Potential Gaps in catabolism of small carbon sources in Halomonas smyrnensis AAD6
Found 69 low-confidence and 58 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 | UYS_RS0206425 | UYS_RS17915 |
| 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 | UYS_RS0214445 | |
| acetate | actP: cation/acetate symporter ActP | UYS_RS0201080 | |
| arabinose | araE: L-arabinose:H+ symporter | UYS_RS0216285 | |
| arabinose | xacC: L-arabinono-1,4-lactonase | UYS_RS0211920 | UYS_RS0206435 |
| arabinose | xacD: L-arabinonate dehydratase | UYS_RS0206420 | UYS_RS0212300 |
| arabinose | xacE: 2-dehydro-3-deoxy-L-arabinonate dehydratase | | |
| asparagine | ans: asparaginase | UYS_RS0206650 | |
| cellobiose | bgl: cellobiase | | |
| cellobiose | SSS-glucose: Sodium/glucose cotransporter | UYS_RS0212935 | UYS_RS0205355 |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | UYS_RS0212190 | UYS_RS0211365 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | UYS_RS0212195 | UYS_RS0211375 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | UYS_RS0212215 | UYS_RS0212205 |
| citrulline | arcC: carbamate kinase | | |
| citrulline | aruF: ornithine/arginine N-succinyltransferase subunit AruAI (AruF) | UYS_RS0208640 | UYS_RS0208635 |
| citrulline | aruG: ornithine/arginine N-succinyltransferase subunit AruAII (AruG) | UYS_RS0208635 | UYS_RS0208640 |
| D-alanine | Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component | UYS_RS0203460 | |
| D-alanine | Pf6N2E2_5403: ABC transporter for D-Alanine, permease component 2 | UYS_RS0203455 | |
| D-alanine | Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component | UYS_RS0203445 | UYS_RS0204000 |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | UYS_RS0203725 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | UYS_RS0206445 | UYS_RS0205325 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | UYS_RS0211160 | |
| deoxyribose | deoK: deoxyribokinase | UYS_RS0207450 | UYS_RS0215875 |
| deoxyribose | deoP: deoxyribose transporter | | |
| fucose | aldA: lactaldehyde dehydrogenase | UYS_RS0209525 | UYS_RS0211640 |
| 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 | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | UYS_RS0211920 | UYS_RS0206435 |
| galactose | sglS: sodium/galactose cotransporter | UYS_RS0212935 | UYS_RS0205355 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | kdgK: 2-keto-3-deoxygluconate kinase | UYS_RS0214580 | UYS_RS0211250 |
| galacturonate | uxaA: D-altronate dehydratase | | |
| galacturonate | uxaB: tagaturonate reductase | UYS_RS0209140 | |
| galacturonate | uxaC: D-galacturonate isomerase | | |
| gluconate | gntA: gluconate TRAP transporter, small permease component | UYS_RS0211580 | |
| gluconate | gntC: gluconate TRAP transporter, periplasmic solute-binding component | UYS_RS0211575 | |
| glucosamine | AO353_21710: glucosaminate ABC transporter, substrate-binding component | | |
| glucosamine | AO353_21715: glucosaminate ABC transporter, permease component 1 | UYS_RS0203995 | UYS_RS0212195 |
| glucosamine | AO353_21720: glucosaminate ABC transporter, permease component 2 | UYS_RS0203995 | UYS_RS0202350 |
| glucosamine | AO353_21725: glucosaminate ABC transporter, ATPase component | UYS_RS0204000 | UYS_RS0212190 |
| glucosamine | kdgK: 2-keto-3-deoxygluconate kinase | UYS_RS0214580 | UYS_RS0211250 |
| glucose | SSS-glucose: Sodium/glucose cotransporter | UYS_RS0212935 | UYS_RS0205355 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | kdgK: 2-keto-3-deoxygluconate kinase | UYS_RS0214580 | UYS_RS0211250 |
| glucuronate | uxaC: D-glucuronate isomerase | | |
| glycerol | glpF: glycerol facilitator glpF | | |
| histidine | hisJ: L-histidine ABC transporter, substrate-binding component HisJ | UYS_RS0211370 | UYS_RS0212205 |
| histidine | hisM: L-histidine ABC transporter, permease component 1 (HisM) | UYS_RS0212200 | UYS_RS0211380 |
| histidine | hisQ: L-histidine ABC transporter, permease component 2 (HisQ) | UYS_RS0212195 | UYS_RS0211375 |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| isoleucine | Bap2: L-isoleucine permease Bap2 | | |
