Potential Gaps in catabolism of small carbon sources in Thermoactinomyces daqus H-18
Found 91 low-confidence and 51 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 | adh: acetaldehyde dehydrogenase (not acylating) | JG50_RS0105030 | JG50_RS0104290 |
| 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 | | |
| alanine | cycA: L-alanine symporter CycA | JG50_RS0115245 | JG50_RS0105800 |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| cellobiose | bglG: cellobiose PTS system, EII-BC or EII-BCA components | | |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | JG50_RS0100590 | JG50_RS0104015 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | JG50_RS0106735 | JG50_RS0104010 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | JG50_RS0100595 | |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | JG50_RS0106740 | JG50_RS0104005 |
| citrulline | arcC: carbamate kinase | | |
| D-alanine | cycA: D-alanine:H+ symporter CycA | JG50_RS0105800 | JG50_RS0109790 |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | glcE: D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) | JG50_RS0103065 | |
| D-lactate | glcF: D-lactate dehydrogenase, FeS subunit GlcF | JG50_RS0116905 | |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
| D-serine | dsdA: D-serine ammonia-lyase | JG50_RS0103020 | JG50_RS0112230 |
| D-serine | dsdX: D-serine transporter DsdX | JG50_RS0113125 | |
| deoxyinosine | adh: acetaldehyde dehydrogenase (not acylating) | JG50_RS0105030 | JG50_RS0104290 |
| deoxyinosine | bmpA: deoxyinosine ABC transporter, substrate-binding component | JG50_RS0103115 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | JG50_RS0101380 | JG50_RS0105740 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | JG50_RS0110475 | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | JG50_RS0107150 | |
| deoxyribose | adh: acetaldehyde dehydrogenase (not acylating) | JG50_RS0105030 | JG50_RS0104290 |
| deoxyribose | deoP: deoxyribose transporter | | |
| ethanol | adh: acetaldehyde dehydrogenase (not acylating) | JG50_RS0105030 | JG50_RS0104290 |
| fucose | aldA: lactaldehyde dehydrogenase | JG50_RS0109305 | JG50_RS0103810 |
| 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 | | |
| fumarate | dctA: fumarate:H+ symporter DctA | JG50_RS0115010 | JG50_RS0113245 |
| galactose | galP: galactose:H+ symporter GalP | | |
| galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | JG50_RS0115695 | |
| galacturonate | eda: 2-keto-3-deoxygluconate 6-phosphate aldolase | JG50_RS0101175 | JG50_RS0102965 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | uxaA: D-altronate dehydratase | | |
| galacturonate | uxaC: D-galacturonate isomerase | | |
| gluconate | gntK: D-gluconate kinase | JG50_RS0113120 | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | JG50_RS0100535 | JG50_RS0108625 |
| 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 | JG50_RS0101170 | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | JG50_RS0105675 | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | PA5503: L-histidine ABC transporter, ATPase component | JG50_RS0106810 | JG50_RS0104015 |
| histidine | PA5504: L-histidine ABC transporter, permease component | JG50_RS0106805 | JG50_RS0110920 |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | JG50_RS0107230 | JG50_RS0107225 |
| isoleucine | Bap2: L-isoleucine permease Bap2 | JG50_RS0115245 | JG50_RS0105800 |
| isoleucine | prpC: 2-methylcitrate synthase | JG50_RS0110880 | |
| isoleucine | prpD: 2-methylcitrate dehydratase | | |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| L-malate | dctA: L-malate:H+ symporter DctA | JG50_RS0115010 | JG50_RS0113245 |
| lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | JG50_RS0115695 | |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | | |
| leucine | leuT: L-leucine:Na+ symporter LeuT | | |
| leucine | liuA: isovaleryl-CoA dehydrogenase | JG50_RS0113945 | JG50_RS0107230 |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | JG50_RS0115085 | JG50_RS0106100 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | JG50_RS0106120 | JG50_RS0114535 |
| lysine | bcd: butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit | JG50_RS0107225 | JG50_RS0107230 |
| lysine | ctfA: butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit | | |
| lysine | ctfB: butanoyl-CoA:acetoacetate CoA-transferase, beta subunit | | |
| lysine | etfA: butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit | JG50_RS0115870 | |
| lysine | etfB: butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit | JG50_RS0115865 | |
| lysine | kal: 3-aminobutyryl-CoA deaminase | | |
