GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Dechlorosoma suillum PS

Found 139 low-confidence and 36 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate dctP: 2-oxoglutarate TRAP transporter, solute receptor component DctP Dsui_3155
2-oxoglutarate dctQ: 2-oxoglutarate TRAP transporter, small permease component DctQ
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase Dsui_0578
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK
4-hydroxybenzoate pobA: 4-hydroxybenzoate 3-monooxygenase
4-hydroxybenzoate praA: protocatechuate 2,3-dioxygenase
4-hydroxybenzoate xylF: 2-hydroxymuconate semialdehyde hydrolase
alanine TRIC: TRIC-type L-alanine transporter Dsui_0014 Dsui_2676
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter
arginine rocA: 1-pyrroline-5-carboxylate dehydrogenase Dsui_0437 Dsui_1464
arginine rocD: ornithine aminotransferase Dsui_3250 Dsui_0023
arginine rocE: L-arginine permease
arginine rocF: arginase Dsui_0671
asparagine ans: asparaginase
cellobiose cbp: cellobiose phosphorylase
cellobiose cdt: cellobiose transporter cdt-1/cdt-2
cellobiose glk: glucokinase Dsui_0801
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component Dsui_0638 Dsui_2068
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 Dsui_0636 Dsui_0637
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline arcC: carbamate kinase
citrulline rocA: 1-pyrroline-5-carboxylate dehydrogenase Dsui_0437 Dsui_1464
citrulline rocD: ornithine aminotransferase Dsui_3250 Dsui_0023
D-alanine cycA: D-alanine:H+ symporter CycA
D-lactate lctP: D-lactate:H+ symporter LctP or LidP
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase Dsui_0728
deoxyinosine deoB: phosphopentomutase Dsui_3057
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase Dsui_2698
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase Dsui_2312 Dsui_0676
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
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 Dsui_1464 Dsui_0437
fucose fucA: L-fuculose-phosphate aldolase FucA Dsui_3380
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 Dsui_0398 Dsui_0083
galactose galK: galactokinase (-1-phosphate forming)
galactose galP: galactose:H+ symporter GalP
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galacturonate dopDH: 2,5-dioxopentanonate dehydrogenase Dsui_0437 Dsui_0105
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate gci: D-galactarolactone cycloisomerase
galacturonate gli: D-galactarolactone isomerase
galacturonate kdgD: 5-dehydro-4-deoxyglucarate dehydratase
galacturonate udh: D-galacturonate dehydrogenase
gluconate gnd: 6-phosphogluconate dehydrogenase, decarboxylating
gluconate gntK: D-gluconate kinase
gluconate gntT: gluconate:H+ symporter GntT
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE)
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) Dsui_1101
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 garL: 5-dehydro-4-deoxy-D-glucarate aldolase Dsui_1977
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate udh: D-glucuronate dehydrogenase
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric)
glycerol glpF: glycerol facilitator glpF
glycerol glpK: glycerol kinase
histidine hutG: N-formiminoglutamate formiminohydrolase Dsui_0671
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
histidine PA5503: L-histidine ABC transporter, ATPase component Dsui_0638 Dsui_2068
histidine PA5504: L-histidine ABC transporter, permease component Dsui_2067
histidine PA5505: L-histidine ABC transporter, substrate-binding component Dsui_2064 Dsui_2066
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
lactose galE: UDP-glucose 4-epimerase Dsui_0398 Dsui_0083
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose glk: glucokinase Dsui_0801
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
lysine davT: 5-aminovalerate aminotransferase Dsui_3250 Dsui_0023
lysine gcdG: succinyl-CoA:glutarate CoA-transferase Dsui_0037 Dsui_1115
lysine lysP: L-lysine:H+ symporter LysP
lysine patA: cadaverine aminotransferase Dsui_3250 Dsui_0023
