Potential Gaps in catabolism of small carbon sources in Thauera aminoaromatica S2
Found 109 low-confidence and 31 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | Psest_0084: 2-oxoglutarate TRAP transporter, fused 4TM/12TM components | C665_RS12495 | |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | C665_RS11725 | C665_RS04340 |
| 4-hydroxybenzoate | pimB: 3-oxopimeloyl-CoA:CoA acetyltransferase | C665_RS04230 | C665_RS03170 |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arginine | prdA: D-proline reductase, prdA component | | |
| arginine | prdB: D-proline reductase, prdB component | | |
| arginine | prdC: D-proline reductase, electron transfer component PrdC | C665_RS10995 | |
| arginine | prdF: proline racemase | | |
| aspartate | dauA: dicarboxylic acid transporter DauA | C665_RS12555 | C665_RS11580 |
| cellobiose | cbp: cellobiose phosphorylase | | |
| cellobiose | cdt: cellobiose transporter cdt-1/cdt-2 | | |
| cellobiose | glk: glucokinase | C665_RS17905 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | C665_RS06460 | C665_RS18755 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | C665_RS06450 | C665_RS18760 |
| citrulline | arcC: carbamate kinase | | |
| citrulline | prdA: D-proline reductase, prdA component | | |
| citrulline | prdB: D-proline reductase, prdB component | | |
| citrulline | prdC: D-proline reductase, electron transfer component PrdC | C665_RS10995 | |
| citrulline | prdF: proline racemase | | |
| D-lactate | glcF: D-lactate dehydrogenase, FeS subunit GlcF | | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| deoxyinosine | deoB: phosphopentomutase | | |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | C665_RS04725 | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | | |
| 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 | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyribose | deoK: deoxyribokinase | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fructose | Slc2a5: fructose:H+ symporter | | |
| fucose | aldA: lactaldehyde dehydrogenase | C665_RS10280 | C665_RS08800 |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | C665_RS02965 | |
| 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 | galE: UDP-glucose 4-epimerase | C665_RS03985 | C665_RS01710 |
| 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 | gci: D-galactarolactone cycloisomerase | | |
| galacturonate | gli: D-galactarolactone isomerase | | |
| galacturonate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | C665_RS13710 | |
| galacturonate | udh: D-galacturonate dehydrogenase | | |
| gluconate | gnd: 6-phosphogluconate dehydrogenase, decarboxylating | | |
| gluconate | gntK: D-gluconate kinase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | C665_RS02440 | |
| glucose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
| glucuronate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | C665_RS13710 | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| glutamate | braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) | C665_RS15470 | C665_RS09040 |
| glutamate | braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) | C665_RS15465 | C665_RS09035 |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | C665_RS14520 | C665_RS10735 |
| glycerol | glpF: glycerol facilitator glpF | | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| lactose | galE: UDP-glucose 4-epimerase | C665_RS03985 | C665_RS01710 |
| lactose | galK: galactokinase (-1-phosphate forming) | | |
| lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| lactose | glk: glucokinase | C665_RS17905 | |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | | |
| lysine | argT: L-lysine ABC transporter, substrate-binding component ArgT | C665_RS06445 | C665_RS19670 |
| lysine | hisM: L-lysine ABC transporter, permease component 1 (HisM) | C665_RS06455 | C665_RS18760 |
| lysine | hisP: L-lysine ABC transporter, ATPase component HisP | C665_RS06460 | C665_RS18755 |
| lysine | hisQ: L-lysine ABC transporter, permease component 2 (HisQ) | C665_RS06450 | C665_RS18760 |
| lysine | patA: cadaverine aminotransferase | C665_RS01920 | C665_RS13470 |
| lysine | patD: 5-aminopentanal dehydrogenase | C665_RS10280 | C665_RS08800 |
| maltose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
| mannitol | manA: mannose-6-phosphate isomerase | C665_RS11925 | |
| mannitol | mt1d: mannitol 1-dehydrogenase | C665_RS10585 | |
| mannitol | PLT5: polyol transporter PLT5 | | |
| mannose | manA: mannose-6-phosphate isomerase | C665_RS11925 | |
| mannose | STP6: mannose:H+ symporter | | |
| 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 | C665_RS03075 | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| myoinositol | mmsA: malonate-semialdehyde dehydrogenase | C665_RS10280 | C665_RS13475 |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | C665_RS02440 | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| phenylacetate | pimB: 3-oxopimeloyl-CoA:CoA acetyltransferase | C665_RS04230 | C665_RS03170 |
| phenylacetate | ppa: phenylacetate permease ppa | C665_RS12865 | C665_RS13515 |
| phenylalanine | pimB: 3-oxopimeloyl-CoA:CoA acetyltransferase | C665_RS04230 | C665_RS03170 |
| proline | prdA: D-proline reductase, prdA component | | |
| proline | prdB: D-proline reductase, prdB component | | |
| proline | prdC: D-proline reductase, electron transfer component PrdC | C665_RS10995 | |
| proline | prdF: proline racemase | | |
| putrescine | gabT: gamma-aminobutyrate transaminase | C665_RS13470 | C665_RS01920 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | C665_RS13470 | C665_RS01920 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | C665_RS10280 | C665_RS00960 |
| putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | C665_RS09750 | |
| rhamnose | aldA: lactaldehyde dehydrogenase | C665_RS10280 | C665_RS08800 |
| 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 | | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| sorbitol | sdh: sorbitol dehydrogenase | C665_RS06220 | C665_RS05895 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
| sucrose | SUS: sucrose synthase | | |
| sucrose | sut: sucrose:proton symporter SUT/SUC | | |
| thymidine | deoA: thymidine phosphorylase DeoA | C665_RS17700 | C665_RS01900 |
| thymidine | deoB: phosphopentomutase | | |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
| trehalose | treF: trehalase | C665_RS11865 | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | C665_RS14635 | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | C665_RS15470 | C665_RS09040 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | C665_RS11695 | C665_RS13475 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | C665_RS18910 | C665_RS06905 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | C665_RS11135 | |
| 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