Potential Gaps in catabolism of small carbon sources in Paenisporosarcina indica PN2
Found 106 low-confidence and 55 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 | adh: acetaldehyde dehydrogenase (not acylating) | GY23_RS12590 | GY23_RS03610 |
| 4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | | |
| 4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | | |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| 4-hydroxybenzoate | pobA: 4-hydroxybenzoate 3-monooxygenase | | |
| 4-hydroxybenzoate | praA: protocatechuate 2,3-dioxygenase | | |
| 4-hydroxybenzoate | praB: 2-hydroxymuconate 6-semialdehyde dehydrogenase | GY23_RS03715 | GY23_RS03610 |
| 4-hydroxybenzoate | praD: 2-oxohex-3-enedioate decarboxylase | | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arginine | bgtB: L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) | | |
| asparagine | glt: aspartate:proton symporter Glt | GY23_RS10025 | GY23_RS10705 |
| aspartate | glt: aspartate:proton symporter Glt | GY23_RS10025 | GY23_RS10705 |
| cellobiose | bgl: cellobiase | GY23_RS12075 | GY23_RS15520 |
| cellobiose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | GY23_RS08100 | GY23_RS08465 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | GY23_RS08460 | GY23_RS12675 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | GY23_RS08105 | GY23_RS03100 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | GY23_RS06995 | GY23_RS12680 |
| citrulline | arcC: carbamate kinase | | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | D-LDH: D-lactate dehydrogenase | GY23_RS03065 | GY23_RS09285 |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
| deoxyinosine | adh: acetaldehyde dehydrogenase (not acylating) | GY23_RS12590 | GY23_RS03610 |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | GY23_RS10205 | GY23_RS09240 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | adh: acetaldehyde dehydrogenase (not acylating) | GY23_RS12590 | GY23_RS03610 |
| deoxyribose | deoP: deoxyribose transporter | | |
| ethanol | adh: acetaldehyde dehydrogenase (not acylating) | GY23_RS12590 | GY23_RS03610 |
| fructose | 1pfk: 1-phosphofructokinase | | |
| fructose | fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components | | |
| fucose | aldA: lactaldehyde dehydrogenase | GY23_RS03610 | GY23_RS12590 |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | GY23_RS09035 | |
| 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 | | |
| 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 | | |
| galacturonate | uxaA: D-altronate dehydratase | | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | GY23_RS12080 | |
| 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 | | |
| glucuronate | uxaC: D-glucuronate isomerase | | |
| glucuronate | uxuA: D-mannonate dehydratase | | |
| glucuronate | uxuB: D-mannonate dehydrogenase | | |
| glutamate | gltP: L-glutamate:cation symporter GltP/GltT | GY23_RS10025 | GY23_RS10705 |
| glycerol | glpF: glycerol facilitator glpF | | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | GY23_RS16175 | GY23_RS06500 |
| histidine | permease: L-histidine permease | GY23_RS06985 | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | GY23_RS06400 | GY23_RS06395 |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | GY23_RS03660 | GY23_RS04790 |
| isoleucine | livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | GY23_RS09725 | |
| isoleucine | livM: L-isoleucine ABC transporter, permease component 2 (LivM/BraE) | GY23_RS09735 | GY23_RS03800 |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | GY23_RS04910 | GY23_RS01470 |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| L-lactate | lutC: L-lactate dehydrogenase, LutC subunit | GY23_RS09250 | |
| 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) | GY23_RS12075 | GY23_RS15520 |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | GY23_RS03660 | GY23_RS04790 |
| leucine | liuA: isovaleryl-CoA dehydrogenase | GY23_RS05200 | GY23_RS06400 |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | GY23_RS04910 | GY23_RS01620 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | GY23_RS14100 | GY23_RS14930 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | GY23_RS01630 | GY23_RS04755 |
| leucine | livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | GY23_RS09725 | |
| leucine | livM: L-leucine ABC transporter, permease component 2 (LivM/BraE) | GY23_RS09735 | GY23_RS03800 |
| lysine | amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) | GY23_RS06905 | GY23_RS09000 |
| lysine | hglS: D-2-hydroxyglutarate synthase | | |
| lysine | lysN: 2-aminoadipate transaminase | GY23_RS02900 | GY23_RS07680 |
| lysine | lysP: L-lysine:H+ symporter LysP | GY23_RS06985 | |
| lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | | |
| maltose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
