Potential Gaps in catabolism of small carbon sources in Martelella endophytica YC6887
Found 75 low-confidence and 37 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | TM49_RS04715 | TM49_RS09420 |
| 4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | | |
| 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 | TM49_RS13160 | |
| arginine | artQ: L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) | TM49_RS20670 | TM49_RS20475 |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | TM49_RS20670 | TM49_RS20475 |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-alanine | Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component | TM49_RS13135 | TM49_RS04330 |
| D-alanine | Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component | TM49_RS13120 | TM49_RS04315 |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | | |
| deoxyinosine | H281DRAFT_01112: deoxynucleoside transporter, permease component 2 | TM49_RS19230 | TM49_RS07030 |
| deoxyinosine | H281DRAFT_01114: deoxynucleoside transporter, substrate-binding component | TM49_RS07020 | |
| deoxyinosine | H281DRAFT_01115: deoxynucleoside transporter, permease component 1 | TM49_RS19225 | TM49_RS07030 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | TM49_RS22215 | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fructose | Slc2a5: fructose:H+ symporter | TM49_RS02240 | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | uxaA: D-altronate dehydratase | TM49_RS08990 | |
| galacturonate | uxaB: tagaturonate reductase | TM49_RS10800 | |
| galacturonate | uxaC: D-galacturonate isomerase | TM49_RS09030 | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | dctQ: D-glucuronate TRAP transporter, small permease component | | |
| glucuronate | uxaC: D-glucuronate isomerase | TM49_RS09030 | |
| glycerol | glpF: glycerol facilitator glpF | TM49_RS08265 | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | | |
| isoleucine | Bap2: L-isoleucine permease Bap2 | | |
| isoleucine | dddA: 3-hydroxypropionate dehydrogenase | TM49_RS09715 | TM49_RS05230 |
| isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | TM49_RS17850 | TM49_RS05305 |
| isoleucine | hpcD: 3-hydroxypropionyl-CoA dehydratase | TM49_RS05305 | |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | TM49_RS14630 | TM49_RS20405 |
| isoleucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| isoleucine | pco: propanyl-CoA oxidase | | |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| L-malate | sdlC: L-malate:Na+ symporter SdlC | | |
| leucine | liuA: isovaleryl-CoA dehydrogenase | TM49_RS21420 | |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | TM49_RS02775 | TM49_RS04790 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | TM49_RS05305 | |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | | |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| leucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| lysine | cadA: lysine decarboxylase | TM49_RS08385 | TM49_RS14505 |
| lysine | glaH: glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD) | | |
| lysine | hisM: L-lysine ABC transporter, permease component 1 (HisM) | TM49_RS20675 | TM49_RS12400 |
| lysine | hisP: L-lysine ABC transporter, ATPase component HisP | TM49_RS20660 | TM49_RS13120 |
| lysine | hisQ: L-lysine ABC transporter, permease component 2 (HisQ) | TM49_RS20670 | TM49_RS20475 |
| lysine | lhgD: L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) | | |
| lysine | patA: cadaverine aminotransferase | TM49_RS08400 | TM49_RS08275 |
| mannitol | mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) | TM49_RS05365 | TM49_RS02475 |
| mannose | STP6: mannose:H+ symporter | TM49_RS02240 | |
| NAG | nagK: N-acetylglucosamine kinase | TM49_RS01780 | TM49_RS02435 |
| NAG | SMc02871: N-acetylglucosamine ABC transporter, permease component 2 | TM49_RS06895 | TM49_RS12245 |
| NAG | SMc02872: N-acetylglucosamine ABC transporter, permease component 1 | TM49_RS06900 | TM49_RS12615 |
| NAG | SMc02873: N-acetylglucosamine ABC transporter, substrate-binding component | | |
| 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 | TM49_RS05305 | |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | TM49_RS05305 | |
| phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | TM49_RS17850 | TM49_RS08775 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | TM49_RS01995 | TM49_RS17855 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | TM49_RS01995 | TM49_RS17855 |
| phenylacetate | paaK: phenylacetate-CoA ligase | TM49_RS17865 | |
| 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 | TM49_RS02450 | TM49_RS13300 |
| phenylalanine | hmgA: homogentisate dioxygenase | | |
| phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| phenylalanine | maiA: maleylacetoacetate isomerase | TM49_RS10720 | |
| phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | | |
| propionate | dddA: 3-hydroxypropionate dehydrogenase | TM49_RS09715 | TM49_RS05230 |
| propionate | hpcD: 3-hydroxypropionyl-CoA dehydratase | TM49_RS05305 | |
| propionate | pco: propanyl-CoA oxidase | | |
| propionate | putP: propionate transporter; proline:Na+ symporter | TM49_RS05585 | |
| putrescine | potB: putrescine ABC transporter, permease component 1 (PotB/PotH) | TM49_RS08030 | TM49_RS09700 |
| putrescine | potC: putrescine ABC transporter, permease component 2 (PotC/PotI) | TM49_RS08025 | TM49_RS15935 |
| putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | | |
| putrescine | puuB: gamma-glutamylputrescine oxidase | TM49_RS00195 | TM49_RS12410 |
| putrescine | puuC: gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase | TM49_RS05310 | TM49_RS05235 |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | snatA: L-serine transporter | TM49_RS16400 | |
| succinate | dauA: succinate:H+ symporter DauA | TM49_RS17060 | |
| threonine | snatA: L-threonine transporter snatA | TM49_RS16400 | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | TM49_RS02450 | TM49_RS13300 |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | TM49_RS10720 | |
| valine | acdH: isobutyryl-CoA dehydrogenase | TM49_RS17845 | |
| valine | Bap2: L-valine permease Bap2 | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | TM49_RS05305 | |
| valine | dddA: 3-hydroxypropionate dehydrogenase | TM49_RS09715 | TM49_RS05230 |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | TM49_RS05305 | |
| valine | hpcD: 3-hydroxypropionyl-CoA dehydratase | TM49_RS05305 | |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | TM49_RS19775 | TM49_RS05235 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | TM49_RS02815 | TM49_RS09795 |
| valine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| valine | pco: propanyl-CoA oxidase | | |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | TM49_RS02240 | |
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