Potential Gaps in catabolism of small carbon sources in Thermobifida halotolerans YIM 90462
Found 100 low-confidence and 66 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | | |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | AMR52_RS11650 | AMR52_RS03260 |
| arabinose | araE: L-arabinose:H+ symporter | AMR52_RS19045 | |
| arabinose | xacB: L-arabinose 1-dehydrogenase | AMR52_RS16130 | AMR52_RS03430 |
| arabinose | xacC: L-arabinono-1,4-lactonase | | |
| arabinose | xacD: L-arabinonate dehydratase | AMR52_RS12095 | AMR52_RS06220 |
| arabinose | xacE: 2-dehydro-3-deoxy-L-arabinonate dehydratase | | |
| arginine | arcC: carbamate kinase | AMR52_RS07290 | |
| arginine | rocE: L-arginine permease | | |
| asparagine | dauA: dicarboxylic acid transporter DauA | AMR52_RS02940 | |
| aspartate | dauA: dicarboxylic acid transporter DauA | AMR52_RS02940 | |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | AMR52_RS01120 | AMR52_RS02570 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | AMR52_RS01125 | |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | AMR52_RS01125 | AMR52_RS10510 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| citrulline | arcC: carbamate kinase | AMR52_RS07290 | |
| D-alanine | cycA: D-alanine:H+ symporter CycA | | |
| D-alanine | dadA: D-alanine dehydrogenase | AMR52_RS03775 | AMR52_RS19010 |
| D-lactate | D-LDH: D-lactate dehydrogenase | AMR52_RS01420 | AMR52_RS05870 |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | AMR52_RS12265 | AMR52_RS12410 |
| deoxyinosine | adh: acetaldehyde dehydrogenase (not acylating) | AMR52_RS16115 | AMR52_RS17885 |
| deoxyinosine | deoB: phosphopentomutase | AMR52_RS05040 | |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | AMR52_RS01895 | AMR52_RS16130 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | adh: acetaldehyde dehydrogenase (not acylating) | AMR52_RS16115 | AMR52_RS17885 |
| deoxyribose | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| ethanol | adh: acetaldehyde dehydrogenase (not acylating) | AMR52_RS16115 | AMR52_RS17885 |
| fructose | glcP: fructose:H+ symporter GlcP | AMR52_RS19045 | |
| fructose | scrK: fructokinase | AMR52_RS17005 | AMR52_RS10310 |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | | |
| fucose | fucI: L-fucose isomerase FucI | | |
| fucose | fucP: L-fucose:H+ symporter FucP | | |
| fucose | fucU: L-fucose mutarotase FucU | AMR52_RS11160 | |
| galactose | galK: galactokinase (-1-phosphate forming) | AMR52_RS20770 | |
| galactose | galP: galactose:H+ symporter GalP | AMR52_RS19045 | |
| galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| galactose | pgmA: alpha-phosphoglucomutase | AMR52_RS15425 | AMR52_RS05040 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | gci: D-galactarolactone cycloisomerase | AMR52_RS07830 | AMR52_RS12095 |
| galacturonate | gli: D-galactarolactone isomerase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | AMR52_RS05045 | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | AMR52_RS07830 | AMR52_RS12095 |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | | |
| glycerol | glpF: glycerol facilitator glpF | | |
| histidine | Ga0059261_1577: L-histidine transporter | AMR52_RS18150 | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | AMR52_RS17905 | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | AMR52_RS02630 | AMR52_RS15620 |
| histidine | hutU: urocanase | | |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | AMR52_RS09775 | AMR52_RS13510 |
| isoleucine | livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) | AMR52_RS18935 | AMR52_RS08450 |
| isoleucine | livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | | |
| isoleucine | livM: L-isoleucine ABC transporter, permease component 2 (LivM/BraE) | AMR52_RS18940 | AMR52_RS08445 |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | AMR52_RS20700 | AMR52_RS22530 |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| L-malate | sdlC: L-malate:Na+ symporter SdlC | | |
| lactose | galK: galactokinase (-1-phosphate forming) | AMR52_RS20770 | |
| lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| lactose | lacP: lactose permease LacP | | |
| lactose | pgmA: alpha-phosphoglucomutase | AMR52_RS15425 | AMR52_RS05040 |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | AMR52_RS09775 | AMR52_RS13510 |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | AMR52_RS22530 | AMR52_RS20700 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | AMR52_RS01315 | AMR52_RS14405 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | AMR52_RS17100 | AMR52_RS20690 |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| leucine | livH: L-leucine ABC transporter, permease component 1 (LivH/BraD) | AMR52_RS18935 | AMR52_RS08450 |
| leucine | livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | | |
| leucine | livM: L-leucine ABC transporter, permease component 2 (LivM/BraE) | AMR52_RS18940 | AMR52_RS08445 |
| lysine | cadA: lysine decarboxylase | | |
| lysine | davD: glutarate semialdehyde dehydrogenase | AMR52_RS13870 | AMR52_RS21235 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | AMR52_RS09085 | AMR52_RS16205 |