| L-lactate | lctO: L-lactate oxidase or 2-monooxygenase | | |
| lactose | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | UYS_RS0211920 | UYS_RS0206435 |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | | |
| leucine | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | UYS_RS0203450 | |
| leucine | aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | UYS_RS0203445 | UYS_RS0204000 |
| leucine | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | UYS_RS0203455 | |
| lysine | argT: L-lysine ABC transporter, substrate-binding component ArgT | UYS_RS0211370 | UYS_RS0212205 |
| lysine | hisM: L-lysine ABC transporter, permease component 1 (HisM) | UYS_RS0212200 | UYS_RS0211380 |
| lysine | hisQ: L-lysine ABC transporter, permease component 2 (HisQ) | UYS_RS0212195 | UYS_RS0211375 |
| lysine | patA: cadaverine aminotransferase | UYS_RS0212955 | UYS_RS0208645 |
| lysine | patD: 5-aminopentanal dehydrogenase | UYS_RS0205480 | UYS_RS0212960 |
| maltose | thuE: maltose ABC transporter, substrate-binding component ThuE | UYS_RS0211705 | |
| maltose | thuF: maltose ABC transporter, permease component 1 (ThuF) | UYS_RS0211700 | UYS_RS0205535 |
| maltose | thuK: maltose ABC transporter, ATPase component ThuK | UYS_RS0205545 | UYS_RS0215895 |
| mannitol | mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE | UYS_RS0215910 | |
| mannitol | mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) | UYS_RS0215905 | UYS_RS0211700 |
| mannitol | mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) | UYS_RS0215900 | UYS_RS0211695 |
| mannose | STP6: mannose:H+ symporter | UYS_RS0216285 | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | UYS_RS0204090 | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| 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 | UYS_RS0210210 | UYS_RS0213615 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | UYS_RS0210210 | UYS_RS0213615 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | UYS_RS0202795 | UYS_RS0202580 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | UYS_RS0202795 | UYS_RS0202580 |
| phenylacetate | paaK: phenylacetate-CoA ligase | UYS_RS0212410 | UYS_RS0214735 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | UYS_RS0210210 | UYS_RS0213615 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| putrescine | gabT: gamma-aminobutyrate transaminase | UYS_RS0212955 | UYS_RS0211785 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | UYS_RS0211785 | UYS_RS0202195 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | UYS_RS0205480 | UYS_RS0210185 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| rhamnose | aldA: lactaldehyde dehydrogenase | UYS_RS0209525 | UYS_RS0211640 |
| rhamnose | rhaA: L-rhamnose isomerase | | |
| rhamnose | rhaB: L-rhamnulokinase | | |
| rhamnose | rhaD: rhamnulose 1-phosphate aldolase | | |
| rhamnose | rhaM: L-rhamnose mutarotase | | |
| ribose | rbsK: ribokinase | UYS_RS0207450 | UYS_RS0215875 |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| sorbitol | mtlK: ABC transporter for polyols MtlEFGK, permease component MtlK | UYS_RS0215895 | UYS_RS0211685 |
| sorbitol | sdh: sorbitol dehydrogenase | UYS_RS0215880 | UYS_RS0211285 |
| sucrose | ams: sucrose hydrolase (invertase) | UYS_RS0211690 | UYS_RS0211680 |
| trehalose | thuE: trehalose ABC transporter, substrate-binding component ThuE | UYS_RS0211705 | |
| trehalose | thuF: trehalose ABC transporter, permease component 1 (ThuF) | UYS_RS0211700 | UYS_RS0205535 |
| trehalose | thuK: trehalose ABC transporter, ATPase component ThuK | UYS_RS0205545 | UYS_RS0211685 |
| trehalose | treF: trehalase | UYS_RS0211690 | UYS_RS0211680 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | UYS_RS0215605 | UYS_RS0209860 |
| valine | Bap2: L-valine permease Bap2 | | |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | UYS_RS0211950 | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | | |
| xylose | xylA: xylose isomerase | | |
| xylose | xylB: xylulokinase | | |
| xylose | xylT: D-xylose transporter | UYS_RS0216285 | |
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