Potential Gaps in catabolism of small carbon sources in Rhodobacter viridis JA737
Found 89 low-confidence and 47 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | dctQ: 2-oxoglutarate TRAP transporter, small permease component DctQ | | |
| 4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | | |
| 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 | | |
| arginine | artM: L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) | C8J30_RS16145 | C8J30_RS12910 |
| arginine | artP: L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA | C8J30_RS16150 | C8J30_RS12895 |
| arginine | gabD: succinate semialdehyde dehydrogenase | C8J30_RS06315 | C8J30_RS10160 |
| arginine | odc: L-ornithine decarboxylase | C8J30_RS06735 | |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | C8J30_RS16150 | C8J30_RS12895 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | C8J30_RS16145 | C8J30_RS12910 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | C8J30_RS16140 | C8J30_RS16145 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | C8J30_RS16135 | C8J30_RS12900 |
| citrulline | arcC: carbamate kinase | | |
| citrulline | gabD: succinate semialdehyde dehydrogenase | C8J30_RS06315 | C8J30_RS10160 |
| citrulline | odc: L-ornithine decarboxylase | C8J30_RS06735 | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-alanine | Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component | C8J30_RS05885 | C8J30_RS00060 |
| D-alanine | Pf6N2E2_5403: ABC transporter for D-Alanine, permease component 2 | C8J30_RS05890 | C8J30_RS00065 |
| D-alanine | Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component | C8J30_RS05900 | C8J30_RS16150 |
| 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 | C8J30_RS03250 | C8J30_RS03120 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fucose | aldA: lactaldehyde dehydrogenase | C8J30_RS14450 | C8J30_RS01350 |
| 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 | C8J30_RS04025 | C8J30_RS03845 |
| 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 | kdgK: 2-keto-3-deoxygluconate kinase | C8J30_RS14070 | |
| 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 | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | C8J30_RS00730 | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | garL: 5-dehydro-4-deoxy-D-glucarate aldolase | C8J30_RS16095 | |
| glucuronate | garR: tartronate semialdehyde reductase | C8J30_RS02305 | C8J30_RS01040 |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| glutamate | aspA: L-aspartate ammonia-lyase | C8J30_RS13165 | |
| glycerol | glpF: glycerol facilitator glpF | | |
| histidine | hisM: L-histidine ABC transporter, permease component 1 (HisM) | C8J30_RS16145 | C8J30_RS12910 |
| histidine | hisP: L-histidine ABC transporter, ATPase component HisP | C8J30_RS16150 | C8J30_RS12895 |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | C8J30_RS02875 | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | C8J30_RS01050 | C8J30_RS00780 |
| isoleucine | livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) | C8J30_RS08775 | C8J30_RS11630 |
| isoleucine | livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | | |
| isoleucine | livM: L-isoleucine ABC transporter, permease component 2 (LivM/BraE) | C8J30_RS05180 | C8J30_RS02040 |
| isoleucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| lactose | klh: periplasmic 3'-ketolactose hydrolase | | |
| lactose | lacA': periplasmic lactose 3-dehydrogenase, LacA subunit | | |
| lactose | lacC': periplasmic lactose 3-dehydrogenase, LacC subunit | | |
| leucine | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | C8J30_RS05895 | C8J30_RS00070 |
| leucine | aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | C8J30_RS05900 | C8J30_RS16150 |
| leucine | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | C8J30_RS05890 | C8J30_RS00065 |
| leucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| lysine | davA: 5-aminovaleramidase | C8J30_RS09125 | C8J30_RS03730 |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase | C8J30_RS06890 | C8J30_RS05595 |
| lysine | hisM: L-lysine ABC transporter, permease component 1 (HisM) | C8J30_RS16145 | C8J30_RS12910 |
| lysine | hisP: L-lysine ABC transporter, ATPase component HisP | C8J30_RS05900 | C8J30_RS16150 |
| mannitol | mtlK: polyol ABC transporter, ATP component MtlK/SmoG | C8J30_RS03245 | C8J30_RS01990 |
| mannose | manP: mannose PTS system, EII-CBA components | C8J30_RS09070 | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | C8J30_RS00730 | |
| 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 | C8J30_RS04555 | C8J30_RS11890 |
| phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | C8J30_RS06890 | C8J30_RS05595 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | C8J30_RS05090 | C8J30_RS12155 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | C8J30_RS05090 | C8J30_RS12155 |
| phenylacetate | paaK: phenylacetate-CoA ligase | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | C8J30_RS11890 | C8J30_RS15415 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylacetate | ppa: phenylacetate permease ppa | C8J30_RS02510 | C8J30_RS03285 |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | fahA: fumarylacetoacetate hydrolase | | |
| phenylalanine | hmgA: homogentisate dioxygenase | | |
| phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| phenylalanine | maiA: maleylacetoacetate isomerase | C8J30_RS00795 | |
| phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
| phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | C8J30_RS11185 | |
| proline | proV: proline ABC transporter, ATPase component ProV | C8J30_RS14465 | C8J30_RS16975 |
| propionate | mctC: propionate:H+ symporter | C8J30_RS03285 | C8J30_RS02510 |
| putrescine | gabD: succinate semialdehyde dehydrogenase | C8J30_RS06315 | C8J30_RS10160 |
| putrescine | potC: putrescine ABC transporter, permease component 2 (PotC/PotI) | C8J30_RS14415 | C8J30_RS09740 |
| putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | C8J30_RS14400 | |
| rhamnose | aldA: lactaldehyde dehydrogenase | C8J30_RS14450 | C8J30_RS01350 |
| rhamnose | rhaA: L-rhamnose isomerase | | |
| rhamnose | rhaB: L-rhamnulokinase | | |
| rhamnose | rhaD: rhamnulose 1-phosphate aldolase | C8J30_RS10870 | |
| rhamnose | rhaM: L-rhamnose mutarotase | | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| serine | snatA: L-serine transporter | C8J30_RS09920 | C8J30_RS09615 |
| threonine | snatA: L-threonine transporter snatA | C8J30_RS09920 | C8J30_RS09615 |
| 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 | C8J30_RS00795 | |
| valine | acdH: isobutyryl-CoA dehydrogenase | C8J30_RS01050 | C8J30_RS00780 |
| valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | C8J30_RS08775 | C8J30_RS11630 |
| valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | | |
| valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | C8J30_RS05180 | C8J30_RS08770 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | C8J30_RS01055 | C8J30_RS10160 |
| valine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | C8J30_RS09070 | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | | |
| 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