Potential Gaps in catabolism of small carbon sources in Moritella dasanensis ArB 0140
Found 81 low-confidence and 51 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 | | |
| 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 | | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arginine | rocF: arginase | | |
| cellobiose | bgl: cellobiase | A923_RS0109830 | |
| citrate | fecB: ferric citrate ABC transporter, substrate-binding component FecB | A923_RS0109885 | |
| citrate | fecC: ferric citrate ABC transporter, permease component 1 (FecC) | A923_RS0109890 | A923_RS0109895 |
| citrate | fecD: ferric citrate ABC transporter, permease component 2 (FecD) | A923_RS0109895 | A923_RS0106425 |
| citrate | fecE: ferric citrate ABC transporter, ATPase component FecE | A923_RS0109900 | A923_RS0119065 |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | A923_RS0121530 | A923_RS0106855 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | A923_RS0121520 | A923_RS0116625 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | A923_RS0121525 | A923_RS0116620 |
| D-alanine | Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component | A923_RS0106870 | |
| D-alanine | Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component | A923_RS0106855 | A923_RS0109795 |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | A923_RS0106030 | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| deoxyribonate | aacS: acetoacetyl-CoA synthetase | A923_RS0100990 | A923_RS0104565 |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | A923_RS0108875 | |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | garK: glycerate 2-kinase | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fucose | aldA: lactaldehyde dehydrogenase | A923_RS0109940 | A923_RS0108515 |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | | |
| fucose | fucI: L-fucose isomerase FucI | | |
| fucose | fucK: L-fuculose kinase FucK | | |
| fucose | fucP: L-fucose:H+ symporter FucP | | |
| fucose | fucU: L-fucose mutarotase FucU | | |
| galactose | galK: galactokinase (-1-phosphate forming) | | |
| galactose | galP: galactose:H+ symporter GalP | | |
| galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| 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 | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | A923_RS0117790 | A923_RS0106150 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | A923_RS0100595 | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
| glucuronate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| histidine | hutV: L-histidine ABC transporter, ATPase component HutV | A923_RS0108545 | A923_RS0118395 |
| histidine | hutX: L-histidine ABC transporter, substrate-binding component HutX | A923_RS0108535 | A923_RS0100760 |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | A923_RS0101015 | |
| isoleucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | A923_RS0101130 | |
| isoleucine | bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | A923_RS0101135 | |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | A923_RS0101140 | A923_RS22235 |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | A923_RS0108700 | A923_RS0119400 |
| L-lactate | lutC: L-lactate dehydrogenase, LutC subunit | A923_RS0106015 | |
| L-lactate | Shew_2731: L-lactate:Na+ symporter, large component | A923_RS0113640 | |
| lactose | galK: galactokinase (-1-phosphate forming) | | |
| lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | A923_RS0109830 | |
| leucine | aacS: acetoacetyl-CoA synthetase | A923_RS0100990 | A923_RS0104565 |
| leucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | A923_RS0101130 | |
| leucine | bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | A923_RS0101135 | |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | A923_RS0101140 | A923_RS22235 |
| lysine | argT: L-lysine ABC transporter, substrate-binding component ArgT | A923_RS0116620 | A923_RS0121525 |
| lysine | hglS: D-2-hydroxyglutarate synthase | | |
| lysine | hisM: L-lysine ABC transporter, permease component 1 (HisM) | A923_RS0121515 | A923_RS0116630 |
| lysine | hisP: L-lysine ABC transporter, ATPase component HisP | A923_RS0121530 | A923_RS0106855 |
| lysine | lysN: 2-aminoadipate transaminase | A923_RS0114085 | A923_RS0118545 |
| maltose | susB: alpha-glucosidase (maltase) | A923_RS0113170 | A923_RS0106605 |
| mannitol | mtlA: mannitol phosphotransferase system, EII-CBA components | | |
| mannitol | mtlD: mannitol-1-phosphate 5-dehydrogenase | | |
| mannose | manA: mannose-6-phosphate isomerase | A923_RS0107980 | |
| mannose | manP: mannose PTS system, EII-CBA components | A923_RS0118060 | |
| 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 | | |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | | |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | A923_RS0106150 | A923_RS0117790 |
| 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 | A923_RS0110330 | A923_RS0112940 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | A923_RS0116325 | A923_RS0110330 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | A923_RS0119825 | A923_RS0119275 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | A923_RS0119825 | A923_RS0119275 |
| phenylacetate | paaK: phenylacetate-CoA ligase | A923_RS0104565 | A923_RS0113825 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aacS: acetoacetyl-CoA synthetase | A923_RS0100990 | A923_RS0104565 |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | A923_RS0102630 | A923_RS0106390 |
| propionate | lctP: propionate permease | A923_RS0106030 | |
| putrescine | gabD: succinate semialdehyde dehydrogenase | A923_RS0109940 | A923_RS0108515 |
| putrescine | gabT: gamma-aminobutyrate transaminase | A923_RS0115325 | A923_RS0118545 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | A923_RS0115325 | A923_RS0118545 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | A923_RS0108515 | A923_RS0109940 |
| pyruvate | yjcH: putative small subunit of pyruvate transporter (yjcH-like) | A923_RS0113635 | |
| rhamnose | aldA: lactaldehyde dehydrogenase | A923_RS0109940 | A923_RS0108515 |
| rhamnose | rhaA: L-rhamnose isomerase | | |
| rhamnose | rhaB: L-rhamnulokinase | | |
| rhamnose | rhaD: rhamnulose 1-phosphate aldolase | | |
| rhamnose | rhaM: L-rhamnose mutarotase | | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsA: D-ribose ABC transporter, ATPase component RbsA | A923_RS0107850 | |
| ribose | rbsB: D-ribose ABC transporter, substrate-binding component RbsB | A923_RS0107860 | |
| ribose | rbsC: D-ribose ABC transporter, permease component RbsC | A923_RS0107855 | |
| sorbitol | mtlA: PTS system for polyols, EII-CBA components | | |
| sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | A923_RS0100300 | A923_RS0105590 |
| sucrose | ams: sucrose hydrolase (invertase) | A923_RS0113170 | A923_RS0106605 |
| trehalose | treC: trehalose-6-phosphate hydrolase | A923_RS0113170 | A923_RS0106605 |
| tyrosine | aacS: acetoacetyl-CoA synthetase | A923_RS0100990 | A923_RS0104565 |
| valine | acdH: isobutyryl-CoA dehydrogenase | A923_RS0101015 | A923_RS0103610 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | A923_RS0112255 | A923_RS0117405 |
| valine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | A923_RS0101130 | |
| valine | bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | A923_RS0101135 | |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | A923_RS0101140 | A923_RS22235 |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | A923_RS0104120 | A923_RS0110330 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | A923_RS0118540 | |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | A923_RS0118060 | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | A923_RS0112565 | A923_RS0117230 |
| xylose | xylA: xylose isomerase | | |
| xylose | xylB: xylulokinase | | |
| xylose | xylT: D-xylose transporter | | |
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