GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Desulfatiglans anilini DSM 4660

Found 164 low-confidence and 60 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate kgtP: 2-oxoglutarate:H+ symporter KgtP
4-hydroxybenzoate bamF: class II benzoyl-CoA reductase, BamF subunit H567_RS0120850 H567_RS29250
4-hydroxybenzoate bamG: class II benzoyl-CoA reductase, BamG subunit H567_RS0103085 H567_RS0110430
4-hydroxybenzoate bamH: class II benzoyl-CoA reductase, BamH subunit H567_RS0102625 H567_RS0103080
4-hydroxybenzoate bamI: class II benzoyl-CoA reductase, BamI subunit H567_RS0120685 H567_RS26855
4-hydroxybenzoate fcbT1: tripartite 4-hydroxybenzoate transporter, substrate-binding component FcbT1 H567_RS0113405
4-hydroxybenzoate fcbT2: tripartite 4-hydroxybenzoate transporter, small DctQ-like component FcbT2
4-hydroxybenzoate gcdH: glutaryl-CoA dehydrogenase H567_RS0110890 H567_RS0117975
4-hydroxybenzoate hcrB: 4-hydroxybenzoyl-CoA reductase, beta subunit H567_RS0121790 H567_RS0120050
4-hydroxybenzoate hcrC: 4-hydroxybenzoyl-CoA reductase, gamma subunit H567_RS0110275 H567_RS0120045
4-hydroxybenzoate pimB: 3-oxopimeloyl-CoA:CoA acetyltransferase H567_RS0110730 H567_RS0115465
alanine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) H567_RS0109120
alanine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) H567_RS0109130 H567_RS0114750
alanine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) H567_RS23995 H567_RS23835
alanine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) H567_RS0109140 H567_RS0107395
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
arginine rocD: ornithine aminotransferase H567_RS0108365 H567_RS0101805
arginine rocE: L-arginine permease
arginine rocF: arginase
asparagine ans: asparaginase H567_RS0110675
asparagine glt: aspartate:proton symporter Glt
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 H567_RS0105135 H567_RS0117690
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline arcC: carbamate kinase
citrulline rocA: 1-pyrroline-5-carboxylate dehydrogenase
citrulline rocD: ornithine aminotransferase H567_RS0108365 H567_RS0101805
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase H567_RS0109920 H567_RS0115845
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 H567_RS0118160
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) H567_RS0113835
deoxyinosine deoB: phosphopentomutase
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine nupC: deoxyinosine:H+ symporter NupC H567_RS0116185
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase H567_RS0117055 H567_RS0117980
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme H567_RS0115950
deoxyribose adh: acetaldehyde dehydrogenase (not acylating) H567_RS0113835
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
ethanol adh: acetaldehyde dehydrogenase (not acylating) H567_RS0113835
fructose 1pfk: 1-phosphofructokinase
fructose fba: fructose 1,6-bisphosphate aldolase H567_RS22300 H567_RS0100630
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
fucose aldA: lactaldehyde dehydrogenase
fucose fucA: L-fuculose-phosphate aldolase FucA H567_RS0109585
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
fumarate dctA: fumarate:H+ symporter DctA
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
galacturonate uxaB: tagaturonate reductase
galacturonate uxaC: D-galacturonate isomerase
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) H567_RS0116780
glucose MFS-glucose: glucose transporter, MFS superfamily
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 H567_RS0101840
glucuronate garR: tartronate semialdehyde reductase
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate udh: D-glucuronate dehydrogenase
glutamate gdhA: glutamate dehydrogenase, NAD-dependent H567_RS0107180
glutamate gltS: L-glutamate:Na+ symporter GltS
glycerol dhaK': dihydroxyacetone kinase, ATP dependent (monomeric)
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 LAT2: L-histidine transporter H567_RS25310
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase H567_RS0110860 H567_RS0104145
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase H567_RS0110895 H567_RS0115475
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase H567_RS0117055 H567_RS0106010
isoleucine livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) H567_RS0109120
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit
isoleucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC H567_RS0102595
L-lactate L-LDH: L-lactate dehydrogenase H567_RS0102105 H567_RS0120690
L-lactate Shew_2731: L-lactate:Na+ symporter, large component
L-malate sdlC: L-malate:Na+ symporter SdlC
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 liuA: isovaleryl-CoA dehydrogenase H567_RS0104145 H567_RS0110860
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit
leucine liuC: 3-methylglutaconyl-CoA hydratase H567_RS0120240 H567_RS0115475
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit H567_RS0117950 H567_RS0106055
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) H567_RS0109120
leucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC H567_RS0102595
lysine davA: 5-aminovaleramidase H567_RS26720 H567_RS0102185
lysine davB: L-lysine 2-monooxygenase
