Potential Gaps in catabolism of small carbon sources in Rhodomicrobium vannielii ATCC 17100
Found 117 low-confidence and 53 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | RVAN_RS07870 | |
| 4-hydroxybenzoate | fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase | RVAN_RS14570 | RVAN_RS02765 |
| 4-hydroxybenzoate | hcrA: 4-hydroxybenzoyl-CoA reductase, alpha subunit | | |
| 4-hydroxybenzoate | hcrB: 4-hydroxybenzoyl-CoA reductase, beta subunit | | |
| 4-hydroxybenzoate | hcrC: 4-hydroxybenzoyl-CoA reductase, gamma subunit | | |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| 4-hydroxybenzoate | pimB: 3-oxopimeloyl-CoA:CoA acetyltransferase | RVAN_RS00115 | RVAN_RS02760 |
| alanine | snatA: L-alanine symporter SnatA | RVAN_RS10695 | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arginine | braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) | RVAN_RS04120 | |
| arginine | braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) | RVAN_RS19490 | RVAN_RS14870 |
| arginine | rocF: arginase | | |
| asparagine | ans: asparaginase | | |
| cellobiose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | RVAN_RS13130 | RVAN_RS13665 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | RVAN_RS10990 | RVAN_RS13660 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | RVAN_RS10985 | |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | RVAN_RS00845 | RVAN_RS13135 |
| citrulline | citrullinase: putative citrullinase | RVAN_RS03875 | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | RVAN_RS10775 | RVAN_RS04340 |
| deoxyinosine | deoB: phosphopentomutase | RVAN_RS06060 | |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | RVAN_RS17490 | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | RVAN_RS07670 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | RVAN_RS14575 | RVAN_RS08300 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | RVAN_RS17275 | |
| deoxyribose | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyribose | deoK: deoxyribokinase | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| ethanol | etoh-dh-nad: ethanol dehydrogenase (NAD(P)) | RVAN_RS05170 | RVAN_RS08470 |
| fructose | Slc2a5: fructose:H+ symporter | | |
| fucose | aldA: lactaldehyde dehydrogenase | RVAN_RS09190 | RVAN_RS11750 |
| 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 | | |
| galactose | galE: UDP-glucose 4-epimerase | RVAN_RS14825 | RVAN_RS00930 |
| 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 | | |
| 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) | | |
| glucose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | dopDH: 2,5-dioxopentanonate dehydrogenase | RVAN_RS11750 | RVAN_RS17095 |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
| glucuronate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | RVAN_RS13320 | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | | |
| glycerol | glpF: glycerol facilitator glpF | | |
| glycerol | glpK: glycerol kinase | | |
| histidine | braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) | RVAN_RS04120 | |
| histidine | braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) | RVAN_RS19490 | RVAN_RS14870 |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| isoleucine | livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) | RVAN_RS04120 | RVAN_RS14865 |
| lactose | galE: UDP-glucose 4-epimerase | RVAN_RS14825 | RVAN_RS00930 |
| lactose | galK: galactokinase (-1-phosphate forming) | | |
| lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| lactose | glk: glucokinase | RVAN_RS02695 | |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | RVAN_RS13615 | |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | RVAN_RS11250 | RVAN_RS17115 |
| leucine | livH: L-leucine ABC transporter, permease component 1 (LivH/BraD) | RVAN_RS04120 | RVAN_RS14865 |
| lysine | davA: 5-aminovaleramidase | RVAN_RS03875 | RVAN_RS13780 |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | davD: glutarate semialdehyde dehydrogenase | RVAN_RS11750 | RVAN_RS09190 |
| lysine | davT: 5-aminovalerate aminotransferase | RVAN_RS10465 | RVAN_RS15510 |
| lysine | fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase | RVAN_RS14570 | RVAN_RS02765 |
| lysine | hisP: L-lysine ABC transporter, ATPase component HisP | RVAN_RS13130 | RVAN_RS13665 |
| maltose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
| maltose | susB: alpha-glucosidase (maltase) | RVAN_RS00535 | |
| mannitol | mt1d: mannitol 1-dehydrogenase | RVAN_RS05300 | RVAN_RS05305 |
| mannitol | PLT5: polyol transporter PLT5 | | |
| mannose | STP6: mannose:H+ symporter | | |
