Potential Gaps in catabolism of small carbon sources in Granulicella tundricola MP5ACTX9
Found 94 low-confidence and 51 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | | |
| 4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | | |
| 4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | | |
| 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 | ACIX9_RS11015 | |
| acetate | dctA: organic acid/proton symporter DctA | ACIX9_RS02550 | ACIX9_RS13655 |
| alanine | cycA: L-alanine symporter CycA | ACIX9_RS08665 | |
| arabinose | araB: ribulokinase | ACIX9_RS06100 | |
| arabinose | araE: L-arabinose:H+ symporter | ACIX9_RS19965 | |
| arginine | rocE: L-arginine permease | ACIX9_RS08665 | |
| arginine | rocF: arginase | | |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | ACIX9_RS08345 | ACIX9_RS19155 |
| 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 | | |
| citrulline | arcC: carbamate kinase | | |
| D-alanine | cycA: D-alanine:H+ symporter CycA | ACIX9_RS08665 | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | D-LDH: D-lactate dehydrogenase | ACIX9_RS17900 | ACIX9_RS22010 |
| D-lactate | larD: D,L-lactic acid transporter | ACIX9_RS08295 | |
| D-serine | cycA: D-serine:H+ symporter CycA | ACIX9_RS08665 | |
| D-serine | dsdA: D-serine ammonia-lyase | ACIX9_RS14955 | ACIX9_RS01950 |
| deoxyinosine | deoB: phosphopentomutase | | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | ACIX9_RS05330 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | ACIX9_RS00675 | ACIX9_RS21300 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | ACIX9_RS03750 | ACIX9_RS20595 |
| deoxyribonate | garK: glycerate 2-kinase | ACIX9_RS24190 | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoK: deoxyribokinase | ACIX9_RS01550 | |
| deoxyribose | deoP: deoxyribose transporter | ACIX9_RS13540 | |
| fucose | fucDH: 2-keto-3-deoxy-L-fuconate 4-dehydrogenase | ACIX9_RS20680 | ACIX9_RS15700 |
| fucose | fuconolactonase: L-fucono-1,5-lactonase | ACIX9_RS20690 | |
| galacturonate | exuT: D-galacturonate transporter ExuT | ACIX9_RS05855 | |
| galacturonate | kdgK: 2-keto-3-deoxygluconate kinase | ACIX9_RS08810 | |
| galacturonate | uxaA: D-altronate dehydratase | | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | ACIX9_RS10350 | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | ACIX9_RS10880 | ACIX9_RS03545 |
| glucosamine | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| glucosamine | nagX: transmembrane glucosamine N-acetyltransferase NagX | ACIX9_RS13455 | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | kdgK: 2-keto-3-deoxygluconate kinase | ACIX9_RS08810 | |
| glucuronate | uxaC: D-glucuronate isomerase | ACIX9_RS10350 | |
| glucuronate | uxuA: D-mannonate dehydratase | | |
| glucuronate | uxuB: D-mannonate dehydrogenase | | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| histidine | permease: L-histidine permease | ACIX9_RS08665 | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | ACIX9_RS02500 | ACIX9_RS12295 |
| isoleucine | Bap2: L-isoleucine permease Bap2 | ACIX9_RS08665 | |
| isoleucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | ACIX9_RS08385 | |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | ACIX9_RS00120 | |
| isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | ACIX9_RS14800 | ACIX9_RS10695 |
| L-lactate | L-LDH: L-lactate dehydrogenase | ACIX9_RS06880 | ACIX9_RS15550 |
| L-lactate | SfMCT: L-lactate transporter SfMCT | ACIX9_RS13685 | |
| lactose | lacP: lactose permease LacP | | |
| leucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | ACIX9_RS08385 | |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | ACIX9_RS00120 | |
| leucine | leuT: L-leucine:Na+ symporter LeuT | | |
| leucine | liuA: isovaleryl-CoA dehydrogenase | ACIX9_RS12295 | ACIX9_RS02500 |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | ACIX9_RS11550 | ACIX9_RS09455 |
| lysine | amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) | ACIX9_RS08285 | ACIX9_RS05935 |
| lysine | hglS: D-2-hydroxyglutarate synthase | | |
| lysine | lat: L-lysine 6-aminotransferase | ACIX9_RS01270 | ACIX9_RS09520 |
