Potential Gaps in catabolism of small carbon sources in Erythrobacter marinus HWDM-33
Found 108 low-confidence and 41 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | AAV99_RS09250 | |
| 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 | | |
| arabinose | araE: L-arabinose:H+ symporter | AAV99_RS11880 | |
| arabinose | xacB: L-arabinose 1-dehydrogenase | AAV99_RS11820 | AAV99_RS06280 |
| arabinose | xacC: L-arabinono-1,4-lactonase | AAV99_RS11825 | |
| arabinose | xacD: L-arabinonate dehydratase | AAV99_RS11830 | AAV99_RS10060 |
| arabinose | xacE: 2-dehydro-3-deoxy-L-arabinonate dehydratase | | |
| arginine | astA: arginine N-succinyltransferase | AAV99_RS11705 | |
| arginine | astC: succinylornithine transaminase | AAV99_RS04900 | AAV99_RS12000 |
| arginine | astE: succinylglutamate desuccinylase | | |
| arginine | rocE: L-arginine permease | | |
| aspartate | glt: aspartate:proton symporter Glt | AAV99_RS02385 | |
| cellobiose | glk: glucokinase | AAV99_RS01385 | AAV99_RS01725 |
| citrate | SLC13A5: citrate:Na+ symporter | AAV99_RS12620 | AAV99_RS12860 |
| citrulline | citrullinase: putative citrullinase | AAV99_RS05660 | |
| citrulline | ocd: ornithine cyclodeaminase | | |
| citrulline | PS417_17590: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| citrulline | PS417_17595: ABC transporter for L-Citrulline, permease component 1 | | |
| citrulline | PS417_17600: ABC transporter for L-Citrulline, permease component 2 | | |
| citrulline | PS417_17605: ABC transporter for L-Citrulline, ATPase component | AAV99_RS11970 | AAV99_RS13340 |
| 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 | AAV99_RS00850 | AAV99_RS10255 |
| deoxyinosine | deoB: phosphopentomutase | AAV99_RS01875 | |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | AAV99_RS00985 | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | AAV99_RS12305 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | AAV99_RS11820 | AAV99_RS08075 |
| 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 | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyribose | deoK: deoxyribokinase | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| 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 | AAV99_RS05995 | |
| fucose | fucU: L-fucose mutarotase FucU | | |
| galactose | dgoA: 2-dehydro-3-deoxy-6-phosphogalactonate aldolase | AAV99_RS01390 | AAV99_RS12340 |
| galactose | dgoD: D-galactonate dehydratase | AAV99_RS11830 | AAV99_RS10060 |
| galactose | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | AAV99_RS11825 | |
| galactose | galdh: D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) | AAV99_RS11820 | AAV99_RS06280 |
| galactose | HP1174: Na+-dependent galactose transporter | AAV99_RS05995 | |
| galacturonate | exuT: D-galacturonate transporter ExuT | AAV99_RS12350 | |
| galacturonate | uxaA: D-altronate dehydratase | | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | | |
| gluconate | gntK: D-gluconate kinase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | AAV99_RS11590 | |
| glucose | glk: glucokinase | AAV99_RS01385 | AAV99_RS01725 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | AAV99_RS12350 | |
| glucuronate | uxaC: D-glucuronate isomerase | | |
| glucuronate | uxuA: D-mannonate dehydratase | | |
| glucuronate | uxuB: D-mannonate dehydrogenase | | |
| glutamate | gdhA: glutamate dehydrogenase, NAD-dependent | AAV99_RS03710 | AAV99_RS02560 |
| glycerol | glpF: glycerol facilitator glpF | AAV99_RS01245 | |
| histidine | Ga0059261_1577: L-histidine transporter | AAV99_RS13360 | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| isoleucine | Bap2: L-isoleucine permease Bap2 | | |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| lactose | glk: glucokinase | AAV99_RS01385 | AAV99_RS01725 |
| lactose | klh: periplasmic 3'-ketolactose hydrolase | | |
| lactose | lacA': periplasmic lactose 3-dehydrogenase, LacA subunit | | |
| lactose | lacB': periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) | AAV99_RS12270 | |
| lactose | lacC': periplasmic lactose 3-dehydrogenase, LacC subunit | | |
| leucine | leuT: L-leucine:Na+ symporter LeuT | | |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | AAV99_RS05725 | AAV99_RS12275 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | AAV99_RS03105 | AAV99_RS05680 |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | AAV99_RS02680 | |
| lysine | davA: 5-aminovaleramidase | AAV99_RS07670 | AAV99_RS05660 |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | davD: glutarate semialdehyde dehydrogenase | AAV99_RS05570 | AAV99_RS10950 |
| lysine | davT: 5-aminovalerate aminotransferase | AAV99_RS04900 | AAV99_RS12000 |
| lysine | fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase | AAV99_RS07705 | AAV99_RS00990 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| maltose | glk: glucokinase | AAV99_RS01385 | AAV99_RS01725 |
| maltose | susB: alpha-glucosidase (maltase) | | |
| mannitol | mt2d: mannitol 2-dehydrogenase | AAV99_RS08075 | AAV99_RS03635 |
| mannitol | PLT5: polyol transporter PLT5 | AAV99_RS11880 | |
| mannose | manA: mannose-6-phosphate isomerase | AAV99_RS05775 | AAV99_RS02555 |
| 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 | | |
| myoinositol | iolT: myo-inositol:H+ symporter | AAV99_RS11880 | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | AAV99_RS11590 | |
| 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 | | |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | AAV99_RS05725 | AAV99_RS05720 |
| phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | AAV99_RS07705 | AAV99_RS00990 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | AAV99_RS12435 | AAV99_RS07710 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | AAV99_RS12435 | AAV99_RS07710 |
| phenylacetate | paaK: phenylacetate-CoA ligase | AAV99_RS07715 | AAV99_RS12450 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | AAV99_RS05725 | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | | |
| propionate | putP: propionate transporter; proline:Na+ symporter | AAV99_RS07660 | |
| putrescine | gabT: gamma-aminobutyrate transaminase | AAV99_RS04900 | AAV99_RS12000 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | AAV99_RS04900 | AAV99_RS12000 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | AAV99_RS05570 | AAV99_RS05185 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| pyruvate | SLC5A8: sodium-coupled pyruvate transporter | | |
| rhamnose | rhaB: L-rhamnulokinase | AAV99_RS00120 | |
| ribose | rbsK: ribokinase | | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | snatA: L-serine transporter | AAV99_RS02880 | |
| sorbitol | sdh: sorbitol dehydrogenase | AAV99_RS12695 | AAV99_RS13520 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | AAV99_RS11880 | |
| sucrose | ams: sucrose hydrolase (invertase) | | |
| threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | AAV99_RS06005 | AAV99_RS06010 |
| threonine | ltaE: L-threonine aldolase | AAV99_RS04660 | AAV99_RS08895 |
| threonine | snatA: L-threonine transporter snatA | AAV99_RS02880 | |
| thymidine | deoA: thymidine phosphorylase DeoA | | |
| thymidine | deoB: phosphopentomutase | AAV99_RS01875 | |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | glk: glucokinase | AAV99_RS01385 | AAV99_RS01725 |
| trehalose | treF: trehalase | AAV99_RS10280 | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | AAV99_RS13300 | AAV99_RS03120 |
| valine | Bap2: L-valine permease Bap2 | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | AAV99_RS13305 | AAV99_RS05725 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | | |
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