| maltose | susB: alpha-glucosidase (maltase) | | |
| mannitol | mtlA: mannitol phosphotransferase system, EII-CBA components | | |
| mannitol | mtlD: mannitol-1-phosphate 5-dehydrogenase | | |
| mannose | manA: mannose-6-phosphate isomerase | | |
| mannose | manP: mannose PTS system, EII-CBA components | | |
| myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | | |
| myoinositol | iolC: 5-dehydro-2-deoxy-D-gluconate kinase | | |
| myoinositol | iolD: 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase | | |
| myoinositol | iolE: scyllo-inosose 2-dehydratase | | |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | | |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | GY23_RS06355 | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| myoinositol | mmsA: malonate-semialdehyde dehydrogenase | GY23_RS06905 | GY23_RS09000 |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | GY23_RS13035 | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | GY23_RS12080 | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| 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 | GY23_RS03600 | GY23_RS14930 |
| phenylacetate | paaK: phenylacetate-CoA ligase | GY23_RS14940 | GY23_RS14200 |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | GY23_RS03600 | GY23_RS03605 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylacetate | ppa: phenylacetate permease ppa | GY23_RS11345 | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | GY23_RS06985 | |
| phenylalanine | iorAB: phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB | | |
| phenylalanine | paaB: phenylacetyl-CoA 1,2-epoxidase, subunit B | | |
| phenylalanine | paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C | | |
| phenylalanine | paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E | | |
| phenylalanine | paaF: 2,3-dehydroadipyl-CoA hydratase | GY23_RS03600 | GY23_RS14930 |
| phenylalanine | paaZ1: oxepin-CoA hydrolase | GY23_RS03600 | GY23_RS03605 |
| phenylalanine | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | GY23_RS04910 | GY23_RS01470 |
| propionate | prpE: propionyl-CoA synthetase | GY23_RS15270 | GY23_RS15365 |
| putrescine | gabD: succinate semialdehyde dehydrogenase | GY23_RS03610 | GY23_RS12590 |
| putrescine | gabT: gamma-aminobutyrate transaminase | GY23_RS07680 | GY23_RS17640 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | GY23_RS17640 | GY23_RS07680 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | GY23_RS03610 | GY23_RS03715 |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | GY23_RS01955 | GY23_RS00375 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase | GY23_RS09270 | GY23_RS13105 |
| rhamnose | LRA6: 2,4-diketo-3-deoxyrhamnonate hydrolase | GY23_RS10290 | GY23_RS00730 |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| sorbitol | scrK: fructokinase | GY23_RS16555 | GY23_RS08840 |
| sorbitol | sdh: sorbitol dehydrogenase | GY23_RS13105 | GY23_RS09030 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
| sucrose | scrK: fructokinase | GY23_RS16555 | GY23_RS08840 |
| sucrose | scrP: sucrose phosphorylase | | |
| sucrose | sut: sucrose:proton symporter SUT/SUC | | |
| threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | GY23_RS04985 | GY23_RS04990 |
| thymidine | adh: acetaldehyde dehydrogenase (not acylating) | GY23_RS12590 | GY23_RS03610 |
| trehalose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
| trehalose | treF: trehalase | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | GY23_RS06985 | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | GY23_RS10290 | GY23_RS03690 |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | GY23_RS06400 | GY23_RS06395 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | GY23_RS14100 | GY23_RS14405 |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | GY23_RS03660 | GY23_RS04790 |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | GY23_RS03600 | GY23_RS14100 |
| valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | GY23_RS09725 | |
| valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | GY23_RS09735 | GY23_RS03800 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | GY23_RS06905 | GY23_RS09000 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | GY23_RS01190 | GY23_RS03205 |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | GY23_RS04910 | GY23_RS01470 |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
| xylitol | xdhA: xylitol dehydrogenase | GY23_RS09030 | GY23_RS09270 |
| xylitol | xylB: xylulokinase | GY23_RS09025 | GY23_RS08540 |
| xylose | xdhA: xylitol dehydrogenase | GY23_RS09030 | GY23_RS09270 |
| xylose | xylB: xylulokinase | GY23_RS09025 | GY23_RS08540 |
| xylose | xylT: D-xylose transporter | | |
| xylose | xyrA: xylitol reductase | GY23_RS02495 | GY23_RS16395 |
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