Potential Gaps in catabolism of small carbon sources in Haloechinothrix alba DSM 45207
Found 97 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 | | |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| acetate | actP: cation/acetate symporter ActP | CHB84_RS05460 | CHB84_RS05500 |
| 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 | CHB84_RS14305 | |
| asparagine | agcS: Probable asparagine:Na+ symporter AgcS | CHB84_RS09695 | |
| aspartate | glt: aspartate:proton symporter Glt | | |
| cellobiose | bgl: cellobiase | | |
| cellobiose | MFS-glucose: glucose transporter, MFS superfamily | | |
| citrate | tctB: citrate/Na+ symporter, small transmembrane component TctB | | |
| citrate | tctC: citrate/Na+ symporter, substrate-binding component TctC | CHB84_RS04375 | CHB84_RS04390 |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | CHB84_RS00100 | CHB84_RS10230 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | CHB84_RS11345 | |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | CHB84_RS00105 | |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| citrulline | arcC: carbamate kinase | | |
| D-alanine | cycA: D-alanine:H+ symporter CycA | | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | D-LDH: D-lactate dehydrogenase | CHB84_RS14550 | CHB84_RS03225 |
| 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 | CHB84_RS11005 | CHB84_RS02110 |
| deoxyinosine | bmpA: deoxyinosine ABC transporter, substrate-binding component | | |
| deoxyinosine | deoB: phosphopentomutase | CHB84_RS04545 | |
| deoxyinosine | nupB: deoxyinosine ABC transporter, permease component 1 | CHB84_RS04455 | |
| deoxyinosine | nupC': deoxyinosine ABC transporter, permease component 2 | CHB84_RS04460 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | CHB84_RS19015 | CHB84_RS19010 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| ethanol | etoh-dh-nad: ethanol dehydrogenase (NAD(P)) | CHB84_RS02895 | CHB84_RS14690 |
| fructose | 1pfk: 1-phosphofructokinase | | |
| fructose | fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components | | |
| fucose | aldA: lactaldehyde dehydrogenase | CHB84_RS02915 | CHB84_RS12510 |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | CHB84_RS12285 | |
| 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 | dctA: fumarate:H+ symporter DctA | | |
| galactose | galK: galactokinase (-1-phosphate forming) | | |
| galactose | galP: galactose:H+ symporter GalP | | |
| galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| galactose | pgmA: alpha-phosphoglucomutase | CHB84_RS01840 | CHB84_RS04545 |
| galacturonate | dopDH: 2,5-dioxopentanonate dehydrogenase | CHB84_RS16915 | CHB84_RS02915 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | gci: D-galactarolactone cycloisomerase | | |
| galacturonate | gli: D-galactarolactone isomerase | | |
| galacturonate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | CHB84_RS06975 | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | CHB84_RS03775 | CHB84_RS15115 |
| glucose | MFS-glucose: glucose transporter, MFS superfamily | | |
| 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 | | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
| glutamate | gluC: L-glutamate ABC transporter, permease component 1 (GluC) | CHB84_RS10220 | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | CHB84_RS12275 | CHB84_RS04605 |
| glycerol | glpF: glycerol facilitator glpF | | |
| histidine | hutG': N-formylglutamate amidohydrolase | | |
| histidine | natB: L-histidine ABC transporter, substrate-binding component NatB | CHB84_RS21595 | |
| histidine | natC: L-histidine ABC transporter, permease component 1 (NatC) | CHB84_RS21580 | |
| histidine | natD: L-histidine ABC transporter, permease component 2 (NatD) | CHB84_RS21575 | CHB84_RS11940 |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | CHB84_RS07335 | CHB84_RS00130 |
| isoleucine | natB: L-isoleucine ABC transporter, substrate-binding component NatB | | |
| isoleucine | natC: L-isoleucine ABC transporter, permease component 1 (NatC) | CHB84_RS21580 | |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | CHB84_RS04620 | CHB84_RS20140 |
| L-lactate | lutC: L-lactate dehydrogenase, LutC subunit | | |
| 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 | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | | |
| lactose | pgmA: alpha-phosphoglucomutase | CHB84_RS01840 | CHB84_RS04545 |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | CHB84_RS07335 | CHB84_RS00130 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | CHB84_RS12015 | CHB84_RS03020 |
| leucine | natB: L-leucine ABC transporter, substrate-binding component NatB | CHB84_RS21595 | |
| leucine | natC: L-leucine ABC transporter, permease component 1 (NatC) | CHB84_RS21580 | |
| lysine | davA: 5-aminovaleramidase | | |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | davD: glutarate semialdehyde dehydrogenase | CHB84_RS16915 | CHB84_RS02915 |
