Potential Gaps in catabolism of small carbon sources in Novosphingobium barchaimii LL02
Found 89 low-confidence and 42 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | V474_RS09075 | |
| 4-hydroxybenzoate | pobA: 4-hydroxybenzoate 3-monooxygenase | | |
| alanine | snatA: L-alanine symporter SnatA | V474_RS07020 | |
| arabinose | Echvi_1880: L-arabinose:Na+ symporter | V474_RS08170 | |
| arabinose | xacC: L-arabinono-1,4-lactonase | V474_RS23735 | V474_RS08205 |
| arabinose | xacD: L-arabinonate dehydratase | V474_RS23740 | V474_RS08210 |
| arginine | astC: succinylornithine transaminase | V474_RS13815 | V474_RS23835 |
| arginine | astE: succinylglutamate desuccinylase | | |
| arginine | rocE: L-arginine permease | | |
| asparagine | ans: asparaginase | V474_RS05990 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | V474_RS07795 | V474_RS11745 |
| 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 | V474_RS06790 | |
| citrulline | ocd: ornithine cyclodeaminase | | |
| D-alanine | cycA: D-alanine:H+ symporter CycA | | |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | V474_RS13280 | V474_RS05525 |
| deoxyinosine | deoB: phosphopentomutase | V474_RS17825 | |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | V474_RS15540 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | V474_RS20390 | V474_RS13330 |
| 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 | | |
| fucose | aldA: lactaldehyde dehydrogenase | V474_RS10060 | V474_RS12520 |
| 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 | V474_RS23750 | V474_RS15975 |
| fucose | fucU: L-fucose mutarotase FucU | | |
| galactose | dgoD: D-galactonate dehydratase | V474_RS08210 | V474_RS23740 |
| galactose | dgoK: 2-dehydro-3-deoxygalactonokinase | V474_RS08870 | V474_RS08595 |
| galactose | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | V474_RS23735 | V474_RS20195 |
| galacturonate | kdgK: 2-keto-3-deoxygluconate kinase | V474_RS08870 | V474_RS08595 |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | V474_RS08775 | |
| gluconate | gntK: D-gluconate kinase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | V474_RS08620 | V474_RS08895 |
| glucuronate | kdgK: 2-keto-3-deoxygluconate kinase | V474_RS08870 | V474_RS08595 |
| glucuronate | uxaC: D-glucuronate isomerase | V474_RS08775 | |
| glucuronate | uxuA: D-mannonate dehydratase | | |
| glutamate | gltP: L-glutamate:cation symporter GltP/GltT | V474_RS22150 | V474_RS15190 |
| glycerol | glpF: glycerol facilitator glpF | | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | V474_RS01300 | V474_RS05240 |
| isoleucine | Bap2: L-isoleucine permease Bap2 | | |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| lactose | dgoD: D-galactonate dehydratase | V474_RS08210 | V474_RS23740 |
| lactose | dgoK: 2-dehydro-3-deoxygalactonokinase | V474_RS08870 | V474_RS08595 |
| lactose | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | V474_RS23735 | V474_RS20195 |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | V474_RS20505 | V474_RS10305 |
| leucine | leuT: L-leucine:Na+ symporter LeuT | | |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | V474_RS01310 | V474_RS16345 |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | V474_RS10040 | V474_RS08255 |
| lysine | cadA: lysine decarboxylase | V474_RS10960 | V474_RS15765 |
| lysine | davT: 5-aminovalerate aminotransferase | V474_RS13815 | V474_RS23835 |
| lysine | gcdH: glutaryl-CoA dehydrogenase | V474_RS05240 | V474_RS22780 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| lysine | patA: cadaverine aminotransferase | V474_RS13815 | V474_RS13220 |
| lysine | patD: 5-aminopentanal dehydrogenase | V474_RS10060 | V474_RS12520 |
| mannitol | mt2d: mannitol 2-dehydrogenase | V474_RS08780 | V474_RS05665 |
| mannitol | PLT5: polyol transporter PLT5 | | |
| mannose | manA: mannose-6-phosphate isomerase | V474_RS00355 | V474_RS00360 |
| mannose | manP: mannose PTS system, EII-CBA components | V474_RS08760 | |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | | |
| myoinositol | iolM: 2-inosose 4-dehydrogenase | | |
| myoinositol | iolN: 2,4-diketo-inositol hydratase | | |
| myoinositol | iolO: 5-dehydro-L-gluconate epimerase | | |
| myoinositol | iolT: myo-inositol:H+ symporter | V474_RS08805 | |
| myoinositol | kdgK: 2-keto-3-deoxygluconate kinase | V474_RS08870 | V474_RS08595 |
| myoinositol | uxaE: D-tagaturonate epimerase | | |
| myoinositol | uxuA: D-mannonate dehydratase | | |
| 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 | paaF: 2,3-dehydroadipyl-CoA hydratase | V474_RS01310 | V474_RS04200 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | V474_RS21625 | V474_RS05390 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | V474_RS21625 | V474_RS05390 |
| phenylacetate | paaK: phenylacetate-CoA ligase | V474_RS19880 | V474_RS07610 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | V474_RS12920 | V474_RS19965 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | hmgA: homogentisate dioxygenase | | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | V474_RS01825 | |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | gabT: gamma-aminobutyrate transaminase | V474_RS13815 | V474_RS23835 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | V474_RS13815 | V474_RS13220 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | V474_RS10060 | V474_RS12520 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | V474_RS01985 | V474_RS08875 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | V474_RS08770 | |
| rhamnose | LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase | V474_RS01280 | V474_RS05665 |
| rhamnose | LRA6: 2,4-diketo-3-deoxyrhamnonate hydrolase | V474_RS24045 | V474_RS15385 |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | snatA: L-serine transporter | V474_RS07020 | |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
| sucrose | ams: sucrose hydrolase (invertase) | V474_RS05265 | |
| threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | V474_RS04460 | V474_RS04455 |
| threonine | ltaE: L-threonine aldolase | V474_RS14035 | V474_RS04295 |
| threonine | snatA: L-threonine transporter snatA | V474_RS07020 | |
| thymidine | deoA: thymidine phosphorylase DeoA | | |
| thymidine | deoB: phosphopentomutase | V474_RS17825 | |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | V474_RS01300 | V474_RS05240 |
| valine | Bap2: L-valine permease Bap2 | | |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | V474_RS10060 | V474_RS22325 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | V474_RS08760 | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | V474_RS19960 | |
| xylose | xylC: xylonolactonase | V474_RS23735 | V474_RS08205 |
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