Potential Gaps in catabolism of small carbon sources in Thauera humireducens SgZ-1
Found 110 low-confidence and 36 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | dctP: 2-oxoglutarate TRAP transporter, solute receptor component DctP | AC731_RS18790 | AC731_RS01690 |
| 2-oxoglutarate | dctQ: 2-oxoglutarate TRAP transporter, small permease component DctQ | | |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | AC731_RS11365 | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arginine | rocF: arginase | AC731_RS16685 | |
| asparagine | dauA: dicarboxylic acid transporter DauA | AC731_RS10565 | |
| aspartate | dauA: dicarboxylic acid transporter DauA | AC731_RS10565 | |
| cellobiose | cbp: cellobiose phosphorylase | | |
| cellobiose | cdt: cellobiose transporter cdt-1/cdt-2 | | |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | AC731_RS03265 | AC731_RS13635 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | AC731_RS03255 | AC731_RS03260 |
| citrulline | arcC: carbamate kinase | | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | AC731_RS16610 | |
| deoxyinosine | deoB: phosphopentomutase | AC731_RS02055 | |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | AC731_RS05125 | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | AC731_RS16830 | AC731_RS08230 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| 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 | AC731_RS17195 | AC731_RS09595 |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | AC731_RS11365 | |
| 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 | dopDH: 2,5-dioxopentanonate dehydrogenase | AC731_RS09755 | AC731_RS17195 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | AC731_RS01010 | |
| gluconate | gnd: 6-phosphogluconate dehydrogenase, decarboxylating | | |
| gluconate | gntA: gluconate TRAP transporter, small permease component | AC731_RS16940 | |
| gluconate | gntB: gluconate TRAP transporter, large permease component | AC731_RS16935 | AC731_RS14355 |
| gluconate | gntK: D-gluconate kinase | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | AC731_RS17645 | |
| glucosamine | SLC2A2: glucosamine transporter SLC2A2 | | |
| glucose | MFS-glucose: glucose transporter, MFS superfamily | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | garL: 5-dehydro-4-deoxy-D-glucarate aldolase | AC731_RS14335 | AC731_RS01010 |
| glucuronate | uxuL: D-glucaro-1,5-lactonase UxuL or UxuF | AC731_RS14360 | |
| glutamate | gdhA: glutamate dehydrogenase, NAD-dependent | AC731_RS13715 | AC731_RS17035 |
| glycerol | dhaD: glycerol dehydrogenase | AC731_RS08230 | AC731_RS16830 |
| glycerol | dhaK': dihydroxyacetone kinase, ATP dependent (monomeric) | | |
| glycerol | glpF: glycerol facilitator glpF | | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| 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) | | |
| lysine | argT: L-lysine ABC transporter, substrate-binding component ArgT | AC731_RS03250 | AC731_RS13625 |
| lysine | davT: 5-aminovalerate aminotransferase | AC731_RS03870 | AC731_RS16685 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | AC731_RS17860 | AC731_RS11725 |
| lysine | gcdH: glutaryl-CoA dehydrogenase | AC731_RS16770 | AC731_RS17095 |
| lysine | hisM: L-lysine ABC transporter, permease component 1 (HisM) | AC731_RS03260 | AC731_RS13630 |
| lysine | hisP: L-lysine ABC transporter, ATPase component HisP | AC731_RS03265 | AC731_RS13635 |
| lysine | hisQ: L-lysine ABC transporter, permease component 2 (HisQ) | AC731_RS03255 | AC731_RS03260 |
| lysine | patA: cadaverine aminotransferase | AC731_RS16685 | AC731_RS03870 |
| lysine | patD: 5-aminopentanal dehydrogenase | AC731_RS17195 | AC731_RS09595 |
| maltose | malA: 6-phospho-alphaglucosidase | | |
| maltose | malEIICBA: maltose phosphotransferase system, EII-CBA components | | |
| mannitol | mt2d: mannitol 2-dehydrogenase | AC731_RS06795 | AC731_RS00590 |
| mannitol | PLT5: polyol transporter PLT5 | | |
| mannose | manA: mannose-6-phosphate isomerase | AC731_RS04970 | |
| 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 | AC731_RS10030 | AC731_RS10085 |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| myoinositol | mmsA: malonate-semialdehyde dehydrogenase | AC731_RS09755 | AC731_RS17195 |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | AC731_RS17645 | |
| 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 | AC731_RS08070 | |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | AC731_RS17460 | AC731_RS14145 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | AC731_RS17425 | AC731_RS03960 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | AC731_RS17425 | AC731_RS03960 |
| phenylacetate | paaK: phenylacetate-CoA ligase | AC731_RS11730 | AC731_RS17130 |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | AC731_RS17835 | AC731_RS17460 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylacetate | ppa: phenylacetate permease ppa | AC731_RS10365 | AC731_RS11880 |
| phenylalanine | iorAB: phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB | AC731_RS18230 | AC731_RS11690 |
| phenylalanine | paaA: phenylacetyl-CoA 1,2-epoxidase, subunit A | | |
| phenylalanine | paaB: phenylacetyl-CoA 1,2-epoxidase, subunit B | | |
| phenylalanine | paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C | | |
| phenylalanine | paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E | AC731_RS08070 | |
| phenylalanine | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | AC731_RS17460 | AC731_RS14145 |
| phenylalanine | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | AC731_RS17425 | AC731_RS03960 |
| phenylalanine | paaJ2: 3-oxoadipyl-CoA thiolase | AC731_RS17425 | AC731_RS03960 |
| phenylalanine | paaZ1: oxepin-CoA hydrolase | AC731_RS17835 | AC731_RS17460 |
| phenylalanine | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| putrescine | gabT: gamma-aminobutyrate transaminase | AC731_RS16685 | AC731_RS03870 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | AC731_RS16685 | AC731_RS03870 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | AC731_RS17195 | AC731_RS01805 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| rhamnose | aldA: lactaldehyde dehydrogenase | AC731_RS17195 | AC731_RS09595 |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | AC731_RS08580 | AC731_RS08065 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | AC731_RS14365 | |
| rhamnose | LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase | AC731_RS14335 | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsK: ribokinase | | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| sorbitol | sdh: sorbitol dehydrogenase | AC731_RS13895 | AC731_RS16830 |
| 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 | AC731_RS12220 | AC731_RS03890 |
| thymidine | deoB: phosphopentomutase | AC731_RS02055 | |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | PsTP: trehalose phosphorylase | | |
| trehalose | TRET1: facilitated trehalose transporter Tret1 | | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | AC731_RS16920 | AC731_RS16910 |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | AC731_RS17945 | AC731_RS08210 |
| valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | AC731_RS15700 | AC731_RS15925 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | AC731_RS09755 | AC731_RS16435 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | AC731_RS11370 | AC731_RS11375 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | AC731_RS13905 | |
| 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