lysine patD: 5-aminopentanal dehydrogenase Dsui_0437 Dsui_1464
maltose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
maltose susB: alpha-glucosidase (maltase)
mannitol mtlA: mannitol phosphotransferase system, EII-CBA components
mannitol mtlD: mannitol-1-phosphate 5-dehydrogenase
mannose manA: mannose-6-phosphate isomerase Dsui_0087
mannose manP: mannose PTS system, EII-CBA components
myoinositol iolB: 5-deoxy-D-glucuronate isomerase
myoinositol iolC: 5-dehydro-2-deoxy-D-gluconate kinase
myoinositol iolD: 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase
myoinositol iolE: scyllo-inosose 2-dehydratase
myoinositol iolG: myo-inositol 2-dehydrogenase
myoinositol iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase Dsui_0050
myoinositol iolT: myo-inositol:H+ symporter
myoinositol mmsA: malonate-semialdehyde dehydrogenase Dsui_0437 Dsui_0105
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) Dsui_1101
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 paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase Dsui_0502 Dsui_1378
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase Dsui_0317 Dsui_3239
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase Dsui_0317 Dsui_3239
phenylacetate paaZ1: oxepin-CoA hydrolase Dsui_0502 Dsui_1378
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylacetate ppa: phenylacetate permease ppa Dsui_0522 Dsui_0290
phenylalanine fahA: fumarylacetoacetate hydrolase
phenylalanine hmgA: homogentisate dioxygenase
phenylalanine HPD: 4-hydroxyphenylpyruvate dioxygenase
phenylalanine maiA: maleylacetoacetate isomerase Dsui_1815
phenylalanine PAH: phenylalanine 4-monooxygenase
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase Dsui_3224
proline put1: proline dehydrogenase
proline putA: L-glutamate 5-semialdeyde dehydrogenase Dsui_0437 Dsui_1464
propionate mctC: propionate:H+ symporter Dsui_0290 Dsui_0522
putrescine gabT: gamma-aminobutyrate transaminase Dsui_3250 Dsui_0023
putrescine patA: putrescine aminotransferase (PatA/SpuC) Dsui_3250 Dsui_0023
putrescine patD: gamma-aminobutyraldehyde dehydrogenase Dsui_0105 Dsui_1464
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
rhamnose aldA: lactaldehyde dehydrogenase Dsui_1464 Dsui_0437
rhamnose LRA1: L-rhamnofuranose dehydrogenase Dsui_2448 Dsui_2538
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase
rhamnose LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsK: ribokinase
ribose rbsU: probable D-ribose transporter RbsU
serine sdaB: L-serine ammonia-lyase Dsui_0728
sorbitol scrK: fructokinase Dsui_0801
sorbitol sdh: sorbitol dehydrogenase Dsui_2448 Dsui_2228
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
sucrose scrK: fructokinase Dsui_0801
sucrose SUS: sucrose synthase
sucrose sut: sucrose:proton symporter SUT/SUC
threonine ltaE: L-threonine aldolase Dsui_1265 Dsui_2254
threonine phtA: L-threonine uptake permease PhtA Dsui_3451
thymidine deoA: thymidine phosphorylase DeoA Dsui_3246
thymidine deoB: phosphopentomutase Dsui_3057
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
trehalose glk: glucokinase Dsui_0801
trehalose PsTP: trehalose phosphorylase
trehalose TRET1: facilitated trehalose transporter Tret1
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine fahA: fumarylacetoacetate hydrolase
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase Dsui_1815
valine bch: 3-hydroxyisobutyryl-CoA hydrolase Dsui_1378 Dsui_0981
valine livH: L-valine ABC transporter, permease component 1 (LivH/BraD) Dsui_0629 Dsui_2060
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) Dsui_0630 Dsui_2061
valine livM: L-valine ABC transporter, permease component 2 (LivM/BraE) Dsui_0628 Dsui_2059
valine mmsA: methylmalonate-semialdehyde dehydrogenase Dsui_0437 Dsui_0105
valine mmsB: 3-hydroxyisobutyrate dehydrogenase Dsui_3436 Dsui_3438
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase
xylose xylA: xylose isomerase
xylose xylB: xylulokinase
xylose xylT: D-xylose transporter

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 (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