GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Dethiosulfovibrio salsuginis USBA 82

Found 146 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 B9Y55_RS03830 B9Y55_RS03095
2-oxoglutarate Psest_0085: 2-oxoglutarate TRAP transporter, solute receptor component B9Y55_RS10400 B9Y55_RS12280
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase
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
acetate pta: phosphate acetyltransferase B9Y55_RS03850 B9Y55_RS03855
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase B9Y55_RS07460
arabinose araE: L-arabinose:H+ symporter
arginine arcC: carbamate kinase B9Y55_RS08870
arginine bgtB: L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) B9Y55_RS01405
asparagine ans: asparaginase B9Y55_RS12600 B9Y55_RS09625
cellobiose bgl: cellobiase
cellobiose glk: glucokinase B9Y55_RS09620
citrate tctB: citrate/Na+ symporter, small transmembrane component TctB
citrate tctC: citrate/Na+ symporter, substrate-binding component TctC B9Y55_RS07260 B9Y55_RS12255
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component B9Y55_RS07490 B9Y55_RS01410
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 B9Y55_RS07495 B9Y55_RS01405
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 B9Y55_RS07495 B9Y55_RS01405
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component B9Y55_RS05805
citrulline arcC: carbamate kinase B9Y55_RS08870
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase B9Y55_RS03840
D-lactate lctP: D-lactate:H+ symporter LctP or LidP
D-serine cycA: D-serine:H+ symporter CycA
deoxyinosine deoB: phosphopentomutase
deoxyinosine H281DRAFT_01112: deoxynucleoside transporter, permease component 2 B9Y55_RS07440 B9Y55_RS11060
deoxyinosine H281DRAFT_01114: deoxynucleoside transporter, substrate-binding component B9Y55_RS07450
deoxyinosine H281DRAFT_01115: deoxynucleoside transporter, permease component 1 B9Y55_RS07435
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
fructose scrK: fructokinase B9Y55_RS11635 B9Y55_RS09620
fructose Slc2a5: fructose:H+ symporter
fucose aldA: lactaldehyde dehydrogenase
fucose fucA: L-fuculose-phosphate aldolase FucA B9Y55_RS07460
fucose fucI: L-fucose isomerase FucI
fucose fucK: L-fuculose kinase FucK B9Y55_RS07455
fucose fucP: L-fucose:H+ symporter FucP
fucose fucU: L-fucose mutarotase FucU
fumarate dctA: fumarate:H+ symporter DctA B9Y55_RS11270
galactose galE: UDP-glucose 4-epimerase B9Y55_RS03335 B9Y55_RS07855
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase B9Y55_RS11070
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
galacturonate uxaB: tagaturonate reductase
galacturonate uxaC: D-galacturonate isomerase
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) B9Y55_RS10585
glucose glk: glucokinase B9Y55_RS09620
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 B9Y55_RS01830
glucuronate garR: tartronate semialdehyde reductase
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 B9Y55_RS03955 B9Y55_RS05100
histidine hutV: L-histidine ABC transporter, ATPase component HutV B9Y55_RS11165 B9Y55_RS07100
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase B9Y55_RS08755
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase B9Y55_RS01195 B9Y55_RS05390
isoleucine livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) B9Y55_RS02595
isoleucine livM: L-isoleucine ABC transporter, permease component 2 (LivM/BraE) B9Y55_RS04290 B9Y55_RS02605
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit
isoleucine pccB: propionyl-CoA carboxylase, beta subunit B9Y55_RS00435
L-lactate lctO: L-lactate oxidase or 2-monooxygenase
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
L-lactate pta: phosphate acetyltransferase B9Y55_RS03850 B9Y55_RS03855
L-malate maeN: malate transporter maeN B9Y55_RS06900
lactose galE: UDP-glucose 4-epimerase B9Y55_RS03335 B9Y55_RS07855
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase B9Y55_RS11070
lactose glk: glucokinase B9Y55_RS09620
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
leucine ilvE: L-leucine transaminase B9Y55_RS11895 B9Y55_RS11880
leucine liuA: isovaleryl-CoA dehydrogenase
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit
leucine liuC: 3-methylglutaconyl-CoA hydratase B9Y55_RS08755
