Potential Gaps in catabolism of small carbon sources in Phyllobacterium endophyticum PEPV15
Found 38 low-confidence and 34 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 | CU100_RS13180 | |
| 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 | CU100_RS13995 | CU100_RS00640 |
| alanine | TRIC: TRIC-type L-alanine transporter | CU100_RS02180 | |
| arabinose | xacD: L-arabinonate dehydratase | CU100_RS02465 | CU100_RS21080 |
| asparagine | ans: asparaginase | CU100_RS08655 | CU100_RS07075 |
| cellobiose | cbp: cellobiose phosphorylase | | |
| citrate | tctB: citrate/Na+ symporter, small transmembrane component TctB | | |
| citrate | tctC: citrate/Na+ symporter, substrate-binding component TctC | CU100_RS04020 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | CU100_RS15815 | CU100_RS15890 |
| D-alanine | AZOBR_RS08260: D-alanine ABC transporter, substrate-binding component | CU100_RS00295 | CU100_RS21275 |
| 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 | CU100_RS26205 | CU100_RS02855 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| ethanol | etoh-dh-nad: ethanol dehydrogenase (NAD(P)) | CU100_RS17315 | CU100_RS15645 |
| galactose | dgoD: D-galactonate dehydratase | CU100_RS02465 | CU100_RS14730 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | uxaA: D-altronate dehydratase | CU100_RS01955 | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | CU100_RS01925 | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | dctQ: D-glucuronate TRAP transporter, small permease component | CU100_RS19465 | |
| glucuronate | uxaC: D-glucuronate isomerase | CU100_RS01925 | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | CU100_RS07895 | CU100_RS07860 |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| lactose | dgoD: D-galactonate dehydratase | CU100_RS02465 | CU100_RS14730 |
| lactose | lacP: lactose permease LacP | | |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | CU100_RS02565 | CU100_RS04335 |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| lysine | hisP: L-lysine ABC transporter, ATPase component HisP | CU100_RS15815 | CU100_RS15890 |
| lysine | lysN: 2-aminoadipate transaminase | CU100_RS21000 | CU100_RS17540 |
| lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | CU100_RS06445 | CU100_RS26250 |
| maltose | susB: alpha-glucosidase (maltase) | CU100_RS19730 | CU100_RS19680 |
| mannitol | mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) | CU100_RS03035 | CU100_RS22610 |
| mannose | man-isomerase: D-mannose isomerase | CU100_RS07035 | |
| 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 | CU100_RS04335 | CU100_RS06475 |
| phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | CU100_RS04880 | CU100_RS23280 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | CU100_RS00240 | CU100_RS04875 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | CU100_RS00240 | CU100_RS04875 |
| phenylacetate | paaK: phenylacetate-CoA ligase | | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | CU100_RS04335 | CU100_RS10670 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | CU100_RS00320 | CU100_RS24600 |
| phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | CU100_RS00295 | CU100_RS21275 |
| phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | CU100_RS21790 | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | | |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | CU100_RS05565 | |
| putrescine | puuB: gamma-glutamylputrescine oxidase | CU100_RS05520 | CU100_RS15510 |
| putrescine | puuC: gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase | CU100_RS25865 | CU100_RS24675 |
| serine | snatA: L-serine transporter | CU100_RS11920 | |
| sucrose | ams: sucrose hydrolase (invertase) | CU100_RS19680 | CU100_RS19730 |
| threonine | snatA: L-threonine transporter snatA | CU100_RS11920 | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | treF: trehalase | CU100_RS19680 | CU100_RS19730 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | CU100_RS07895 | CU100_RS07860 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | CU100_RS00345 | CU100_RS08050 |
| xylitol | Dshi_0546: xylitol ABC transporter, ATPase component | CU100_RS03040 | CU100_RS19250 |
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