Potential Gaps in catabolism of small carbon sources in Alicycliphilus denitrificans K601
Found 90 low-confidence and 28 medium-confidence steps on the best paths for 62 pathways.
Pathway | Step | Best candidate | 2nd candidate |
2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | ALIDE2_RS10370 | ALIDE2_RS20480 |
4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | ALIDE2_RS15500 | |
4-hydroxybenzoate | pobA: 4-hydroxybenzoate 3-monooxygenase | | |
4-hydroxybenzoate | praA: protocatechuate 2,3-dioxygenase | | |
arabinose | araA: L-arabinose isomerase | | |
arabinose | araB: ribulokinase | | |
arabinose | araD: L-ribulose-5-phosphate epimerase | | |
arabinose | araE: L-arabinose:H+ symporter | | |
cellobiose | cbp: cellobiose phosphorylase | | |
cellobiose | cdt: cellobiose transporter cdt-1/cdt-2 | | |
cellobiose | glk: glucokinase | ALIDE2_RS02800 | |
citrate | citA: citrate:H+ symporter CitA | ALIDE2_RS10370 | ALIDE2_RS20480 |
citrulline | arcC: carbamate kinase | | |
deoxyinosine | deoB: phosphopentomutase | | |
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 | ALIDE2_RS09190 | ALIDE2_RS00675 |
deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | ALIDE2_RS11445 | |
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 | 1pfk: 1-phosphofructokinase | | |
fructose | fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components | | |
fucose | aldA: lactaldehyde dehydrogenase | ALIDE2_RS07695 | ALIDE2_RS07670 |
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 | | |
fucose | fucU: L-fucose mutarotase FucU | | |
galactose | galE: UDP-glucose 4-epimerase | ALIDE2_RS04205 | ALIDE2_RS02195 |
galactose | galK: galactokinase (-1-phosphate forming) | | |
galactose | galP: galactose:H+ symporter GalP | | |
galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
galacturonate | exuT: D-galacturonate transporter ExuT | | |
galacturonate | udh: D-galacturonate dehydrogenase | | |
galacturonate | uxuL: D-galactaro-1,5-lactonase (UxuL or UxuF) | | |
glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | ALIDE2_RS03360 | |
glucose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
glucuronate | udh: D-glucuronate dehydrogenase | | |
glucuronate | uxuL: D-glucaro-1,5-lactonase UxuL or UxuF | | |
glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | ALIDE2_RS21655 | |
glycerol | glpF: glycerol facilitator glpF | | |
lactose | galE: UDP-glucose 4-epimerase | ALIDE2_RS04205 | ALIDE2_RS02195 |
lactose | galK: galactokinase (-1-phosphate forming) | | |
lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
lactose | glk: glucokinase | ALIDE2_RS02800 | |
lactose | lacP: lactose permease LacP | | |
lactose | lacZ: lactase (homomeric) | | |
lysine | argT: L-lysine ABC transporter, substrate-binding component ArgT | ALIDE2_RS18840 | ALIDE2_RS08490 |
lysine | davD: glutarate semialdehyde dehydrogenase | ALIDE2_RS08540 | ALIDE2_RS18720 |
lysine | davT: 5-aminovalerate aminotransferase | ALIDE2_RS17550 | ALIDE2_RS06730 |
lysine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | ALIDE2_RS08370 | ALIDE2_RS05800 |
lysine | hisM: L-lysine ABC transporter, permease component 1 (HisM) | ALIDE2_RS18830 | ALIDE2_RS08495 |
lysine | hisP: L-lysine ABC transporter, ATPase component HisP | ALIDE2_RS18825 | ALIDE2_RS03245 |
lysine | hisQ: L-lysine ABC transporter, permease component 2 (HisQ) | ALIDE2_RS18835 | ALIDE2_RS17655 |
lysine | patA: cadaverine aminotransferase | ALIDE2_RS17550 | |
lysine | patD: 5-aminopentanal dehydrogenase | ALIDE2_RS01490 | ALIDE2_RS07695 |
maltose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
maltose | susB: alpha-glucosidase (maltase) | | |
mannitol | mtlA: mannitol phosphotransferase system, EII-CBA components | | |
mannose | manA: mannose-6-phosphate isomerase | ALIDE2_RS03430 | |
mannose | manP: mannose PTS system, EII-CBA components | | |
myoinositol | iolD: 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase | | |
myoinositol | iolE: scyllo-inosose 2-dehydratase | | |
myoinositol | iolG: myo-inositol 2-dehydrogenase | | |
myoinositol | iolT: myo-inositol:H+ symporter | | |
NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | ALIDE2_RS03360 | |
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 | ALIDE2_RS02480 | ALIDE2_RS05570 |
phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
phenylacetate | ppa: phenylacetate permease ppa | ALIDE2_RS20490 | |
phenylalanine | hmgA: homogentisate dioxygenase | | |
phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | ALIDE2_RS18235 | |
phenylalanine | QDPR: 6,7-dihydropteridine reductase | | |
propionate | putP: propionate transporter; proline:Na+ symporter | ALIDE2_RS15465 | |
putrescine | gabT: gamma-aminobutyrate transaminase | ALIDE2_RS23265 | ALIDE2_RS17550 |
putrescine | patA: putrescine aminotransferase (PatA/SpuC) | ALIDE2_RS23265 | ALIDE2_RS17550 |
putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | ALIDE2_RS07695 | ALIDE2_RS07670 |
putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
rhamnose | aldA: lactaldehyde dehydrogenase | ALIDE2_RS07695 | ALIDE2_RS07670 |
rhamnose | LRA1: L-rhamnofuranose dehydrogenase | ALIDE2_RS12795 | ALIDE2_RS01550 |
rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
rhamnose | LRA3: L-rhamnonate dehydratase | ALIDE2_RS08545 | ALIDE2_RS14310 |
rhamnose | LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase | ALIDE2_RS08535 | ALIDE2_RS02575 |
rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
ribose | rbsK: ribokinase | | |
ribose | rbsU: probable D-ribose transporter RbsU | | |
sorbitol | mtlA: PTS system for polyols, EII-CBA components | | |
sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | ALIDE2_RS09190 | ALIDE2_RS21380 |
sucrose | scrK: fructokinase | | |
sucrose | SUS: sucrose synthase | | |
sucrose | sut: sucrose:proton symporter SUT/SUC | | |
threonine | ltaE: L-threonine aldolase | ALIDE2_RS10600 | |
thymidine | deoA: thymidine phosphorylase DeoA | ALIDE2_RS16720 | ALIDE2_RS13560 |
thymidine | deoB: phosphopentomutase | | |
thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
thymidine | nupG: thymidine permease NupG/XapB | | |
trehalose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
trehalose | treF: trehalase | ALIDE2_RS02810 | |
tryptophan | aroP: tryptophan:H+ symporter AroP | ALIDE2_RS12155 | |
tyrosine | hmgA: homogentisate dioxygenase | | |
valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | ALIDE2_RS08370 | ALIDE2_RS05800 |
valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | ALIDE2_RS14285 | ALIDE2_RS01100 |
xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | | |
xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | ALIDE2_RS12685 | |
xylose | xylA: xylose isomerase | | |
xylose | xylB: xylulokinase | | |
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