Potential Gaps in catabolism of small carbon sources in Rhodobacter johrii JA192
Found 71 low-confidence and 55 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 | C8J29_RS20745 | C8J29_RS09375 |
| 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 | C8J29_RS16510 | |
| alanine | snatA: L-alanine symporter SnatA | C8J29_RS06105 | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arabinose | xacB: L-arabinose 1-dehydrogenase | C8J29_RS15950 | C8J29_RS19185 |
| arabinose | xacD: L-arabinonate dehydratase | C8J29_RS07520 | C8J29_RS18010 |
| arabinose | xacE: 2-dehydro-3-deoxy-L-arabinonate dehydratase | C8J29_RS14935 | |
| arginine | bgtB: L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) | | |
| arginine | odc: L-ornithine decarboxylase | C8J29_RS01770 | |
| arginine | puuD: gamma-glutamyl-gamma-aminobutyrate hydrolase | C8J29_RS07905 | C8J29_RS01825 |
| citrate | tctB: citrate/Na+ symporter, small transmembrane component TctB | | |
| citrate | tctC: citrate/Na+ symporter, substrate-binding component TctC | C8J29_RS17865 | C8J29_RS18095 |
| citrulline | arcC: carbamate kinase | | |
| citrulline | odc: L-ornithine decarboxylase | C8J29_RS01770 | |
| citrulline | PS417_17590: ABC transporter for L-Citrulline, periplasmic substrate-binding component | C8J29_RS08570 | |
| citrulline | PS417_17595: ABC transporter for L-Citrulline, permease component 1 | C8J29_RS17490 | C8J29_RS14955 |
| citrulline | PS417_17600: ABC transporter for L-Citrulline, permease component 2 | C8J29_RS08580 | |
| citrulline | PS417_17605: ABC transporter for L-Citrulline, ATPase component | C8J29_RS08565 | C8J29_RS17495 |
| citrulline | puuD: gamma-glutamyl-gamma-aminobutyrate hydrolase | C8J29_RS07905 | C8J29_RS01825 |
| D-alanine | Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component | C8J29_RS00485 | C8J29_RS18260 |
| D-alanine | Pf6N2E2_5403: ABC transporter for D-Alanine, permease component 2 | C8J29_RS18265 | C8J29_RS00490 |
| D-alanine | Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component | C8J29_RS00500 | C8J29_RS19225 |
| 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 | C8J29_RS10320 | C8J29_RS02890 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| ethanol | etoh-dh-nad: ethanol dehydrogenase (NAD(P)) | C8J29_RS14180 | C8J29_RS02520 |
| fucose | fucD: L-fuconate dehydratase | C8J29_RS21790 | |
| fucose | fuconolactonase: L-fucono-1,5-lactonase | | |
| fucose | fucP: L-fucose:H+ symporter FucP | | |
| fucose | fucU: L-fucose mutarotase FucU | | |
| galactose | galP: galactose:H+ symporter GalP | | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | gci: D-galactarolactone cycloisomerase | C8J29_RS21155 | C8J29_RS17975 |
| galacturonate | gli: D-galactarolactone isomerase | | |
| galacturonate | udh: D-galacturonate dehydrogenase | | |
| gluconate | gntA: gluconate TRAP transporter, small permease component | C8J29_RS20245 | |
| gluconate | gntC: gluconate TRAP transporter, periplasmic solute-binding component | C8J29_RS20255 | C8J29_RS09155 |
| gluconate | gntK: D-gluconate kinase | | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | C8J29_RS04180 | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | dctP: D-glucuronate TRAP transporter, solute receptor component | C8J29_RS09155 | C8J29_RS20255 |
| glucuronate | dctQ: D-glucuronate TRAP transporter, small permease component | | |
| glucuronate | kdgK: 2-keto-3-deoxygluconate kinase | C8J29_RS09170 | C8J29_RS18460 |
| glucuronate | uxaC: D-glucuronate isomerase | C8J29_RS09160 | |
| histidine | hutG': N-formylglutamate amidohydrolase | | |
| histidine | PA5503: L-histidine ABC transporter, ATPase component | C8J29_RS07285 | C8J29_RS14945 |
| histidine | PA5504: L-histidine ABC transporter, permease component | C8J29_RS07290 | |
| histidine | PA5505: L-histidine ABC transporter, substrate-binding component | C8J29_RS07295 | |
| isoleucine | livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) | C8J29_RS18430 | C8J29_RS14190 |
| isoleucine | livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | | |
| isoleucine | livM: L-isoleucine ABC transporter, permease component 2 (LivM/BraE) | C8J29_RS03030 | C8J29_RS18425 |
| L-lactate | Shew_2731: L-lactate:Na+ symporter, large component | C8J29_RS09630 | |
