Potential Gaps in catabolism of small carbon sources in Kocuria turfanensis HO-9042
Found 55 low-confidence and 63 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | AYX06_RS08060 | AYX06_RS16275 |
| 4-hydroxybenzoate | pcaB: 3-carboxymuconate cycloisomerase | AYX06_RS05800 | |
| 4-hydroxybenzoate | pcaD: 3-oxoadipate enol-lactone hydrolase | AYX06_RS19670 with AYX06_RS18615 | AYX06_RS05795 |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | AYX06_RS09015 | AYX06_RS09820 |
| arabinose | gguA: L-arabinose ABC transporter, ATPase component GguA | AYX06_RS12005 | AYX06_RS15290 |
| arabinose | gguB: L-arabinose ABC transporter, permease component GguB | AYX06_RS12010 | |
| arginine | gbamidase: guanidinobutyramidase | AYX06_RS15485 | AYX06_RS08180 |
| arginine | kauB: 4-guanidinobutyraldehyde dehydrogenase | AYX06_RS09260 | AYX06_RS16305 |
| arginine | rocE: L-arginine permease | AYX06_RS16200 | AYX06_RS08205 |
| asparagine | ans: asparaginase | AYX06_RS06760 | AYX06_RS14405 |
| asparagine | glt: aspartate:proton symporter Glt | AYX06_RS00120 | AYX06_RS16315 |
| aspartate | glt: aspartate:proton symporter Glt | AYX06_RS00120 | AYX06_RS16315 |
| cellobiose | cebE: cellobiose ABC transporter, substrate-binding component CebE | AYX06_RS11255 | |
| cellobiose | glk: glucokinase | AYX06_RS00415 | AYX06_RS06820 |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | AYX06_RS06170 | AYX06_RS17570 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | AYX06_RS08215 | |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | AYX06_RS17565 | AYX06_RS08215 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| citrulline | arcC: carbamate kinase | | |
| citrulline | put1: proline dehydrogenase | AYX06_RS08775 | AYX06_RS07690 |
| citrulline | putA: L-glutamate 5-semialdeyde dehydrogenase | AYX06_RS08775 | AYX06_RS07690 |
| D-alanine | cycA: D-alanine:H+ symporter CycA | AYX06_RS08205 | AYX06_RS16200 |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | D-LDH: D-lactate dehydrogenase | AYX06_RS06610 | AYX06_RS13185 |
| D-serine | cycA: D-serine:H+ symporter CycA | AYX06_RS08205 | AYX06_RS16200 |
| D-serine | dsdA: D-serine ammonia-lyase | AYX06_RS15515 | |
| deoxyinosine | adh: acetaldehyde dehydrogenase (not acylating) | AYX06_RS16305 | AYX06_RS14125 |
| deoxyinosine | bmpA: deoxyinosine ABC transporter, substrate-binding component | AYX06_RS15285 | |
| deoxyinosine | deoB: phosphopentomutase | AYX06_RS16260 | AYX06_RS05575 |
| deoxyinosine | nupB: deoxyinosine ABC transporter, permease component 1 | AYX06_RS15295 | |
| deoxyinosine | nupC': deoxyinosine ABC transporter, permease component 2 | AYX06_RS15300 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | AYX06_RS10315 | AYX06_RS07900 |
| 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) | AYX06_RS16305 | AYX06_RS14125 |
| deoxyribose | deoP: deoxyribose transporter | | |
| ethanol | adh: acetaldehyde dehydrogenase (not acylating) | AYX06_RS16305 | AYX06_RS14125 |
| fructose | 1pfk: 1-phosphofructokinase | AYX06_RS14810 | |
| 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 | | |
| galactose | gguA: galactose ABC transporter, ATPase component GguA | AYX06_RS12005 | AYX06_RS15290 |
| galactose | gguB: galactose ABC transporter, permease component GguB | AYX06_RS12010 | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | udh: D-galacturonate dehydrogenase | | |
| galacturonate | uxuL: D-galactaro-1,5-lactonase (UxuL or UxuF) | AYX06_RS13455 | |
| gluconate | gntK: D-gluconate kinase | AYX06_RS11135 | |
| gluconate | gntT: gluconate:H+ symporter GntT | AYX06_RS01670 | AYX06_RS11120 |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucose | glk: glucokinase | AYX06_RS00415 | AYX06_RS06820 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| glucuronate | uxuL: D-glucaro-1,5-lactonase UxuL or UxuF | AYX06_RS13455 | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | AYX06_RS02845 | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | AYX06_RS13270 | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| histidine | permease: L-histidine permease | AYX06_RS16200 | AYX06_RS08205 |
