GapMind for catabolism of small carbon sources

 

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.

Links

Downloads

Related tools

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:

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:

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:

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