Potential Gaps in catabolism of small carbon sources in Sphingopyxis terrae UI2
Found 106 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 | CCK86_RS15735 | CCK86_RS05265 |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| 4-hydroxybenzoate | pobA: 4-hydroxybenzoate 3-monooxygenase | | |
| 4-hydroxybenzoate | praA: protocatechuate 2,3-dioxygenase | | |
| 4-hydroxybenzoate | praC: 2-hydroxymuconate tautomerase | CCK86_RS05915 | |
| alanine | snatA: L-alanine symporter SnatA | CCK86_RS06405 | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | CCK86_RS08050 | |
| arginine | adiA: arginine decarboxylase (AdiA/SpeA) | | |
| arginine | patD: gamma-aminobutyraldehyde dehydrogenase | CCK86_RS04530 | CCK86_RS11115 |
| arginine | rocE: L-arginine permease | CCK86_RS04360 | |
| asparagine | ans: asparaginase | CCK86_RS07050 | CCK86_RS05545 |
| cellobiose | glk: glucokinase | CCK86_RS14305 | |
| citrate | SLC13A5: citrate:Na+ symporter | CCK86_RS03645 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | CCK86_RS01525 | CCK86_RS02665 |
| 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 | | |
| citrulline | rocD: ornithine aminotransferase | CCK86_RS13855 | CCK86_RS14315 |
| D-alanine | cycA: D-alanine:H+ symporter CycA | CCK86_RS04360 | |
| D-alanine | dadA: D-alanine dehydrogenase | CCK86_RS04205 | |
| D-lactate | D-LDH: D-lactate dehydrogenase | CCK86_RS00525 | CCK86_RS14530 |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
| D-serine | cycA: D-serine:H+ symporter CycA | CCK86_RS04360 | |
| deoxyinosine | deoB: phosphopentomutase | CCK86_RS00985 | |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | CCK86_RS11190 | CCK86_RS08045 |
| 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 | | |
| fructose | fruP: fructose porter FruP | CCK86_RS01055 | |
| fructose | scrK: fructokinase | | |
| fucose | fdh: L-fucose 1-dehydrogenase | CCK86_RS08045 | CCK86_RS06570 |
| fucose | fuconolactonase: L-fucono-1,5-lactonase | CCK86_RS08015 | |
| fucose | fucP: L-fucose:H+ symporter FucP | CCK86_RS01055 | |
| fucose | fucU: L-fucose mutarotase FucU | | |
| galactose | galE: UDP-glucose 4-epimerase | CCK86_RS10055 | CCK86_RS10065 |
| galactose | galK: galactokinase (-1-phosphate forming) | | |
| galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| galacturonate | exuT: D-galacturonate transporter ExuT | CCK86_RS10005 | |
| galacturonate | kdgK: 2-keto-3-deoxygluconate kinase | CCK86_RS09970 | CCK86_RS15685 |
| galacturonate | uxaA: D-altronate dehydratase | CCK86_RS08030 | |
| 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) | CCK86_RS01830 | CCK86_RS16725 |
| glucose | glk: glucokinase | CCK86_RS14305 | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | CCK86_RS10005 | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
| glucuronate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | CCK86_RS02070 | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| glutamate | gltP: L-glutamate:cation symporter GltP/GltT | CCK86_RS10215 | CCK86_RS03490 |
| glycerol | glpF: glycerol facilitator glpF | CCK86_RS06320 | |
| isoleucine | Bap2: L-isoleucine permease Bap2 | CCK86_RS04360 | |
| L-lactate | lctO: L-lactate oxidase or 2-monooxygenase | CCK86_RS04860 | |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| lactose | glk: glucokinase | CCK86_RS14305 | |
| lactose | klh: periplasmic 3'-ketolactose hydrolase | | |
| lactose | lacA': periplasmic lactose 3-dehydrogenase, LacA subunit | | |
| lactose | lacB': periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) | CCK86_RS04065 | |
| lactose | lacC': periplasmic lactose 3-dehydrogenase, LacC subunit | | |
| leucine | leuT: L-leucine:Na+ symporter LeuT | | |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | CCK86_RS10770 | CCK86_RS06600 |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | CCK86_RS10770 | |
| lysine | davA: 5-aminovaleramidase | CCK86_RS14580 | CCK86_RS10675 |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | lysP: L-lysine:H+ symporter LysP | CCK86_RS04360 | |
| maltose | glk: glucokinase | CCK86_RS14305 | |
| 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 | CCK86_RS15010 | CCK86_RS14080 |
| 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 | CCK86_RS08050 | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | CCK86_RS01830 | CCK86_RS16725 |
| 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 | CCK86_RS06600 | CCK86_RS04290 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | CCK86_RS14895 | CCK86_RS07375 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | CCK86_RS14895 | CCK86_RS07375 |
| phenylacetate | paaK: phenylacetate-CoA ligase | CCK86_RS14725 | CCK86_RS12100 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | CCK86_RS04290 | CCK86_RS06600 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | CCK86_RS04360 | |
| phenylalanine | hmgA: homogentisate dioxygenase | | |
| phenylalanine | maiA: maleylacetoacetate isomerase | CCK86_RS01885 | CCK86_RS12885 |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | | |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | CCK86_RS04530 | CCK86_RS11115 |
| putrescine | potB: putrescine ABC transporter, permease component 1 (PotB/PotH) | CCK86_RS14335 | |
| putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | CCK86_RS14340 | |
| pyruvate | SLC5A8: sodium-coupled pyruvate transporter | | |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | CCK86_RS12270 | CCK86_RS06570 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase | CCK86_RS10505 | CCK86_RS08025 |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsK: ribokinase | | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | snatA: L-serine transporter | CCK86_RS06405 | |
| sorbitol | scrK: fructokinase | | |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
| sucrose | ams: sucrose hydrolase (invertase) | | |
| sucrose | glk: glucokinase | CCK86_RS14305 | |
| threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | CCK86_RS10370 | CCK86_RS10365 |
| threonine | ltaE: L-threonine aldolase | CCK86_RS03575 | CCK86_RS14630 |
| threonine | snatA: L-threonine transporter snatA | CCK86_RS06405 | |
| thymidine | deoA: thymidine phosphorylase DeoA | | |
| thymidine | deoB: phosphopentomutase | CCK86_RS00985 | |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| trehalose | glk: glucokinase | CCK86_RS14305 | |
| trehalose | treF: trehalase | | |
| tryptophan | hpaH: anthranilate 3-monooxygenase (hydroxylase), FADH2-dependent | | |
| tryptophan | kynA: tryptophan 2,3-dioxygenase | CCK86_RS11990 | |
| tryptophan | kynB: kynurenine formamidase | CCK86_RS09985 | CCK86_RS04100 |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | CCK86_RS04360 | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | CCK86_RS01885 | CCK86_RS12885 |
| valine | acdH: isobutyryl-CoA dehydrogenase | CCK86_RS06610 | CCK86_RS00605 |
| valine | Bap2: L-valine permease Bap2 | CCK86_RS04360 | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | CCK86_RS06605 | CCK86_RS06600 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | | |
| xylose | DKDP-dehydrog: D-2-keto-3-deoxypentoate dehydrogenase | CCK86_RS08025 | CCK86_RS06535 |
| xylose | xad: D-xylonate dehydratase | CCK86_RS01415 | |
| xylose | xdh: D-xylose dehydrogenase | CCK86_RS11190 | CCK86_RS06535 |
| xylose | xylC: xylonolactonase | CCK86_RS07365 | |
| xylose | xylT: D-xylose transporter | CCK86_RS08050 | |
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