Potential Gaps in catabolism of small carbon sources in Sporolactobacillus vineae SL153
Found 104 low-confidence and 43 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 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 | xylF: 2-hydroxymuconate semialdehyde hydrolase | | |
| acetate | actP: cation/acetate symporter ActP | RH97_RS08865 | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | RH97_RS04785 | |
| arginine | gabD: succinate semialdehyde dehydrogenase | RH97_RS06550 | RH97_RS05970 |
| arginine | patA: putrescine aminotransferase (PatA/SpuC) | RH97_RS10690 | RH97_RS02445 |
| arginine | patD: gamma-aminobutyraldehyde dehydrogenase | RH97_RS02580 | RH97_RS06550 |
| arginine | rocE: L-arginine permease | RH97_RS02150 | RH97_RS12570 |
| cellobiose | bgl: cellobiase | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | RH97_RS08095 | RH97_RS07910 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | RH97_RS02560 | |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | RH97_RS02560 | RH97_RS08090 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | RH97_RS08085 | |
| citrulline | citrullinase: putative citrullinase | RH97_RS09270 | |
| citrulline | rocA: 1-pyrroline-5-carboxylate dehydrogenase | RH97_RS02580 | RH97_RS06770 |
| citrulline | rocD: ornithine aminotransferase | RH97_RS08100 | RH97_RS02445 |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | RH97_RS04705 | RH97_RS03700 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoK: deoxyribokinase | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fructose | levDE: fructose PTS system (fructose 6-phosphate forming), EII-AB component | RH97_RS02405 | |
| fructose | levF: fructose PTS system (fructose 6-phosphate forming), EII-C component | RH97_RS02400 | RH97_RS10975 |
| fructose | levG: fructose PTS system (fructose 6-phosphate forming), EII-D component | RH97_RS02395 | RH97_RS10980 |
| fucose | aldA: lactaldehyde dehydrogenase | RH97_RS02580 | RH97_RS06550 |
| 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 | RH97_RS04785 | |
| galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| galacturonate | dopDH: 2,5-dioxopentanonate dehydrogenase | RH97_RS06550 | RH97_RS05000 |
| 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 | | |
| 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 | garR: tartronate semialdehyde reductase | RH97_RS02125 | RH97_RS06075 |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| histidine | PA5503: L-histidine ABC transporter, ATPase component | RH97_RS08020 | RH97_RS05715 |
| histidine | PA5505: L-histidine ABC transporter, substrate-binding component | RH97_RS05705 | RH97_RS08015 |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | RH97_RS08905 | |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | RH97_RS10585 | RH97_RS04110 |
| isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | RH97_RS08930 | RH97_RS07390 |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | RH97_RS03700 | RH97_RS10960 |
| isoleucine | prpC: 2-methylcitrate synthase | RH97_RS00850 | |
| lactose | galK: galactokinase (-1-phosphate forming) | | |
| lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| lactose | lacP: lactose permease LacP | | |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | RH97_RS10585 | RH97_RS04110 |
| leucine | liuA: isovaleryl-CoA dehydrogenase | RH97_RS08905 | |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | RH97_RS09550 | RH97_RS08700 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | RH97_RS08930 | RH97_RS07390 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | | |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| lysine | davA: 5-aminovaleramidase | RH97_RS09110 | RH97_RS09270 |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | davD: glutarate semialdehyde dehydrogenase | RH97_RS06550 | RH97_RS02580 |
| lysine | glaH: glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD) | | |
| maltose | malI: maltose transporter | RH97_RS10790 | |
| 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 | | |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | | |
| 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 | RH97_RS08930 | RH97_RS07390 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | RH97_RS08930 | RH97_RS07390 |
| phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | RH97_RS08935 | RH97_RS05205 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | RH97_RS08940 | RH97_RS04710 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | RH97_RS08940 | RH97_RS04710 |
| phenylacetate | paaK: phenylacetate-CoA ligase | RH97_RS07385 | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | RH97_RS08930 | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | RH97_RS12640 | RH97_RS11340 |
| 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 | | |
| proline | proY: proline:H+ symporter | RH97_RS11340 | RH97_RS12640 |
| proline | put1: proline dehydrogenase | | |
| proline | putA: L-glutamate 5-semialdeyde dehydrogenase | RH97_RS02580 | RH97_RS06770 |
| propionate | lctP: propionate permease | RH97_RS07375 | |
| propionate | prpC: 2-methylcitrate synthase | RH97_RS00850 | |
| propionate | prpE: propionyl-CoA synthetase | RH97_RS04870 | RH97_RS04695 |
| putrescine | gabD: succinate semialdehyde dehydrogenase | RH97_RS06550 | RH97_RS05970 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | RH97_RS10690 | RH97_RS02445 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | RH97_RS02580 | RH97_RS06550 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| pyruvate | mctC: pyruvate symporter MctC | RH97_RS08865 | |
| rhamnose | aldA: lactaldehyde dehydrogenase | RH97_RS02580 | RH97_RS06550 |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | RH97_RS03700 | RH97_RS09595 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | | |
| rhamnose | LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase | | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsK: ribokinase | | |
| ribose | rbsU: probable D-ribose transporter RbsU | RH97_RS08635 | |
| serine | serP: L-serine permease SerP | RH97_RS12560 | RH97_RS12640 |
| threonine | prpC: 2-methylcitrate synthase | RH97_RS00850 | |
| threonine | tdcB: L-threonine dehydratase | RH97_RS06685 | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | thuE: trehalose ABC transporter, substrate-binding component ThuE | RH97_RS07355 | |
| trehalose | thuK: trehalose ABC transporter, ATPase component ThuK | RH97_RS12055 | RH97_RS01755 |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | RH97_RS12640 | RH97_RS12560 |
| tyrosine | fahA: fumarylacetoacetate hydrolase | | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | RH97_RS08905 | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | RH97_RS08930 | |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | RH97_RS10585 | RH97_RS04110 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | RH97_RS02125 | RH97_RS06075 |
| valine | prpC: 2-methylcitrate synthase | RH97_RS00850 | |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | RH97_RS05185 | RH97_RS13340 |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | RH97_RS07450 | |
| xylose | xylA: xylose isomerase | | |
| xylose | xylB: xylulokinase | | |
| xylose | xylT: D-xylose transporter | RH97_RS04785 | |
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