Potential Gaps in catabolism of small carbon sources in Planococcus halocryophilus Or1
Found 109 low-confidence and 53 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | Psest_0084: 2-oxoglutarate TRAP transporter, fused 4TM/12TM components | B481_RS11125 | |
| 4-hydroxybenzoate | adh: acetaldehyde dehydrogenase (not acylating) | B481_RS12395 | B481_RS02440 |
| 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 | B481_RS03760 | B481_RS12395 |
| 4-hydroxybenzoate | praD: 2-oxohex-3-enedioate decarboxylase | | |
| acetate | actP: cation/acetate symporter ActP | B481_RS01795 | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | chvE: L-arabinose ABC transporter, substrate-binding component ChvE | B481_RS07005 | B481_RS06975 |
| arginine | putA: L-glutamate 5-semialdeyde dehydrogenase | B481_RS03760 | B481_RS14250 |
| asparagine | ans: asparaginase | B481_RS09400 | |
| citrate | tctB: citrate/Na+ symporter, small transmembrane component TctB | | |
| citrate | tctC: citrate/Na+ symporter, substrate-binding component TctC | B481_RS12490 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | B481_RS11695 | B481_RS04230 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | B481_RS12325 | B481_RS17055 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | B481_RS17055 | B481_RS14065 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | B481_RS11685 | B481_RS17045 |
| citrulline | citrullinase: putative citrullinase | | |
| citrulline | putA: L-glutamate 5-semialdeyde dehydrogenase | B481_RS03760 | B481_RS14250 |
| D-alanine | cycA: D-alanine:H+ symporter CycA | B481_RS11840 | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | larD: D,L-lactic acid transporter | B481_RS05350 | |
| D-serine | cycA: D-serine:H+ symporter CycA | B481_RS11840 | |
| deoxyinosine | adh: acetaldehyde dehydrogenase (not acylating) | B481_RS12395 | B481_RS02440 |
| deoxyinosine | deoD: deoxyinosine phosphorylase | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | B481_RS09125 | B481_RS03755 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | B481_RS12345 | |
| deoxyribose | adh: acetaldehyde dehydrogenase (not acylating) | B481_RS12395 | B481_RS02440 |
| deoxyribose | deoP: deoxyribose transporter | | |
| ethanol | adh: acetaldehyde dehydrogenase (not acylating) | B481_RS12395 | B481_RS02440 |
| fructose | 1pfk: 1-phosphofructokinase | | |
| 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 | | |
| galactose | chvE: galactose ABC transporter, substrate-binding component ChvE | B481_RS07005 | B481_RS06975 |
| galactose | galK: galactokinase (-1-phosphate forming) | | |
| galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| galactose | pgmA: alpha-phosphoglucomutase | B481_RS16765 | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | kdgK: 2-keto-3-deoxygluconate kinase | B481_RS08110 | |
| galacturonate | uxaA: D-altronate dehydratase | B481_RS08010 | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | | |
| 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 | B481_RS08085 | B481_RS12005 |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | B481_RS08100 | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | B481_RS04335 | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| histidine | PA5503: L-histidine ABC transporter, ATPase component | B481_RS03930 | B481_RS08935 |
| histidine | PA5505: L-histidine ABC transporter, substrate-binding component | B481_RS08925 | B481_RS03920 |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | B481_RS04440 | B481_RS04445 |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | B481_RS10835 | B481_RS07835 |
| isoleucine | brnQ: L-isoleucine:cation symporter BrnQ/BraZ/BraB | B481_RS17140 | |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | B481_RS16025 | B481_RS10635 |
| L-lactate | L-LDH: L-lactate dehydrogenase | B481_RS02505 | |
| L-lactate | SfMCT: L-lactate transporter SfMCT | B481_RS07565 | |
| lactose | klh: periplasmic 3'-ketolactose hydrolase | | |
| lactose | lacA': periplasmic lactose 3-dehydrogenase, LacA subunit | | |
| lactose | lacB': periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) | | |
| lactose | lacC': periplasmic lactose 3-dehydrogenase, LacC subunit | | |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | B481_RS10835 | B481_RS07835 |
| leucine | brnQ: L-leucine:Na+ symporter BrnQ/BraB | B481_RS17140 | |
| leucine | liuA: isovaleryl-CoA dehydrogenase | B481_RS15775 | B481_RS04445 |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | B481_RS16025 | B481_RS10635 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | B481_RS00445 | B481_RS12835 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | B481_RS10625 | B481_RS16165 |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| lysine | amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) | B481_RS04030 | B481_RS11595 |
