Potential Gaps in catabolism of small carbon sources in Novosphingobium fuchskuhlense FNE08-7
Found 106 low-confidence and 40 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | AQZ52_RS12650 | AQZ52_RS16895 |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| alanine | snatA: L-alanine symporter SnatA | AQZ52_RS02210 | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arabinose | xacB: L-arabinose 1-dehydrogenase | AQZ52_RS00360 | AQZ52_RS00270 |
| arabinose | xacC: L-arabinono-1,4-lactonase | AQZ52_RS04370 | |
| arabinose | xacD: L-arabinonate dehydratase | AQZ52_RS11390 | AQZ52_RS11825 |
| arabinose | xacE: 2-dehydro-3-deoxy-L-arabinonate dehydratase | | |
| arginine | adiA: arginine decarboxylase (AdiA/SpeA) | | |
| arginine | puuC: gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase | AQZ52_RS13160 | AQZ52_RS14300 |
| arginine | puuD: gamma-glutamyl-gamma-aminobutyrate hydrolase | | |
| arginine | rocE: L-arginine permease | AQZ52_RS05130 | |
| asparagine | ans: asparaginase | AQZ52_RS03840 | |
| cellobiose | glk: glucokinase | AQZ52_RS12325 | AQZ52_RS13465 |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | citrullinase: putative citrullinase | AQZ52_RS05060 | |
| citrulline | PS417_17590: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| citrulline | PS417_17595: ABC transporter for L-Citrulline, permease component 1 | | |
| citrulline | PS417_17600: ABC transporter for L-Citrulline, permease component 2 | | |
| citrulline | PS417_17605: ABC transporter for L-Citrulline, ATPase component | AQZ52_RS15605 | AQZ52_RS11530 |
| citrulline | rocD: ornithine aminotransferase | AQZ52_RS13575 | AQZ52_RS01040 |
| D-alanine | cycA: D-alanine:H+ symporter CycA | AQZ52_RS05130 | |
| D-alanine | dadA: D-alanine dehydrogenase | AQZ52_RS12840 | |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
| D-serine | cycA: D-serine:H+ symporter CycA | AQZ52_RS05130 | |
| D-serine | dsdA: D-serine ammonia-lyase | AQZ52_RS15185 | AQZ52_RS05140 |
| deoxyinosine | deoB: phosphopentomutase | AQZ52_RS04445 | |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | | |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | AQZ52_RS16175 | AQZ52_RS04935 |
| deoxyribonate | garK: glycerate 2-kinase | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | AQZ52_RS13760 | |
| deoxyribose | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | AQZ52_RS16175 | AQZ52_RS04935 |
| deoxyribose | drdehyd-alpha: 2-deoxy-D-ribose dehydrogenase, alpha subunit | AQZ52_RS13495 | AQZ52_RS13050 |
| deoxyribose | drdehyd-beta: 2-deoxy-D-ribose dehydrogenase, beta subunit | AQZ52_RS13490 | AQZ52_RS13045 |
| deoxyribose | drdehyd-cytc: 2-deoxyribose-D dehydrogenase, cytochrome c component | | |
| deoxyribose | garK: glycerate 2-kinase | | |
| deoxyribose | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | AQZ52_RS13760 | |
| fructose | fruP: fructose porter FruP | AQZ52_RS11580 | |
| 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 | AQZ52_RS11580 | |
| fucose | fucU: L-fucose mutarotase FucU | | |
| fumarate | sdcL: fumarate:Na+ symporter SdcL | AQZ52_RS17015 | |
| galactose | galE: UDP-glucose 4-epimerase | AQZ52_RS03630 | AQZ52_RS01005 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | kdgK: 2-keto-3-deoxygluconate kinase | | |
| galacturonate | uxaA: D-altronate dehydratase | | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | | |
| gluconate | gntK: D-gluconate kinase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | AQZ52_RS14760 | |
| glucose | glk: glucokinase | AQZ52_RS12325 | AQZ52_RS13465 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | AQZ52_RS11390 | |
| glucuronate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | AQZ52_RS09010 | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | AQZ52_RS11345 | |
| glycerol | glpF: glycerol facilitator glpF | | |
| histidine | Ga0059261_1577: L-histidine transporter | AQZ52_RS10590 | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| isoleucine | Bap2: L-isoleucine permease Bap2 | AQZ52_RS05130 | |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| L-malate | sdlC: L-malate:Na+ symporter SdlC | AQZ52_RS17015 | |
| lactose | galE: UDP-glucose 4-epimerase | AQZ52_RS03630 | AQZ52_RS01005 |
