Potential Gaps in catabolism of small carbon sources in Bacillus coahuilensis m4-4
Found 136 low-confidence and 41 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | Psest_0085: 2-oxoglutarate TRAP transporter, solute receptor component | M44_RS10455 | |
| 4-hydroxybenzoate | adh: acetaldehyde dehydrogenase (not acylating) | M44_RS14855 | M44_RS16260 |
| 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 | praB: 2-hydroxymuconate 6-semialdehyde dehydrogenase | M44_RS04450 | M44_RS14855 |
| 4-hydroxybenzoate | praD: 2-oxohex-3-enedioate decarboxylase | | |
| acetate | satP: acetate/proton symporter satP | M44_RS17885 | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | chvE: L-arabinose ABC transporter, substrate-binding component ChvE | M44_RS14675 | |
| arginine | bgtB: L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) | | |
| arginine | putA: L-glutamate 5-semialdeyde dehydrogenase | M44_RS04450 | M44_RS16260 |
| asparagine | agcS: Probable asparagine:Na+ symporter AgcS | M44_RS04855 | M44_RS08680 |
| asparagine | ans: asparaginase | M44_RS05115 | |
| aspartate | glt: aspartate:proton symporter Glt | | |
| citrate | acn: aconitase | | |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | M44_RS04570 | M44_RS17840 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | M44_RS04565 | M44_RS17865 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | M44_RS17835 | M44_RS04565 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| citrulline | citrullinase: putative citrullinase | | |
| citrulline | putA: L-glutamate 5-semialdeyde dehydrogenase | M44_RS04450 | M44_RS16260 |
| D-alanine | cycA: D-alanine:H+ symporter CycA | | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | D-LDH: D-lactate dehydrogenase | M44_RS16615 | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | | |
| deoxyinosine | adh: acetaldehyde dehydrogenase (not acylating) | M44_RS14855 | M44_RS16260 |
| deoxyribonate | atoA: acetoacetyl-CoA transferase, A subunit | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | M44_RS05005 | |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | garK: glycerate 2-kinase | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | adh: acetaldehyde dehydrogenase (not acylating) | M44_RS14855 | M44_RS16260 |
| deoxyribose | deoK: deoxyribokinase | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| ethanol | adh: acetaldehyde dehydrogenase (not acylating) | M44_RS14855 | M44_RS16260 |
| fructose | Slc2a5: fructose:H+ symporter | | |
| fucose | aldA: lactaldehyde dehydrogenase | M44_RS04450 | M44_RS06330 |
| 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 | | |
| fumarate | Dshi_1195: TRAP transporter for succinate, fumarate, L-malate, and 2-oxoglutarate, substrate-binding component | | |
| galactose | chvE: galactose ABC transporter, substrate-binding component ChvE | M44_RS14675 | |
| galactose | galE: UDP-glucose 4-epimerase | M44_RS16710 | M44_RS15595 |
| galactose | galK: galactokinase (-1-phosphate forming) | | |
| galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| galacturonate | dopDH: 2,5-dioxopentanonate dehydrogenase | M44_RS14855 | M44_RS04450 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | gci: D-galactarolactone cycloisomerase | | |
| galacturonate | gli: D-galactarolactone isomerase | | |
| galacturonate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | | |
| galacturonate | udh: D-galacturonate dehydrogenase | | |
| gluconate | gntK: D-gluconate kinase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | M44_RS03225 | M44_RS18445 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | dopDH: 2,5-dioxopentanonate dehydrogenase | M44_RS14855 | M44_RS04450 |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
| glucuronate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| glutamate | gltS: L-glutamate:Na+ symporter GltS | | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | | |
| glycerol | glpF: glycerol facilitator glpF | | |
| glycerol | glpK: glycerol kinase | | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
| histidine | PA5503: L-histidine ABC transporter, ATPase component | M44_RS16460 | M44_RS14780 |
| histidine | PA5505: L-histidine ABC transporter, substrate-binding component | M44_RS16470 | M44_RS14285 |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | M44_RS16995 | M44_RS17000 |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | M44_RS05005 | M44_RS07285 |
| isoleucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | M44_RS10915 | |
| isoleucine | pccB: propionyl-CoA carboxylase, beta subunit | | |
| L-malate | Dshi_1195: TRAP transporter for succinate, fumarate, L-malate, and 2-oxoglutarate, substrate-binding component | | |
| lactose | galE: UDP-glucose 4-epimerase | M44_RS16710 | M44_RS15595 |
| 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) | M44_RS14320 | |
