Potential Gaps in catabolism of small carbon sources in Algoriphagus machipongonensis PR1
Found 86 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 | 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 | xylF: 2-hydroxymuconate semialdehyde hydrolase | | |
| acetate | actP: cation/acetate symporter ActP | ALPR1_RS02865 | |
| arabinose | Echvi_1880: L-arabinose:Na+ symporter | ALPR1_RS12485 | ALPR1_RS16525 |
| arabinose | xacB: L-arabinose 1-dehydrogenase | ALPR1_RS16160 | ALPR1_RS17925 |
| arabinose | xacC: L-arabinono-1,4-lactonase | ALPR1_RS03685 | |
| arginine | rocE: L-arginine permease | | |
| arginine | rocF: arginase | ALPR1_RS12720 | |
| cellobiose | bgl: cellobiase | | |
| cellobiose | glk: glucokinase | ALPR1_RS14545 | ALPR1_RS05845 |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | ALPR1_RS09775 | ALPR1_RS13410 |
| 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 | larD: D,L-lactic acid transporter | ALPR1_RS19200 | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | ALPR1_RS03120 | |
| deoxyinosine | deoB: phosphopentomutase | ALPR1_RS10665 | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | ALPR1_RS10400 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | ALPR1_RS17925 | ALPR1_RS12235 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | garK: glycerate 2-kinase | ALPR1_RS10625 | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoP: deoxyribose transporter | ALPR1_RS13860 | |
| ethanol | etoh-dh-nad: ethanol dehydrogenase (NAD(P)) | ALPR1_RS01365 | ALPR1_RS12235 |
| fucose | fucD: L-fuconate dehydratase | ALPR1_RS11090 | |
| fucose | fucDH: 2-keto-3-deoxy-L-fuconate 4-dehydrogenase | ALPR1_RS13840 | ALPR1_RS17925 |
| fucose | fuconolactonase: L-fucono-1,5-lactonase | ALPR1_RS13850 | |
| galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | ALPR1_RS05850 | ALPR1_RS20085 |
| glucose | glk: glucokinase | ALPR1_RS14545 | ALPR1_RS05845 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | dctP: D-glucuronate TRAP transporter, solute receptor component | ALPR1_RS17480 | |
| glucuronate | dctQ: D-glucuronate TRAP transporter, small permease component | | |
| glucuronate | uxuB: D-mannonate dehydrogenase | | |
| glutamate | gdhA: glutamate dehydrogenase, NAD-dependent | ALPR1_RS03870 | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | ALPR1_RS19190 | |
| histidine | permease: L-histidine permease | | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | ALPR1_RS02465 | ALPR1_RS19205 |
| isoleucine | Bap2: L-isoleucine permease Bap2 | | |
| isoleucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | ALPR1_RS18330 | ALPR1_RS02675 |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | ALPR1_RS14510 | ALPR1_RS12815 |
| isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | ALPR1_RS16285 | ALPR1_RS01095 |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | ALPR1_RS17925 | ALPR1_RS16160 |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | ALPR1_RS12520 | ALPR1_RS12915 |
| L-lactate | Shew_2732: L-lactate:Na+ symporter, small component | ALPR1_RS02870 | |
| lactose | glk: glucokinase | ALPR1_RS14545 | ALPR1_RS05845 |
| lactose | klh: periplasmic 3'-ketolactose hydrolase | ALPR1_RS07255 | ALPR1_RS15135 |
| lactose | lacB': periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) | ALPR1_RS18010 | ALPR1_RS11665 |
| lactose | lacC': periplasmic lactose 3-dehydrogenase, LacC subunit | ALPR1_RS17980 | ALPR1_RS18960 |
| leucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | ALPR1_RS18330 | ALPR1_RS02675 |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | ALPR1_RS14510 | ALPR1_RS12815 |
| leucine | leuT: L-leucine:Na+ symporter LeuT | | |
| leucine | liuA: isovaleryl-CoA dehydrogenase | ALPR1_RS19205 | ALPR1_RS02465 |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | ALPR1_RS12520 | ALPR1_RS12915 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | ALPR1_RS14955 | ALPR1_RS04635 |
| lysine | cadA: lysine decarboxylase | ALPR1_RS02910 | |
