GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Sulfuritalea hydrogenivorans DSM 22779

Found 124 low-confidence and 35 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
4-hydroxybenzoate hcrA: 4-hydroxybenzoyl-CoA reductase, alpha subunit
4-hydroxybenzoate hcrB: 4-hydroxybenzoyl-CoA reductase, beta subunit
4-hydroxybenzoate hcrC: 4-hydroxybenzoyl-CoA reductase, gamma subunit
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK
alanine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) SUTH_RS01380
alanine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) SUTH_RS01375 SUTH_RS00445
alanine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) SUTH_RS01370 SUTH_RS00450
alanine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) SUTH_RS06110 SUTH_RS01360
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 SUTH_RS05840 SUTH_RS08615
arginine rocD: ornithine aminotransferase SUTH_RS15840 SUTH_RS17015
arginine rocE: L-arginine permease
arginine rocF: arginase SUTH_RS08390
asparagine ans: asparaginase
cellobiose cbp: cellobiose phosphorylase
cellobiose cdt: cellobiose transporter cdt-1/cdt-2
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component SUTH_RS00295 SUTH_RS13600
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 SUTH_RS00300
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline arcC: carbamate kinase
citrulline rocA: 1-pyrroline-5-carboxylate dehydrogenase SUTH_RS05840 SUTH_RS08615
citrulline rocD: ornithine aminotransferase SUTH_RS15840 SUTH_RS17015
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 SUTH_RS17910
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) SUTH_RS08615 SUTH_RS05840
deoxyinosine deoB: phosphopentomutase
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase SUTH_RS08025
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase SUTH_RS08230 SUTH_RS01455
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate garK: glycerate 2-kinase
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme SUTH_RS14325
deoxyribose adh: acetaldehyde dehydrogenase (not acylating) SUTH_RS08615 SUTH_RS05840
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
ethanol adh: acetaldehyde dehydrogenase (not acylating) SUTH_RS08615 SUTH_RS05840
fructose Slc2a5: fructose:H+ symporter
fucose aldA: lactaldehyde dehydrogenase SUTH_RS15235 SUTH_RS08615
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 SUTH_RS16630 SUTH_RS20285
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 SUTH_RS08615 SUTH_RS05840
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate gci: D-galactarolactone cycloisomerase
galacturonate gli: D-galactarolactone isomerase
galacturonate kdgD: 5-dehydro-4-deoxyglucarate dehydratase SUTH_RS12045
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) SUTH_RS02960
glucose MFS-glucose: glucose transporter, MFS superfamily
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate garK: glycerate 2-kinase
glucuronate garL: 5-dehydro-4-deoxy-D-glucarate aldolase SUTH_RS08605 SUTH_RS12045
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate udh: D-glucuronate dehydrogenase
glutamate gdhA: glutamate dehydrogenase, NAD-dependent
glycerol glpF: glycerol facilitator glpF
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
histidine permease: L-histidine permease
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
lactose galE: UDP-glucose 4-epimerase SUTH_RS16630 SUTH_RS20285
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
lysine davT: 5-aminovalerate aminotransferase SUTH_RS05530 SUTH_RS17015
lysine lysP: L-lysine:H+ symporter LysP
lysine patA: cadaverine aminotransferase SUTH_RS05530 SUTH_RS15840
lysine patD: 5-aminopentanal dehydrogenase SUTH_RS08615 SUTH_RS05840
maltose malA: 6-phospho-alphaglucosidase
maltose malEIICBA: maltose phosphotransferase system, EII-CBA components
mannitol mt2d: mannitol 2-dehydrogenase SUTH_RS08230 SUTH_RS13160
mannitol PLT5: polyol transporter PLT5
mannose manA: mannose-6-phosphate isomerase SUTH_RS16880
mannose STP6: mannose:H+ symporter
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 SUTH_RS03815
myoinositol iolT: myo-inositol:H+ symporter
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) SUTH_RS02960
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components
phenylacetate ppa: phenylacetate permease ppa SUTH_RS00905
proline davT: 5-aminovalerate aminotransferase SUTH_RS05530 SUTH_RS17015
proline prdA: D-proline reductase, prdA component
proline prdB: D-proline reductase, prdB component
proline prdC: D-proline reductase, electron transfer component PrdC
proline prdF: proline racemase
propionate mctC: propionate:H+ symporter SUTH_RS00905
putrescine gabT: gamma-aminobutyrate transaminase SUTH_RS05530 SUTH_RS17015
putrescine patA: putrescine aminotransferase (PatA/SpuC) SUTH_RS05530 SUTH_RS15840
putrescine patD: gamma-aminobutyraldehyde dehydrogenase SUTH_RS08615 SUTH_RS05840
putrescine potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) SUTH_RS11370
rhamnose aldA: lactaldehyde dehydrogenase SUTH_RS15235 SUTH_RS08615
rhamnose rhaA: L-rhamnose isomerase
rhamnose rhaB: L-rhamnulokinase
rhamnose rhaD: rhamnulose 1-phosphate aldolase SUTH_RS15235
rhamnose rhaM: L-rhamnose mutarotase
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsK: ribokinase
ribose rbsU: probable D-ribose transporter RbsU
serine sdaB: L-serine ammonia-lyase SUTH_RS17910
sorbitol sdh: sorbitol dehydrogenase SUTH_RS08230 SUTH_RS11655
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
sucrose SUS: sucrose synthase
sucrose sut: sucrose:proton symporter SUT/SUC
threonine adh: acetaldehyde dehydrogenase (not acylating) SUTH_RS08615 SUTH_RS05840
threonine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) SUTH_RS01380
threonine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) SUTH_RS01375 SUTH_RS00445
threonine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) SUTH_RS01370 SUTH_RS00450
threonine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) SUTH_RS06110 SUTH_RS01360
threonine ltaE: L-threonine aldolase SUTH_RS03505
thymidine adh: acetaldehyde dehydrogenase (not acylating) SUTH_RS08615 SUTH_RS05840
thymidine deoA: thymidine phosphorylase DeoA SUTH_RS05550
thymidine deoB: phosphopentomutase
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
trehalose MFS-glucose: glucose transporter, MFS superfamily
trehalose treF: trehalase SUTH_RS10195
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
valine bch: 3-hydroxyisobutyryl-CoA hydrolase SUTH_RS15075 SUTH_RS10290
valine livH: L-valine ABC transporter, permease component 1 (LivH/BraD) SUTH_RS01375 SUTH_RS00445
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) SUTH_RS01380
valine livM: L-valine ABC transporter, permease component 2 (LivM/BraE) SUTH_RS01370 SUTH_RS00450
valine mmsA: methylmalonate-semialdehyde dehydrogenase SUTH_RS12545 SUTH_RS08615
valine mmsB: 3-hydroxyisobutyrate dehydrogenase SUTH_RS15105 SUTH_RS15110
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase SUTH_RS11655
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:

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