Potential Gaps in catabolism of small carbon sources in Hyphomicrobium sulfonivorans WDL6
Found 145 low-confidence and 35 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 | APY04_RS10505 | |
| 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 | | |
| alanine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | APY04_RS10585 | |
| alanine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | APY04_RS10560 | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | APY04_RS04925 | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arginine | rocD: ornithine aminotransferase | APY04_RS01040 | APY04_RS02685 |
| arginine | rocF: arginase | | |
| asparagine | ans: asparaginase | APY04_RS07835 | |
| cellobiose | bgl: cellobiase | | |
| cellobiose | MFS-glucose: glucose transporter, MFS superfamily | | |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | APY04_RS02705 | APY04_RS07015 |
| 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 | APY04_RS13220 | |
| citrulline | citrullinase: putative citrullinase | APY04_RS09935 | |
| citrulline | rocD: ornithine aminotransferase | APY04_RS01040 | APY04_RS02685 |
| D-alanine | AZOBR_RS08245: D-alanine ABC transporter, ATPase component 1 | APY04_RS10570 | APY04_RS08115 |
| D-alanine | AZOBR_RS08260: D-alanine ABC transporter, substrate-binding component | APY04_RS10585 | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | APY04_RS06705 | APY04_RS13150 |
| deoxyinosine | deoB: phosphopentomutase | APY04_RS16370 | |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | APY04_RS04885 | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
| deoxyribonate | aacS: acetoacetyl-CoA synthetase | APY04_RS00535 | APY04_RS01545 |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | APY04_RS10945 | |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyribose | deoK: deoxyribokinase | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fructose | 1pfk: 1-phosphofructokinase | | |
| fructose | fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components | | |
| fucose | aldA: lactaldehyde dehydrogenase | APY04_RS06730 | APY04_RS13805 |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | APY04_RS04925 | |
| 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 | | |
| galactose | galK: galactokinase (-1-phosphate forming) | | |
| galactose | galP: galactose:H+ symporter GalP | | |
| galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| galactose | pgmA: alpha-phosphoglucomutase | APY04_RS10600 | APY04_RS16370 |
| galacturonate | dopDH: 2,5-dioxopentanonate dehydrogenase | APY04_RS10965 | APY04_RS06730 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | gci: D-galactarolactone cycloisomerase | | |
| galacturonate | gli: D-galactarolactone isomerase | | |
| galacturonate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | | |
| galacturonate | udh: D-galacturonate dehydrogenase | | |
| gluconate | gnd: 6-phosphogluconate dehydrogenase, decarboxylating | | |
| gluconate | gntK: D-gluconate kinase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | SLC2A2: glucosamine transporter SLC2A2 | | |
| glucose | MFS-glucose: glucose transporter, MFS superfamily | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | dopDH: 2,5-dioxopentanonate dehydrogenase | APY04_RS10965 | APY04_RS06730 |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
| glucuronate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| glutamate | gdhA: glutamate dehydrogenase, NAD-dependent | APY04_RS12410 | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | APY04_RS09545 | APY04_RS04105 |
| isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | APY04_RS00565 | APY04_RS07375 |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | APY04_RS10300 | APY04_RS12550 |
| isoleucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| 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) | | |
| lactose | pgmA: alpha-phosphoglucomutase | APY04_RS10600 | APY04_RS16370 |
| leucine | aacS: acetoacetyl-CoA synthetase | APY04_RS00535 | APY04_RS01545 |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | APY04_RS01365 | APY04_RS04340 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | APY04_RS10815 | APY04_RS07375 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | APY04_RS01350 | |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| leucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| lysine | amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) | APY04_RS10965 | APY04_RS06730 |
| lysine | hglS: D-2-hydroxyglutarate synthase | | |
| lysine | lat: L-lysine 6-aminotransferase | APY04_RS02685 | APY04_RS00380 |
