Potential Gaps in catabolism of small carbon sources in Luteimonas huabeiensis HB2
Found 90 low-confidence and 38 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | ligA: protocatechuate 4,5-dioxygenase, alpha subunit | | |
| 4-hydroxybenzoate | ligB: protocatechuate 4,5-dioxygenase, beta subunit | | |
| 4-hydroxybenzoate | ligC: 2-hydroxy-4-carboxymuconate-6-semialdehyde dehydrogenase | | |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | Z164_RS0103015 | Z164_RS0106850 |
| 4-hydroxybenzoate | pobA: 4-hydroxybenzoate 3-monooxygenase | | |
| arabinose | araE: L-arabinose:H+ symporter | Z164_RS0116495 | |
| arabinose | xacB: L-arabinose 1-dehydrogenase | Z164_RS0111850 | Z164_RS20265 |
| arabinose | xacC: L-arabinono-1,4-lactonase | | |
| arabinose | xacD: L-arabinonate dehydratase | Z164_RS0114625 | Z164_RS0110905 |
| arabinose | xacE: 2-dehydro-3-deoxy-L-arabinonate dehydratase | | |
| arginine | rocD: ornithine aminotransferase | Z164_RS0103700 | Z164_RS0104555 |
| arginine | rocE: L-arginine permease | | |
| citrate | cit1: citrate:H+ symporter Cit1 | Z164_RS0115710 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | Z164_RS0118440 | Z164_RS22615 |
| 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 | | |
| citrulline | citrullinase: putative citrullinase | Z164_RS0108045 | |
| citrulline | rocD: ornithine aminotransferase | Z164_RS0103700 | Z164_RS0104555 |
| D-alanine | cycA: D-alanine:H+ symporter CycA | | |
| D-alanine | dadA: D-alanine dehydrogenase | Z164_RS0111790 | |
| D-lactate | D-LDH: D-lactate dehydrogenase | Z164_RS0101235 | Z164_RS0101230 |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | Z164_RS0100460 | Z164_RS20710 |
| deoxyinosine | deoB: phosphopentomutase | Z164_RS0100865 | Z164_RS0111380 |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | Z164_RS0112790 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | Z164_RS20265 | Z164_RS0107970 |
| 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 | deoP: deoxyribose transporter | Z164_RS0116790 | |
| fucose | aldA: lactaldehyde dehydrogenase | Z164_RS0100050 | Z164_RS0110845 |
| 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 | Z164_RS0116790 | |
| fucose | fucU: L-fucose mutarotase FucU | | |
| galactose | galK: galactokinase (-1-phosphate forming) | | |
| galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| galacturonate | kdgK: 2-keto-3-deoxygluconate kinase | Z164_RS0100220 | Z164_RS0116795 |
| galacturonate | uxaA: D-altronate dehydratase | | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | Z164_RS0117200 | |
| gluconate | gntK: D-gluconate kinase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | nagX: transmembrane glucosamine N-acetyltransferase NagX | Z164_RS0101630 | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | Z164_RS0117185 | |
| glucuronate | kdgK: 2-keto-3-deoxygluconate kinase | Z164_RS0100220 | Z164_RS0116795 |
| glucuronate | uxaC: D-glucuronate isomerase | Z164_RS0117200 | |
| glucuronate | uxuB: D-mannonate dehydrogenase | Z164_RS0117325 | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | | |
| glycerol | glpF: glycerol facilitator glpF | | |
| glycerol | glpK: glycerol kinase | | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | Z164_RS0109600 | Z164_RS0109400 |
| isoleucine | Bap2: L-isoleucine permease Bap2 | | |
| lactose | galK: galactokinase (-1-phosphate forming) | | |
| lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| lactose | lacP: lactose permease LacP | | |
| leucine | leuT: L-leucine:Na+ symporter LeuT | | |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | Z164_RS0109700 | |
| lysine | cadA: lysine decarboxylase | Z164_RS0109990 | |
| lysine | davD: glutarate semialdehyde dehydrogenase | Z164_RS0109520 | Z164_RS0100050 |
| lysine | davT: 5-aminovalerate aminotransferase | Z164_RS0103700 | Z164_RS0104555 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | | |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| lysine | patA: cadaverine aminotransferase | Z164_RS0104555 | Z164_RS0103700 |
| lysine | patD: 5-aminopentanal dehydrogenase | Z164_RS0109520 | Z164_RS0100050 |
| maltose | susB: alpha-glucosidase (maltase) | | |
| mannitol | mt2d: mannitol 2-dehydrogenase | Z164_RS0117325 | Z164_RS0113310 |
| mannitol | PLT5: polyol transporter PLT5 | | |
| mannose | gluP: mannose:Na+ symporter | Z164_RS0116790 | Z164_RS0101610 |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | Z164_RS0117470 | |
| myoinositol | iolM: 2-inosose 4-dehydrogenase | Z164_RS0114950 | Z164_RS0100045 |
| myoinositol | iolN: 2,4-diketo-inositol hydratase | | |
| myoinositol | iolO: 5-dehydro-L-gluconate epimerase | | |
| myoinositol | iolT: myo-inositol:H+ symporter | Z164_RS0116495 | |
| myoinositol | kdgK: 2-keto-3-deoxygluconate kinase | Z164_RS0100220 | Z164_RS0116795 |
| myoinositol | uxaE: D-tagaturonate epimerase | | |
| myoinositol | uxuB: D-mannonate dehydrogenase | Z164_RS0117325 | |
| 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 | Z164_RS0106175 | Z164_RS0104740 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | Z164_RS0106175 | Z164_RS0104740 |
| phenylacetate | paaK: phenylacetate-CoA ligase | Z164_RS0108910 | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | Z164_RS0109725 | Z164_RS0104740 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | Z164_RS0108005 | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | Z164_RS0101700 | |
| propionate | putP: propionate transporter; proline:Na+ symporter | Z164_RS0112435 | |
| putrescine | gabT: gamma-aminobutyrate transaminase | Z164_RS0103700 | Z164_RS0104555 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | Z164_RS0104555 | Z164_RS0103700 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | Z164_RS0100050 | Z164_RS0109520 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| rhamnose | aldA: lactaldehyde dehydrogenase | Z164_RS0100050 | Z164_RS0110845 |
| 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 | rbsU: probable D-ribose transporter RbsU | | |
| serine | serP: L-serine permease SerP | | |
| sorbitol | sdh: sorbitol dehydrogenase | Z164_RS20265 | Z164_RS0100150 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
| sucrose | ams: sucrose hydrolase (invertase) | | |
| threonine | tdcC: L-threonine:H+ symporter TdcC | | |
| thymidine | deoB: phosphopentomutase | Z164_RS0100865 | Z164_RS0111380 |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| trehalose | treF: trehalase | Z164_RS0103465 | |
| tryptophan | antA: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA | Z164_RS0106875 | |
| tryptophan | antB: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB | Z164_RS0106870 | |
| tryptophan | antC: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC | Z164_RS0106865 | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | kynB: kynurenine formamidase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | Z164_RS0109600 | Z164_RS0109400 |
| valine | Bap2: L-valine permease Bap2 | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | Z164_RS0106175 | Z164_RS0104740 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | Z164_RS0109520 | Z164_RS0100050 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | Z164_RS0107975 | |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
| xylitol | xdhA: xylitol dehydrogenase | Z164_RS0113310 | Z164_RS20265 |
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