| lysine | kamD: L-beta-lysine 5,6-aminomutase, alpha subunit | | |
| mannose | manP: mannose PTS system, EII-CBA components | JG50_RS0105050 | |
| myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | JG50_RS0109750 | |
| myoinositol | iolC: 5-dehydro-2-deoxy-D-gluconate kinase | JG50_RS0101180 | |
| myoinositol | iolD: 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase | | |
| myoinositol | iolE: scyllo-inosose 2-dehydratase | | |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | JG50_RS0100080 | |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | JG50_RS0107145 | |
| myoinositol | iolT: myo-inositol:H+ symporter | JG50_RS0101670 | |
| myoinositol | mmsA: malonate-semialdehyde dehydrogenase | JG50_RS0104290 | JG50_RS0103810 |
| NAG | nagPcb: N-acetylglucosamine phosphotransferase system, EII-CB component NagP | JG50_RS0108625 | JG50_RS0100535 |
| phenylacetate | paaB: phenylacetyl-CoA 1,2-epoxidase, subunit B | JG50_RS0109265 | |
| phenylacetate | paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C | JG50_RS0109270 | |
| phenylacetate | paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E | | |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | JG50_RS0105825 | JG50_RS0106695 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | JG50_RS0105830 | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | ARO10: phenylpyruvate decarboxylase | JG50_RS0116720 | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | JG50_RS0115245 | JG50_RS0106285 |
| phenylalanine | paaB: phenylacetyl-CoA 1,2-epoxidase, subunit B | JG50_RS0109265 | |
| phenylalanine | paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C | JG50_RS0109270 | |
| phenylalanine | paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E | | |
| phenylalanine | paaF: 2,3-dehydroadipyl-CoA hydratase | JG50_RS0105825 | JG50_RS0106695 |
| phenylalanine | paaZ1: oxepin-CoA hydrolase | JG50_RS0105830 | |
| phenylalanine | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | pad-dh: phenylacetaldehyde dehydrogenase | JG50_RS0103810 | JG50_RS0109305 |
| proline | opuBA: proline ABC transporter, ATPase component OpuBA/BusAA | JG50_RS0117690 | JG50_RS0103930 |
| propionate | prpC: 2-methylcitrate synthase | JG50_RS0110880 | |
| propionate | prpD: 2-methylcitrate dehydratase | | |
| propionate | prpE: propionyl-CoA synthetase | JG50_RS0110160 | JG50_RS0105805 |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | gabT: gamma-aminobutyrate transaminase | JG50_RS0105185 | JG50_RS0110325 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | JG50_RS0114245 | JG50_RS0105185 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | JG50_RS0103810 | JG50_RS0109305 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | JG50_RS0103655 | JG50_RS0101475 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | JG50_RS0101170 | |
| rhamnose | LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase | JG50_RS0103655 | JG50_RS0104760 |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | serP: L-serine permease SerP | JG50_RS0105800 | JG50_RS0115245 |
| sorbitol | mtlA: PTS system for polyols, EII-CBA components | JG50_RS0112780 | |
| sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | JG50_RS0111700 | JG50_RS0103655 |
| succinate | dctA: succinate:H+ symporter DctA | JG50_RS0115010 | JG50_RS0113245 |
| sucrose | ams: sucrose hydrolase (invertase) | JG50_RS0115665 | |
| threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | JG50_RS0100555 | JG50_RS0100560 |
| threonine | tdcC: L-threonine:H+ symporter TdcC | | |
| thymidine | adh: acetaldehyde dehydrogenase (not acylating) | JG50_RS0105030 | JG50_RS0104290 |
| trehalose | treC: trehalose-6-phosphate hydrolase | JG50_RS0115665 | JG50_RS0113770 |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | JG50_RS0105800 | JG50_RS0106285 |
| tyrosine | fahA: fumarylacetoacetate hydrolase | JG50_RS0101375 | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | JG50_RS0107230 | JG50_RS0107225 |
| valine | Bap2: L-valine permease Bap2 | JG50_RS0115245 | JG50_RS0105800 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | JG50_RS0105830 | JG50_RS0106115 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | JG50_RS0104290 | JG50_RS0103810 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | JG50_RS0115150 | JG50_RS0109685 |
| valine | prpC: 2-methylcitrate synthase | JG50_RS0110880 | |
| valine | prpD: 2-methylcitrate dehydratase | | |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | JG50_RS0105050 | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | | |
| 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