Potential Gaps in catabolism of small carbon sources in Xenophilus azovorans DSM 13620
Found 80 low-confidence and 43 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 | Q392_RS30055 | |
2-oxoglutarate | Psest_0085: 2-oxoglutarate TRAP transporter, solute receptor component | Q392_RS30060 | |
4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | Q392_RS24240 | Q392_RS02605 |
4-hydroxybenzoate | praA: protocatechuate 2,3-dioxygenase | | |
alanine | snatA: L-alanine symporter SnatA | Q392_RS18140 | |
arabinose | araE: L-arabinose:H+ symporter | | |
arabinose | xacB: L-arabinose 1-dehydrogenase | Q392_RS13490 | Q392_RS03415 |
arabinose | xacC: L-arabinono-1,4-lactonase | Q392_RS10520 | Q392_RS08560 |
arabinose | xacE: 2-dehydro-3-deoxy-L-arabinonate dehydratase | | |
arginine | braC: ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC | Q392_RS28895 | Q392_RS05395 |
arginine | braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) | Q392_RS11640 | Q392_RS28475 |
arginine | braF: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) | Q392_RS23140 | Q392_RS27095 |
arginine | braG: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) | Q392_RS11630 | Q392_RS09840 |
cellobiose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
citrate | tctB: citrate/Na+ symporter, small transmembrane component TctB | | |
citrate | tctC: citrate/Na+ symporter, substrate-binding component TctC | Q392_RS03185 | Q392_RS19490 |
citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | Q392_RS15975 | Q392_RS21800 |
citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | Q392_RS27605 | Q392_RS21810 |
citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | Q392_RS21810 | Q392_RS15970 |
citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
citrulline | arcC: carbamate kinase | | |
D-alanine | Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component | Q392_RS33980 | |
D-alanine | Pf6N2E2_5403: ABC transporter for D-Alanine, permease component 2 | Q392_RS21810 | |
D-alanine | Pf6N2E2_5404: ABC transporter for D-Alanine, permease component 1 | Q392_RS27605 | Q392_RS24095 |
D-serine | cycA: D-serine:H+ symporter CycA | | |
D-serine | dsdA: D-serine ammonia-lyase | Q392_RS25660 | Q392_RS29285 |
deoxyinosine | deoB: phosphopentomutase | Q392_RS14970 | |
deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
deoxyinosine | deoD: deoxyinosine phosphorylase | | |
deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | Q392_RS30315 | Q392_RS21195 |
deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | Q392_RS02710 | Q392_RS18505 |
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 | Slc2a5: fructose:H+ symporter | | |
fucose | fdh: L-fucose 1-dehydrogenase | Q392_RS06765 | Q392_RS09845 |
fucose | fucD: L-fuconate dehydratase | Q392_RS27400 | Q392_RS10550 |
fucose | fuconolactonase: L-fucono-1,5-lactonase | | |
fucose | fucP: L-fucose:H+ symporter FucP | | |
fucose | fucU: L-fucose mutarotase FucU | | |
galactose | dgoD: D-galactonate dehydratase | Q392_RS10365 | Q392_RS08305 |
galactose | galdh: D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) | Q392_RS13490 | Q392_RS03415 |
galactose | galP: galactose:H+ symporter GalP | | |
galacturonate | exuT: D-galacturonate transporter ExuT | | |
glucosamine | AO353_21710: glucosaminate ABC transporter, substrate-binding component | | |
glucosamine | AO353_21715: glucosaminate ABC transporter, permease component 1 | Q392_RS21815 | Q392_RS27605 |
glucosamine | AO353_21720: glucosaminate ABC transporter, permease component 2 | Q392_RS24095 | Q392_RS27605 |
glucosamine | AO353_21725: glucosaminate ABC transporter, ATPase component | Q392_RS15975 | Q392_RS21800 |
glucosamine | glucosaminate-lyase: glucosaminate ammonia-lyase | Q392_RS09755 | Q392_RS11670 |
glucosamine | kdgA: 2-keto-3-deoxygluconate-6-phosphate aldolase EC:4.1.2.14 | Q392_RS10445 | Q392_RS10375 |
glucosamine | kdgK: 2-keto-3-deoxygluconate kinase | Q392_RS21790 | |
glucose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
glucuronate | dctQ: D-glucuronate TRAP transporter, small permease component | | |
glycerol | glpF: glycerol facilitator glpF | Q392_RS23180 | |
histidine | aapP: L-histidine ABC transporter, ATPase component AapP | Q392_RS21800 | Q392_RS24100 |
histidine | aapQ: L-histidine ABC transporter, permease component 1 (AapQ) | Q392_RS24090 | Q392_RS21810 |
lactose | dgoD: D-galactonate dehydratase | Q392_RS10365 | Q392_RS08305 |
