Potential Gaps in catabolism of small carbon sources in Megamonas funiformis YIT 11815
Found 117 low-confidence and 50 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | | |
| 4-hydroxybenzoate | ald-dh-CoA: acetaldehyde dehydrogenase, acylating | | |
| 4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | | |
| 4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | | |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | HMPREF9454_RS08985 | |
| 4-hydroxybenzoate | pobA: 4-hydroxybenzoate 3-monooxygenase | | |
| 4-hydroxybenzoate | praA: protocatechuate 2,3-dioxygenase | | |
| 4-hydroxybenzoate | xylF: 2-hydroxymuconate semialdehyde hydrolase | | |
| acetate | acs: acetyl-CoA synthetase, AMP-forming | | |
| acetate | dctA: organic acid/proton symporter DctA | HMPREF9454_RS02310 | HMPREF9454_RS11160 |
| arginine | gabD: succinate semialdehyde dehydrogenase | HMPREF9454_RS09545 | |
| arginine | gabT: gamma-aminobutyrate transaminase | HMPREF9454_RS05550 | HMPREF9454_RS02955 |
| arginine | patA: putrescine aminotransferase (PatA/SpuC) | HMPREF9454_RS07540 | HMPREF9454_RS05550 |
| arginine | patD: gamma-aminobutyraldehyde dehydrogenase | | |
| arginine | rocE: L-arginine permease | HMPREF9454_RS12410 | HMPREF9454_RS10885 |
| cellobiose | bgl: cellobiase | HMPREF9454_RS07115 | |
| cellobiose | glk: glucokinase | HMPREF9454_RS09110 | HMPREF9454_RS10520 |
| cellobiose | MFS-glucose: glucose transporter, MFS superfamily | HMPREF9454_RS09490 | HMPREF9454_RS09235 |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | HMPREF9454_RS06810 | HMPREF9454_RS00035 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | HMPREF9454_RS06815 | HMPREF9454_RS06960 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | HMPREF9454_RS06815 | HMPREF9454_RS06960 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | HMPREF9454_RS06820 | |
| citrulline | arcC: carbamate kinase | | |
| citrulline | rocA: 1-pyrroline-5-carboxylate dehydrogenase | | |
| citrulline | rocD: ornithine aminotransferase | HMPREF9454_RS02955 | HMPREF9454_RS05550 |
| D-alanine | cycA: D-alanine:H+ symporter CycA | HMPREF9454_RS00495 | HMPREF9454_RS10885 |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
| D-serine | cycA: D-serine:H+ symporter CycA | HMPREF9454_RS10885 | HMPREF9454_RS00495 |
| D-serine | dsdA: D-serine ammonia-lyase | HMPREF9454_RS12015 | |
| deoxyinosine | ald-dh-CoA: acetaldehyde dehydrogenase, acylating | | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | HMPREF9454_RS06580 | |
| deoxyribonate | aacS: acetoacetyl-CoA synthetase | | |
| deoxyribonate | atoB: acetyl-CoA C-acetyltransferase | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | HMPREF9454_RS05535 | HMPREF9454_RS06485 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | HMPREF9454_RS08595 | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | ald-dh-CoA: acetaldehyde dehydrogenase, acylating | | |
| deoxyribose | deoK: deoxyribokinase | HMPREF9454_RS01920 | |
| ethanol | ald-dh-CoA: acetaldehyde dehydrogenase, acylating | | |
| ethanol | etoh-dh-nad: ethanol dehydrogenase (NAD(P)) | HMPREF9454_RS12050 | HMPREF9454_RS08145 |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | HMPREF9454_RS12520 | HMPREF9454_RS08755 |
| fucose | fucO: L-lactaldehyde reductase | HMPREF9454_RS08145 | HMPREF9454_RS08515 |
| fumarate | dctA: fumarate:H+ symporter DctA | HMPREF9454_RS02310 | HMPREF9454_RS11160 |
| galactose | galK: galactokinase (-1-phosphate forming) | | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | uxaC: D-galacturonate isomerase | | |
| gluconate | gntK: D-gluconate kinase | HMPREF9454_RS09200 | HMPREF9454_RS09495 |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | HMPREF9454_RS07765 | HMPREF9454_RS01155 |
| glucose | glk: glucokinase | HMPREF9454_RS09110 | HMPREF9454_RS10520 |
| glucose | MFS-glucose: glucose transporter, MFS superfamily | HMPREF9454_RS09490 | HMPREF9454_RS09235 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | uxaC: D-glucuronate isomerase | | |
| glycerol | dhaD: glycerol dehydrogenase | HMPREF9454_RS12050 | HMPREF9454_RS08145 |
| glycerol | dhaL: dihydroxyacetone:PEP phosphotransferase, subunit L | HMPREF9454_RS07855 | HMPREF9454_RS08745 |
| glycerol | dhaM: dihydroxyacetone:PEP phosphotransferase, subunit M | HMPREF9454_RS12415 | |
| glycerol | glpF: glycerol facilitator glpF | | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| histidine | PA5503: L-histidine ABC transporter, ATPase component | HMPREF9454_RS00035 | HMPREF9454_RS06810 |
| histidine | PA5504: L-histidine ABC transporter, permease component | HMPREF9454_RS00040 | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | | |
| isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | HMPREF9454_RS11665 | |
| isoleucine | fadA: 2-methylacetoacetyl-CoA thiolase | | |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | HMPREF9454_RS06290 | HMPREF9454_RS06485 |
| isoleucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | HMPREF9454_RS08625 | |
| isoleucine | pccB: propionyl-CoA carboxylase, beta subunit | HMPREF9454_RS11355 | |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| L-malate | sdlC: L-malate:Na+ symporter SdlC | HMPREF9454_RS04425 | |
| lactose | galK: galactokinase (-1-phosphate forming) | | |
| lactose | glk: glucokinase | HMPREF9454_RS09110 | HMPREF9454_RS10520 |
| lactose | lacS: lactose permease LacS | HMPREF9454_RS04285 | HMPREF9454_RS04275 |
| leucine | aacS: acetoacetyl-CoA synthetase | | |
| leucine | atoB: acetyl-CoA C-acetyltransferase | | |
