Potential Gaps in catabolism of small carbon sources in Verminephrobacter eiseniae EF01-2
Found 46 low-confidence and 33 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | VEIS_RS06105 | VEIS_RS02515 |
| 4-hydroxybenzoate | ligK: 4-oxalocitramalate aldolase | VEIS_RS07560 | VEIS_RS19305 |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| alanine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | VEIS_RS09160 | VEIS_RS02980 |
| arabinose | xacC: L-arabinono-1,4-lactonase | VEIS_RS04500 | VEIS_RS12530 |
| arginine | odc: L-ornithine decarboxylase | VEIS_RS16955 | |
| cellobiose | bgl: cellobiase | VEIS_RS04640 | |
| citrate | tctB: citrate/Na+ symporter, small transmembrane component TctB | | |
| citrate | tctC: citrate/Na+ symporter, substrate-binding component TctC | VEIS_RS01960 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | VEIS_RS01685 | VEIS_RS09705 |
| citrulline | arcC: carbamate kinase | | |
| citrulline | odc: L-ornithine decarboxylase | VEIS_RS16955 | |
| D-alanine | cycA: D-alanine:H+ symporter CycA | VEIS_RS13795 | |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
| D-serine | cycA: D-serine:H+ symporter CycA | VEIS_RS13795 | |
| D-serine | dsdA: D-serine ammonia-lyase | VEIS_RS02600 | VEIS_RS10515 |
| deoxyinosine | deoB: phosphopentomutase | | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | | |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | VEIS_RS03125 | |
| deoxyribose | deoP: deoxyribose transporter | | |
| galactose | dgoK: 2-dehydro-3-deoxygalactonokinase | | |
| galactose | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | VEIS_RS04500 | VEIS_RS07190 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | VEIS_RS13340 | |
| galacturonate | uxuL: D-galactaro-1,5-lactonase (UxuL or UxuF) | VEIS_RS12530 | VEIS_RS04500 |
| gluconate | gadh2: gluconate 2-dehydrogenase cytochrome c subunit | | |
| gluconate | gadh3: gluconate 2-dehydrogenase subunit 3 | VEIS_RS07775 | |
| gluconate | kguD: 2-keto-6-phosphogluconate reductase | VEIS_RS10120 | VEIS_RS06385 |
| gluconate | kguT: 2-ketogluconate transporter | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | VEIS_RS06790 | VEIS_RS13435 |
| glucosamine | SLC2A2: glucosamine transporter SLC2A2 | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | VEIS_RS18270 | VEIS_RS03120 |
| glutamate | gdhA: glutamate dehydrogenase, NAD-dependent | VEIS_RS08285 | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | VEIS_RS09880 | |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| lactose | dgoK: 2-dehydro-3-deoxygalactonokinase | | |
| lactose | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | VEIS_RS04500 | VEIS_RS07190 |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | | |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | VEIS_RS11830 | VEIS_RS16510 |
| lysine | davD: glutarate semialdehyde dehydrogenase | VEIS_RS19570 | VEIS_RS10490 |
| lysine | davT: 5-aminovalerate aminotransferase | VEIS_RS09290 | VEIS_RS15235 |
| lysine | fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase | VEIS_RS24060 | VEIS_RS08750 |
| lysine | hisM: L-lysine ABC transporter, permease component 1 (HisM) | VEIS_RS09420 | VEIS_RS01680 |
| lysine | hisP: L-lysine ABC transporter, ATPase component HisP | VEIS_RS01685 | VEIS_RS16195 |
| lysine | hisQ: L-lysine ABC transporter, permease component 2 (HisQ) | VEIS_RS09415 | VEIS_RS01675 |
| lysine | patA: cadaverine aminotransferase | VEIS_RS09290 | VEIS_RS08300 |
| maltose | susB: alpha-glucosidase (maltase) | | |
| mannitol | mt2d: mannitol 2-dehydrogenase | VEIS_RS15405 | VEIS_RS10145 |
| mannitol | mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE | VEIS_RS15425 | VEIS_RS16570 |
| mannitol | mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) | VEIS_RS15420 | VEIS_RS09190 |
| mannitol | mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) | VEIS_RS15415 | VEIS_RS09855 |
| mannitol | mtlK: polyol ABC transporter, ATP component MtlK/SmoG | VEIS_RS04665 | VEIS_RS21870 |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | VEIS_RS09040 | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | VEIS_RS06795 | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | VEIS_RS06790 | VEIS_RS13435 |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | VEIS_RS24060 | VEIS_RS08750 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | VEIS_RS18635 | VEIS_RS19085 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | iorAB: phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB | VEIS_RS18395 | VEIS_RS19805 |
| phenylalanine | paaH: 3-hydroxyadipyl-CoA dehydrogenase | VEIS_RS24060 | VEIS_RS08750 |
| phenylalanine | paaZ1: oxepin-CoA hydrolase | VEIS_RS18635 | VEIS_RS19085 |
| phenylalanine | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| sucrose | ams: sucrose hydrolase (invertase) | | |
| threonine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | VEIS_RS09160 | VEIS_RS02980 |
| thymidine | deoA: thymidine phosphorylase DeoA | | |
| thymidine | deoB: phosphopentomutase | | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | treF: trehalase | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | VEIS_RS17155 | VEIS_RS04310 |
| xylitol | xdhA: xylitol dehydrogenase | VEIS_RS17275 | VEIS_RS13060 |
| xylose | xylC: xylonolactonase | VEIS_RS12530 | VEIS_RS04500 |
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