Potential Gaps in catabolism of small carbon sources in Collimonas pratensis Ter91
Found 48 low-confidence and 35 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | pcaC: 4-carboxymuconolactone decarboxylase | CPter91_RS03290 | CPter91_RS00680 |
| 4-hydroxybenzoate | pcaH: protocatechuate 3,4-dioxygenase, alpha subunit | CPter91_RS03300 | CPter91_RS03305 |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | CPter91_RS05910 | |
| 4-hydroxybenzoate | pobA: 4-hydroxybenzoate 3-monooxygenase | | |
| alanine | TRIC: TRIC-type L-alanine transporter | CPter91_RS02645 | CPter91_RS06100 |
| arginine | rocE: L-arginine permease | | |
| arginine | rocF: arginase | CPter91_RS24995 | |
| cellobiose | bgl: cellobiase | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | CPter91_RS16520 | CPter91_RS22715 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | CPter91_RS17330 | CPter91_RS02010 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | CPter91_RS17330 | CPter91_RS16515 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | CPter91_RS04830 | CPter91_RS04835 |
| citrulline | arcC: carbamate kinase | | |
| D-alanine | cycA: D-alanine:H+ symporter CycA | | |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | CPter91_RS06370 | CPter91_RS09680 |
| deoxyinosine | deoB: phosphopentomutase | | |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | CPter91_RS07315 | CPter91_RS24970 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | CPter91_RS19920 | CPter91_RS09345 |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| galactose | dgoK: 2-dehydro-3-deoxygalactonokinase | CPter91_RS22765 | CPter91_RS14175 |
| galacturonate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | | |
| galacturonate | uxuL: D-galactaro-1,5-lactonase (UxuL or UxuF) | CPter91_RS04060 | CPter91_RS04875 |
| glucosamine | nagK: N-acetylglucosamine kinase | CPter91_RS15505 | CPter91_RS07255 |
| glucosamine | nagX: transmembrane glucosamine N-acetyltransferase NagX | CPter91_RS10035 | |
| glucosamine | SMc02869: N-acetylglucosamine ABC transporter, ATPase component | CPter91_RS15500 | CPter91_RS18465 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | garL: 5-dehydro-4-deoxy-D-glucarate aldolase | CPter91_RS10075 | CPter91_RS08085 |
| glucuronate | uxuL: D-glucaro-1,5-lactonase UxuL or UxuF | CPter91_RS04060 | CPter91_RS22845 |
| histidine | PA5504: L-histidine ABC transporter, permease component | CPter91_RS20975 | |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| lactose | dgoK: 2-dehydro-3-deoxygalactonokinase | CPter91_RS22765 | CPter91_RS14175 |
| lactose | lacP: lactose permease LacP | | |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| lysine | patA: cadaverine aminotransferase | CPter91_RS25065 | CPter91_RS23610 |
| lysine | patD: 5-aminopentanal dehydrogenase | CPter91_RS01785 | CPter91_RS18175 |
| maltose | susB: alpha-glucosidase (maltase) | | |
| mannitol | mt2d: mannitol 2-dehydrogenase | CPter91_RS18470 | CPter91_RS21865 |
| mannitol | mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE | CPter91_RS18445 | |
| mannitol | mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) | CPter91_RS18450 | |
| mannitol | mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) | CPter91_RS18455 | CPter91_RS10200 |
| mannitol | mtlK: polyol ABC transporter, ATP component MtlK/SmoG | CPter91_RS18465 | CPter91_RS01695 |
| NAG | nagK: N-acetylglucosamine kinase | CPter91_RS15505 | CPter91_RS07255 |
| NAG | SMc02869: N-acetylglucosamine ABC transporter, ATPase component | CPter91_RS15500 | CPter91_RS18465 |
| 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 | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | CPter91_RS02885 | CPter91_RS03835 |
| phenylacetate | paaK: phenylacetate-CoA ligase | | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | CPter91_RS02965 | CPter91_RS02885 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | CPter91_RS14485 | |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | CPter91_RS01775 | CPter91_RS19620 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | CPter91_RS18175 | CPter91_RS25040 |
| putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | CPter91_RS03560 | |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | CPter91_RS19730 | CPter91_RS21865 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase | CPter91_RS24970 | CPter91_RS10730 |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| sucrose | ams: sucrose hydrolase (invertase) | | |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | CPter91_RS04940 | CPter91_RS04935 |
| threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | CPter91_RS17570 | CPter91_RS07560 |
| threonine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | CPter91_RS17565 | CPter91_RS10935 |
| threonine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | CPter91_RS10935 | CPter91_RS17560 |
| thymidine | deoA: thymidine phosphorylase DeoA | CPter91_RS05835 | |
| thymidine | deoB: phosphopentomutase | | |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | CPter91_RS02960 | CPter91_RS24540 |
| valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | CPter91_RS17570 | CPter91_RS07560 |
| valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | CPter91_RS04940 | CPter91_RS04935 |
| valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | CPter91_RS17565 | CPter91_RS07555 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | CPter91_RS08550 | CPter91_RS19755 |
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