Potential Gaps in catabolism of small carbon sources in Pontibacter lucknowensis DM9
Found 99 low-confidence and 48 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 | pcaB: 3-carboxymuconate cycloisomerase | | |
| 4-hydroxybenzoate | pcaC: 4-carboxymuconolactone decarboxylase | BW972_RS06905 | |
| 4-hydroxybenzoate | pcaG: protocatechuate 3,4-dioxygenase, beta subunit | BW972_RS06900 | |
| 4-hydroxybenzoate | pcaH: protocatechuate 3,4-dioxygenase, alpha subunit | | |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| 4-hydroxybenzoate | pobA: 4-hydroxybenzoate 3-monooxygenase | | |
| acetate | dctA: organic acid/proton symporter DctA | BW972_RS10625 | |
| arabinose | araE: L-arabinose:H+ symporter | BW972_RS16070 | |
| arabinose | xacB: L-arabinose 1-dehydrogenase | BW972_RS06240 | BW972_RS14020 |
| arabinose | xacC: L-arabinono-1,4-lactonase | BW972_RS17120 | |
| arabinose | xacD: L-arabinonate dehydratase | | |
| arabinose | xacE: 2-dehydro-3-deoxy-L-arabinonate dehydratase | | |
| arginine | rocE: L-arginine permease | | |
| cellobiose | bgl: cellobiase | | |
| cellobiose | glk: glucokinase | BW972_RS15830 | |
| citrate | SLC13A5: citrate:Na+ symporter | BW972_RS00225 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | BW972_RS13795 | BW972_RS01130 |
| 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 | lctP: D-lactate:H+ symporter LctP or LidP | | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | BW972_RS18740 | |
| deoxyinosine | deoB: phosphopentomutase | BW972_RS12575 | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | BW972_RS17810 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | BW972_RS11755 | BW972_RS08620 |
| 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)) | BW972_RS17115 | BW972_RS13000 |
| fructose | 1pfk: 1-phosphofructokinase | BW972_RS07980 | |
| fructose | fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components | | |
| fucose | aldA: lactaldehyde dehydrogenase | BW972_RS08600 | BW972_RS04225 |
| 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 | BW972_RS07765 | |
| fucose | fucU: L-fucose mutarotase FucU | | |
| fumarate | dctA: fumarate:H+ symporter DctA | BW972_RS10625 | BW972_RS00955 |
| galacturonate | uxaA: D-altronate dehydratase | | |
| galacturonate | uxaB: tagaturonate reductase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucose | glk: glucokinase | BW972_RS15830 | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | BW972_RS16010 | |
| glucuronate | uxuB: D-mannonate dehydrogenase | | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | BW972_RS15735 | |
| glycerol | glpF: glycerol facilitator glpF | | |
| glycerol | glpK: glycerol kinase | | |
| histidine | permease: L-histidine permease | | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | BW972_RS04615 | BW972_RS02870 |
| isoleucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | BW972_RS06070 | BW972_RS04795 |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | BW972_RS00415 | BW972_RS18605 |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | BW972_RS11755 | BW972_RS06930 |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | BW972_RS08095 | BW972_RS07085 |
| L-lactate | L-LDH: L-lactate dehydrogenase | BW972_RS15220 | |
| L-malate | dctA: L-malate:H+ symporter DctA | BW972_RS10625 | BW972_RS00955 |
| lactose | glk: glucokinase | BW972_RS15830 | |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | | |
| leucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | BW972_RS06070 | BW972_RS04795 |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | BW972_RS00415 | BW972_RS18605 |
| leucine | liuA: isovaleryl-CoA dehydrogenase | BW972_RS02870 | BW972_RS04615 |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | BW972_RS08095 | BW972_RS17835 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | BW972_RS01390 | BW972_RS15030 |
| lysine | davA: 5-aminovaleramidase | BW972_RS17410 | |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | davD: glutarate semialdehyde dehydrogenase | BW972_RS04225 | BW972_RS14090 |
| lysine | davT: 5-aminovalerate aminotransferase | BW972_RS12460 | BW972_RS08485 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | BW972_RS13280 | |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| maltose | glk: glucokinase | BW972_RS15830 | |