lactose | galdh: D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) | Q392_RS13490 | Q392_RS03415 |
lactose | glk: glucokinase | Q392_RS00640 | Q392_RS29650 |
lactose | lacP: lactose permease LacP | | |
lactose | lacZ: lactase (homomeric) | | |
lysine | davT: 5-aminovalerate aminotransferase | Q392_RS30555 | Q392_RS21065 |
lysine | lysP: L-lysine:H+ symporter LysP | | |
lysine | patA: cadaverine aminotransferase | Q392_RS30555 | Q392_RS30065 |
lysine | patD: 5-aminopentanal dehydrogenase | Q392_RS25600 | Q392_RS22195 |
maltose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
maltose | susB: alpha-glucosidase (maltase) | Q392_RS00875 | |
mannitol | mt2d: mannitol 2-dehydrogenase | Q392_RS21200 | Q392_RS26790 |
mannitol | mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE | Q392_RS21220 | |
mannitol | mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) | Q392_RS21215 | Q392_RS16585 |
mannitol | mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) | Q392_RS21210 | Q392_RS16590 |
mannitol | mtlK: polyol ABC transporter, ATP component MtlK/SmoG | Q392_RS18270 | Q392_RS21205 |
mannose | manA: mannose-6-phosphate isomerase | Q392_RS24500 | |
mannose | manP: mannose PTS system, EII-CBA components | | |
myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | | |
myoinositol | iolC: 5-dehydro-2-deoxy-D-gluconate kinase | Q392_RS21790 | |
myoinositol | iolD: 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase | | |
myoinositol | iolE: scyllo-inosose 2-dehydratase | | |
myoinositol | iolG: myo-inositol 2-dehydrogenase | Q392_RS13310 | |
myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | Q392_RS21790 | |
myoinositol | iolT: myo-inositol:H+ symporter | | |
NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | Q392_RS08770 | |
NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | Q392_RS20100 | |
phenylacetate | ppa: phenylacetate permease ppa | Q392_RS22915 | |
phenylalanine | iorAB: phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB | Q392_RS04890 | |
phenylalanine | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | Q392_RS20100 | |
propionate | lctP: propionate permease | Q392_RS27120 | |
putrescine | gabT: gamma-aminobutyrate transaminase | Q392_RS31975 | Q392_RS06435 |
putrescine | patA: putrescine aminotransferase (PatA/SpuC) | Q392_RS31975 | Q392_RS06435 |
putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | Q392_RS19250 | Q392_RS19065 |
rhamnose | LRA1: L-rhamnofuranose dehydrogenase | Q392_RS26790 | Q392_RS09845 |
rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
rhamnose | LRA3: L-rhamnonate dehydratase | Q392_RS27400 | Q392_RS10550 |
rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
ribose | rbsA: D-ribose ABC transporter, ATPase component RbsA | Q392_RS00635 | Q392_RS28405 |
ribose | rbsB: D-ribose ABC transporter, substrate-binding component RbsB | Q392_RS00625 | |
ribose | rbsK: ribokinase | | |
sucrose | SUS: sucrose synthase | | |
sucrose | sut: sucrose:proton symporter SUT/SUC | | |
threonine | snatA: L-threonine transporter snatA | Q392_RS18140 | |
thymidine | deoA: thymidine phosphorylase DeoA | Q392_RS22305 | Q392_RS21700 |
thymidine | deoB: phosphopentomutase | Q392_RS14970 | |
thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
thymidine | nupG: thymidine permease NupG/XapB | | |
trehalose | glk: glucokinase | Q392_RS00640 | Q392_RS29650 |
trehalose | PsTP: trehalose phosphorylase | | |
trehalose | TRET1: facilitated trehalose transporter Tret1 | | |
tryptophan | andAb: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin subunit AndAb | Q392_RS08950 | Q392_RS03885 |
tryptophan | aroP: tryptophan:H+ symporter AroP | | |
tryptophan | kyn: kynureninase | | |
valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | Q392_RS28895 | Q392_RS05395 |
valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | Q392_RS11640 | Q392_RS01960 |
valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | Q392_RS06815 | Q392_RS06060 |
xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
xylitol | xdhA: xylitol dehydrogenase | Q392_RS13490 | Q392_RS27430 |
xylose | xad: D-xylonate dehydratase | Q392_RS10365 | Q392_RS08305 |
xylose | xylC: xylonolactonase | Q392_RS10520 | Q392_RS08560 |
xylose | xylT: D-xylose transporter | | |
Confidence: high confidence medium confidence low confidence
This GapMind analysis is from Apr 09 2024. 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