| lactose | glk: glucokinase | AQZ52_RS12325 | AQZ52_RS13465 |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | AQZ52_RS13405 | AQZ52_RS13355 |
| leucine | leuT: L-leucine:Na+ symporter LeuT | | |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | AQZ52_RS00510 | AQZ52_RS15005 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | AQZ52_RS16345 | AQZ52_RS03785 |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | AQZ52_RS13010 | |
| lysine | cadA: lysine decarboxylase | AQZ52_RS11980 | |
| lysine | davD: glutarate semialdehyde dehydrogenase | AQZ52_RS13580 | AQZ52_RS07445 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | AQZ52_RS00705 | AQZ52_RS12995 |
| lysine | gcdH: glutaryl-CoA dehydrogenase | AQZ52_RS16335 | AQZ52_RS11475 |
| lysine | lysP: L-lysine:H+ symporter LysP | AQZ52_RS05130 | |
| lysine | patA: cadaverine aminotransferase | AQZ52_RS01405 | AQZ52_RS01040 |
| lysine | patD: 5-aminopentanal dehydrogenase | AQZ52_RS13160 | AQZ52_RS14300 |
| maltose | glk: glucokinase | AQZ52_RS12325 | AQZ52_RS13465 |
| mannitol | mt2d: mannitol 2-dehydrogenase | AQZ52_RS12235 | AQZ52_RS16770 |
| mannitol | PLT5: polyol transporter PLT5 | | |
| mannose | manP: mannose PTS system, EII-CBA components | | |
| myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | | |
| myoinositol | iolC: 5-dehydro-2-deoxy-D-gluconate kinase | | |
| myoinositol | iolD: 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase | | |
| myoinositol | iolE: scyllo-inosose 2-dehydratase | | |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | | |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | AQZ52_RS14760 | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| 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 | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | AQZ52_RS03795 | AQZ52_RS13185 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | AQZ52_RS03795 | AQZ52_RS13185 |
| phenylacetate | paaK: phenylacetate-CoA ligase | AQZ52_RS00450 | AQZ52_RS12120 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | AQZ52_RS17100 | AQZ52_RS13795 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | AQZ52_RS05130 | |
| phenylalanine | hmgA: homogentisate dioxygenase | | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | | |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | puuC: gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase | AQZ52_RS13160 | AQZ52_RS14300 |
| putrescine | puuD: gamma-glutamyl-gamma-aminobutyrate hydrolase | | |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| pyruvate | SLC5A8: sodium-coupled pyruvate transporter | | |
| rhamnose | rhaM: L-rhamnose mutarotase | | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsK: ribokinase | | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | snatA: L-serine transporter | AQZ52_RS02210 | |
| sorbitol | sdh: sorbitol dehydrogenase | AQZ52_RS05170 | AQZ52_RS12260 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
| succinate | sdc: succinate:Na+ symporter Sdc | AQZ52_RS17015 | |
| sucrose | ams: sucrose hydrolase (invertase) | AQZ52_RS12300 | |
| sucrose | glk: glucokinase | AQZ52_RS12325 | AQZ52_RS13465 |
| threonine | snatA: L-threonine transporter snatA | AQZ52_RS02210 | |
| threonine | tdcE: 2-ketobutyrate formate-lyase | | |
| thymidine | deoA: thymidine phosphorylase DeoA | | |
| thymidine | deoB: phosphopentomutase | AQZ52_RS04445 | |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| trehalose | glk: glucokinase | AQZ52_RS12325 | AQZ52_RS13465 |
| trehalose | treF: trehalase | AQZ52_RS12300 | AQZ52_RS02535 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | AQZ52_RS05130 | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | AQZ52_RS05130 | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | AQZ52_RS00520 | AQZ52_RS11475 |
| valine | Bap2: L-valine permease Bap2 | AQZ52_RS05130 | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | AQZ52_RS00515 | AQZ52_RS00510 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | | |
| xylose | xylA: xylose isomerase | | |
| xylose | xylB: xylulokinase | | |
| xylose | xylT: D-xylose transporter | AQZ52_RS14505 | |
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