| leucine | liuA: isovaleryl-CoA dehydrogenase | | |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | HMPREF9454_RS08625 | |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | | |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | HMPREF9454_RS11355 | |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| leucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| lysine | amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) | | |
| lysine | hglS: D-2-hydroxyglutarate synthase | | |
| lysine | lat: L-lysine 6-aminotransferase | HMPREF9454_RS02955 | HMPREF9454_RS05550 |
| lysine | lysN: 2-aminoadipate transaminase | HMPREF9454_RS11865 | HMPREF9454_RS07540 |
| lysine | lysP: L-lysine:H+ symporter LysP | HMPREF9454_RS10885 | HMPREF9454_RS00495 |
| lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | HMPREF9454_RS05330 | |
| maltose | glk: glucokinase | HMPREF9454_RS09110 | HMPREF9454_RS10520 |
| maltose | MFS-glucose: glucose transporter, MFS superfamily | HMPREF9454_RS09490 | HMPREF9454_RS09235 |
| mannitol | mtlD: mannitol-1-phosphate 5-dehydrogenase | HMPREF9454_RS11680 | |
| mannose | mannokinase: D-mannose kinase | HMPREF9454_RS09110 | |
| myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | | |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | HMPREF9454_RS06040 | HMPREF9454_RS04395 |
| myoinositol | iolT: myo-inositol:H+ symporter | HMPREF9454_RS09490 | HMPREF9454_RS09235 |
| myoinositol | mmsA: malonate-semialdehyde dehydrogenase | | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | HMPREF9454_RS07765 | HMPREF9454_RS01155 |
| 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 | HMPREF9454_RS11665 | |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | HMPREF9454_RS11665 | |
| phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | HMPREF9454_RS06290 | HMPREF9454_RS05535 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | | |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | | |
| phenylacetate | paaK: phenylacetate-CoA ligase | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | HMPREF9454_RS11665 | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aacS: acetoacetyl-CoA synthetase | | |
| phenylalanine | atoB: acetyl-CoA C-acetyltransferase | | |
| phenylalanine | fahA: fumarylacetoacetate hydrolase | HMPREF9454_RS01860 | |
| phenylalanine | hmgA: homogentisate dioxygenase | | |
| phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| phenylalanine | maiA: maleylacetoacetate isomerase | | |
| phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
| phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | | |
| proline | put1: proline dehydrogenase | | |
| proline | putA: L-glutamate 5-semialdeyde dehydrogenase | | |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | HMPREF9454_RS08625 | |
| propionate | pccB: propionyl-CoA carboxylase, beta subunit | HMPREF9454_RS11355 | |
| propionate | prpE: propionyl-CoA synthetase | | |
| propionate | putP: propionate transporter; proline:Na+ symporter | HMPREF9454_RS09855 | |
| putrescine | gabD: succinate semialdehyde dehydrogenase | HMPREF9454_RS09545 | |
| putrescine | gabT: gamma-aminobutyrate transaminase | HMPREF9454_RS05550 | HMPREF9454_RS02955 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | HMPREF9454_RS07540 | HMPREF9454_RS05550 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | | |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| pyruvate | SLC5A8: sodium-coupled pyruvate transporter | | |
| rhamnose | fucO: L-lactaldehyde reductase | HMPREF9454_RS08145 | HMPREF9454_RS08515 |
| rhamnose | rhaA: L-rhamnose isomerase | | |
| rhamnose | rhaM: L-rhamnose mutarotase | | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsK: ribokinase | HMPREF9454_RS01920 | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| succinate | sdc: succinate:Na+ symporter Sdc | HMPREF9454_RS04425 | |
| threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | HMPREF9454_RS11885 | HMPREF9454_RS11890 |
| threonine | kbl: glycine C-acetyltransferase (2-amino-3-ketobutyrate CoA-ligase) | HMPREF9454_RS00740 | |
| threonine | tdh: L-threonine 3-dehydrogenase | HMPREF9454_RS08145 | HMPREF9454_RS08515 |
| thymidine | ald-dh-CoA: acetaldehyde dehydrogenase, acylating | | |
| trehalose | glk: glucokinase | HMPREF9454_RS09110 | HMPREF9454_RS10520 |
| trehalose | MFS-glucose: glucose transporter, MFS superfamily | HMPREF9454_RS09490 | HMPREF9454_RS09235 |
| trehalose | treF: trehalase | HMPREF9454_RS06060 | HMPREF9454_RS09460 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | HMPREF9454_RS00495 | HMPREF9454_RS10885 |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aacS: acetoacetyl-CoA synthetase | | |
| tyrosine | atoB: acetyl-CoA C-acetyltransferase | | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | HMPREF9454_RS01860 | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | HMPREF9454_RS11665 | |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | HMPREF9454_RS11665 | |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | | |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | HMPREF9454_RS09545 | |
| valine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | HMPREF9454_RS08625 | |
| valine | pccB: propionyl-CoA carboxylase, beta subunit | HMPREF9454_RS11355 | |
| xylitol | EIIA-Axl: xylitol PTS, enzyme IIA (EIIA-Axl) | HMPREF9454_RS05440 | |
| xylitol | EIIB-Axl: xylitol PTS, enzyme IIB (EIIB-Axl) | HMPREF9454_RS05435 | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | HMPREF9454_RS05425 | |
| xylose | xylA: xylose isomerase | | |
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