Potential Gaps in catabolism of small carbon sources in Halomonas salina B6
Found 89 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 | | |
| acetate | actP: cation/acetate symporter ActP | BN1003_RS09400 | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arabinose | xacB: L-arabinose 1-dehydrogenase | BN1003_RS09075 | BN1003_RS05720 |
| arabinose | xacC: L-arabinono-1,4-lactonase | | |
| arabinose | xacD: L-arabinonate dehydratase | BN1003_RS05580 | BN1003_RS07290 |
| arabinose | xacE: 2-dehydro-3-deoxy-L-arabinonate dehydratase | | |
| arginine | gabT: gamma-aminobutyrate transaminase | BN1003_RS17975 | BN1003_RS11280 |
| asparagine | ans: asparaginase | BN1003_RS13260 | BN1003_RS15240 |
| cellobiose | cbp: cellobiose phosphorylase | | |
| cellobiose | cdt: cellobiose transporter cdt-1/cdt-2 | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | BN1003_RS05870 | BN1003_RS01390 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | BN1003_RS05855 | BN1003_RS02485 |
| citrulline | aruF: ornithine/arginine N-succinyltransferase subunit AruAI (AruF) | BN1003_RS05025 | |
| citrulline | aruG: ornithine/arginine N-succinyltransferase subunit AruAII (AruG) | BN1003_RS05025 | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-alanine | Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component | BN1003_RS01610 | |
| D-alanine | Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component | BN1003_RS01595 | BN1003_RS02475 |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | BN1003_RS10165 | BN1003_RS02660 |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | BN1003_RS13590 | BN1003_RS10965 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | BN1003_RS01330 | |
| deoxyribose | deoK: deoxyribokinase | BN1003_RS14215 | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fucose | aldA: lactaldehyde dehydrogenase | BN1003_RS17970 | BN1003_RS18195 |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | BN1003_RS01910 | |
| 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 | dgoK: 2-dehydro-3-deoxygalactonokinase | BN1003_RS06060 | BN1003_RS06715 |
| galactose | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | | |
| galactose | galdh: D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) | BN1003_RS09075 | BN1003_RS05720 |
| galactose | galP: galactose:H+ symporter GalP | | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | kdgK: 2-keto-3-deoxygluconate kinase | BN1003_RS06715 | BN1003_RS14215 |
| 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) | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | BN1003_RS02385 | |
| glucose | MFS-glucose: glucose transporter, MFS superfamily | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | garL: 5-dehydro-4-deoxy-D-glucarate aldolase | | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | BN1003_RS06065 | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| histidine | hisJ: L-histidine ABC transporter, substrate-binding component HisJ | BN1003_RS11755 | BN1003_RS05855 |
| histidine | hisM: L-histidine ABC transporter, permease component 1 (HisM) | BN1003_RS05860 | BN1003_RS01405 |
| histidine | hisQ: L-histidine ABC transporter, permease component 2 (HisQ) | BN1003_RS05865 | BN1003_RS01400 |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| isoleucine | livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) | BN1003_RS13575 | BN1003_RS09910 |
| isoleucine | livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | | |
| isoleucine | livM: L-isoleucine ABC transporter, permease component 2 (LivM/BraE) | BN1003_RS00930 | |
| lactose | dgoK: 2-dehydro-3-deoxygalactonokinase | BN1003_RS06060 | BN1003_RS06715 |
| lactose | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | | |
| lactose | galdh: D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) | BN1003_RS09075 | BN1003_RS05720 |
| 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) | BN1003_RS01600 | |
| leucine | aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | BN1003_RS01595 | BN1003_RS02475 |
| leucine | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | BN1003_RS01605 | |
| lysine | argT: L-lysine ABC transporter, substrate-binding component ArgT | BN1003_RS01395 | BN1003_RS11755 |
| lysine | davA: 5-aminovaleramidase | BN1003_RS06225 | BN1003_RS06495 |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | hisM: L-lysine ABC transporter, permease component 1 (HisM) | BN1003_RS05860 | BN1003_RS01405 |
| lysine | hisQ: L-lysine ABC transporter, permease component 2 (HisQ) | BN1003_RS05865 | BN1003_RS01400 |
| maltose | thuE: maltose ABC transporter, substrate-binding component ThuE | BN1003_RS06410 | |
| maltose | thuF: maltose ABC transporter, permease component 1 (ThuF) | BN1003_RS06405 | BN1003_RS10945 |
| maltose | thuK: maltose ABC transporter, ATPase component ThuK | BN1003_RS10955 | BN1003_RS06390 |
| mannitol | mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE | BN1003_RS10940 | |
| mannitol | mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) | BN1003_RS10945 | |
| mannitol | mtlK: polyol ABC transporter, ATP component MtlK/SmoG | BN1003_RS10955 | BN1003_RS06390 |
| mannose | manA: mannose-6-phosphate isomerase | BN1003_RS06955 | |
| mannose | manP: mannose PTS system, EII-CBA components | BN1003_RS06310 | |
| 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 | BN1003_RS00790 | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | BN1003_RS02385 | |
| 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 | BN1003_RS10785 | BN1003_RS18225 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | BN1003_RS18215 | BN1003_RS18225 |
| phenylacetate | paaK: phenylacetate-CoA ligase | BN1003_RS15960 | BN1003_RS11840 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | BN1003_RS18225 | BN1003_RS10785 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| putrescine | gabT: gamma-aminobutyrate transaminase | BN1003_RS17975 | BN1003_RS11280 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| rhamnose | aldA: lactaldehyde dehydrogenase | BN1003_RS17970 | BN1003_RS18195 |
| 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 | rbsK: ribokinase | BN1003_RS14215 | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | BN1003_RS00935 | |
| serine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | BN1003_RS00925 | BN1003_RS13575 |
| serine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | | |
| sorbitol | mtlK: ABC transporter for polyols MtlEFGK, permease component MtlK | BN1003_RS10955 | BN1003_RS06390 |
| sucrose | ams: sucrose hydrolase (invertase) | BN1003_RS06395 | |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | BN1003_RS00935 | |
| threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | BN1003_RS00925 | BN1003_RS13575 |
| threonine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | | |
| threonine | ltaE: L-threonine aldolase | BN1003_RS01955 | BN1003_RS06920 |
| trehalose | thuE: trehalose ABC transporter, substrate-binding component ThuE | BN1003_RS06410 | |
| trehalose | thuF: trehalose ABC transporter, permease component 1 (ThuF) | BN1003_RS06405 | BN1003_RS10945 |
| trehalose | thuK: trehalose ABC transporter, ATPase component ThuK | BN1003_RS06390 | BN1003_RS10955 |
| trehalose | treF: trehalase | BN1003_RS06395 | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | BN1003_RS15950 | BN1003_RS16630 |
| valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | BN1003_RS13575 | BN1003_RS09910 |
| valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | | |
| valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | BN1003_RS00930 | |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
| xylitol | xdhA: xylitol dehydrogenase | BN1003_RS09075 | BN1003_RS10965 |
| xylose | xylA: xylose isomerase | | |
| 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