Potential Gaps in catabolism of small carbon sources in Lacinutrix himadriensis E4-9a
Found 115 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 | | |
| 4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | | |
| 4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | AMD28_RS08005 | |
| 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 | AMD28_RS06010 | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arginine | rocE: L-arginine permease | | |
| arginine | rocF: arginase | | |
| cellobiose | bgl: cellobiase | | |
| 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 | AMD28_RS08690 | AMD28_RS16625 |
| 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 | AMD28_RS09535 | AMD28_RS13745 |
| 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 | AMD28_RS14865 | AMD28_RS08105 |
| deoxyinosine | deoB: phosphopentomutase | AMD28_RS01325 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | AMD28_RS14015 | AMD28_RS09705 |
| 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 | AMD28_RS12245 | |
| ethanol | etoh-dh-nad: ethanol dehydrogenase (NAD(P)) | AMD28_RS14410 | AMD28_RS14450 |
| fructose | Slc2a5: fructose:H+ symporter | | |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | | |
| fucose | fucK: L-fuculose kinase FucK | | |
| fumarate | SLC26dg: fumarate transporter SLC26dg | AMD28_RS03750 | |
| galactose | galK: galactokinase (-1-phosphate forming) | | |
| galactose | galP: galactose:H+ symporter GalP | | |
| galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| galacturonate | exuT: D-galacturonate transporter ExuT | AMD28_RS09735 | |
| galacturonate | uxaA: D-altronate dehydratase | | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | AMD28_RS11815 | |
| 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 | AMD28_RS09735 | |
| glucuronate | uxaC: D-glucuronate isomerase | | |
| glucuronate | uxuA: D-mannonate dehydratase | | |
| glucuronate | uxuB: D-mannonate dehydrogenase | AMD28_RS14395 | |
| glutamate | gdhA: glutamate dehydrogenase, NAD-dependent | AMD28_RS11685 | AMD28_RS05825 |
| glycerol | glpF: glycerol facilitator glpF | AMD28_RS12020 | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | AMD28_RS13410 | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | permease: L-histidine permease | | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | AMD28_RS04680 | AMD28_RS05185 |
| isoleucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | AMD28_RS14910 | AMD28_RS04760 |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | AMD28_RS16375 | AMD28_RS04765 |
| isoleucine | brnQ: L-isoleucine:cation symporter BrnQ/BraZ/BraB | AMD28_RS00295 | |
| isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | AMD28_RS12825 | AMD28_RS01405 |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | AMD28_RS14015 | AMD28_RS09740 |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | AMD28_RS05795 | AMD28_RS11080 |
| L-lactate | L-LDH: L-lactate dehydrogenase | AMD28_RS12235 | AMD28_RS03565 |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| L-malate | sdlC: L-malate:Na+ symporter SdlC | | |
| lactose | galK: galactokinase (-1-phosphate forming) | | |
| lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| lactose | glk: glucokinase | | |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | | |
| leucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | AMD28_RS14910 | AMD28_RS04760 |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | AMD28_RS16375 | AMD28_RS04765 |
| leucine | brnQ: L-leucine:Na+ symporter BrnQ/BraB | AMD28_RS00295 | |
| leucine | liuA: isovaleryl-CoA dehydrogenase | AMD28_RS04680 | AMD28_RS05185 |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | AMD28_RS05795 | AMD28_RS11080 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | AMD28_RS12825 | |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | AMD28_RS13295 | AMD28_RS05800 |
| lysine | hglS: D-2-hydroxyglutarate synthase | | |
| lysine | lat: L-lysine 6-aminotransferase | AMD28_RS05570 | |
| lysine | lysN: 2-aminoadipate transaminase | AMD28_RS15745 | AMD28_RS08075 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | AMD28_RS15065 | |
| maltose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
| mannitol | PLT5: polyol transporter PLT5 | | |
| mannose | manA: mannose-6-phosphate isomerase | AMD28_RS16110 | AMD28_RS10020 |
| 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 | | |
| myoinositol | uxaE: D-tagaturonate epimerase | | |
| myoinositol | uxuA: D-mannonate dehydratase | | |
| myoinositol | uxuB: D-mannonate dehydrogenase | AMD28_RS14395 | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | AMD28_RS11815 | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | AMD28_RS12825 | AMD28_RS01405 |
| 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 | AMD28_RS12825 | AMD28_RS01405 |
| proline | proY: proline:H+ symporter | | |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | AMD28_RS05795 | AMD28_RS11080 |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | gabT: gamma-aminobutyrate transaminase | AMD28_RS05570 | AMD28_RS17420 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | AMD28_RS05570 | AMD28_RS17420 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | AMD28_RS04480 | AMD28_RS06035 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| pyruvate | yjcH: putative small subunit of pyruvate transporter (yjcH-like) | AMD28_RS06015 | |
| rhamnose | rhaA: L-rhamnose isomerase | | |
| rhamnose | rhaB: L-rhamnulokinase | AMD28_RS12270 | |
| rhamnose | rhaD: rhamnulose 1-phosphate aldolase | AMD28_RS12260 | |
| rhamnose | rhaM: L-rhamnose mutarotase | | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsA: D-ribose ABC transporter, ATPase component RbsA | AMD28_RS14385 | |
| ribose | rbsB: D-ribose ABC transporter, substrate-binding component RbsB | AMD28_RS14380 | |
| ribose | rbsC: D-ribose ABC transporter, permease component RbsC | AMD28_RS14390 | |
| ribose | rbsK: ribokinase | | |
| serine | snatA: L-serine transporter | AMD28_RS14305 | |
| sorbitol | sdh: sorbitol dehydrogenase | AMD28_RS14395 | AMD28_RS09705 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
| succinate | sdc: succinate:Na+ symporter Sdc | | |
| sucrose | scrP: sucrose phosphorylase | | |
| sucrose | sut: sucrose:proton symporter SUT/SUC | | |
| threonine | gcvT: glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) | | |
| threonine | snatA: L-threonine transporter snatA | AMD28_RS14305 | |
| thymidine | deoA: thymidine phosphorylase DeoA | | |
| thymidine | deoB: phosphopentomutase | AMD28_RS01325 | |
| 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 | AMD28_RS04680 | AMD28_RS05185 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | | |
| valine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | AMD28_RS14910 | AMD28_RS04760 |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | AMD28_RS16375 | AMD28_RS04765 |
| valine | brnQ: L-valine:cation symporter BrnQ/BraZ/BraB | AMD28_RS00295 | |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | AMD28_RS12830 | AMD28_RS12825 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | AMD28_RS04480 | AMD28_RS02025 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | | |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | AMD28_RS05795 | AMD28_RS11080 |
| 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 | | |
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