Potential Gaps in catabolism of small carbon sources in Granulicella mallensis MP5ACTX8
Found 72 low-confidence and 55 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | ACIX8_RS14560 | ACIX8_RS04810 |
| 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 | ACIX8_RS16595 | |
| acetate | dctA: organic acid/proton symporter DctA | ACIX8_RS06205 | ACIX8_RS09550 |
| alanine | snatA: L-alanine symporter SnatA | ACIX8_RS02975 | |
| arabinose | araB: ribulokinase | ACIX8_RS23605 | ACIX8_RS14455 |
| arabinose | araE: L-arabinose:H+ symporter | ACIX8_RS04220 | ACIX8_RS11205 |
| arginine | rocE: L-arginine permease | | |
| arginine | rocF: arginase | | |
| asparagine | ans: asparaginase | ACIX8_RS00185 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | ACIX8_RS02065 | ACIX8_RS18020 |
| 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 | dadA: D-alanine dehydrogenase | | |
| D-lactate | D-LDH: D-lactate dehydrogenase | ACIX8_RS14090 | ACIX8_RS02120 |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | ACIX8_RS00375 | ACIX8_RS20995 |
| deoxyinosine | deoB: phosphopentomutase | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | ACIX8_RS18095 | ACIX8_RS00525 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | ACIX8_RS10765 | |
| deoxyribonate | garK: glycerate 2-kinase | ACIX8_RS10770 | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoP: deoxyribose transporter | ACIX8_RS14615 | |
| fucose | fucP: L-fucose:H+ symporter FucP | ACIX8_RS14615 | ACIX8_RS19365 |
| galacturonate | exuT: D-galacturonate transporter ExuT | ACIX8_RS16740 | ACIX8_RS04750 |
| galacturonate | kdgK: 2-keto-3-deoxygluconate kinase | ACIX8_RS18080 | ACIX8_RS04655 |
| galacturonate | uxaA: D-altronate dehydratase | | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | ACIX8_RS08215 | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | ACIX8_RS04660 | ACIX8_RS04705 |
| glucosamine | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | ACIX8_RS04750 | |
| glucuronate | kdgK: 2-keto-3-deoxygluconate kinase | ACIX8_RS18080 | ACIX8_RS04655 |
| glucuronate | uxaC: D-glucuronate isomerase | ACIX8_RS08215 | |
| glucuronate | uxuB: D-mannonate dehydrogenase | | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | ACIX8_RS12585 | |
| histidine | hutG': N-formylglutamate amidohydrolase | | |
| histidine | LAT2: L-histidine transporter | ACIX8_RS13580 | ACIX8_RS07745 |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | ACIX8_RS18780 | ACIX8_RS10450 |
| isoleucine | Bap2: L-isoleucine permease Bap2 | | |
| isoleucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | ACIX8_RS06540 | |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | ACIX8_RS23965 | |
| isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | ACIX8_RS02780 | ACIX8_RS18945 |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | ACIX8_RS10280 | ACIX8_RS18095 |
| L-lactate | lutC: L-lactate dehydrogenase, LutC subunit | ACIX8_RS05495 | |
| lactose | lacP: lactose permease LacP | | |
| leucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | ACIX8_RS06540 | |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | ACIX8_RS23965 | |
| leucine | leuT: L-leucine:Na+ symporter LeuT | | |
| leucine | liuA: isovaleryl-CoA dehydrogenase | ACIX8_RS10450 | ACIX8_RS18780 |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | ACIX8_RS11400 | ACIX8_RS07735 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | ACIX8_RS18955 | |
| lysine | hglS: D-2-hydroxyglutarate synthase | | |
| lysine | lysN: 2-aminoadipate transaminase | ACIX8_RS10465 | ACIX8_RS09750 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | ACIX8_RS09760 | |
| mannitol | manA: mannose-6-phosphate isomerase | ACIX8_RS19360 | ACIX8_RS10470 |
| mannitol | mt1d: mannitol 1-dehydrogenase | ACIX8_RS04060 | |
| mannitol | PLT5: polyol transporter PLT5 | ACIX8_RS11205 | ACIX8_RS13440 |
| mannose | gluP: mannose:Na+ symporter | ACIX8_RS17830 | ACIX8_RS19365 |
| mannose | manA: mannose-6-phosphate isomerase | ACIX8_RS19360 | ACIX8_RS10470 |
| 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 | ACIX8_RS22815 | |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | ACIX8_RS05660 | |
| myoinositol | iolT: myo-inositol:H+ symporter | ACIX8_RS04220 | ACIX8_RS11205 |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | ACIX8_RS04660 | ACIX8_RS04705 |
| 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 | ACIX8_RS02780 | ACIX8_RS18945 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | ACIX8_RS18945 | ACIX8_RS02780 |
| phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | ACIX8_RS10250 | ACIX8_RS18095 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | ACIX8_RS05900 | |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | ACIX8_RS05900 | |
| phenylacetate | paaK: phenylacetate-CoA ligase | | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | ACIX8_RS18945 | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | maiA: maleylacetoacetate isomerase | | |
| phenylalanine | PAH: phenylalanine 4-monooxygenase | ACIX8_RS13750 | |
| phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | ACIX8_RS11795 | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | | |
| putrescine | gabD: succinate semialdehyde dehydrogenase | ACIX8_RS16850 | ACIX8_RS07595 |
| putrescine | gabT: gamma-aminobutyrate transaminase | ACIX8_RS09750 | ACIX8_RS13335 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | ACIX8_RS13335 | ACIX8_RS10415 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | ACIX8_RS16850 | ACIX8_RS07595 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | ACIX8_RS04740 | |
| rhamnose | rhaB: L-rhamnulokinase | ACIX8_RS05535 | |
| rhamnose | rhaM: L-rhamnose mutarotase | ACIX8_RS05490 | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | ACIX8_RS05515 | |
| serine | snatA: L-serine transporter | ACIX8_RS02975 | |
| sorbitol | sdh: sorbitol dehydrogenase | ACIX8_RS10710 | ACIX8_RS17355 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | ACIX8_RS11205 | ACIX8_RS04220 |
| succinate | dctA: succinate:H+ symporter DctA | ACIX8_RS06205 | ACIX8_RS09550 |
| sucrose | ams: sucrose hydrolase (invertase) | ACIX8_RS17600 | ACIX8_RS22440 |
| threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | ACIX8_RS04905 | ACIX8_RS04895 |
| threonine | snatA: L-threonine transporter snatA | ACIX8_RS02975 | |
| thymidine | deoB: phosphopentomutase | | |
| trehalose | treF: trehalase | ACIX8_RS17600 | ACIX8_RS22440 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | ACIX8_RS18780 | ACIX8_RS10450 |
| valine | Bap2: L-valine permease Bap2 | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | ACIX8_RS02780 | |
| valine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | ACIX8_RS06540 | |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | ACIX8_RS23965 | |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | ACIX8_RS02780 | ACIX8_RS18945 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | ACIX8_RS06770 | ACIX8_RS16850 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | | |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | ACIX8_RS11205 | ACIX8_RS13440 |
| xylitol | xdhA: xylitol dehydrogenase | ACIX8_RS17355 | ACIX8_RS21155 |
| xylose | xylA: xylose isomerase | | |
| xylose | xylT: D-xylose transporter | ACIX8_RS04220 | ACIX8_RS11205 |
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