GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Desulfoscipio geothermicus DSM 3669

Found 144 low-confidence and 47 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 BM299_RS04570 BM299_RS16955
2-oxoglutarate Psest_0085: 2-oxoglutarate TRAP transporter, solute receptor component BM299_RS08865 BM299_RS12820
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
acetate actP: cation/acetate symporter ActP
alanine cycA: L-alanine symporter CycA
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase BM299_RS05060
arabinose araE: L-arabinose:H+ symporter
arginine gabD: succinate semialdehyde dehydrogenase BM299_RS16640
arginine gabT: gamma-aminobutyrate transaminase BM299_RS02525 BM299_RS00590
arginine patD: gamma-aminobutyraldehyde dehydrogenase
arginine rocE: L-arginine permease
asparagine ans: asparaginase
asparagine glnP: L-asparagine ABC transporter, fused permease and substrate-binding components GlnP
aspartate glt: aspartate:proton symporter Glt
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 BM299_RS00225 BM299_RS18035
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 BM299_RS05465 BM299_RS18040
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 BM299_RS05465 BM299_RS18040
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component BM299_RS18045 BM299_RS08595
citrulline arcC: carbamate kinase
citrulline put1: proline dehydrogenase BM299_RS03410
citrulline putA: L-glutamate 5-semialdeyde dehydrogenase
citrulline rocD: ornithine aminotransferase BM299_RS04985 BM299_RS08235
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate glcE: D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) BM299_RS10985 BM299_RS04225
D-lactate glcF: D-lactate dehydrogenase, FeS subunit GlcF BM299_RS10990
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase BM299_RS07595
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase BM299_RS12585 BM299_RS17970
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate garK: glycerate 2-kinase
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components BM299_RS10520
fucose fucA: L-fuculose-phosphate aldolase FucA BM299_RS05060
fucose fucI: L-fucose isomerase FucI
fucose fucK: L-fuculose kinase FucK
fucose fucO: L-lactaldehyde reductase BM299_RS08815 BM299_RS11945
fucose fucP: L-fucose:H+ symporter FucP
fucose fucU: L-fucose mutarotase FucU
fumarate Dshi_1194: TRAP transporter for succinate, fumarate, L-malate, and 2-oxoglutarate, fused 4TM/12TM components BM299_RS04570 BM299_RS16955
fumarate Dshi_1195: TRAP transporter for succinate, fumarate, L-malate, and 2-oxoglutarate, substrate-binding component BM299_RS16950
galactose galK: galactokinase (-1-phosphate forming)
galactose galP: galactose:H+ symporter GalP
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galacturonate eda: 2-keto-3-deoxygluconate 6-phosphate aldolase
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate kdgK: 2-keto-3-deoxygluconate kinase
galacturonate uxaA: D-altronate dehydratase BM299_RS07255
galacturonate uxaB: tagaturonate reductase
galacturonate uxaC: D-galacturonate isomerase
gluconate gntA: gluconate TRAP transporter, small permease component BM299_RS11935 BM299_RS07270
gluconate gntB: gluconate TRAP transporter, large permease component BM299_RS09255 BM299_RS11930
gluconate gntC: gluconate TRAP transporter, periplasmic solute-binding component BM299_RS11940 BM299_RS09265
gluconate gntK: D-gluconate kinase
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE)
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) BM299_RS08430
glucose MFS-glucose: glucose transporter, MFS superfamily
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate dopDH: 2,5-dioxopentanonate dehydrogenase
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate kdgD: 5-dehydro-4-deoxyglucarate dehydratase
glucuronate udh: D-glucuronate dehydrogenase
glutamate glnP: L-glutamate ABC transporter, fused permease and substrate-binding components GlnP
glycerol dhaK': dihydroxyacetone kinase, ATP dependent (monomeric)
glycerol glpF: glycerol facilitator glpF
histidine hutG: N-formiminoglutamate formiminohydrolase BM299_RS01320
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
histidine hutV: L-histidine ABC transporter, ATPase component HutV BM299_RS08565 BM299_RS03860
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase BM299_RS11335 BM299_RS06015
isoleucine Bap2: L-isoleucine permease Bap2
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase BM299_RS07795 BM299_RS07900
isoleucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit BM299_RS06260
L-lactate lctO: L-lactate oxidase or 2-monooxygenase BM299_RS04190
L-malate Dshi_1194: TRAP transporter for succinate, fumarate, L-malate, and 2-oxoglutarate, fused 4TM/12TM components BM299_RS04570 BM299_RS16955
