GapMind for catabolism of small carbon sources

 

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.

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