| lysine | hglS: D-2-hydroxyglutarate synthase | | |
| lysine | lysN: 2-aminoadipate transaminase | B481_RS09195 | B481_RS11625 |
| lysine | lysP: L-lysine:H+ symporter LysP | B481_RS11840 | |
| lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | | |
| mannose | manA: mannose-6-phosphate isomerase | | |
| mannose | manP: mannose PTS system, EII-CBA components | B481_RS02290 | |
| 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 | B481_RS04485 | B481_RS01095 |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| myoinositol | mmsA: malonate-semialdehyde dehydrogenase | B481_RS04030 | B481_RS11595 |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | | |
| phenylacetate | paaA: phenylacetyl-CoA 1,2-epoxidase, subunit A | | |
| 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 | B481_RS12835 | B481_RS02710 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | B481_RS00285 | B481_RS12835 |
| phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | B481_RS04435 | B481_RS14455 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | B481_RS12860 | B481_RS09545 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | B481_RS12860 | B481_RS09545 |
| phenylacetate | paaK: phenylacetate-CoA ligase | B481_RS02700 | B481_RS00435 |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylacetate | ppa: phenylacetate permease ppa | B481_RS01795 | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | B481_RS11840 | |
| phenylalanine | fahA: fumarylacetoacetate hydrolase | B481_RS08050 | |
| phenylalanine | hmgA: homogentisate dioxygenase | | |
| phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| phenylalanine | maiA: maleylacetoacetate isomerase | | |
| phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
| phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | B481_RS03880 | |
| proline | putA: L-glutamate 5-semialdeyde dehydrogenase | B481_RS03760 | B481_RS14250 |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | B481_RS16025 | B481_RS10635 |
| propionate | putP: propionate transporter; proline:Na+ symporter | B481_RS14345 | |
| putrescine | gabT: gamma-aminobutyrate transaminase | B481_RS08685 | B481_RS05620 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | B481_RS08685 | B481_RS02835 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | B481_RS03760 | B481_RS12395 |
| putrescine | potA: putrescine ABC transporter, ATPase component (PotA/PotG) | B481_RS06795 | B481_RS11735 |
| putrescine | potB: putrescine ABC transporter, permease component 1 (PotB/PotH) | | |
| pyruvate | mctC: pyruvate symporter MctC | B481_RS01795 | |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | B481_RS10305 | B481_RS01230 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | B481_RS08010 | B481_RS08100 |
| 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 | B481_RS07000 | B481_RS01495 |
| ribose | rbsB: D-ribose ABC transporter, substrate-binding component RbsB | B481_RS12915 | |
| ribose | rbsC: D-ribose ABC transporter, permease component RbsC | B481_RS12910 | B481_RS01490 |
| serine | serP: L-serine permease SerP | B481_RS11840 | |
| sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | B481_RS10305 | B481_RS01065 |
| succinate | sdc: succinate:Na+ symporter Sdc | | |
| sucrose | 1pfk: 1-phosphofructokinase | | |
| sucrose | ams: sucrose hydrolase (invertase) | B481_RS03350 | B481_RS06785 |
| threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | B481_RS15985 | |
| threonine | tdcC: L-threonine:H+ symporter TdcC | | |
| thymidine | adh: acetaldehyde dehydrogenase (not acylating) | B481_RS12395 | B481_RS02440 |
| trehalose | treF: trehalase | B481_RS03660 | B481_RS06785 |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | B481_RS11840 | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | B481_RS08050 | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | B481_RS04440 | B481_RS15775 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | B481_RS00445 | B481_RS12835 |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | B481_RS10835 | B481_RS07835 |
| valine | brnQ: L-valine:cation symporter BrnQ/BraZ/BraB | B481_RS17140 | |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | B481_RS00445 | B481_RS12835 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | B481_RS04030 | B481_RS11595 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | B481_RS01105 | B481_RS10995 |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | B481_RS16025 | B481_RS10635 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | B481_RS02290 | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | B481_RS00905 | |
| xylose | xdh: D-xylose dehydrogenase | B481_RS10305 | B481_RS11895 |
| xylose | xylC: xylonolactonase | | |
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