Potential Gaps in catabolism of small carbon sources in Jeotgalibacillus soli P9
Found 83 low-confidence and 45 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | KP78_RS02020 | |
| 4-hydroxybenzoate | pobA: 4-hydroxybenzoate 3-monooxygenase | | |
| 4-hydroxybenzoate | praA: protocatechuate 2,3-dioxygenase | | |
| 4-hydroxybenzoate | praB: 2-hydroxymuconate 6-semialdehyde dehydrogenase | KP78_RS11775 | KP78_RS01230 |
| acetate | actP: cation/acetate symporter ActP | KP78_RS05035 | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arginine | bgtB: L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) | | |
| cellobiose | bgl: cellobiase | KP78_RS12720 | KP78_RS17575 |
| citrate | SLC13A5: citrate:Na+ symporter | KP78_RS08705 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | KP78_RS15160 | KP78_RS02250 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | KP78_RS02245 | |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | KP78_RS15165 | KP78_RS02245 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| citrulline | arcC: carbamate kinase | | |
| D-alanine | cycA: D-alanine:H+ symporter CycA | KP78_RS07720 | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | D-LDH: D-lactate dehydrogenase | KP78_RS10085 | KP78_RS04325 |
| D-lactate | larD: D,L-lactic acid transporter | KP78_RS11850 | |
| D-serine | cycA: D-serine:H+ symporter CycA | KP78_RS07720 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | KP78_RS13615 | KP78_RS07170 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| 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 | 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 | | |
| gluconate | gntT: gluconate:H+ symporter GntT | KP78_RS01635 | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
| glucuronate | udh: D-glucuronate dehydrogenase | KP78_RS04360 | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | KP78_RS04485 | KP78_RS05500 |
| histidine | PA5503: L-histidine ABC transporter, ATPase component | KP78_RS06965 | KP78_RS18135 |
| histidine | PA5505: L-histidine ABC transporter, substrate-binding component | KP78_RS18125 | KP78_RS04710 |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | KP78_RS05640 | KP78_RS15755 |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | KP78_RS11215 | KP78_RS06595 |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | KP78_RS15385 | KP78_RS10715 |
| L-lactate | SfMCT: L-lactate transporter SfMCT | KP78_RS08180 | KP78_RS01415 |
| lactose | galK: galactokinase (-1-phosphate forming) | | |
| lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | KP78_RS12720 | KP78_RS17575 |
| leucine | liuA: isovaleryl-CoA dehydrogenase | KP78_RS15755 | KP78_RS05645 |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | KP78_RS10715 | KP78_RS15385 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | KP78_RS09200 | KP78_RS13650 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | KP78_RS10875 | KP78_RS15145 |
| lysine | davA: 5-aminovaleramidase | KP78_RS10330 | |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | davD: glutarate semialdehyde dehydrogenase | KP78_RS01230 | KP78_RS12295 |
| lysine | davT: 5-aminovalerate aminotransferase | KP78_RS10035 | KP78_RS04910 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | KP78_RS12575 | KP78_RS12420 |
| lysine | gcdH: glutaryl-CoA dehydrogenase | KP78_RS05645 | KP78_RS05640 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| mannose | manA: mannose-6-phosphate isomerase | KP78_RS00900 | |
| mannose | manP: mannose PTS system, EII-CBA components | KP78_RS05465 | |
| myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | | |
| myoinositol | iolC: 5-dehydro-2-deoxy-D-gluconate kinase | KP78_RS01460 | |
| myoinositol | iolD: 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase | | |
| myoinositol | iolE: scyllo-inosose 2-dehydratase | KP78_RS06240 | |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | KP78_RS06250 | KP78_RS04825 |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | KP78_RS05700 | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| myoinositol | mmsA: malonate-semialdehyde dehydrogenase | KP78_RS13035 | KP78_RS01230 |
| 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 | KP78_RS13650 | KP78_RS16750 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | KP78_RS09045 | KP78_RS12595 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | KP78_RS18175 | KP78_RS14985 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | KP78_RS14985 | KP78_RS18175 |
| phenylacetate | paaK: phenylacetate-CoA ligase | KP78_RS16760 | KP78_RS09195 |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | KP78_RS16750 | KP78_RS12595 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylacetate | ppa: phenylacetate permease ppa | KP78_RS05035 | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | fahA: fumarylacetoacetate hydrolase | | |
| phenylalanine | hmgA: homogentisate dioxygenase | | |
| phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| phenylalanine | maiA: maleylacetoacetate isomerase | | |
| phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
| phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | | |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | KP78_RS15385 | KP78_RS10715 |
| propionate | putP: propionate transporter; proline:Na+ symporter | KP78_RS07580 | |
| putrescine | gabT: gamma-aminobutyrate transaminase | KP78_RS10035 | KP78_RS04910 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | KP78_RS17775 | KP78_RS04910 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | KP78_RS11775 | KP78_RS12295 |
| pyruvate | mctC: pyruvate symporter MctC | KP78_RS05035 | |
| 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 | rbsA: D-ribose ABC transporter, ATPase component RbsA | KP78_RS04870 | KP78_RS05680 |
| ribose | rbsB: D-ribose ABC transporter, substrate-binding component RbsB | KP78_RS04880 | |
| ribose | rbsC: D-ribose ABC transporter, permease component RbsC | KP78_RS04875 | KP78_RS05685 |
| serine | serP: L-serine permease SerP | | |
| sorbitol | sdh: sorbitol dehydrogenase | KP78_RS02335 | KP78_RS05185 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
| threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | KP78_RS15485 | KP78_RS15490 |
| threonine | ltaE: L-threonine aldolase | KP78_RS05785 | |
| threonine | tdcC: L-threonine:H+ symporter TdcC | | |
| trehalose | treC: trehalose-6-phosphate hydrolase | KP78_RS06445 | KP78_RS12070 |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | KP78_RS15755 | KP78_RS05640 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | KP78_RS12595 | KP78_RS13650 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | KP78_RS13035 | KP78_RS01230 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | KP78_RS12630 | KP78_RS01645 |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | KP78_RS15385 | KP78_RS10715 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | KP78_RS05465 | |
| xylose | xylA: xylose isomerase | | |
| xylose | xylB: xylulokinase | KP78_RS17820 | |
| 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