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | | |
| glycerol | glpF: glycerol facilitator glpF | B9Z44_RS14135 | |
| glycerol | glpK: glycerol kinase | | |
| histidine | braC: ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC | B9Z44_RS00730 | |
| histidine | braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) | B9Z44_RS04220 | B9Z44_RS12865 |
| histidine | braF: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) | B9Z44_RS05725 | B9Z44_RS04215 |
| histidine | braG: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) | B9Z44_RS05720 | B9Z44_RS04210 |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| lactose | klh: periplasmic 3'-ketolactose hydrolase | | |
| lactose | lacA': periplasmic lactose 3-dehydrogenase, LacA subunit | | |
| lactose | lacB': periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) | B9Z44_RS01490 | B9Z44_RS03615 |
| lactose | lacC': periplasmic lactose 3-dehydrogenase, LacC subunit | | |
| lysine | davD: glutarate semialdehyde dehydrogenase | B9Z44_RS11745 | B9Z44_RS01610 |
| lysine | davT: 5-aminovalerate aminotransferase | B9Z44_RS03080 | B9Z44_RS03845 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | B9Z44_RS06760 | B9Z44_RS01590 |
| lysine | lysP: L-lysine:H+ symporter LysP | B9Z44_RS14795 | |
| lysine | patA: cadaverine aminotransferase | B9Z44_RS03080 | |
| lysine | patD: 5-aminopentanal dehydrogenase | B9Z44_RS11550 | B9Z44_RS11745 |
| maltose | susB: alpha-glucosidase (maltase) | | |
| mannitol | mtlA: mannitol phosphotransferase system, EII-CBA components | | |
| mannitol | mtlD: mannitol-1-phosphate 5-dehydrogenase | | |
| mannose | man-isomerase: D-mannose isomerase | | |
| mannose | scrK: fructokinase | B9Z44_RS13905 | |
| 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 | B9Z44_RS12880 | |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | B9Z44_RS06845 | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | B9Z44_RS08880 | |
| 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 | | |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | B9Z44_RS01330 | B9Z44_RS14765 |
| phenylacetate | paaK: phenylacetate-CoA ligase | B9Z44_RS08455 | B9Z44_RS06550 |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | B9Z44_RS01330 | B9Z44_RS06755 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylacetate | ppa: phenylacetate permease ppa | B9Z44_RS05450 | |
| phenylalanine | hmgA: homogentisate dioxygenase | | |
| phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | B9Z44_RS12925 | |
| phenylalanine | maiA: maleylacetoacetate isomerase | B9Z44_RS13915 | B9Z44_RS05020 |
| phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
| phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | B9Z44_RS01090 | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | | |
| proline | put1: proline dehydrogenase | | |
| proline | putA: L-glutamate 5-semialdeyde dehydrogenase | B9Z44_RS11550 | B9Z44_RS07890 |
| propionate | lctP: propionate permease | B9Z44_RS10395 | |
| putrescine | gabT: gamma-aminobutyrate transaminase | B9Z44_RS03080 | B9Z44_RS03845 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | B9Z44_RS03080 | |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | B9Z44_RS11550 | B9Z44_RS11745 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | B9Z44_RS13785 | B9Z44_RS01350 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | B9Z44_RS02125 | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsK: ribokinase | | |
| serine | sdaB: L-serine ammonia-lyase | B9Z44_RS09005 | B9Z44_RS09180 |
| sorbitol | scrK: fructokinase | B9Z44_RS13905 | |
| sorbitol | sdh: sorbitol dehydrogenase | B9Z44_RS01380 | B9Z44_RS03965 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
| sucrose | ams: sucrose hydrolase (invertase) | | |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | B9Z44_RS00730 | |
| threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | B9Z44_RS04225 | B9Z44_RS05730 |
| threonine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | B9Z44_RS04220 | B9Z44_RS12865 |
| threonine | tdcE: 2-ketobutyrate formate-lyase | | |
| thymidine | adh: acetaldehyde dehydrogenase (not acylating) | B9Z44_RS11745 | B9Z44_RS11550 |
| thymidine | deoA: thymidine phosphorylase DeoA | B9Z44_RS10795 | |
| thymidine | deoB: phosphopentomutase | | |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | treF: trehalase | | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | B9Z44_RS12925 | |
| tyrosine | maiA: maleylacetoacetate isomerase | B9Z44_RS13915 | B9Z44_RS05020 |
| valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | B9Z44_RS00730 | B9Z44_RS12855 |
| valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | B9Z44_RS04220 | B9Z44_RS12865 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | B9Z44_RS07890 | B9Z44_RS11745 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | B9Z44_RS11970 | B9Z44_RS08180 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | | |
| xylose | DKDP-dehydrog: D-2-keto-3-deoxypentoate dehydrogenase | B9Z44_RS03530 | B9Z44_RS06590 |
| xylose | gtsA: xylose ABC transporter, periplasmic substrate-binding component GtsA | B9Z44_RS13790 | |
| xylose | gtsB: xylose ABC transporter, permease component 1 GtsB | B9Z44_RS13800 | |
| xylose | gtsC: xylose ABC transporter, permease component 2 GtsC | B9Z44_RS13805 | |
| xylose | xad: D-xylonate dehydratase | B9Z44_RS13860 | B9Z44_RS01485 |
| xylose | xdh: D-xylose dehydrogenase | B9Z44_RS12885 | B9Z44_RS09995 |
| xylose | xylC: xylonolactonase | | |
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