Potential Gaps in catabolism of small carbon sources in Endozoicomonas montiporae CL-33
Found 83 low-confidence and 49 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | Psest_0084: 2-oxoglutarate TRAP transporter, fused 4TM/12TM components | EZMO1_RS05295 | EZMO1_RS14610 |
| 2-oxoglutarate | Psest_0085: 2-oxoglutarate TRAP transporter, solute receptor component | EZMO1_RS14605 | EZMO1_RS05290 |
| 4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | EZMO1_RS06720 | EZMO1_RS02235 |
| 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 | EZMO1_RS06715 | |
| acetate | actP: cation/acetate symporter ActP | | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | EZMO1_RS03780 | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | EZMO1_RS25170 | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arginine | gabT: gamma-aminobutyrate transaminase | EZMO1_RS05155 | EZMO1_RS05305 |
| arginine | puuD: gamma-glutamyl-gamma-aminobutyrate hydrolase | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | EZMO1_RS20800 | EZMO1_RS08085 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | EZMO1_RS08100 | EZMO1_RS17260 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | EZMO1_RS08095 | EZMO1_RS17260 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | EZMO1_RS08090 | |
| citrulline | rocD: ornithine aminotransferase | EZMO1_RS05305 | EZMO1_RS22405 |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-alanine | Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component | EZMO1_RS20815 | |
| D-alanine | Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component | EZMO1_RS20800 | EZMO1_RS08085 |
| D-lactate | D-LDH: D-lactate dehydrogenase | EZMO1_RS02600 | EZMO1_RS01150 |
| 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 | EZMO1_RS12070 | EZMO1_RS04575 |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | EZMO1_RS15100 | EZMO1_RS06035 |
| 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 | fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components | EZMO1_RS08275 | |
| fucose | fucI: L-fucose isomerase FucI | | |
| fucose | HSERO_RS05260: ABC transporter for L-fucose, substrate-binding component | EZMO1_RS03790 | |
| galactose | galP: galactose:H+ symporter GalP | | |
| galacturonate | eda: 2-keto-3-deoxygluconate 6-phosphate aldolase | | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | kdgK: 2-keto-3-deoxygluconate kinase | | |
| galacturonate | uxaA: D-altronate dehydratase | | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | | |
| gluconate | gnd: 6-phosphogluconate dehydrogenase, decarboxylating | EZMO1_RS12720 | |
| gluconate | gntK: D-gluconate kinase | EZMO1_RS19995 | |
| gluconate | gntT: gluconate:H+ symporter GntT | EZMO1_RS19165 | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | EZMO1_RS01415 | EZMO1_RS18400 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | EZMO1_RS08745 | EZMO1_RS03920 |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | garL: 5-dehydro-4-deoxy-D-glucarate aldolase | EZMO1_RS02240 | EZMO1_RS15485 |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| histidine | aapM: L-histidine ABC transporter, permease component 2 (AapM) | EZMO1_RS20805 | EZMO1_RS17260 |
| histidine | aapP: L-histidine ABC transporter, ATPase component AapP | EZMO1_RS20800 | EZMO1_RS08085 |
| histidine | aapQ: L-histidine ABC transporter, permease component 1 (AapQ) | EZMO1_RS20810 | EZMO1_RS00975 |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
| isoleucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | EZMO1_RS24355 | |
| isoleucine | bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | EZMO1_RS24350 | |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | EZMO1_RS02395 | EZMO1_RS08330 |
| isoleucine | prpB: 2-methylisocitrate lyase | EZMO1_RS12020 | |
| L-lactate | SfMCT: L-lactate transporter SfMCT | EZMO1_RS22730 | |
| lactose | lacP: lactose permease LacP | | |
| leucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | EZMO1_RS24355 | |
