Potential Gaps in catabolism of small carbon sources in Rhodobacter maris JA276
Found 95 low-confidence and 61 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 | CRO22_RS00730 | CRO22_RS10285 |
| 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 | araE: L-arabinose:H+ symporter | | |
| arabinose | xacB: L-arabinose 1-dehydrogenase | CRO22_RS14095 | CRO22_RS14510 |
| arabinose | xacC: L-arabinono-1,4-lactonase | | |
| arabinose | xacD: L-arabinonate dehydratase | CRO22_RS06545 | CRO22_RS05670 |
| arabinose | xacE: 2-dehydro-3-deoxy-L-arabinonate dehydratase | | |
| arginine | artM: L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) | CRO22_RS13220 | CRO22_RS16315 |
| arginine | artQ: L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) | CRO22_RS13225 | CRO22_RS16320 |
| arginine | gabD: succinate semialdehyde dehydrogenase | CRO22_RS15345 | CRO22_RS14815 |
| arginine | odc: L-ornithine decarboxylase | CRO22_RS15245 | |
| arginine | puuB: gamma-glutamylputrescine oxidase | CRO22_RS16290 | CRO22_RS13255 |
| citrate | SLC13A5: citrate:Na+ symporter | CRO22_RS11140 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | CRO22_RS13235 | CRO22_RS16330 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | CRO22_RS13220 | CRO22_RS06045 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | CRO22_RS13225 | CRO22_RS13220 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | CRO22_RS13230 | CRO22_RS16325 |
| citrulline | arcC: carbamate kinase | | |
| citrulline | gabD: succinate semialdehyde dehydrogenase | CRO22_RS15345 | CRO22_RS14815 |
| citrulline | odc: L-ornithine decarboxylase | CRO22_RS15245 | |
| citrulline | puuB: gamma-glutamylputrescine oxidase | CRO22_RS16290 | CRO22_RS13255 |
| D-alanine | dadA: D-alanine dehydrogenase | CRO22_RS13150 | |
| D-alanine | Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component | CRO22_RS03095 | |
| D-alanine | Pf6N2E2_5403: ABC transporter for D-Alanine, permease component 2 | CRO22_RS03090 | |
| D-alanine | Pf6N2E2_5404: ABC transporter for D-Alanine, permease component 1 | CRO22_RS03085 | CRO22_RS06045 |
| D-alanine | Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component | CRO22_RS03080 | CRO22_RS13180 |
| 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 | | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | CRO22_RS14510 | CRO22_RS12655 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoK: deoxyribokinase | CRO22_RS09440 | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fucose | aldA: lactaldehyde dehydrogenase | CRO22_RS10475 | CRO22_RS11970 |
| 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 | | |
| galactose | galE: UDP-glucose 4-epimerase | CRO22_RS14585 | CRO22_RS16005 |
| galactose | galK: galactokinase (-1-phosphate forming) | | |
| galactose | galP: galactose:H+ symporter GalP | | |
| galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | uxaA: D-altronate dehydratase | CRO22_RS06990 | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | CRO22_RS06945 | |
| gluconate | gntK: D-gluconate kinase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | CRO22_RS11860 | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | dctQ: D-glucuronate TRAP transporter, small permease component | CRO22_RS06955 | |
| glucuronate | uxaC: D-glucuronate isomerase | CRO22_RS06945 | |
| glutamate | aspA: L-aspartate ammonia-lyase | CRO22_RS00535 | |
| histidine | aapJ: L-histidine ABC transporter, substrate-binding component AapJ | CRO22_RS03095 | |
| histidine | aapM: L-histidine ABC transporter, permease component 2 (AapM) | CRO22_RS03085 | CRO22_RS13185 |
| histidine | aapP: L-histidine ABC transporter, ATPase component AapP | CRO22_RS03080 | CRO22_RS13180 |
| histidine | aapQ: L-histidine ABC transporter, permease component 1 (AapQ) | CRO22_RS03090 | CRO22_RS06045 |
| 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 | CRO22_RS10865 | CRO22_RS11805 |
| isoleucine | livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) | CRO22_RS11435 | CRO22_RS07975 |
| isoleucine | livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | | |
| isoleucine | livM: L-isoleucine ABC transporter, permease component 2 (LivM/BraE) | CRO22_RS13790 | CRO22_RS12850 |
| isoleucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| L-lactate | Shew_2731: L-lactate:Na+ symporter, large component | CRO22_RS01330 | |
| L-lactate | Shew_2732: L-lactate:Na+ symporter, small component | CRO22_RS01335 | |
| lactose | klh: periplasmic 3'-ketolactose hydrolase | | |
| lactose | lacA': periplasmic lactose 3-dehydrogenase, LacA subunit | | |