| lysine | lysN: 2-aminoadipate transaminase | APY04_RS08820 | APY04_RS02685 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| maltose | malA: 6-phospho-alphaglucosidase | | |
| maltose | malEIICBA: maltose phosphotransferase system, EII-CBA components | | |
| mannitol | mtlA: mannitol phosphotransferase system, EII-CBA components | | |
| mannitol | mtlD: mannitol-1-phosphate 5-dehydrogenase | | |
| mannose | manP: mannose PTS system, EII-CBA components | | |
| 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 | | |
| myoinositol | mmsA: malonate-semialdehyde dehydrogenase | APY04_RS10965 | APY04_RS06730 |
| 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 | paaF: 2,3-dehydroadipyl-CoA hydratase | APY04_RS07375 | APY04_RS10815 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | APY04_RS07375 | APY04_RS00565 |
| phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | APY04_RS00565 | APY04_RS03320 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | APY04_RS12555 | APY04_RS12615 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | APY04_RS12555 | APY04_RS12615 |
| phenylacetate | paaK: phenylacetate-CoA ligase | APY04_RS00535 | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | APY04_RS07375 | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aacS: acetoacetyl-CoA synthetase | APY04_RS00535 | APY04_RS01545 |
| phenylalanine | fahA: fumarylacetoacetate hydrolase | | |
| phenylalanine | hmgA: homogentisate dioxygenase | | |
| phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | APY04_RS10560 | APY04_RS13100 |
| phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | APY04_RS10585 | |
| phenylalanine | maiA: maleylacetoacetate isomerase | | |
| phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
| phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | APY04_RS07600 | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | APY04_RS04120 | |
| proline | AZOBR_RS08245: proline ABC transporter, ATPase component 1 | APY04_RS10570 | APY04_RS08115 |
| proline | AZOBR_RS08260: proline ABC transporter, substrate-binding component | APY04_RS10585 | |
| propionate | lctP: propionate permease | APY04_RS01325 | |
| putrescine | gabD: succinate semialdehyde dehydrogenase | APY04_RS10965 | APY04_RS06730 |
| putrescine | gabT: gamma-aminobutyrate transaminase | APY04_RS01040 | APY04_RS02685 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | APY04_RS01040 | APY04_RS00380 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | APY04_RS06730 | APY04_RS13805 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | APY04_RS01590 | APY04_RS10300 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | | |
| rhamnose | LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase | APY04_RS10300 | APY04_RS12550 |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsK: ribokinase | | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | APY04_RS10585 | |
| serine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | APY04_RS10560 | |
| serine | sdaB: L-serine ammonia-lyase | APY04_RS13150 | APY04_RS06705 |
| sorbitol | mtlA: PTS system for polyols, EII-CBA components | | |
| sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | APY04_RS01590 | APY04_RS10300 |
| sucrose | ams: sucrose hydrolase (invertase) | | |
| sucrose | MFS-glucose: glucose transporter, MFS superfamily | | |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | APY04_RS10585 | |
| threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | APY04_RS10560 | |
| threonine | tdcE: 2-ketobutyrate formate-lyase | | |
| thymidine | deoA: thymidine phosphorylase DeoA | | |
| thymidine | deoB: phosphopentomutase | APY04_RS16370 | |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | MFS-glucose: glucose transporter, MFS superfamily | | |
| trehalose | treF: trehalase | APY04_RS03185 | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aacS: acetoacetyl-CoA synthetase | APY04_RS00535 | APY04_RS01545 |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | APY04_RS09545 | APY04_RS04105 |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | APY04_RS00565 | APY04_RS10815 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | APY04_RS10965 | APY04_RS06730 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | APY04_RS11010 | |
| 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 | APY04_RS15335 | |
| xylose | xylA: xylose isomerase | | |
| xylose | xylB: xylulokinase | | |
| xylose | xylT: D-xylose transporter | | |
Confidence: high confidence medium confidence low confidence
This GapMind analysis is from Apr 09 2024. 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