| lysine | lysN: 2-aminoadipate transaminase | ACIX9_RS14145 | ACIX9_RS16955 |
| lysine | lysP: L-lysine:H+ symporter LysP | ACIX9_RS08665 | |
| lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | | |
| mannitol | manA: mannose-6-phosphate isomerase | ACIX9_RS08435 | ACIX9_RS14140 |
| mannitol | mt1d: mannitol 1-dehydrogenase | ACIX9_RS15190 | ACIX9_RS18140 |
| mannitol | PLT5: polyol transporter PLT5 | | |
| mannose | gluP: mannose:Na+ symporter | ACIX9_RS19715 | ACIX9_RS10875 |
| mannose | manA: mannose-6-phosphate isomerase | ACIX9_RS08435 | ACIX9_RS14140 |
| 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 | ACIX9_RS20475 | |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | | |
| myoinositol | iolT: myo-inositol:H+ symporter | ACIX9_RS19965 | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | ACIX9_RS10880 | ACIX9_RS03545 |
| 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 | ACIX9_RS14800 | ACIX9_RS05545 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | ACIX9_RS05545 | ACIX9_RS14800 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | ACIX9_RS10690 | ACIX9_RS05110 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | ACIX9_RS10690 | ACIX9_RS05110 |
| phenylacetate | paaK: phenylacetate-CoA ligase | | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | ACIX9_RS05545 | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | ACIX9_RS08665 | |
| phenylalanine | fahA: fumarylacetoacetate hydrolase | ACIX9_RS20670 | |
| phenylalanine | hmgA: homogentisate dioxygenase | | |
| phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| phenylalanine | maiA: maleylacetoacetate isomerase | | |
| phenylalanine | PAH: phenylalanine 4-monooxygenase | ACIX9_RS10475 | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | | |
| proline | N515DRAFT_2924: proline transporter | ACIX9_RS17310 | |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | gabT: gamma-aminobutyrate transaminase | ACIX9_RS01270 | ACIX9_RS09520 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | ACIX9_RS16955 | ACIX9_RS01270 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | ACIX9_RS13865 | ACIX9_RS05935 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| pyruvate | SLC5A8: sodium-coupled pyruvate transporter | | |
| rhamnose | rhaB: L-rhamnulokinase | ACIX9_RS03130 | |
| rhamnose | rhaD: rhamnulose 1-phosphate aldolase | ACIX9_RS03125 | |
| rhamnose | rhaM: L-rhamnose mutarotase | | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | ACIX9_RS03095 | |
| ribose | rbsK: ribokinase | ACIX9_RS01550 | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | snatA: L-serine transporter | ACIX9_RS16220 | |
| sorbitol | sdh: sorbitol dehydrogenase | ACIX9_RS14225 | ACIX9_RS10320 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
| sucrose | ams: sucrose hydrolase (invertase) | ACIX9_RS02275 | ACIX9_RS05530 |
| threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | ACIX9_RS15380 | ACIX9_RS15395 |
| threonine | phtA: L-threonine uptake permease PhtA | ACIX9_RS22020 | |
| thymidine | deoB: phosphopentomutase | | |
| thymidine | nupC: thymidine permease NupC | ACIX9_RS05330 | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | ACIX9_RS08665 | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | ACIX9_RS20670 | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | ACIX9_RS02500 | ACIX9_RS12295 |
| valine | Bap2: L-valine permease Bap2 | ACIX9_RS08665 | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | ACIX9_RS14800 | |
| valine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | ACIX9_RS08385 | |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | ACIX9_RS00120 | |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | ACIX9_RS14800 | ACIX9_RS05545 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | ACIX9_RS01250 | ACIX9_RS13865 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | | |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
| xylitol | xdhA: xylitol dehydrogenase | ACIX9_RS21510 | ACIX9_RS08175 |
| xylose | xylT: D-xylose transporter | ACIX9_RS19965 | |
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