| mannitol | mtlA: mannitol phosphotransferase system, EII-CBA components | | |
| mannitol | mtlD: mannitol-1-phosphate 5-dehydrogenase | | |
| mannose | manA: mannose-6-phosphate isomerase | BW972_RS18955 | BW972_RS01880 |
| 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 | BW972_RS16070 | |
| myoinositol | uxaE: D-tagaturonate epimerase | | |
| myoinositol | uxuB: D-mannonate dehydrogenase | | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagK: N-acetylglucosamine kinase | | |
| phenylacetate | paaB: phenylacetyl-CoA 1,2-epoxidase, subunit B | BW972_RS13485 | |
| phenylacetate | paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C | BW972_RS13480 | |
| phenylacetate | paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E | BW972_RS13460 | |
| phenylacetate | paaK: phenylacetate-CoA ligase | | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | BW972_RS04095 | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | iorAB: phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB | | |
| phenylalanine | paaB: phenylacetyl-CoA 1,2-epoxidase, subunit B | BW972_RS13485 | |
| phenylalanine | paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C | BW972_RS13480 | |
| phenylalanine | paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E | BW972_RS13460 | |
| phenylalanine | paaZ1: oxepin-CoA hydrolase | BW972_RS04095 | |
| proline | ectP: proline transporter EctP | BW972_RS12200 | |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | BW972_RS08095 | BW972_RS07085 |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | gabT: gamma-aminobutyrate transaminase | BW972_RS12460 | BW972_RS08485 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | BW972_RS12460 | BW972_RS03895 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | BW972_RS08600 | BW972_RS04225 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| pyruvate | actP: large subunit of pyruvate transporter (actP-like) | BW972_RS01200 | |
| pyruvate | yjcH: putative small subunit of pyruvate transporter (yjcH-like) | BW972_RS01205 | |
| rhamnose | aldA: lactaldehyde dehydrogenase | BW972_RS08600 | BW972_RS04225 |
| rhamnose | rhaA: L-rhamnose isomerase | | |
| rhamnose | rhaB: L-rhamnulokinase | | |
| rhamnose | rhaD: rhamnulose 1-phosphate aldolase | | |
| 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 | BW972_RS00540 | |
| sorbitol | mtlA: PTS system for polyols, EII-CBA components | | |
| sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | BW972_RS11755 | BW972_RS06930 |
| succinate | dctA: succinate:H+ symporter DctA | BW972_RS10625 | BW972_RS00955 |
| sucrose | ams: sucrose hydrolase (invertase) | BW972_RS16760 | BW972_RS12720 |
| sucrose | glk: glucokinase | BW972_RS15830 | |
| threonine | snatA: L-threonine transporter snatA | BW972_RS00540 | |
| thymidine | deoA: thymidine phosphorylase DeoA | | |
| thymidine | deoB: phosphopentomutase | BW972_RS12575 | |
| trehalose | glk: glucokinase | BW972_RS15830 | |
| tryptophan | antA: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA | | |
| tryptophan | antB: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB | | |
| tryptophan | antC: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC | | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | kynA: tryptophan 2,3-dioxygenase | BW972_RS08710 | |
| tryptophan | kynB: kynurenine formamidase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | BW972_RS04615 | BW972_RS02870 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | BW972_RS16605 | |
| valine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | BW972_RS06070 | BW972_RS04795 |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | BW972_RS00415 | BW972_RS18605 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | BW972_RS08600 | BW972_RS04225 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | | |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | BW972_RS08095 | BW972_RS07085 |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | BW972_RS16070 | |
| xylitol | xdhA: xylitol dehydrogenase | BW972_RS06930 | BW972_RS06320 |
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