| lactose | lacB': periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) | CRO22_RS13030 | |
| lactose | lacC': periplasmic lactose 3-dehydrogenase, LacC subunit | | |
| leucine | livH: L-leucine ABC transporter, permease component 1 (LivH/BraD) | CRO22_RS11435 | CRO22_RS07975 |
| leucine | livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | | |
| leucine | livM: L-leucine ABC transporter, permease component 2 (LivM/BraE) | CRO22_RS13790 | CRO22_RS12850 |
| leucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| lysine | davA: 5-aminovaleramidase | CRO22_RS04160 | CRO22_RS06295 |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase | CRO22_RS06210 | CRO22_RS03430 |
| lysine | hisM: L-lysine ABC transporter, permease component 1 (HisM) | CRO22_RS13220 | CRO22_RS16315 |
| lysine | hisQ: L-lysine ABC transporter, permease component 2 (HisQ) | CRO22_RS13225 | CRO22_RS06045 |
| mannitol | mt2d: mannitol 2-dehydrogenase | CRO22_RS06980 | CRO22_RS02400 |
| mannitol | mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) | CRO22_RS05175 | CRO22_RS14500 |
| mannitol | mtlK: polyol ABC transporter, ATP component MtlK/SmoG | CRO22_RS05180 | CRO22_RS07640 |
| mannose | manP: mannose PTS system, EII-CBA components | CRO22_RS14780 | |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | | |
| 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 | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | CRO22_RS11860 | |
| 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 | CRO22_RS16395 | |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | CRO22_RS09335 | CRO22_RS02520 |
| phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | CRO22_RS06210 | CRO22_RS03430 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | CRO22_RS13625 | CRO22_RS02395 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | CRO22_RS13625 | CRO22_RS02395 |
| phenylacetate | paaK: phenylacetate-CoA ligase | | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | CRO22_RS02520 | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | fahA: fumarylacetoacetate hydrolase | | |
| phenylalanine | hmgA: homogentisate dioxygenase | | |
| phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| phenylalanine | maiA: maleylacetoacetate isomerase | | |
| phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
| phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | | |
| proline | natB: proline ABC transporter, substrate-binding component NatB | CRO22_RS12830 | |
| proline | natC: proline ABC transporter, permease component 1 (NatC) | | |
| proline | natD: proline ABC transporter, permease component 2 (NatD) | CRO22_RS12845 | |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | gabD: succinate semialdehyde dehydrogenase | CRO22_RS15345 | CRO22_RS14815 |
| putrescine | potC: putrescine ABC transporter, permease component 2 (PotC/PotI) | CRO22_RS01275 | CRO22_RS01760 |
| putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | CRO22_RS01750 | |
| putrescine | puuB: gamma-glutamylputrescine oxidase | CRO22_RS16290 | CRO22_RS13255 |
| rhamnose | aldA: lactaldehyde dehydrogenase | CRO22_RS10475 | CRO22_RS11970 |
| rhamnose | rhaA: L-rhamnose isomerase | | |
| rhamnose | rhaB: L-rhamnulokinase | | |
| rhamnose | rhaD: rhamnulose 1-phosphate aldolase | CRO22_RS06765 | |
| rhamnose | rhaM: L-rhamnose mutarotase | | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsK: ribokinase | CRO22_RS09440 | |
| serine | snatA: L-serine transporter | CRO22_RS16965 | CRO22_RS05425 |
| sorbitol | sdh: sorbitol dehydrogenase | CRO22_RS14510 | CRO22_RS09910 |
| threonine | snatA: L-threonine transporter snatA | CRO22_RS16965 | CRO22_RS05425 |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| 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 | CRO22_RS10865 | CRO22_RS11805 |
| valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | CRO22_RS11435 | CRO22_RS07975 |
| valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | | |
| valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | CRO22_RS13790 | CRO22_RS11430 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | CRO22_RS10870 | CRO22_RS11970 |
| valine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
| xylitol | xdhA: xylitol dehydrogenase | CRO22_RS14510 | CRO22_RS12655 |
| xylose | xylF: ABC transporter for xylose, substrate binding component xylF | CRO22_RS09235 | |
| xylose | xylG: ABC transporter for xylose, ATP-binding component xylG | CRO22_RS06780 | CRO22_RS10415 |
| xylose | xylH: ABC transporter for xylose, permease component xylH | CRO22_RS06775 | CRO22_RS09240 |
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