Potential Gaps in catabolism of small carbon sources in Lacinutrix mariniflava AKS432
Found 105 low-confidence and 50 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | | |
| 4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | | |
| 4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | ASC44_RS11605 | |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| 4-hydroxybenzoate | pobA: 4-hydroxybenzoate 3-monooxygenase | | |
| 4-hydroxybenzoate | praA: protocatechuate 2,3-dioxygenase | | |
| 4-hydroxybenzoate | xylF: 2-hydroxymuconate semialdehyde hydrolase | | |
| acetate | actP: cation/acetate symporter ActP | ASC44_RS03815 | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | ASC44_RS15965 | |
| arginine | rocE: L-arginine permease | | |
| arginine | rocF: arginase | | |
| cellobiose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | ASC44_RS06965 | ASC44_RS16995 |
| 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 | | |
| D-alanine | cycA: D-alanine:H+ symporter CycA | | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | D-LDH: D-lactate dehydrogenase | ASC44_RS01470 | ASC44_RS07615 |
| D-lactate | larD: D,L-lactic acid transporter | ASC44_RS06705 | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | ASC44_RS13055 | ASC44_RS11500 |
| deoxyinosine | deoB: phosphopentomutase | ASC44_RS15015 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | ASC44_RS01645 | ASC44_RS16305 |
| 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 | deoK: deoxyribokinase | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| ethanol | etoh-dh-nad: ethanol dehydrogenase (NAD(P)) | ASC44_RS02130 | ASC44_RS02225 |
| fructose | glcP: fructose:H+ symporter GlcP | ASC44_RS15965 | |
| fructose | scrK: fructokinase | ASC44_RS02120 | |
| fucose | aldA: lactaldehyde dehydrogenase | ASC44_RS02470 | ASC44_RS03840 |
| 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 | | |
| fumarate | SLC26dg: fumarate transporter SLC26dg | ASC44_RS16920 | |
| galactose | sglS: sodium/galactose cotransporter | ASC44_RS00595 | |
| galacturonate | exuT: D-galacturonate transporter ExuT | ASC44_RS13605 | |
| galacturonate | uxaA: D-altronate dehydratase | | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | | |
| gluconate | edd: phosphogluconate dehydratase | ASC44_RS11480 | |
| 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) | ASC44_RS10115 | |
| glucose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | ASC44_RS13605 | |
| glucuronate | uxaC: D-glucuronate isomerase | | |
| glucuronate | uxuB: D-mannonate dehydrogenase | ASC44_RS02115 | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | ASC44_RS06715 | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | ASC44_RS01260 | |
| histidine | permease: L-histidine permease | | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | ASC44_RS13260 | ASC44_RS13900 |
| isoleucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | ASC44_RS02400 | ASC44_RS13355 |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | ASC44_RS17155 | ASC44_RS13360 |
| isoleucine | brnQ: L-isoleucine:cation symporter BrnQ/BraZ/BraB | ASC44_RS08080 | |
| isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | ASC44_RS12240 | ASC44_RS09760 |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | ASC44_RS01645 | ASC44_RS13610 |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | ASC44_RS03655 | ASC44_RS09380 |
| L-lactate | lctO: L-lactate oxidase or 2-monooxygenase | | |
| L-malate | sdlC: L-malate:Na+ symporter SdlC | | |
| lactose | glk: glucokinase | | |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | ASC44_RS00550 | |
| leucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | ASC44_RS02400 | ASC44_RS13355 |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | ASC44_RS17155 | ASC44_RS13360 |
| leucine | brnQ: L-leucine:Na+ symporter BrnQ/BraB | ASC44_RS08080 | |
| leucine | liuA: isovaleryl-CoA dehydrogenase | ASC44_RS13260 | ASC44_RS13900 |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | ASC44_RS03655 | ASC44_RS17230 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | ASC44_RS09760 | ASC44_RS12240 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | ASC44_RS01120 | ASC44_RS03660 |
