Potential Gaps in catabolism of small carbon sources in Bacillus horneckiae 1P01SC
Found 91 low-confidence and 42 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | Psest_0084: 2-oxoglutarate TRAP transporter, fused 4TM/12TM components | CWS20_RS15130 | CWS20_RS16195 |
| 2-oxoglutarate | Psest_0085: 2-oxoglutarate TRAP transporter, solute receptor component | CWS20_RS15120 | CWS20_RS18075 |
| 4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | CWS20_RS24275 | CWS20_RS24270 |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | CWS20_RS20970 | |
| 4-hydroxybenzoate | pobA: 4-hydroxybenzoate 3-monooxygenase | | |
| 4-hydroxybenzoate | praA: protocatechuate 2,3-dioxygenase | | |
| acetate | actP: cation/acetate symporter ActP | CWS20_RS18950 | |
| 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 | cbp: cellobiose phosphorylase | | |
| cellobiose | cdt: cellobiose transporter cdt-1/cdt-2 | | |
| citrate | citM: citrate:cation:H+ symporter CitM | CWS20_RS08370 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | CWS20_RS25265 | CWS20_RS13430 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | CWS20_RS25260 | CWS20_RS06310 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | CWS20_RS25260 | CWS20_RS18615 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | CWS20_RS25255 | CWS20_RS13420 |
| citrulline | arcC: carbamate kinase | | |
| D-alanine | cycA: D-alanine:H+ symporter CycA | CWS20_RS24220 | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-serine | cycA: D-serine:H+ symporter CycA | CWS20_RS24220 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | CWS20_RS27195 | CWS20_RS01530 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fucose | aldA: lactaldehyde dehydrogenase | CWS20_RS10330 | CWS20_RS13150 |
| 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 | | |
| galacturonate | uxaA: D-altronate dehydratase | CWS20_RS14035 | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | CWS20_RS26950 | |
| glucose | MFS-glucose: glucose transporter, MFS superfamily | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | garL: 5-dehydro-4-deoxy-D-glucarate aldolase | | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| histidine | PA5503: L-histidine ABC transporter, ATPase component | CWS20_RS16280 | CWS20_RS11520 |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | CWS20_RS14685 | CWS20_RS14680 |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | CWS20_RS25225 | CWS20_RS05470 |
| 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) | | |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | CWS20_RS25225 | CWS20_RS05470 |
| leucine | liuA: isovaleryl-CoA dehydrogenase | CWS20_RS11290 | CWS20_RS14685 |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | CWS20_RS25120 | CWS20_RS21840 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | CWS20_RS26305 | CWS20_RS09920 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | CWS20_RS21850 | CWS20_RS25290 |
| lysine | cadA: lysine decarboxylase | CWS20_RS12350 | |
| lysine | davD: glutarate semialdehyde dehydrogenase | CWS20_RS10330 | CWS20_RS24280 |
| lysine | davT: 5-aminovalerate aminotransferase | CWS20_RS20380 | CWS20_RS14815 |
| lysine | gcdH: glutaryl-CoA dehydrogenase | CWS20_RS19005 | CWS20_RS14680 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| lysine | patA: cadaverine aminotransferase | CWS20_RS20380 | CWS20_RS16520 |
| lysine | patD: 5-aminopentanal dehydrogenase | CWS20_RS13150 | CWS20_RS10330 |
| maltose | MAL11: maltose permease | | |
| mannitol | mtlA: mannitol phosphotransferase system, EII-CBA components | | |
| mannitol | mtlD: mannitol-1-phosphate 5-dehydrogenase | | |
| mannose | manA: mannose-6-phosphate isomerase | | |
| mannose | manP: mannose PTS system, EII-CBA components | CWS20_RS04945 | |
| 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 | CWS20_RS23655 | |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | CWS20_RS14645 | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | CWS20_RS26950 | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| 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 | CWS20_RS08920 | CWS20_RS04890 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | CWS20_RS01265 | CWS20_RS25770 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | CWS20_RS01265 | CWS20_RS04885 |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | CWS20_RS03965 | CWS20_RS25745 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylacetate | ppa: phenylacetate permease ppa | CWS20_RS18950 | |
| phenylalanine | livF: L-phenylalanine ABC transporter, ATPase component 1 (LivF) | CWS20_RS00560 | CWS20_RS12840 |
| phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | CWS20_RS00575 | CWS20_RS12825 |
| phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | CWS20_RS00580 | |
| phenylalanine | livM: L-phenylalanine ABC transporter, permease component 2 (LivM) | CWS20_RS12830 | CWS20_RS00570 |
| phenylalanine | maiA: maleylacetoacetate isomerase | | |
| phenylalanine | PAH: phenylalanine 4-monooxygenase | CWS20_RS03265 | |
| phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | CWS20_RS04670 | |
| propionate | prpE: propionyl-CoA synthetase | CWS20_RS16265 | CWS20_RS23850 |
| putrescine | gabD: succinate semialdehyde dehydrogenase | CWS20_RS10330 | CWS20_RS13150 |
| putrescine | gabT: gamma-aminobutyrate transaminase | CWS20_RS23900 | CWS20_RS20380 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | CWS20_RS23900 | CWS20_RS20860 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | CWS20_RS10330 | CWS20_RS13150 |
| pyruvate | mctC: pyruvate symporter MctC | CWS20_RS18950 | |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | CWS20_RS02995 | CWS20_RS09090 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | CWS20_RS14035 | |
| rhamnose | LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase | CWS20_RS26225 | CWS20_RS04045 |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsA: D-ribose ABC transporter, ATPase component RbsA | CWS20_RS04520 | CWS20_RS15540 |
| ribose | rbsB: D-ribose ABC transporter, substrate-binding component RbsB | CWS20_RS04530 | |
| ribose | rbsC: D-ribose ABC transporter, permease component RbsC | CWS20_RS04525 | CWS20_RS15535 |
| sorbitol | scrK: fructokinase | CWS20_RS20735 | CWS20_RS24110 |
| sorbitol | sdh: sorbitol dehydrogenase | CWS20_RS01290 | CWS20_RS27175 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
| sucrose | ams: sucrose hydrolase (invertase) | CWS20_RS23670 | CWS20_RS17885 |
| threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | CWS20_RS10995 | CWS20_RS11000 |
| trehalose | PsTP: trehalose phosphorylase | | |
| trehalose | TRET1: facilitated trehalose transporter Tret1 | | |
| tryptophan | mhpD: 2-hydroxypentadienoate hydratase | CWS20_RS24275 | CWS20_RS24270 |
| tryptophan | nbaE: 2-aminomuconate 6-semialdehyde dehydrogenase | CWS20_RS24280 | CWS20_RS04070 |
| tryptophan | nbaF: 2-aminomuconate deaminase | CWS20_RS11805 | CWS20_RS18330 |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | CWS20_RS14685 | CWS20_RS14680 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | CWS20_RS09920 | CWS20_RS08920 |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | CWS20_RS25225 | CWS20_RS05470 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | CWS20_RS13930 | CWS20_RS26700 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | CWS20_RS04945 | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | CWS20_RS01290 | CWS20_RS27175 |
| xylose | xylA: xylose isomerase | | |
| xylose | xylB: xylulokinase | CWS20_RS24865 | |
| 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