Potential Gaps in catabolism of small carbon sources in Dyadobacter tibetensis Y620-1
Found 75 low-confidence and 52 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | X939_RS0102780 | |
| 4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | | |
| 4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | X939_RS22465 | |
| 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 | X939_RS0121495 | |
| acetate | dctA: organic acid/proton symporter DctA | X939_RS0107610 | X939_RS0105660 |
| arabinose | Echvi_1880: L-arabinose:Na+ symporter | X939_RS0104810 | X939_RS0110740 |
| arginine | rocE: L-arginine permease | | |
| arginine | rocF: arginase | | |
| cellobiose | bgl: cellobiase | X939_RS0106735 | |
| cellobiose | glk: glucokinase | X939_RS0118470 | X939_RS0107285 |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | X939_RS0120890 | X939_RS0121095 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | | |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | | |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| D-alanine | cycA: D-alanine:H+ symporter CycA | | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | larD: D,L-lactic acid transporter | X939_RS0108570 | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | X939_RS0117325 | X939_RS0114125 |
| deoxyinosine | deoB: phosphopentomutase | X939_RS0105135 | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | | |
| deoxyribonate | aacS: acetoacetyl-CoA synthetase | X939_RS0107425 | X939_RS0109710 |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | X939_RS0105700 | X939_RS0115790 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoP: deoxyribose transporter | X939_RS0117630 | |
| ethanol | etoh-dh-nad: ethanol dehydrogenase (NAD(P)) | X939_RS0101125 | X939_RS0111485 |
| fucose | fucD: L-fuconate dehydratase | | |
| fucose | fucDH: 2-keto-3-deoxy-L-fuconate 4-dehydrogenase | X939_RS0104630 | X939_RS0111250 |
| galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| gluconate | gntK: D-gluconate kinase | X939_RS0113300 | |
| glucosamine | nagK: N-acetylglucosamine kinase | X939_RS0118470 | X939_RS0107285 |
| glucose | glk: glucokinase | X939_RS0118470 | X939_RS0107285 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | X939_RS0102575 | X939_RS0104335 |
| glucuronate | uxuB: D-mannonate dehydrogenase | X939_RS0113100 | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | X939_RS0103910 | X939_RS0106825 |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
| histidine | hutH: histidine ammonia-lyase | X939_RS0103885 | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| histidine | permease: L-histidine permease | | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | X939_RS0114560 | X939_RS0119550 |
| isoleucine | Bap2: L-isoleucine permease Bap2 | | |
| isoleucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | X939_RS0120795 | |
| isoleucine | bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | X939_RS0108605 | X939_RS0120105 |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | X939_RS0104565 | X939_RS0102400 |
| isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | X939_RS0115225 | X939_RS0101630 |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | X939_RS0109760 | X939_RS0108310 |
| L-lactate | larD: D,L-lactic acid transporter LarD | X939_RS0108570 | |
| L-lactate | lldG: L-lactate dehydrogenase, LldG subunit | X939_RS0104595 | |
| lactose | glk: glucokinase | X939_RS0118470 | X939_RS0107285 |
| lactose | klh: periplasmic 3'-ketolactose hydrolase | X939_RS0114470 | |
| lactose | lacB': periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) | X939_RS0120070 | X939_RS0112220 |
| lactose | lacC': periplasmic lactose 3-dehydrogenase, LacC subunit | X939_RS0104740 | X939_RS0103065 |
| leucine | aacS: acetoacetyl-CoA synthetase | X939_RS0107425 | X939_RS0109710 |
| leucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | X939_RS0120795 | |
| leucine | bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | X939_RS0108605 | X939_RS0120105 |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | X939_RS0104565 | X939_RS0102400 |
| leucine | leuT: L-leucine:Na+ symporter LeuT | | |
| leucine | liuA: isovaleryl-CoA dehydrogenase | X939_RS0119550 | X939_RS0114560 |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | X939_RS0109760 | X939_RS0108310 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | X939_RS0109475 | X939_RS0101630 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | X939_RS0108515 | X939_RS0119410 |
| lysine | hglS: D-2-hydroxyglutarate synthase | | |
| lysine | lysN: 2-aminoadipate transaminase | X939_RS0114440 | X939_RS0120435 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | X939_RS0118010 | X939_RS0110690 |
| maltose | glk: glucokinase | X939_RS0118470 | X939_RS0107285 |
| mannitol | PLT5: polyol transporter PLT5 | | |
| mannose | manA: mannose-6-phosphate isomerase | X939_RS0103720 | X939_RS0110035 |
| mannose | manP: mannose PTS system, EII-CBA components | | |
| myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | X939_RS0104790 | |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | X939_RS0104795 | X939_RS0117100 |
| myoinositol | PS417_11885: myo-inositol ABC transporter, substrate-binding component | X939_RS0110160 | |
| myoinositol | PS417_11895: myo-inositol ABC transporter, permease component | X939_RS0121530 | X939_RS0116935 |
| NAG | nagK: N-acetylglucosamine kinase | X939_RS0118470 | X939_RS0107285 |
| 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 | X939_RS0114445 | |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | X939_RS0109475 | X939_RS0101630 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | X939_RS0109475 | X939_RS0110100 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | X939_RS0119830 | X939_RS0102770 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | X939_RS0119830 | X939_RS0102770 |
| phenylacetate | paaK: phenylacetate-CoA ligase | X939_RS0104125 | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aacS: acetoacetyl-CoA synthetase | X939_RS0107425 | X939_RS0109710 |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | maiA: maleylacetoacetate isomerase | | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | X939_RS0112120 | |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | X939_RS0109760 | X939_RS0108310 |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | gabT: gamma-aminobutyrate transaminase | X939_RS0120435 | X939_RS0102485 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | X939_RS0103685 | X939_RS0100145 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| pyruvate | SLC5A8: sodium-coupled pyruvate transporter | X939_RS0112035 | |
| serine | serP: L-serine permease SerP | | |
| sorbitol | sdh: sorbitol dehydrogenase | X939_RS0113100 | X939_RS0112630 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | X939_RS0108280 | |
| sucrose | ams: sucrose hydrolase (invertase) | X939_RS22210 | |
| threonine | tdcC: L-threonine:H+ symporter TdcC | | |
| thymidine | deoA: thymidine phosphorylase DeoA | | |
| thymidine | deoB: phosphopentomutase | X939_RS0105135 | |
| trehalose | glk: glucokinase | X939_RS0118470 | X939_RS0107285 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aacS: acetoacetyl-CoA synthetase | X939_RS0107425 | X939_RS0109710 |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | X939_RS0114560 | X939_RS0119550 |
| valine | Bap2: L-valine permease Bap2 | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | | |
| valine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | X939_RS0120795 | |
| valine | bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | X939_RS0108605 | X939_RS0120105 |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | X939_RS0104565 | X939_RS0102400 |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | X939_RS0101630 | X939_RS0109475 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | | |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | X939_RS0109760 | X939_RS0108310 |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | X939_RS0108280 | |
| xylitol | xdhA: xylitol dehydrogenase | X939_RS0112630 | X939_RS0105700 |
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