| leucine | atoA: acetoacetyl-CoA transferase, A subunit | | |
| leucine | ilvE: L-leucine transaminase | M44_RS00340 | M44_RS14625 |
| leucine | liuA: isovaleryl-CoA dehydrogenase | M44_RS16995 | M44_RS17000 |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | M44_RS10915 | |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | M44_RS04960 | M44_RS04440 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | | |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| leucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| lysine | davA: 5-aminovaleramidase | M44_RS04225 | |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | davT: 5-aminovalerate aminotransferase | M44_RS13910 | M44_RS22870 |
| lysine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | M44_RS04440 | M44_RS12670 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | | |
| lysine | gcdH: glutaryl-CoA dehydrogenase | M44_RS17000 | M44_RS16995 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| mannitol | mt2d: mannitol 2-dehydrogenase | M44_RS07285 | M44_RS05005 |
| mannitol | PLT5: polyol transporter PLT5 | | |
| mannose | man-isomerase: D-mannose isomerase | | |
| mannose | STP6: mannose:H+ symporter | | |
| myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | | |
| myoinositol | iolC: 5-dehydro-2-deoxy-D-gluconate kinase | M44_RS01700 | |
| 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 | | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| myoinositol | mmsA: malonate-semialdehyde dehydrogenase | M44_RS14855 | M44_RS04450 |
| 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 | M44_RS04440 | M44_RS12670 |
| phenylacetate | paaK: phenylacetate-CoA ligase | | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | M44_RS04445 | M44_RS04440 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | iorAB: phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB | | |
| phenylalanine | paaA: phenylacetyl-CoA 1,2-epoxidase, subunit A | | |
| phenylalanine | paaB: phenylacetyl-CoA 1,2-epoxidase, subunit B | | |
| phenylalanine | paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C | | |
| phenylalanine | paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E | | |
| phenylalanine | paaF: 2,3-dehydroadipyl-CoA hydratase | M44_RS04440 | M44_RS12670 |
| phenylalanine | paaZ1: oxepin-CoA hydrolase | M44_RS04445 | M44_RS04440 |
| phenylalanine | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| proline | putA: L-glutamate 5-semialdeyde dehydrogenase | M44_RS04450 | M44_RS16260 |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | M44_RS10915 | |
| propionate | pccB: propionyl-CoA carboxylase, beta subunit | | |
| putrescine | gabT: gamma-aminobutyrate transaminase | M44_RS13910 | M44_RS03565 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | M44_RS13910 | |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | M44_RS04450 | M44_RS14855 |
| pyruvate | SLC5A8: sodium-coupled pyruvate transporter | | |
| rhamnose | aldA: lactaldehyde dehydrogenase | M44_RS04450 | M44_RS06330 |
| 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 | serP: L-serine permease SerP | | |
| sorbitol | sdh: sorbitol dehydrogenase | M44_RS07285 | M44_RS05005 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
| succinate | satP: succinate:H+ symporter SatP | M44_RS17885 | |
| threonine | aldA: lactaldehyde dehydrogenase | M44_RS04450 | M44_RS06330 |
| threonine | tdcC: L-threonine:H+ symporter TdcC | | |
| threonine | tynA: aminoacetone oxidase | | |
| thymidine | adh: acetaldehyde dehydrogenase (not acylating) | M44_RS14855 | M44_RS16260 |
| thymidine | deoA: thymidine phosphorylase DeoA | M44_RS26570 | |
| trehalose | treC: trehalose-6-phosphate hydrolase | M44_RS15400 | M44_RS01580 |
| tryptophan | tnaA: tryptophanase | | |
| tryptophan | tnaT: tryptophan:Na+ symporter TnaT | M44_RS16560 | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | atoA: acetoacetyl-CoA transferase, A subunit | | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | M44_RS16995 | M44_RS17000 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | M44_RS04440 | M44_RS13525 |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | M44_RS04440 | M44_RS12670 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | M44_RS14855 | M44_RS16260 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | M44_RS12690 | |
| valine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | M44_RS10915 | |
| valine | pccB: propionyl-CoA carboxylase, beta subunit | | |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | | |
| xylose | xylA: xylose isomerase | | |
| xylose | xylB: xylulokinase | | |
| xylose | xylF: ABC transporter for xylose, substrate binding component xylF | M44_RS14675 | |
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.
Links
Downloads
Related tools
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