L-malate Dshi_1195: TRAP transporter for succinate, fumarate, L-malate, and 2-oxoglutarate, substrate-binding component BM299_RS16950
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)
leucine leuT: L-leucine:Na+ symporter LeuT BM299_RS01110
leucine liuA: isovaleryl-CoA dehydrogenase BM299_RS06015 BM299_RS06045
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit BM299_RS06260
leucine liuC: 3-methylglutaconyl-CoA hydratase BM299_RS10405 BM299_RS07795
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit BM299_RS10410 BM299_RS09155
leucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
lysine cadA: lysine decarboxylase
lysine davD: glutarate semialdehyde dehydrogenase
lysine gcdG: succinyl-CoA:glutarate CoA-transferase BM299_RS01175
lysine gcdH: glutaryl-CoA dehydrogenase BM299_RS11335 BM299_RS06045
lysine lysP: L-lysine:H+ symporter LysP
lysine patD: 5-aminopentanal dehydrogenase
maltose malAP: maltose permease BM299_RS01700
maltose susB: alpha-glucosidase (maltase)
mannitol mtlA: mannitol phosphotransferase system, EII-CBA components
mannitol mtlD: mannitol-1-phosphate 5-dehydrogenase
mannose manP: mannose PTS system, EII-CBA components BM299_RS10520
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 BM299_RS02705
myoinositol iolT: myo-inositol:H+ symporter
myoinositol mmsA: malonate-semialdehyde dehydrogenase
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) BM299_RS08430
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 paaF: 2,3-dehydroadipyl-CoA hydratase BM299_RS07795 BM299_RS18360
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase BM299_RS17115 BM299_RS00890
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase BM299_RS17115 BM299_RS00890
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase BM299_RS00245 BM299_RS10405
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine paaA: phenylacetyl-CoA 1,2-epoxidase, subunit A
phenylalanine paaB: phenylacetyl-CoA 1,2-epoxidase, subunit B
phenylalanine paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C
phenylalanine paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E
phenylalanine paaF: 2,3-dehydroadipyl-CoA hydratase BM299_RS07795 BM299_RS18360
phenylalanine paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase BM299_RS17115 BM299_RS00890
phenylalanine paaJ2: 3-oxoadipyl-CoA thiolase BM299_RS17115 BM299_RS00890
phenylalanine paaZ1: oxepin-CoA hydrolase BM299_RS00245 BM299_RS10405
phenylalanine paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
proline hutV: proline ABC transporter, ATPase component HutV BM299_RS08565 BM299_RS03860
proline hutW: proline ABC transporter, permease component HutW BM299_RS03855 BM299_RS08570
proline put1: proline dehydrogenase BM299_RS03410
proline putA: L-glutamate 5-semialdeyde dehydrogenase
propionate pccA: propionyl-CoA carboxylase, alpha subunit BM299_RS06260
putrescine gabD: succinate semialdehyde dehydrogenase BM299_RS16640
putrescine gabT: gamma-aminobutyrate transaminase BM299_RS02525 BM299_RS00590
putrescine patD: gamma-aminobutyraldehyde dehydrogenase
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose fucO: L-lactaldehyde reductase BM299_RS08815 BM299_RS11945
rhamnose LRA1: L-rhamnofuranose dehydrogenase BM299_RS05100 BM299_RS12585
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase BM299_RS07255 BM299_RS11820
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 serP: L-serine permease SerP
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase BM299_RS05100 BM299_RS00600
succinate Dshi_1194: TRAP transporter for succinate, fumarate, L-malate, and 2-oxoglutarate, fused 4TM/12TM components BM299_RS04570 BM299_RS16955
succinate Dshi_1195: TRAP transporter for succinate, fumarate, L-malate, and 2-oxoglutarate, substrate-binding component BM299_RS16950
sucrose ams: sucrose hydrolase (invertase)
sucrose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components BM299_RS10520
threonine pccA: propionyl-CoA carboxylase, alpha subunit BM299_RS06260
threonine tdcC: L-threonine:H+ symporter TdcC
threonine tdcE: 2-ketobutyrate formate-lyase
thymidine nupG: thymidine permease NupG/XapB
trehalose PsTP: trehalose phosphorylase
trehalose TRET1: facilitated trehalose transporter Tret1
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine fahA: fumarylacetoacetate hydrolase
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase BM299_RS11335 BM299_RS06015
valine Bap2: L-valine permease Bap2
valine bch: 3-hydroxyisobutyryl-CoA hydrolase BM299_RS10405 BM299_RS07900
valine mmsA: methylmalonate-semialdehyde dehydrogenase
valine mmsB: 3-hydroxyisobutyrate dehydrogenase BM299_RS16945
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
valine pccA: propionyl-CoA carboxylase, alpha subunit BM299_RS06260
xylitol fruI: xylitol PTS, enzyme IIABC (FruI) BM299_RS10520
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 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