| isoleucine | Bap2: L-isoleucine permease Bap2 | AYX06_RS16200 | AYX06_RS08205 |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | AYX06_RS13360 | AYX06_RS00480 |
| lactose | glk: glucokinase | AYX06_RS00415 | AYX06_RS06820 |
| lactose | lacP: lactose permease LacP | | |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | AYX06_RS13360 | AYX06_RS00480 |
| leucine | leuT: L-leucine:Na+ symporter LeuT | AYX06_RS06135 | |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | AYX06_RS12215 | AYX06_RS11835 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | AYX06_RS10100 | AYX06_RS08340 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | AYX06_RS12210 | AYX06_RS16330 |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| lysine | davA: 5-aminovaleramidase | AYX06_RS15485 | AYX06_RS08180 |
| lysine | davD: glutarate semialdehyde dehydrogenase | AYX06_RS14125 | AYX06_RS09260 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | AYX06_RS10090 | AYX06_RS01285 |
| maltose | glk: glucokinase | AYX06_RS00415 | AYX06_RS06820 |
| mannose | manP: mannose PTS system, EII-CBA components | AYX06_RS14815 | |
| myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | AYX06_RS15060 | |
| myoinositol | iolE: scyllo-inosose 2-dehydratase | AYX06_RS15005 | |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | AYX06_RS15015 | AYX06_RS10015 |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | AYX06_RS08340 | AYX06_RS10100 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | AYX06_RS08340 | AYX06_RS10100 |
| phenylacetate | ppa: phenylacetate permease ppa | AYX06_RS16640 | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | AYX06_RS08205 | AYX06_RS16200 |
| phenylalanine | paaF: 2,3-dehydroadipyl-CoA hydratase | AYX06_RS08340 | AYX06_RS10100 |
| phenylalanine | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | AYX06_RS08340 | AYX06_RS10100 |
| proline | put1: proline dehydrogenase | AYX06_RS08775 | AYX06_RS07690 |
| proline | putA: L-glutamate 5-semialdeyde dehydrogenase | AYX06_RS08775 | AYX06_RS07690 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| rhamnose | rhaM: L-rhamnose mutarotase | AYX06_RS10195 | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | serP: L-serine permease SerP | AYX06_RS16200 | AYX06_RS08205 |
| sorbitol | mtlA: PTS system for polyols, EII-CBA components | AYX06_RS05555 | |
| sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | AYX06_RS10315 | AYX06_RS11945 |
| sucrose | 1pfk: 1-phosphofructokinase | AYX06_RS14810 | |
| sucrose | ams: sucrose hydrolase (invertase) | AYX06_RS09180 | AYX06_RS06495 |
| threonine | adh: acetaldehyde dehydrogenase (not acylating) | AYX06_RS16305 | AYX06_RS14125 |
| threonine | RR42_RS28305: L-threonine:H+ symporter | AYX06_RS16200 | AYX06_RS08205 |
| thymidine | adh: acetaldehyde dehydrogenase (not acylating) | AYX06_RS16305 | AYX06_RS14125 |
| thymidine | deoB: phosphopentomutase | AYX06_RS16260 | AYX06_RS05575 |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | glk: glucokinase | AYX06_RS00415 | AYX06_RS06820 |
| trehalose | treF: trehalase | AYX06_RS06495 | AYX06_RS08420 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | AYX06_RS08205 | AYX06_RS16200 |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | AYX06_RS08205 | AYX06_RS16200 |
| tyrosine | fahA: fumarylacetoacetate hydrolase | | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | Bap2: L-valine permease Bap2 | AYX06_RS16200 | AYX06_RS08205 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | AYX06_RS14040 | AYX06_RS10100 |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | AYX06_RS13360 | AYX06_RS00480 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | AYX06_RS15030 | AYX06_RS10045 |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | AYX06_RS14980 | AYX06_RS10665 |
| xylose | xylG: ABC transporter for xylose, ATP-binding component xylG | AYX06_RS12005 | AYX06_RS15290 |
| xylose | xylH: ABC transporter for xylose, permease component xylH | AYX06_RS12010 | |
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