Potential Gaps in catabolism of small carbon sources in Bacillus okhensis Kh10-101
Found 68 low-confidence and 43 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 | LQ50_RS19920 | LQ50_RS04695 |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| acetate | actP: cation/acetate symporter ActP | LQ50_RS18325 | |
| arginine | bgtB: L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) | | |
| citrate | citM: citrate:cation:H+ symporter CitM | LQ50_RS19660 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | LQ50_RS00390 | LQ50_RS02930 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | LQ50_RS00395 | |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | LQ50_RS00395 | |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | LQ50_RS24565 | |
| citrulline | citrullinase: putative citrullinase | LQ50_RS10825 | |
| D-alanine | cycA: D-alanine:H+ symporter CycA | | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | D-LDH: D-lactate dehydrogenase | LQ50_RS13735 | LQ50_RS09640 |
| D-lactate | larD: D,L-lactic acid transporter | LQ50_RS14610 | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | LQ50_RS19725 | LQ50_RS09165 |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | LQ50_RS07860 | LQ50_RS14895 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | LQ50_RS14880 | LQ50_RS05305 |
| deoxyribose | deoP: deoxyribose transporter | | |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | LQ50_RS02720 | LQ50_RS18960 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | | |
| glucosamine | nagPcb: N-acetylglucosamine phosphotransferase system, EII-CB component NagP | LQ50_RS03430 | LQ50_RS06805 |
| glucosamine | nagX: transmembrane glucosamine N-acetyltransferase NagX | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | uxuB: D-mannonate dehydrogenase | | |
| histidine | PA5503: L-histidine ABC transporter, ATPase component | LQ50_RS02930 | LQ50_RS00035 |
| histidine | PA5505: L-histidine ABC transporter, substrate-binding component | LQ50_RS00040 | LQ50_RS02920 |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | LQ50_RS17965 | LQ50_RS15570 |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | LQ50_RS13820 | LQ50_RS06600 |
| isoleucine | brnQ: L-isoleucine:cation symporter BrnQ/BraZ/BraB | LQ50_RS14475 | LQ50_RS07840 |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | LQ50_RS07860 | LQ50_RS14895 |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | LQ50_RS13935 | LQ50_RS15565 |
| L-lactate | SfMCT: L-lactate transporter SfMCT | LQ50_RS14640 | LQ50_RS09895 |
| lactose | lacP: lactose permease LacP | | |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | LQ50_RS13820 | LQ50_RS06600 |
| leucine | brnQ: L-leucine:Na+ symporter BrnQ/BraB | LQ50_RS14475 | LQ50_RS07840 |
| leucine | liuA: isovaleryl-CoA dehydrogenase | LQ50_RS15570 | LQ50_RS17965 |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | LQ50_RS13935 | LQ50_RS15565 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | LQ50_RS15545 | LQ50_RS20175 |
| lysine | davA: 5-aminovaleramidase | LQ50_RS03445 | |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | LQ50_RS15550 | LQ50_RS05955 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | | |
| lysine | gcdH: glutaryl-CoA dehydrogenase | LQ50_RS17965 | LQ50_RS15570 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| mannose | manA: mannose-6-phosphate isomerase | LQ50_RS20965 | |
| mannose | manP: mannose PTS system, EII-CBA components | LQ50_RS03465 | |
| myoinositol | PS417_11895: myo-inositol ABC transporter, permease component | LQ50_RS06900 | LQ50_RS02730 |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | | |
| NAG | nagPcb: N-acetylglucosamine phosphotransferase system, EII-CB component NagP | LQ50_RS03430 | LQ50_RS06805 |
| 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 | LQ50_RS05955 | LQ50_RS15550 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | LQ50_RS18060 | LQ50_RS05955 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | LQ50_RS11705 | LQ50_RS04800 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | LQ50_RS11705 | LQ50_RS19530 |
| phenylacetate | paaK: phenylacetate-CoA ligase | LQ50_RS05970 | LQ50_RS05965 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| 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 | LQ50_RS08080 | |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | LQ50_RS13935 | LQ50_RS15565 |
| propionate | prpE: propionyl-CoA synthetase | LQ50_RS12660 | LQ50_RS00925 |
| propionate | putP: propionate transporter; proline:Na+ symporter | LQ50_RS04230 | |
| putrescine | gabT: gamma-aminobutyrate transaminase | LQ50_RS13745 | LQ50_RS03535 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | LQ50_RS03535 | LQ50_RS17375 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | LQ50_RS22865 | LQ50_RS10540 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| pyruvate | yjcH: putative small subunit of pyruvate transporter (yjcH-like) | | |
| rhamnose | rhaA: L-rhamnose isomerase | | |
| rhamnose | rhaB: L-rhamnulokinase | LQ50_RS02715 | |
| rhamnose | rhaM: L-rhamnose mutarotase | | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsB: D-ribose ABC transporter, substrate-binding component RbsB | LQ50_RS02425 | LQ50_RS06910 |
| ribose | rbsC: D-ribose ABC transporter, permease component RbsC | LQ50_RS06900 | LQ50_RS02730 |
| serine | serP: L-serine permease SerP | | |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | LQ50_RS13580 | |
| threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | LQ50_RS21920 | LQ50_RS21925 |
| threonine | tdcC: L-threonine:H+ symporter TdcC | | |
| trehalose | treF: trehalase | LQ50_RS21555 | LQ50_RS06810 |
| tryptophan | antA: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA | | |
| tryptophan | antB: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB | | |
| tryptophan | antC: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC | | |
| tryptophan | tnaT: tryptophan:Na+ symporter TnaT | LQ50_RS04625 | LQ50_RS15590 |
| 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 | LQ50_RS17965 | LQ50_RS15570 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | LQ50_RS18060 | |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | LQ50_RS13820 | LQ50_RS06600 |
| valine | brnQ: L-valine:cation symporter BrnQ/BraZ/BraB | LQ50_RS14475 | LQ50_RS07840 |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | LQ50_RS15550 | LQ50_RS05955 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | LQ50_RS06530 | LQ50_RS18900 |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | LQ50_RS13935 | LQ50_RS15565 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | LQ50_RS03465 | |
| xylose | aldA: (glycol)aldehyde dehydrogenase | LQ50_RS13740 | LQ50_RS17640 |
| xylose | xylC: xylonolactonase | LQ50_RS19655 | |
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