GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Cupriavidus basilensis 4G11

Found 51 low-confidence and 44 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
arabinose araE: L-arabinose:H+ symporter
arabinose xacB: L-arabinose 1-dehydrogenase RR42_RS30145 RR42_RS25125
arabinose xacC: L-arabinono-1,4-lactonase RR42_RS30140 RR42_RS33665
arginine artJ: L-arginine ABC transporter, periplasmic substrate-binding component ArtJ/HisJ/ArtI/AotJ/ArgT RR42_RS29645 RR42_RS34315
arginine rocF: arginase RR42_RS02455 RR42_RS14625
cellobiose mglB: glucose ABC transporter, substrate-binding component
cellobiose mglC: glucose ABC transporter, permease component (MglC) RR42_RS03365 RR42_RS32890
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component RR42_RS29660 RR42_RS34305
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 RR42_RS29655 RR42_RS04400
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 RR42_RS29650 RR42_RS04400
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component RR42_RS29645 RR42_RS31745
citrulline arcC: carbamate kinase
D-serine cycA: D-serine:H+ symporter CycA RR42_RS28305 RR42_RS33495
deoxyinosine deoB: phosphopentomutase RR42_RS13475
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter RR42_RS25070 RR42_RS04270
deoxyribose deoxyribonate-transport: 2-deoxy-D-ribonate transporter RR42_RS25070 RR42_RS04270
deoxyribose drdehyd-beta: 2-deoxy-D-ribose dehydrogenase, beta subunit RR42_RS09125 RR42_RS25790
deoxyribose drdehyd-cytc: 2-deoxyribose-D dehydrogenase, cytochrome c component RR42_RS10775 RR42_RS21615
fucose fdh: L-fucose 1-dehydrogenase RR42_RS24995 RR42_RS21135
fucose fucD: L-fuconate dehydratase RR42_RS26650 RR42_RS00275
fucose fuconolactonase: L-fucono-1,5-lactonase
fucose fucU: L-fucose mutarotase FucU
fucose HSERO_RS05255: ABC transporter for L-fucose, permease component RR42_RS03365 RR42_RS32890
fucose HSERO_RS05260: ABC transporter for L-fucose, substrate-binding component
galactose dgoA: 2-dehydro-3-deoxy-6-phosphogalactonate aldolase RR42_RS28865
galactose dgoD: D-galactonate dehydratase RR42_RS33950 RR42_RS18585
galactose dgoK: 2-dehydro-3-deoxygalactonokinase RR42_RS28860 RR42_RS09470
galactose galdh: D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) RR42_RS30145 RR42_RS25125
galactose galP: galactose:H+ symporter GalP
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) RR42_RS09880 RR42_RS01460
glucosamine SLC2A2: glucosamine transporter SLC2A2
glucose mglB: glucose ABC transporter, substrate-binding component
glucose mglC: glucose ABC transporter, permease component (MglC) RR42_RS03365 RR42_RS32890
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) RR42_RS13815 RR42_RS16760
lactose dgoA: 2-dehydro-3-deoxy-6-phosphogalactonate aldolase RR42_RS28865
lactose dgoD: D-galactonate dehydratase RR42_RS33950 RR42_RS18585
lactose dgoK: 2-dehydro-3-deoxygalactonokinase RR42_RS28860 RR42_RS09470
lactose galdh: D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) RR42_RS30145 RR42_RS25125
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric) RR42_RS30175 RR42_RS26860
lysine patA: cadaverine aminotransferase RR42_RS26850 RR42_RS26160
lysine patD: 5-aminopentanal dehydrogenase RR42_RS27780 RR42_RS26255
maltose mglB: glucose ABC transporter, substrate-binding component
maltose mglC: glucose ABC transporter, permease component (MglC) RR42_RS03365 RR42_RS32890
maltose susB: alpha-glucosidase (maltase)
mannitol mt2d: mannitol 2-dehydrogenase RR42_RS34965 RR42_RS09405
mannitol PLT5: polyol transporter PLT5
mannose man-isomerase: D-mannose isomerase RR42_RS28130
myoinositol iolG: myo-inositol 2-dehydrogenase
myoinositol iolM: 2-inosose 4-dehydrogenase RR42_RS09405 RR42_RS35005
myoinositol iolN: 2,4-diketo-inositol hydratase
myoinositol iolO: 5-dehydro-L-gluconate epimerase
myoinositol PS417_11885: myo-inositol ABC transporter, substrate-binding component RR42_RS03370
myoinositol PS417_11895: myo-inositol ABC transporter, permease component RR42_RS03365 RR42_RS32890
myoinositol uxaE: D-tagaturonate epimerase
myoinositol uxuB: D-mannonate dehydrogenase RR42_RS34965
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) RR42_RS09880 RR42_RS01460
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components
phenylacetate ppa: phenylacetate permease ppa RR42_RS06400
phenylalanine PPDCalpha: phenylpyruvate decarboxylase, alpha subunit RR42_RS33045 RR42_RS10655
phenylalanine PPDCbeta: phenylpyruvate decarboxylase, beta subunit RR42_RS33050 RR42_RS10660
propionate lctP: propionate permease RR42_RS21280 RR42_RS14610
putrescine patA: putrescine aminotransferase (PatA/SpuC) RR42_RS27405 RR42_RS01575
putrescine patD: gamma-aminobutyraldehyde dehydrogenase RR42_RS26255 RR42_RS21485
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
rhamnose aldA: lactaldehyde dehydrogenase RR42_RS25010 RR42_RS27780
rhamnose LRA1: L-rhamnofuranose dehydrogenase RR42_RS21790 RR42_RS33710
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase RR42_RS23065 RR42_RS26650
rhamnose LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase RR42_RS26640 RR42_RS29120
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsK: ribokinase RR42_RS28860
ribose rbsU: probable D-ribose transporter RbsU
sorbitol sdh: sorbitol dehydrogenase RR42_RS21790 RR42_RS31670
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
sucrose ams: sucrose hydrolase (invertase)
thymidine deoB: phosphopentomutase RR42_RS13475
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
trehalose mglB: glucose ABC transporter, substrate-binding component
trehalose mglC: glucose ABC transporter, permease component (MglC) RR42_RS03365 RR42_RS32890
tryptophan antA: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA RR42_RS23500
tryptophan antB: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB RR42_RS23495
tryptophan antC: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC RR42_RS23490 RR42_RS32665
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase RR42_RS09405 RR42_RS35005
xylose HDOP-hydrol: 5-hydroxy-2,4-dioxopentanonate hydrolase RR42_RS00385 RR42_RS05150
xylose xad: D-xylonate dehydratase RR42_RS18585 RR42_RS33950
xylose xylF: ABC transporter for xylose, substrate binding component xylF
xylose xylH: ABC transporter for xylose, permease component xylH RR42_RS03365 RR42_RS32890

Confidence: high confidence medium confidence low confidence

This GapMind analysis is from Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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