| lysine | gcdH: glutaryl-CoA dehydrogenase | AMR52_RS12140 | AMR52_RS17090 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| lysine | patA: cadaverine aminotransferase | AMR52_RS07295 | AMR52_RS05940 |
| mannitol | mtlA: mannitol phosphotransferase system, EII-CBA components | | |
| mannitol | mtlD: mannitol-1-phosphate 5-dehydrogenase | | |
| mannose | manP: mannose PTS system, EII-CBA components | | |
| myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | | |
| myoinositol | iolC: 5-dehydro-2-deoxy-D-gluconate kinase | AMR52_RS09825 | |
| myoinositol | iolD: 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase | | |
| myoinositol | iolE: scyllo-inosose 2-dehydratase | | |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | AMR52_RS07680 | |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | AMR52_RS09825 | |
| myoinositol | iolT: myo-inositol:H+ symporter | AMR52_RS19045 | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | AMR52_RS05045 | |
| 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 | AMR52_RS01315 | AMR52_RS14405 |
| phenylacetate | paaK: phenylacetate-CoA ligase | AMR52_RS11500 | AMR52_RS18260 |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | AMR52_RS14495 | AMR52_RS18880 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylacetate | ppa: phenylacetate permease ppa | AMR52_RS03190 | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| 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 | | |
| phenylalanine | paaF: 2,3-dehydroadipyl-CoA hydratase | AMR52_RS01315 | AMR52_RS14405 |
| phenylalanine | paaK: phenylacetate-CoA ligase | AMR52_RS11500 | AMR52_RS18260 |
| phenylalanine | paaZ1: oxepin-CoA hydrolase | AMR52_RS14495 | AMR52_RS18880 |
| phenylalanine | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | pad-dh: phenylacetaldehyde dehydrogenase | AMR52_RS16115 | AMR52_RS10345 |
| phenylalanine | PPDCalpha: phenylpyruvate decarboxylase, alpha subunit | AMR52_RS09770 | AMR52_RS13520 |
| phenylalanine | PPDCbeta: phenylpyruvate decarboxylase, beta subunit | AMR52_RS24355 | AMR52_RS13515 |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | AMR52_RS20700 | AMR52_RS22530 |
| putrescine | gabT: gamma-aminobutyrate transaminase | AMR52_RS01840 | AMR52_RS10340 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | AMR52_RS10340 | AMR52_RS07295 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| rhamnose | rhaM: L-rhamnose mutarotase | AMR52_RS11160 | |
| rhamnose | rhaP: L-rhamnose ABC transporter, permease component 1 (RhaP) | AMR52_RS11170 | AMR52_RS11175 |
| rhamnose | rhaS: L-rhamnose ABC transporter, substrate-binding component RhaS | AMR52_RS11165 | |
| rhamnose | rhaT': L-rhamnose ABC transporter, ATPase component RhaT | AMR52_RS11180 | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | | |
| serine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | AMR52_RS08450 | AMR52_RS12120 |
| serine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | AMR52_RS08445 | AMR52_RS12125 |
| sorbitol | mtlF: ABC transporter for polyols MtlEFGK, permease component MtlF | AMR52_RS08270 | AMR52_RS23410 |
| sorbitol | mtlK: ABC transporter for polyols MtlEFGK, permease component MtlK | AMR52_RS12205 | AMR52_RS10350 |
| sorbitol | scrK: fructokinase | AMR52_RS17005 | AMR52_RS10310 |
| sorbitol | sdh: sorbitol dehydrogenase | AMR52_RS14540 | AMR52_RS01895 |
| succinate | dauA: succinate:H+ symporter DauA | AMR52_RS02940 | |
| sucrose | ams: sucrose hydrolase (invertase) | AMR52_RS02690 | AMR52_RS12195 |
| threonine | adh: acetaldehyde dehydrogenase (not acylating) | AMR52_RS16115 | AMR52_RS17885 |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | | |
| threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | AMR52_RS08450 | AMR52_RS12120 |
| threonine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | AMR52_RS08445 | AMR52_RS12125 |
| threonine | ltaE: L-threonine aldolase | AMR52_RS05300 | |
| thymidine | adh: acetaldehyde dehydrogenase (not acylating) | AMR52_RS16115 | AMR52_RS17885 |
| thymidine | deoA: thymidine phosphorylase DeoA | | |
| thymidine | deoB: phosphopentomutase | AMR52_RS05040 | |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | treF: trehalase | AMR52_RS02690 | AMR52_RS12195 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | AMR52_RS01465 | AMR52_RS13355 |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | AMR52_RS11475 | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | AMR52_RS14495 | AMR52_RS14435 |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | AMR52_RS09775 | AMR52_RS13510 |
| valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | AMR52_RS18935 | AMR52_RS08450 |
| valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | | |
| valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | AMR52_RS18940 | AMR52_RS08445 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | AMR52_RS01825 | AMR52_RS12145 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | AMR52_RS18725 | |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | AMR52_RS20700 | AMR52_RS22530 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | AMR52_RS08280 | AMR52_RS18830 |
| xylose | xylB: xylulokinase | | |
| xylose | xylT: D-xylose transporter | AMR52_RS19045 | |
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