Potential Gaps in catabolism of small carbon sources in Sphingobium czechense LL01
Found 84 low-confidence and 41 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | V473_RS16690 | V473_RS17920 |
| alanine | alsT: L-alanine symporter AlsT/DagA | V473_RS03915 | |
| arabinose | araE: L-arabinose:H+ symporter | V473_RS05365 | |
| arabinose | xacC: L-arabinono-1,4-lactonase | V473_RS13380 | V473_RS16695 |
| arabinose | xacD: L-arabinonate dehydratase | V473_RS11950 | V473_RS12050 |
| arginine | adiA: arginine decarboxylase (AdiA/SpeA) | | |
| arginine | patA: putrescine aminotransferase (PatA/SpuC) | V473_RS20290 | V473_RS02290 |
| arginine | patD: gamma-aminobutyraldehyde dehydrogenase | V473_RS05540 | V473_RS05490 |
| arginine | rocE: L-arginine permease | | |
| asparagine | ans: asparaginase | V473_RS09330 | |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | V473_RS03740 | V473_RS00455 |
| 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 | citrullinase: putative citrullinase | V473_RS09535 | |
| citrulline | ocd: ornithine cyclodeaminase | | |
| D-alanine | cycA: D-alanine:H+ symporter CycA | | |
| D-lactate | D-LDH: D-lactate dehydrogenase | V473_RS06300 | V473_RS08145 |
| 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 | V473_RS10210 | V473_RS11265 |
| deoxyinosine | deoB: phosphopentomutase | V473_RS03920 | |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | V473_RS05375 | V473_RS18075 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | garK: glycerate 2-kinase | | |
| deoxyribose | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyribose | deoK: deoxyribokinase | | |
| deoxyribose | deoP: deoxyribose transporter | V473_RS17505 | |
| fructose | glcP: fructose:H+ symporter GlcP | V473_RS05365 | |
| fucose | fdh: L-fucose 1-dehydrogenase | V473_RS19030 | V473_RS08785 |
| galactose | dgoD: D-galactonate dehydratase | V473_RS11950 | V473_RS05420 |
| galactose | dgoK: 2-dehydro-3-deoxygalactonokinase | V473_RS04255 | V473_RS11945 |
| galactose | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | V473_RS13380 | V473_RS05370 |
| galacturonate | uxaA: D-altronate dehydratase | V473_RS17515 | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | V473_RS05430 | |
| 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) | V473_RS11055 | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | V473_RS05425 | |
| glucuronate | uxaC: D-glucuronate isomerase | V473_RS05430 | |
| glucuronate | uxuB: D-mannonate dehydrogenase | V473_RS05435 | |
| glycerol | glpF: glycerol facilitator glpF | | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | V473_RS03945 | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| isoleucine | Bap2: L-isoleucine permease Bap2 | | |
| L-lactate | L-LDH: L-lactate dehydrogenase | V473_RS02790 | V473_RS03950 |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| lactose | dgoD: D-galactonate dehydratase | V473_RS11950 | V473_RS05420 |
| lactose | dgoK: 2-dehydro-3-deoxygalactonokinase | V473_RS04255 | V473_RS11945 |
| lactose | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | V473_RS13380 | V473_RS05370 |
| lactose | lacP: lactose permease LacP | | |
| leucine | leuT: L-leucine:Na+ symporter LeuT | | |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | V473_RS08215 | V473_RS18100 |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| lysine | cadA: lysine decarboxylase | V473_RS17630 | V473_RS02020 |
| lysine | davT: 5-aminovalerate aminotransferase | V473_RS02290 | V473_RS18720 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | V473_RS05465 | V473_RS08220 |
| lysine | gcdH: glutaryl-CoA dehydrogenase | V473_RS17395 | V473_RS17555 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| lysine | patA: cadaverine aminotransferase | V473_RS02290 | V473_RS20290 |
| lysine | patD: 5-aminopentanal dehydrogenase | V473_RS05540 | V473_RS05490 |
| mannitol | mt2d: mannitol 2-dehydrogenase | V473_RS05435 | V473_RS15960 |
| mannitol | PLT5: polyol transporter PLT5 | V473_RS05365 | |
| mannose | gluP: mannose:Na+ symporter | V473_RS13390 | V473_RS17505 |
| mannose | man-isomerase: D-mannose isomerase | | |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | V473_RS20215 | |
| myoinositol | iolM: 2-inosose 4-dehydrogenase | | |
| myoinositol | iolN: 2,4-diketo-inositol hydratase | | |
| myoinositol | iolO: 5-dehydro-L-gluconate epimerase | | |
| myoinositol | iolT: myo-inositol:H+ symporter | V473_RS05365 | |
| myoinositol | uxaE: D-tagaturonate epimerase | | |
| myoinositol | uxuB: D-mannonate dehydrogenase | V473_RS05435 | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | V473_RS11055 | |
| 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 | paaK: phenylacetate-CoA ligase | V473_RS18160 | V473_RS05200 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | V473_RS08215 | V473_RS05770 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | maiA: maleylacetoacetate isomerase | V473_RS00260 | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | V473_RS19685 | |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | V473_RS20290 | V473_RS02290 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | V473_RS05540 | V473_RS05490 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | V473_RS15930 | |
| ribose | rbsK: ribokinase | | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | snatA: L-serine transporter | V473_RS13055 | |
| sorbitol | sdh: sorbitol dehydrogenase | V473_RS16930 | V473_RS05715 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | V473_RS05365 | |
| sucrose | ams: sucrose hydrolase (invertase) | V473_RS17575 | |
| threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | V473_RS11540 | V473_RS11545 |
| threonine | ltaE: L-threonine aldolase | V473_RS15155 | V473_RS09495 |
| threonine | snatA: L-threonine transporter snatA | V473_RS13055 | |
| thymidine | deoA: thymidine phosphorylase DeoA | | |
| thymidine | deoB: phosphopentomutase | V473_RS03920 | |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| tryptophan | antA: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA | V473_RS08335 | V473_RS20080 |
| tryptophan | antB: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB | V473_RS08330 | |
| tryptophan | antC: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC | | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | kyn: kynureninase | | |
| tryptophan | kynA: tryptophan 2,3-dioxygenase | | |
| tryptophan | kynB: kynurenine formamidase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | maiA: maleylacetoacetate isomerase | V473_RS00260 | |
| valine | Bap2: L-valine permease Bap2 | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | V473_RS04400 | V473_RS04380 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | V473_RS19030 | |
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