Potential Gaps in catabolism of small carbon sources in Kocuria flava HO-9041
Found 71 low-confidence and 58 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | AS188_RS03520 | AS188_RS01290 |
| 4-hydroxybenzoate | pcaB: 3-carboxymuconate cycloisomerase | AS188_RS10175 | AS188_RS14100 |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | AS188_RS02005 | AS188_RS08185 |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | AS188_RS02770 | AS188_RS06680 |
| arginine | adiA: arginine decarboxylase (AdiA/SpeA) | | |
| arginine | gabT: gamma-aminobutyrate transaminase | AS188_RS01315 | AS188_RS05905 |
| arginine | rocE: L-arginine permease | AS188_RS02160 | AS188_RS01250 |
| arginine | speB: agmatinase | AS188_RS05070 | |
| asparagine | glt: aspartate:proton symporter Glt | AS188_RS08795 | AS188_RS08005 |
| aspartate | glt: aspartate:proton symporter Glt | AS188_RS08795 | AS188_RS08005 |
| cellobiose | bgl: cellobiase | | |
| cellobiose | glk: glucokinase | AS188_RS09060 | AS188_RS10390 |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | AS188_RS14460 | AS188_RS13325 |
| 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 | arcC: carbamate kinase | | |
| citrulline | gabT: gamma-aminobutyrate transaminase | AS188_RS01315 | AS188_RS05905 |
| citrulline | odc: L-ornithine decarboxylase | | |
| D-alanine | cycA: D-alanine:H+ symporter CycA | AS188_RS01250 | AS188_RS03395 |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | D-LDH: D-lactate dehydrogenase | AS188_RS14825 | AS188_RS05040 |
| D-serine | cycA: D-serine:H+ symporter CycA | AS188_RS03395 | AS188_RS02160 |
| D-serine | dsdA: D-serine ammonia-lyase | AS188_RS07060 | |
| deoxyinosine | deoB: phosphopentomutase | AS188_RS13880 | AS188_RS07950 |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | AS188_RS02195 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | AS188_RS04270 | AS188_RS09780 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoK: deoxyribokinase | AS188_RS08840 | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fructose | 1pfk: 1-phosphofructokinase | AS188_RS06515 | |
| fucose | aldA: lactaldehyde dehydrogenase | AS188_RS07995 | AS188_RS00910 |
| 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 | | |
| galactose | galP: galactose:H+ symporter GalP | AS188_RS02770 | AS188_RS06680 |
| galacturonate | dopDH: 2,5-dioxopentanonate dehydrogenase | AS188_RS05910 | AS188_RS01305 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | garD: meso-galactarate dehydratase (L-threo-forming) GarD | | |
| galacturonate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | AS188_RS08430 | |
| galacturonate | udh: D-galacturonate dehydrogenase | | |
| galacturonate | uxuL: D-galactaro-1,5-lactonase (UxuL or UxuF) | AS188_RS05230 | |
| gluconate | gntK: D-gluconate kinase | AS188_RS03425 | |
| gluconate | gntT: gluconate:H+ symporter GntT | AS188_RS03410 | AS188_RS04325 |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | AS188_RS13850 | |
| glucose | glk: glucokinase | AS188_RS09060 | AS188_RS10390 |
| 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 | AS188_RS00895 | AS188_RS08430 |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | AS188_RS11245 | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | AS188_RS05070 | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| histidine | permease: L-histidine permease | AS188_RS02160 | AS188_RS01250 |
| isoleucine | Bap2: L-isoleucine permease Bap2 | AS188_RS02160 | AS188_RS01250 |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | AS188_RS05130 | AS188_RS09120 |
| lactose | glk: glucokinase | AS188_RS09060 | AS188_RS10390 |
| lactose | lacP: lactose permease LacP | | |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | AS188_RS05130 | AS188_RS09120 |
| leucine | leuT: L-leucine:Na+ symporter LeuT | AS188_RS14420 | |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | AS188_RS04440 | AS188_RS07980 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | AS188_RS02285 | AS188_RS15810 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | AS188_RS04435 | AS188_RS08020 |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| lysine | davD: glutarate semialdehyde dehydrogenase | AS188_RS01305 | AS188_RS05910 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | AS188_RS15800 | AS188_RS02275 |
| lysine | patA: cadaverine aminotransferase | AS188_RS08625 | AS188_RS05905 |
| maltose | glk: glucokinase | AS188_RS09060 | AS188_RS10390 |
| mannose | manP: mannose PTS system, EII-CBA components | AS188_RS06520 | |
| myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | AS188_RS06755 | |
| myoinositol | iolE: scyllo-inosose 2-dehydratase | AS188_RS06705 | |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | AS188_RS06715 | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | AS188_RS13850 | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | AS188_RS01390 | AS188_RS02285 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | AS188_RS02285 | AS188_RS15810 |
| phenylacetate | ppa: phenylacetate permease ppa | AS188_RS08290 | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | AS188_RS01250 | AS188_RS03395 |
| phenylalanine | paaF: 2,3-dehydroadipyl-CoA hydratase | AS188_RS01390 | AS188_RS02285 |
| phenylalanine | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | AS188_RS02285 | AS188_RS15810 |
| phenylalanine | pad-dh: phenylacetaldehyde dehydrogenase | AS188_RS11615 | AS188_RS00910 |
| proline | put1: proline dehydrogenase | AS188_RS01650 | AS188_RS00540 |
| proline | putA: L-glutamate 5-semialdeyde dehydrogenase | AS188_RS01650 | AS188_RS00540 |
| putrescine | gabT: gamma-aminobutyrate transaminase | AS188_RS01315 | AS188_RS05905 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| rhamnose | aldA: lactaldehyde dehydrogenase | AS188_RS07995 | AS188_RS00910 |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | AS188_RS05710 | AS188_RS04765 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | | |
| rhamnose | LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase | AS188_RS00895 | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsK: ribokinase | AS188_RS08840 | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | AS188_RS02565 | AS188_RS03480 |
| sucrose | 1pfk: 1-phosphofructokinase | AS188_RS06515 | |
| sucrose | ams: sucrose hydrolase (invertase) | AS188_RS02605 | AS188_RS14710 |
| threonine | tdcC: L-threonine:H+ symporter TdcC | AS188_RS01560 | |
| thymidine | deoB: phosphopentomutase | AS188_RS13880 | AS188_RS07950 |
| thymidine | nupC: thymidine permease NupC | AS188_RS02195 | |
| trehalose | glk: glucokinase | AS188_RS09060 | AS188_RS10390 |
| trehalose | treF: trehalase | AS188_RS14710 | AS188_RS02420 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | AS188_RS01250 | AS188_RS03395 |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | AS188_RS01250 | AS188_RS03395 |
| tyrosine | fahA: fumarylacetoacetate hydrolase | | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | Bap2: L-valine permease Bap2 | AS188_RS02160 | AS188_RS01250 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | AS188_RS05805 | AS188_RS15810 |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | AS188_RS05130 | AS188_RS09120 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | AS188_RS06730 | AS188_RS02220 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | AS188_RS02215 | AS188_RS04900 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | AS188_RS06520 | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | AS188_RS07440 | AS188_RS07990 |
| xylose | xylA: xylose isomerase | | |
| xylose | xylB: xylulokinase | | |
| xylose | xylT: D-xylose transporter | AS188_RS02770 | AS188_RS06680 |
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