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit B9Y55_RS00435
leucine liuE: hydroxymethylglutaryl-CoA lyase B9Y55_RS05475
leucine livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) B9Y55_RS02595
leucine livM: L-leucine ABC transporter, permease component 2 (LivM/BraE) B9Y55_RS04290 B9Y55_RS02605
lysine amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd)
lysine bgtB: L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) B9Y55_RS01405
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase B9Y55_RS01850
lysine lysN: 2-aminoadipate transaminase B9Y55_RS11880 B9Y55_RS01600
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase
maltose glk: glucokinase B9Y55_RS09620
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
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
myoinositol iolT: myo-inositol:H+ symporter
myoinositol mmsA: malonate-semialdehyde dehydrogenase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) B9Y55_RS10585
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 B9Y55_RS08755
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase B9Y55_RS08755
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase B9Y55_RS01195 B9Y55_RS05390
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase B9Y55_RS03080
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase B9Y55_RS03080
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine fahA: fumarylacetoacetate hydrolase
phenylalanine hmgA: homogentisate dioxygenase
phenylalanine HPD: 4-hydroxyphenylpyruvate dioxygenase
phenylalanine maiA: maleylacetoacetate isomerase
phenylalanine PAH: phenylalanine 4-monooxygenase
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase
phenylalanine QDPR: 6,7-dihydropteridine reductase
proline hutV: proline ABC transporter, ATPase component HutV B9Y55_RS11165 B9Y55_RS07100
proline hutW: proline ABC transporter, permease component HutW B9Y55_RS11170 B9Y55_RS07095
proline hutX: proline ABC transporter, substrate-binding component HutX B9Y55_RS01760 B9Y55_RS11160
proline put1: proline dehydrogenase
proline putA: L-glutamate 5-semialdeyde dehydrogenase
propionate pccA: propionyl-CoA carboxylase, alpha subunit
propionate pccB: propionyl-CoA carboxylase, beta subunit B9Y55_RS00435
propionate prpE: propionyl-CoA synthetase
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabD: succinate semialdehyde dehydrogenase B9Y55_RS10265
putrescine gabT: gamma-aminobutyrate transaminase B9Y55_RS03105 B9Y55_RS03640
putrescine patA: putrescine aminotransferase (PatA/SpuC) B9Y55_RS03105 B9Y55_RS01850
putrescine patD: gamma-aminobutyraldehyde dehydrogenase
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose aldA: lactaldehyde dehydrogenase
rhamnose rhaA: L-rhamnose isomerase
rhamnose rhaD: rhamnulose 1-phosphate aldolase
rhamnose rhaM: L-rhamnose mutarotase
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 B9Y55_RS01195
succinate sdc: succinate:Na+ symporter Sdc
sucrose ams: sucrose hydrolase (invertase)
sucrose glk: glucokinase B9Y55_RS09620
threonine tdcC: L-threonine:H+ symporter TdcC
thymidine deoB: phosphopentomutase
thymidine nupG: thymidine permease NupG/XapB
trehalose glk: glucokinase B9Y55_RS09620
trehalose treF: trehalase
tryptophan tnaA: tryptophanase
tryptophan trpP: energy-coupling factor transporter, tryptophan-specific (S) component TrpP
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
valine bch: 3-hydroxyisobutyryl-CoA hydrolase B9Y55_RS08755
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase B9Y55_RS08755
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) B9Y55_RS02595
valine livM: L-valine ABC transporter, permease component 2 (LivM/BraE) B9Y55_RS04290 B9Y55_RS02605
valine mmsA: methylmalonate-semialdehyde dehydrogenase
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine pccA: propionyl-CoA carboxylase, alpha subunit
valine pccB: propionyl-CoA carboxylase, beta subunit B9Y55_RS00435
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase
xylose xylA: xylose isomerase
xylose xylB: xylulokinase B9Y55_RS07465
xylose xylT: D-xylose transporter

Confidence: high confidence medium confidence low confidence

This GapMind analysis is from Sep 24 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