Potential Gaps in catabolism of small carbon sources in Oceanisphaera arctica V1-41
Found 81 low-confidence and 37 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | pcaB: 3-carboxymuconate cycloisomerase | | |
| 4-hydroxybenzoate | pcaC: 4-carboxymuconolactone decarboxylase | | |
| 4-hydroxybenzoate | pcaD: 3-oxoadipate enol-lactone hydrolase | UN63_RS00235 | |
| 4-hydroxybenzoate | pcaG: protocatechuate 3,4-dioxygenase, beta subunit | | |
| 4-hydroxybenzoate | pcaH: protocatechuate 3,4-dioxygenase, alpha subunit | | |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | UN63_RS00150 | |
| 4-hydroxybenzoate | pobA: 4-hydroxybenzoate 3-monooxygenase | | |
| acetate | actP: cation/acetate symporter ActP | | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arginine | gabT: gamma-aminobutyrate transaminase | UN63_RS03985 | UN63_RS03445 |
| cellobiose | bgl: cellobiase | | |
| cellobiose | ptsG: glucose PTS, enzyme IICB | UN63_RS03845 | |
| citrate | tctB: citrate/Na+ symporter, small transmembrane component TctB | UN63_RS05295 | |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | UN63_RS03180 | UN63_RS13375 |
| citrulline | gabT: gamma-aminobutyrate transaminase | UN63_RS03985 | UN63_RS03445 |
| citrulline | odc: L-ornithine decarboxylase | UN63_RS14765 | |
| D-alanine | Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component | UN63_RS01075 | |
| D-alanine | Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component | UN63_RS01060 | UN63_RS12580 |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| deoxyinosine | adh: acetaldehyde dehydrogenase (not acylating) | UN63_RS03525 | UN63_RS03450 |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | UN63_RS13315 | |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | UN63_RS11135 | |
| deoxyribose | adh: acetaldehyde dehydrogenase (not acylating) | UN63_RS03525 | UN63_RS03450 |
| deoxyribose | deoP: deoxyribose transporter | | |
| ethanol | adh: acetaldehyde dehydrogenase (not acylating) | UN63_RS03525 | UN63_RS03450 |
| fucose | aldA: lactaldehyde dehydrogenase | UN63_RS14965 | UN63_RS08875 |
| 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 | uxaA: D-altronate dehydratase | | |
| galacturonate | uxaB: tagaturonate reductase | | |
| gluconate | edd: phosphogluconate dehydratase | UN63_RS11410 | UN63_RS14440 |
| gluconate | gntK: D-gluconate kinase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | nagP: N-acetylglucosamine transporter NagP | | |
| glucosamine | nagX: transmembrane glucosamine N-acetyltransferase NagX | | |
| glucose | ptsG: glucose PTS, enzyme IICB | UN63_RS03845 | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | dctP: D-glucuronate TRAP transporter, solute receptor component | UN63_RS14385 | UN63_RS11875 |
| glucuronate | dctQ: D-glucuronate TRAP transporter, small permease component | | |
| glycerol | glpF: glycerol facilitator glpF | | |
| histidine | aapM: L-histidine ABC transporter, permease component 2 (AapM) | UN63_RS01065 | UN63_RS13375 |
| histidine | aapQ: L-histidine ABC transporter, permease component 1 (AapQ) | UN63_RS01070 | UN63_RS12585 |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | UN63_RS03090 | UN63_RS07065 |
| isoleucine | prpD: 2-methylcitrate dehydratase | | |
| lactose | galK: galactokinase (-1-phosphate forming) | | |
| lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| lactose | glk: glucokinase | UN63_RS00805 | |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | | |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | UN63_RS03090 | UN63_RS07065 |
| lysine | argT: L-lysine ABC transporter, substrate-binding component ArgT | UN63_RS02420 | UN63_RS03185 |
| lysine | hisM: L-lysine ABC transporter, permease component 1 (HisM) | UN63_RS03175 | UN63_RS13370 |
| lysine | hisP: L-lysine ABC transporter, ATPase component HisP | UN63_RS03190 | UN63_RS01060 |
| lysine | hisQ: L-lysine ABC transporter, permease component 2 (HisQ) | UN63_RS03180 | UN63_RS13375 |
| lysine | patA: cadaverine aminotransferase | UN63_RS12600 | UN63_RS03535 |
| lysine | patD: 5-aminopentanal dehydrogenase | UN63_RS03450 | UN63_RS08090 |
| maltose | ptsG: glucose PTS, enzyme IICB | UN63_RS03845 | |
| maltose | susB: alpha-glucosidase (maltase) | | |
| mannitol | mtlA: mannitol phosphotransferase system, EII-CBA components | | |
| mannitol | mtlD: mannitol-1-phosphate 5-dehydrogenase | | |
| mannose | manA: mannose-6-phosphate isomerase | UN63_RS10555 | |
| mannose | manP: mannose PTS system, EII-CBA components | UN63_RS01635 | |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | | |
| myoinositol | iolM: 2-inosose 4-dehydrogenase | | |
| myoinositol | iolN: 2,4-diketo-inositol hydratase | | |
| myoinositol | iolO: 5-dehydro-L-gluconate epimerase | | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| myoinositol | uxaE: D-tagaturonate epimerase | | |
| NAG | nagP: N-acetylglucosamine transporter NagP | | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| propionate | prpD: 2-methylcitrate dehydratase | | |
| putrescine | gabT: gamma-aminobutyrate transaminase | UN63_RS03985 | UN63_RS03445 |
| pyruvate | SLC5A8: sodium-coupled pyruvate transporter | | |
| rhamnose | aldA: lactaldehyde dehydrogenase | UN63_RS14965 | UN63_RS08875 |
| 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 | UN63_RS08345 | |
| ribose | rbsB: D-ribose ABC transporter, substrate-binding component RbsB | UN63_RS08335 | |
| ribose | rbsC: D-ribose ABC transporter, permease component RbsC | UN63_RS08340 | |
| serine | sdaB: L-serine ammonia-lyase | UN63_RS11405 | UN63_RS06625 |
| sorbitol | mtlA: PTS system for polyols, EII-CBA components | | |
| sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | UN63_RS16365 | UN63_RS08970 |
| sucrose | ams: sucrose hydrolase (invertase) | | |
| thymidine | adh: acetaldehyde dehydrogenase (not acylating) | UN63_RS03525 | UN63_RS03450 |
| trehalose | ptsG: glucose PTS, enzyme IICB | UN63_RS03845 | |
| trehalose | treF: trehalase | | |
| tryptophan | antA: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA | UN63_RS00170 | |
| tryptophan | antB: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB | UN63_RS00165 | |
| tryptophan | antC: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC | UN63_RS00160 | |
| tryptophan | kyn: kynureninase | | |
| tryptophan | kynA: tryptophan 2,3-dioxygenase | | |
| tryptophan | kynB: kynurenine formamidase | | |
| tryptophan | pcaD: 3-oxoadipate enol-lactone hydrolase | UN63_RS00235 | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | UN63_RS08990 | UN63_RS13340 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | UN63_RS08980 | |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | UN63_RS03090 | UN63_RS07065 |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | UN63_RS10750 | UN63_RS14495 |
| valine | prpD: 2-methylcitrate dehydratase | | |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | UN63_RS01635 | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | UN63_RS11715 | |
| 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.
Links
Downloads
Related tools
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