| lysine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | CHB84_RS03020 | CHB84_RS21025 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | CHB84_RS03990 | CHB84_RS09615 |
| lysine | gcdH: glutaryl-CoA dehydrogenase | CHB84_RS03285 | CHB84_RS20145 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| maltose | MAL11: maltose permease | | |
| mannitol | mt2d: mannitol 2-dehydrogenase | CHB84_RS03845 | CHB84_RS03815 |
| mannitol | mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE | CHB84_RS03830 | |
| mannitol | mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) | CHB84_RS03835 | |
| mannitol | mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) | CHB84_RS03840 | CHB84_RS12305 |
| mannitol | mtlK: polyol ABC transporter, ATP component MtlK/SmoG | CHB84_RS03850 | CHB84_RS12290 |
| mannitol | scrK: fructokinase | CHB84_RS03805 | CHB84_RS05370 |
| mannose | manP: mannose PTS system, EII-CBA components | | |
| myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | CHB84_RS05380 | |
| myoinositol | iolE: scyllo-inosose 2-dehydratase | CHB84_RS05395 | |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | CHB84_RS05370 | |
| myoinositol | PGA1_c07300: myo-inositol ABC transport, substrate-binding component | CHB84_RS05400 | |
| myoinositol | PGA1_c07310: myo-inositol ABC transporter, permease component | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | CHB84_RS03775 | CHB84_RS15115 |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | CHB84_RS03020 | CHB84_RS04900 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | paaF: 2,3-dehydroadipyl-CoA hydratase | CHB84_RS03020 | CHB84_RS04900 |
| phenylalanine | pad-dh: phenylacetaldehyde dehydrogenase | CHB84_RS02915 | CHB84_RS19545 |
| phenylalanine | PPDCalpha: phenylpyruvate decarboxylase, alpha subunit | CHB84_RS00120 | |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | CHB84_RS04620 | CHB84_RS20140 |
| propionate | putP: propionate transporter; proline:Na+ symporter | CHB84_RS11455 | |
| putrescine | gabT: gamma-aminobutyrate transaminase | CHB84_RS16910 | CHB84_RS19235 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | CHB84_RS19235 | CHB84_RS09600 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | CHB84_RS02915 | CHB84_RS19545 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| pyruvate | actP: large subunit of pyruvate transporter (actP-like) | CHB84_RS05460 | CHB84_RS05500 |
| pyruvate | yjcH: putative small subunit of pyruvate transporter (yjcH-like) | CHB84_RS05465 | |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | CHB84_RS19015 | CHB84_RS19540 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | | |
| rhamnose | LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase | CHB84_RS03845 | CHB84_RS03955 |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | CHB84_RS21595 | |
| serine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | CHB84_RS21580 | CHB84_RS11945 |
| sorbitol | mtlK: ABC transporter for polyols MtlEFGK, permease component MtlK | CHB84_RS03850 | CHB84_RS12290 |
| sorbitol | scrK: fructokinase | CHB84_RS03805 | CHB84_RS05370 |
| succinate | sdc: succinate:Na+ symporter Sdc | | |
| sucrose | ams: sucrose hydrolase (invertase) | CHB84_RS12475 | |
| sucrose | MFS-glucose: glucose transporter, MFS superfamily | | |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | CHB84_RS21595 | |
| threonine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | CHB84_RS21580 | CHB84_RS11945 |
| thymidine | deoB: phosphopentomutase | CHB84_RS04545 | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | MFS-glucose: glucose transporter, MFS superfamily | | |
| trehalose | treF: trehalase | CHB84_RS05975 | CHB84_RS12475 |
| tryptophan | tnaA: tryptophanase | | |
| tryptophan | tnaT: tryptophan:Na+ symporter TnaT | CHB84_RS17435 | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | CHB84_RS04900 | CHB84_RS20905 |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | CHB84_RS07335 | CHB84_RS00130 |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | CHB84_RS03020 | CHB84_RS21025 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | CHB84_RS05390 | CHB84_RS12430 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | CHB84_RS16120 | CHB84_RS06325 |
| valine | natB: L-valine ABC transporter, substrate-binding component NatB | | |
| valine | natC: L-valine ABC transporter, permease component 1 (NatC) | CHB84_RS21580 | |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | CHB84_RS04620 | CHB84_RS20140 |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
| xylitol | xdhA: xylitol dehydrogenase | CHB84_RS03815 | CHB84_RS05425 |
| xylose | xdhA: xylitol dehydrogenase | CHB84_RS03815 | CHB84_RS05425 |
| xylose | xylT: D-xylose transporter | | |
| xylose | xyrA: xylitol reductase | CHB84_RS02190 | |
Confidence: high confidence medium confidence low confidence
This GapMind analysis is from Apr 09 2024. 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