| 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 | RVAN_RS10740 | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| phenylacetate | fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase | RVAN_RS14570 | RVAN_RS02765 |
| phenylacetate | paaK: phenylacetate-CoA ligase | RVAN_RS04370 | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | padB: phenylacetyl-CoA dehydrogenase, PadB subunit | | |
| phenylacetate | padC: phenylacetyl-CoA dehydrogenase, PadC subunit | RVAN_RS20755 | |
| phenylacetate | padD: phenylacetyl-CoA dehydrogenase, PadD subunit | | |
| phenylacetate | padE: phenylglyoxylate dehydrogenase, gamma subunit | | |
| phenylacetate | padF: phenylglyoxylate dehydrogenase, delta subunit | | |
| phenylacetate | padG: phenylglyoxylate dehydrogenase, alpha subunit | | |
| phenylacetate | padH: phenylglyoxylate dehydrogenase, epsilon subunit | | |
| phenylacetate | padI: phenylglyoxylate dehydrogenase, beta subunit | | |
| phenylacetate | pimB: 3-oxopimeloyl-CoA:CoA acetyltransferase | RVAN_RS00115 | RVAN_RS02760 |
| phenylalanine | fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase | RVAN_RS14570 | RVAN_RS02765 |
| phenylalanine | iorAB: phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB | RVAN_RS03470 | |
| phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | RVAN_RS04120 | RVAN_RS14865 |
| phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | RVAN_RS04095 | |
| phenylalanine | padB: phenylacetyl-CoA dehydrogenase, PadB subunit | | |
| phenylalanine | padC: phenylacetyl-CoA dehydrogenase, PadC subunit | RVAN_RS20755 | |
| phenylalanine | padD: phenylacetyl-CoA dehydrogenase, PadD subunit | | |
| phenylalanine | padE: phenylglyoxylate dehydrogenase, gamma subunit | | |
| phenylalanine | padF: phenylglyoxylate dehydrogenase, delta subunit | | |
| phenylalanine | padG: phenylglyoxylate dehydrogenase, alpha subunit | | |
| phenylalanine | padH: phenylglyoxylate dehydrogenase, epsilon subunit | | |
| phenylalanine | padI: phenylglyoxylate dehydrogenase, beta subunit | | |
| phenylalanine | pimB: 3-oxopimeloyl-CoA:CoA acetyltransferase | RVAN_RS00115 | RVAN_RS02760 |
| propionate | lctP: propionate permease | RVAN_RS04455 | |
| putrescine | gabT: gamma-aminobutyrate transaminase | RVAN_RS10465 | RVAN_RS15555 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | RVAN_RS09190 | RVAN_RS11750 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| rhamnose | aldA: lactaldehyde dehydrogenase | RVAN_RS09190 | RVAN_RS11750 |
| rhamnose | rhaA: L-rhamnose isomerase | | |
| rhamnose | rhaB: L-rhamnulokinase | | |
| rhamnose | rhaD: rhamnulose 1-phosphate aldolase | | |
| rhamnose | rhaM: L-rhamnose mutarotase | | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsK: ribokinase | | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | snatA: L-serine transporter | RVAN_RS10695 | |
| sorbitol | sdh: sorbitol dehydrogenase | RVAN_RS13210 | RVAN_RS00205 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
| sucrose | SUS: sucrose synthase | | |
| sucrose | sut: sucrose:proton symporter SUT/SUC | | |
| threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | RVAN_RS00150 | RVAN_RS00155 |
| threonine | ltaE: L-threonine aldolase | RVAN_RS03675 | |
| threonine | snatA: L-threonine transporter snatA | RVAN_RS10695 | |
| thymidine | deoA: thymidine phosphorylase DeoA | | |
| thymidine | deoB: phosphopentomutase | RVAN_RS06060 | |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| thymidine | nupC: thymidine permease NupC | RVAN_RS07670 | |
| trehalose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
| trehalose | treF: trehalase | RVAN_RS06100 | RVAN_RS16690 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | RVAN_RS13205 | |
| tyrosine | Ac3H11_1692: L-tyrosine ABC transporter, ATPase component 2 | RVAN_RS14875 | RVAN_RS04105 |
| tyrosine | Ac3H11_1694: L-tyrosine ABC transporter, permease component 2 | RVAN_RS19490 | RVAN_RS14870 |
| tyrosine | Ac3H11_1695: L-tyrosine ABC transporter, permease component 1 | RVAN_RS04120 | RVAN_RS14865 |
| tyrosine | Ac3H11_2396: L-tyrosine ABC transporter, substrate-binding component component | RVAN_RS04095 | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | RVAN_RS01040 | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | RVAN_RS04120 | RVAN_RS09275 |
| valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | RVAN_RS19490 | RVAN_RS14870 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | RVAN_RS17095 | RVAN_RS09190 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | RVAN_RS17110 | RVAN_RS04520 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | | |
| 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