| leucine | bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | EZMO1_RS24350 | |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | EZMO1_RS02395 | EZMO1_RS08330 |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | EZMO1_RS20260 | EZMO1_RS03360 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | EZMO1_RS12715 | EZMO1_RS20265 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | EZMO1_RS03350 | EZMO1_RS20275 |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| lysine | davA: 5-aminovaleramidase | EZMO1_RS24040 | |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | davT: 5-aminovalerate aminotransferase | EZMO1_RS05155 | EZMO1_RS05305 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| mannitol | mtlA: mannitol phosphotransferase system, EII-CBA components | | |
| mannitol | mtlD: mannitol-1-phosphate 5-dehydrogenase | | |
| mannose | manA: mannose-6-phosphate isomerase | EZMO1_RS14095 | |
| mannose | manP: mannose PTS system, EII-CBA components | EZMO1_RS08275 | |
| 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 | EZMO1_RS22545 | |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | | |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | EZMO1_RS18450 | EZMO1_RS18455 |
| myoinositol | PS417_11885: myo-inositol ABC transporter, substrate-binding component | | |
| myoinositol | PS417_11895: myo-inositol ABC transporter, permease component | EZMO1_RS03795 | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | EZMO1_RS01415 | EZMO1_RS18400 |
| 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 | EZMO1_RS06810 | |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | EZMO1_RS12715 | EZMO1_RS06580 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | EZMO1_RS04945 | EZMO1_RS12715 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | EZMO1_RS13395 | EZMO1_RS06595 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | EZMO1_RS13395 | EZMO1_RS06595 |
| phenylacetate | paaK: phenylacetate-CoA ligase | EZMO1_RS06510 | EZMO1_RS18090 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | EZMO1_RS12715 | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | maiA: maleylacetoacetate isomerase | | |
| phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | EZMO1_RS12125 | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | EZMO1_RS19525 | EZMO1_RS04780 |
| propionate | prpB: 2-methylisocitrate lyase | EZMO1_RS12020 | |
| propionate | putP: propionate transporter; proline:Na+ symporter | EZMO1_RS21675 | EZMO1_RS08230 |
| putrescine | gabT: gamma-aminobutyrate transaminase | EZMO1_RS05155 | EZMO1_RS05305 |
| putrescine | puuD: gamma-glutamyl-gamma-aminobutyrate hydrolase | | |
| pyruvate | yjcH: putative small subunit of pyruvate transporter (yjcH-like) | EZMO1_RS21545 | |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | EZMO1_RS15100 | EZMO1_RS06710 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | | |
| rhamnose | LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase | EZMO1_RS02240 | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsK: ribokinase | | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| sorbitol | mtlA: PTS system for polyols, EII-CBA components | | |
| sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | EZMO1_RS15100 | EZMO1_RS06035 |
| sucrose | ams: sucrose hydrolase (invertase) | EZMO1_RS01190 | |
| trehalose | treF: trehalase | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| tyrosine | tyrP: Tyrosine permease | EZMO1_RS21610 | EZMO1_RS24605 |
| valine | acdH: isobutyryl-CoA dehydrogenase | EZMO1_RS12710 | EZMO1_RS03345 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | EZMO1_RS11875 | EZMO1_RS20265 |
| valine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | EZMO1_RS24355 | |
| valine | bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | EZMO1_RS24350 | |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | EZMO1_RS02395 | EZMO1_RS08330 |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | EZMO1_RS13400 | EZMO1_RS12715 |
| valine | prpB: 2-methylisocitrate lyase | EZMO1_RS12020 | |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | EZMO1_RS08275 | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | EZMO1_RS01345 | |
| xylose | xylA: xylose isomerase | | |
| xylose | xylB: xylulokinase | | |
| xylose | xylE_Tm: ABC transporter for xylose, substrate binding component xylE | EZMO1_RS03790 | |
| xylose | xylF_Tm: ABC transporter for xylose, permease component xylF | EZMO1_RS03795 | |
| xylose | xylK_Tm: ABC transporter for xylose, ATP binding component xylK | EZMO1_RS03800 | |
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