| lysine | davD: glutarate semialdehyde dehydrogenase | ALPR1_RS01205 | ALPR1_RS06445 |
| lysine | davT: 5-aminovalerate aminotransferase | ALPR1_RS03490 | ALPR1_RS09710 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | | |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| lysine | patD: 5-aminopentanal dehydrogenase | ALPR1_RS01205 | ALPR1_RS06860 |
| maltose | glk: glucokinase | ALPR1_RS14545 | ALPR1_RS05845 |
| maltose | susB: alpha-glucosidase (maltase) | | |
| mannitol | mt2d: mannitol 2-dehydrogenase | ALPR1_RS17925 | ALPR1_RS16160 |
| mannitol | PLT5: polyol transporter PLT5 | | |
| mannose | man-isomerase: D-mannose isomerase | | |
| mannose | STP6: mannose:H+ symporter | | |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | ALPR1_RS05730 | |
| myoinositol | iolM: 2-inosose 4-dehydrogenase | | |
| myoinositol | iolN: 2,4-diketo-inositol hydratase | | |
| myoinositol | iolO: 5-dehydro-L-gluconate epimerase | ALPR1_RS16075 | ALPR1_RS11655 |
| myoinositol | iolT: myo-inositol:H+ symporter | ALPR1_RS10185 | ALPR1_RS12850 |
| myoinositol | uxaE: D-tagaturonate epimerase | | |
| myoinositol | uxuB: D-mannonate dehydrogenase | | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | ALPR1_RS20075 | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | ALPR1_RS05850 | ALPR1_RS20085 |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| 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 | ALPR1_RS16785 | |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | ALPR1_RS16285 | |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | ALPR1_RS16285 | ALPR1_RS05015 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | ALPR1_RS01085 | ALPR1_RS13240 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | ALPR1_RS01085 | ALPR1_RS13240 |
| phenylacetate | paaK: phenylacetate-CoA ligase | ALPR1_RS19255 | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | maiA: maleylacetoacetate isomerase | | |
| phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | ALPR1_RS00415 | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | | |
| proline | ectP: proline transporter EctP | ALPR1_RS00845 | ALPR1_RS01370 |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | ALPR1_RS12520 | ALPR1_RS12915 |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | gabT: gamma-aminobutyrate transaminase | ALPR1_RS03490 | ALPR1_RS09710 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | ALPR1_RS01205 | ALPR1_RS06860 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| pyruvate | actP: large subunit of pyruvate transporter (actP-like) | ALPR1_RS02865 | |
| pyruvate | yjcH: putative small subunit of pyruvate transporter (yjcH-like) | ALPR1_RS02870 | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | snatA: L-serine transporter | ALPR1_RS14825 | |
| sorbitol | sdh: sorbitol dehydrogenase | ALPR1_RS16070 | ALPR1_RS08420 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | ALPR1_RS12850 | |
| sucrose | ams: sucrose hydrolase (invertase) | ALPR1_RS10225 | |
| threonine | snatA: L-threonine transporter snatA | ALPR1_RS14825 | |
| thymidine | deoA: thymidine phosphorylase DeoA | ALPR1_RS03280 | |
| thymidine | deoB: phosphopentomutase | ALPR1_RS10665 | |
| trehalose | glk: glucokinase | ALPR1_RS14545 | ALPR1_RS05845 |
| 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 | ALPR1_RS02465 | ALPR1_RS19205 |
| valine | Bap2: L-valine permease Bap2 | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | | |
| valine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | ALPR1_RS18330 | ALPR1_RS02675 |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | ALPR1_RS14510 | ALPR1_RS12815 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | ALPR1_RS01205 | ALPR1_RS06860 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | | |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | ALPR1_RS12520 | ALPR1_RS12915 |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
| xylitol | xdhA: xylitol dehydrogenase | ALPR1_RS16070 | ALPR1_RS08420 |
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