| lysine | davA: 5-aminovaleramidase | ASC44_RS11230 | |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | davD: glutarate semialdehyde dehydrogenase | ASC44_RS02470 | ASC44_RS06355 |
| lysine | davT: 5-aminovalerate aminotransferase | ASC44_RS17360 | ASC44_RS00280 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | | |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| maltose | glk: glucokinase | | |
| mannitol | PLT5: polyol transporter PLT5 | | |
| mannitol | scrK: fructokinase | ASC44_RS02120 | |
| mannose | manA: mannose-6-phosphate isomerase | ASC44_RS11095 | ASC44_RS14075 |
| mannose | manP: mannose PTS system, EII-CBA components | | |
| 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 | ASC44_RS15965 | |
| myoinositol | uxaE: D-tagaturonate epimerase | | |
| myoinositol | uxuB: D-mannonate dehydrogenase | ASC44_RS02115 | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | ASC44_RS10115 | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | ASC44_RS09760 | ASC44_RS12240 |
| phenylacetate | paaK: phenylacetate-CoA ligase | | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | iorAB: phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB | | |
| phenylalanine | paaF: 2,3-dehydroadipyl-CoA hydratase | ASC44_RS09760 | ASC44_RS12240 |
| proline | proY: proline:H+ symporter | | |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | ASC44_RS03655 | ASC44_RS09380 |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | gabT: gamma-aminobutyrate transaminase | ASC44_RS17360 | ASC44_RS00280 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | ASC44_RS17360 | ASC44_RS00280 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | ASC44_RS02470 | ASC44_RS06355 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| pyruvate | actP: large subunit of pyruvate transporter (actP-like) | ASC44_RS03815 | |
| pyruvate | yjcH: putative small subunit of pyruvate transporter (yjcH-like) | ASC44_RS03820 | |
| rhamnose | aldA: lactaldehyde dehydrogenase | ASC44_RS02470 | ASC44_RS03840 |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | ASC44_RS01645 | ASC44_RS17255 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | | |
| rhamnose | LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase | | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsA: D-ribose ABC transporter, ATPase component RbsA | ASC44_RS02105 | |
| ribose | rbsB: D-ribose ABC transporter, substrate-binding component RbsB | ASC44_RS02100 | |
| ribose | rbsC: D-ribose ABC transporter, permease component RbsC | ASC44_RS02110 | |
| ribose | rbsK: ribokinase | | |
| serine | snatA: L-serine transporter | ASC44_RS00800 | ASC44_RS03665 |
| sorbitol | mtlA: PTS system for polyols, EII-CBA components | | |
| sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | ASC44_RS01645 | ASC44_RS17255 |
| succinate | sdc: succinate:Na+ symporter Sdc | | |
| sucrose | ams: sucrose hydrolase (invertase) | | |
| sucrose | glcP: fructose:H+ symporter GlcP | ASC44_RS15965 | |
| sucrose | scrK: fructokinase | ASC44_RS02120 | |
| threonine | snatA: L-threonine transporter snatA | ASC44_RS00800 | ASC44_RS03665 |
| thymidine | deoA: thymidine phosphorylase DeoA | | |
| thymidine | deoB: phosphopentomutase | ASC44_RS15015 | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
| trehalose | treF: trehalase | | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | ASC44_RS13260 | ASC44_RS14880 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | ASC44_RS09760 | ASC44_RS12240 |
| valine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | ASC44_RS02400 | ASC44_RS13355 |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | ASC44_RS17155 | ASC44_RS13360 |
| valine | brnQ: L-valine:cation symporter BrnQ/BraZ/BraB | ASC44_RS08080 | |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | ASC44_RS03840 | ASC44_RS02025 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | | |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | ASC44_RS03655 | ASC44_RS09380 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | ASC44_RS02225 | |
| xylose | xylA: xylose isomerase | | |
| xylose | xylB: xylulokinase | | |
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.
Links
Downloads
Related tools
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