lysine davD: glutarate semialdehyde dehydrogenase
lysine davT: 5-aminovalerate aminotransferase H567_RS0101805 H567_RS0108365
lysine gcdG: succinyl-CoA:glutarate CoA-transferase H567_RS0117995
lysine gcdH: glutaryl-CoA dehydrogenase H567_RS0110890 H567_RS0117975
lysine lysP: L-lysine:H+ symporter LysP
maltose malA: 6-phospho-alphaglucosidase
maltose malEIICBA: maltose phosphotransferase system, EII-CBA components
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 nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) H567_RS0116780
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 H567_RS0110895 H567_RS0115475
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase H567_RS0110065 H567_RS0110730
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase H567_RS0110065 H567_RS0115465
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase H567_RS0115155 H567_RS0115475
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine livF: L-phenylalanine ABC transporter, ATPase component 1 (LivF) H567_RS0109140 H567_RS0107395
phenylalanine livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK H567_RS0109120
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 H567_RS0110895 H567_RS0115475
phenylalanine paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase H567_RS0110065 H567_RS0110730
phenylalanine paaJ2: 3-oxoadipyl-CoA thiolase H567_RS0110065 H567_RS0115465
phenylalanine paaZ1: oxepin-CoA hydrolase H567_RS0115155 H567_RS0115475
phenylalanine paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
proline HSERO_RS00870: proline ABC transporter, substrate-binding component
proline HSERO_RS00885: proline ABC transporter, permease component 1 H567_RS0109125 H567_RS0114745
proline HSERO_RS00895: proline ABC transporter, ATPase component 1 H567_RS23995 H567_RS0114755
proline HSERO_RS00900: proline ABC transporter, ATPase component 2 H567_RS0109140 H567_RS0108405
proline put1: proline dehydrogenase H567_RS0114335
proline putA: L-glutamate 5-semialdeyde dehydrogenase
propionate pccA: propionyl-CoA carboxylase, alpha subunit
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabD: succinate semialdehyde dehydrogenase
putrescine gabT: gamma-aminobutyrate transaminase H567_RS0102770 H567_RS0101805
putrescine patA: putrescine aminotransferase (PatA/SpuC) H567_RS0102770 H567_RS0101805
putrescine patD: gamma-aminobutyraldehyde dehydrogenase
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate yjcH: putative small subunit of pyruvate transporter (yjcH-like) H567_RS0111510
rhamnose aldA: lactaldehyde dehydrogenase
rhamnose LRA1: L-rhamnofuranose dehydrogenase H567_RS0106010 H567_RS0117980
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 braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) H567_RS0109120
serine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) H567_RS0109130 H567_RS0114750
serine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) H567_RS23995 H567_RS23835
serine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) H567_RS0109140 H567_RS0107395
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase H567_RS0117055 H567_RS0106010
succinate satP: succinate:H+ symporter SatP H567_RS0121480
sucrose ams: sucrose hydrolase (invertase)
sucrose MFS-glucose: glucose transporter, MFS superfamily
threonine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) H567_RS0109120
threonine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) H567_RS0109130 H567_RS0114750
threonine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) H567_RS23995 H567_RS23835
threonine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) H567_RS0109140 H567_RS0107395
threonine pccA: propionyl-CoA carboxylase, alpha subunit
threonine tdcE: 2-ketobutyrate formate-lyase
thymidine adh: acetaldehyde dehydrogenase (not acylating) H567_RS0113835
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupC: thymidine permease NupC H567_RS0116185
trehalose PsTP: trehalose phosphorylase
trehalose TRET1: facilitated trehalose transporter Tret1
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine Ac3H11_1692: L-tyrosine ABC transporter, ATPase component 2 H567_RS0109140 H567_RS0108405
tyrosine Ac3H11_1693: L-tyrosine ABC transporter, ATPase component 1 H567_RS23995 H567_RS23835
tyrosine Ac3H11_1695: L-tyrosine ABC transporter, permease component 1 H567_RS0109125 H567_RS0114745
tyrosine Ac3H11_2396: L-tyrosine ABC transporter, substrate-binding component component
tyrosine fahA: fumarylacetoacetate hydrolase H567_RS24120
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase H567_RS0110860 H567_RS0104145
valine bch: 3-hydroxyisobutyryl-CoA hydrolase H567_RS0118000 H567_RS0120240
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) H567_RS0109120
valine livM: L-valine ABC transporter, permease component 2 (LivM/BraE) H567_RS0109130 H567_RS0114750
valine mmsA: methylmalonate-semialdehyde dehydrogenase
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine pccA: propionyl-CoA carboxylase, alpha subunit
valine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC H567_RS0102595
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase H567_RS0113835
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