| L-lactate | Shew_2732: L-lactate:Na+ symporter, small component | C8J29_RS09635 | |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | C8J29_RS06000 | |
| leucine | livH: L-leucine ABC transporter, permease component 1 (LivH/BraD) | C8J29_RS18430 | C8J29_RS14190 |
| leucine | livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | | |
| leucine | livM: L-leucine ABC transporter, permease component 2 (LivM/BraE) | C8J29_RS03030 | C8J29_RS18425 |
| lysine | argT: L-lysine ABC transporter, substrate-binding component ArgT | C8J29_RS08570 | |
| lysine | davA: 5-aminovaleramidase | C8J29_RS09850 | C8J29_RS20260 |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | davT: 5-aminovalerate aminotransferase | C8J29_RS17815 | C8J29_RS01855 |
| lysine | fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase | C8J29_RS15150 | C8J29_RS02600 |
| lysine | hisM: L-lysine ABC transporter, permease component 1 (HisM) | C8J29_RS08580 | C8J29_RS17490 |
| lysine | hisQ: L-lysine ABC transporter, permease component 2 (HisQ) | C8J29_RS14955 | C8J29_RS14950 |
| maltose | susB: alpha-glucosidase (maltase) | C8J29_RS15940 | C8J29_RS03850 |
| myoinositol | iatA: myo-inositol ABC transporter, ATPase component IatA | C8J29_RS17445 | C8J29_RS16570 |
| myoinositol | ibpA: myo-inositol ABC transporter, substrate-binding component IbpA | | |
| myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | | |
| myoinositol | iolD: 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase | | |
| myoinositol | iolE: scyllo-inosose 2-dehydratase | | |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | C8J29_RS20205 | C8J29_RS20590 |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | C8J29_RS04180 | |
| 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 | C8J29_RS16095 | C8J29_RS18410 |
| phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | C8J29_RS15150 | C8J29_RS02600 |
| phenylacetate | paaK: phenylacetate-CoA ligase | C8J29_RS12885 | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | C8J29_RS04835 | C8J29_RS04225 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylacetate | ppa: phenylacetate permease ppa | C8J29_RS13465 | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | fahA: fumarylacetoacetate hydrolase | C8J29_RS07505 | |
| phenylalanine | hmgA: homogentisate dioxygenase | | |
| phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| phenylalanine | maiA: maleylacetoacetate isomerase | C8J29_RS13380 | |
| phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | | |
| propionate | mctC: propionate:H+ symporter | C8J29_RS13465 | |
| putrescine | potB: putrescine ABC transporter, permease component 1 (PotB/PotH) | C8J29_RS03615 | C8J29_RS06665 |
| putrescine | potC: putrescine ABC transporter, permease component 2 (PotC/PotI) | C8J29_RS03610 | C8J29_RS06660 |
| putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | C8J29_RS03605 | |
| putrescine | puuD: gamma-glutamyl-gamma-aminobutyrate hydrolase | C8J29_RS07905 | C8J29_RS01825 |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | C8J29_RS02405 | C8J29_RS07095 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | C8J29_RS21790 | C8J29_RS17975 |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| serine | snatA: L-serine transporter | C8J29_RS06105 | |
| sucrose | ams: sucrose hydrolase (invertase) | C8J29_RS15940 | C8J29_RS11535 |
| threonine | snatA: L-threonine transporter snatA | C8J29_RS06105 | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | treF: trehalase | C8J29_RS15940 | C8J29_RS11535 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | C8J29_RS07505 | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | C8J29_RS13380 | |
| valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | C8J29_RS18430 | C8J29_RS14190 |
| valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | | |
| valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | C8J29_RS03030 | C8J29_RS18425 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | C8J29_RS06470 | C8J29_RS02515 |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
| xylitol | xdhA: xylitol dehydrogenase | C8J29_RS17990 | C8J29_RS18470 |
| 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