GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Desulfitobacterium hafniense DCB-2

Found 142 low-confidence and 58 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate dctM: 2-oxoglutarate TRAP transporter, large permease component DctM DHAF_RS05355 DHAF_RS23125
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 DHAF_RS06240 DHAF_RS10310
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK DHAF_RS18240 DHAF_RS07395
4-hydroxybenzoate pobA: 4-hydroxybenzoate 3-monooxygenase
4-hydroxybenzoate praA: protocatechuate 2,3-dioxygenase
4-hydroxybenzoate xylF: 2-hydroxymuconate semialdehyde hydrolase DHAF_RS07750
acetate actP: cation/acetate symporter ActP
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase DHAF_RS18790
arabinose araE: L-arabinose:H+ symporter
arginine gabT: gamma-aminobutyrate transaminase DHAF_RS03890 DHAF_RS16705
arginine patA: putrescine aminotransferase (PatA/SpuC) DHAF_RS03890 DHAF_RS16705
arginine patD: gamma-aminobutyraldehyde dehydrogenase DHAF_RS13220 DHAF_RS10840
arginine rocE: L-arginine permease DHAF_RS12190 DHAF_RS06640
asparagine ans: asparaginase DHAF_RS15300
asparagine ansP: L-asparagine permease AnsP DHAF_RS06640 DHAF_RS12190
aspartate peb1C: aspartate ABC transporter, ATPase component Peb1C DHAF_RS05220 DHAF_RS23680
aspartate peb1D: aspartate ABC transporter, permease component 2 (Peb1D) DHAF_RS05235 DHAF_RS23685
cellobiose cbp: cellobiose phosphorylase
cellobiose cbpC: cellobiose ABC transporter, substrate-binding component CbpC
citrate citE: citrate lyase, citryl-ACP lyase component CitE DHAF_RS15385 DHAF_RS04530
citrate tctB: citrate/Na+ symporter, small transmembrane component TctB
citrate tctC: citrate/Na+ symporter, substrate-binding component TctC DHAF_RS09800
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component DHAF_RS22710 DHAF_RS11405
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 DHAF_RS22715 DHAF_RS23685
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 DHAF_RS23685 DHAF_RS03765
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component DHAF_RS23690 DHAF_RS18955
citrulline arcC: carbamate kinase
citrulline rocA: 1-pyrroline-5-carboxylate dehydrogenase DHAF_RS13220
citrulline rocD: ornithine aminotransferase DHAF_RS16705 DHAF_RS03890
D-alanine cycA: D-alanine:H+ symporter CycA DHAF_RS12190 DHAF_RS06640
D-alanine dadA: D-alanine dehydrogenase
D-serine cycA: D-serine:H+ symporter CycA DHAF_RS06640 DHAF_RS12190
deoxyinosine bmpA: deoxyinosine ABC transporter, substrate-binding component DHAF_RS11210
deoxyinosine nupB: deoxyinosine ABC transporter, permease component 1 DHAF_RS11200
deoxyribonate aacS: acetoacetyl-CoA synthetase DHAF_RS18135 DHAF_RS01655
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase DHAF_RS19070
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
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) DHAF_RS02645 DHAF_RS13285
fructose 1pfk: 1-phosphofructokinase
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
fucose fucA: L-fuculose-phosphate aldolase FucA
fucose fucI: L-fucose isomerase FucI
fucose fucK: L-fuculose kinase FucK
fucose fucO: L-lactaldehyde reductase DHAF_RS02645 DHAF_RS10835
fucose fucP: L-fucose:H+ symporter FucP
fucose fucU: L-fucose mutarotase FucU
fumarate sdcL: fumarate:Na+ symporter SdcL DHAF_RS01040
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 DHAF_RS09835
galacturonate exuT: D-galacturonate transporter ExuT DHAF_RS05095
galacturonate kdgK: 2-keto-3-deoxygluconate kinase
galacturonate uxaA: D-altronate dehydratase DHAF_RS16340
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)
glucose MFS-glucose: glucose transporter, MFS superfamily DHAF_RS09440
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT DHAF_RS05095
glucuronate garL: 5-dehydro-4-deoxy-D-glucarate aldolase
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate udh: D-glucuronate dehydrogenase
glutamate gltL: L-glutamate ABC transporter, ATPase component (GltL/GluA/BztD/GlnQ/AatP/PEB1C) DHAF_RS23680 DHAF_RS05220
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric)
glycerol glpF: glycerol facilitator glpF DHAF_RS09525
histidine hutG: N-formiminoglutamate formiminohydrolase DHAF_RS00930
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
histidine PA5503: L-histidine ABC transporter, ATPase component DHAF_RS07420 DHAF_RS03775
histidine PA5504: L-histidine ABC transporter, permease component DHAF_RS07415
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase DHAF_RS14315 DHAF_RS14305
isoleucine brnQ: L-isoleucine:cation symporter BrnQ/BraZ/BraB DHAF_RS11265
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase DHAF_RS14270 DHAF_RS18210
isoleucine epi: methylmalonyl-CoA epimerase
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase DHAF_RS19070 DHAF_RS03090
isoleucine mcm-small: methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit DHAF_RS13505 DHAF_RS14625
isoleucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit DHAF_RS17500
isoleucine pccB: propionyl-CoA carboxylase, beta subunit
L-lactate L-LDH: L-lactate dehydrogenase DHAF_RS08965 DHAF_RS22055
L-malate sdlC: L-malate:Na+ symporter SdlC DHAF_RS01040
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 aacS: acetoacetyl-CoA synthetase DHAF_RS18135 DHAF_RS01655
leucine brnQ: L-leucine:Na+ symporter BrnQ/BraB DHAF_RS11265
leucine liuA: isovaleryl-CoA dehydrogenase DHAF_RS14305 DHAF_RS14315
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit DHAF_RS17500
leucine liuC: 3-methylglutaconyl-CoA hydratase DHAF_RS18210 DHAF_RS14270
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
lysine davA: 5-aminovaleramidase
lysine davB: L-lysine 2-monooxygenase
lysine davT: 5-aminovalerate aminotransferase DHAF_RS03890 DHAF_RS16705
lysine gcdG: succinyl-CoA:glutarate CoA-transferase DHAF_RS01625
lysine gcdH: glutaryl-CoA dehydrogenase DHAF_RS14305 DHAF_RS14315
lysine lysP: L-lysine:H+ symporter LysP DHAF_RS06640 DHAF_RS12190
maltose MFS-glucose: glucose transporter, MFS superfamily DHAF_RS09440
maltose susB: alpha-glucosidase (maltase) DHAF_RS15960 DHAF_RS02450
mannitol mtlA: mannitol phosphotransferase system, EII-CBA components
mannitol mtlD: mannitol-1-phosphate 5-dehydrogenase
mannose manA: mannose-6-phosphate isomerase DHAF_RS04205
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 DHAF_RS24105 DHAF_RS13175
myoinositol iolT: myo-inositol:H+ symporter DHAF_RS09440
myoinositol mmsA: malonate-semialdehyde dehydrogenase DHAF_RS13220
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
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 DHAF_RS14270 DHAF_RS18210
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase DHAF_RS18210 DHAF_RS14270
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase DHAF_RS14275 DHAF_RS03095
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase DHAF_RS14275 DHAF_RS03095
phenylacetate paaK: phenylacetate-CoA ligase DHAF_RS17250 DHAF_RS18135
phenylacetate paaZ1: oxepin-CoA hydrolase DHAF_RS18210
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine iorAB: phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB
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 DHAF_RS14270 DHAF_RS18210
phenylalanine paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase DHAF_RS18210 DHAF_RS14270
phenylalanine paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase DHAF_RS14275 DHAF_RS03095
phenylalanine paaJ2: 3-oxoadipyl-CoA thiolase DHAF_RS14275 DHAF_RS03095
phenylalanine paaZ1: oxepin-CoA hydrolase DHAF_RS18210
phenylalanine paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
proline put1: proline dehydrogenase
proline putA: L-glutamate 5-semialdeyde dehydrogenase DHAF_RS13220
propionate epi: methylmalonyl-CoA epimerase
propionate mcm-small: methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit DHAF_RS13505 DHAF_RS14625
propionate pccA: propionyl-CoA carboxylase, alpha subunit DHAF_RS17500
propionate pccB: propionyl-CoA carboxylase, beta subunit
putrescine gabT: gamma-aminobutyrate transaminase DHAF_RS03890 DHAF_RS16705
putrescine patA: putrescine aminotransferase (PatA/SpuC) DHAF_RS03890 DHAF_RS16705
putrescine patD: gamma-aminobutyraldehyde dehydrogenase DHAF_RS13220 DHAF_RS10840
putrescine potB: putrescine ABC transporter, permease component 1 (PotB/PotH) DHAF_RS12790
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose fucO: L-lactaldehyde reductase DHAF_RS02645 DHAF_RS10835
rhamnose LRA1: L-rhamnofuranose dehydrogenase DHAF_RS19070 DHAF_RS12765
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase DHAF_RS16340 DHAF_RS22085
rhamnose LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase DHAF_RS10310
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsK: ribokinase
ribose rbsU: probable D-ribose transporter RbsU
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase DHAF_RS19070 DHAF_RS10450
succinate sdc: succinate:Na+ symporter Sdc DHAF_RS01040
sucrose ams: sucrose hydrolase (invertase)
sucrose MFS-glucose: glucose transporter, MFS superfamily DHAF_RS09440
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) DHAF_RS20135 DHAF_RS20130
threonine ltaE: L-threonine aldolase DHAF_RS05420 DHAF_RS24045
thymidine nupG: thymidine permease NupG/XapB
trehalose MFS-glucose: glucose transporter, MFS superfamily DHAF_RS09440
trehalose treF: trehalase
tryptophan aroP: tryptophan:H+ symporter AroP DHAF_RS06640 DHAF_RS12190
tyrosine aacS: acetoacetyl-CoA synthetase DHAF_RS18135 DHAF_RS01655
tyrosine aroP: L-tyrosine transporter (AroP/FywP) DHAF_RS06640 DHAF_RS12190
tyrosine fahA: fumarylacetoacetate hydrolase DHAF_RS15245
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase DHAF_RS14315 DHAF_RS14305
valine bch: 3-hydroxyisobutyryl-CoA hydrolase DHAF_RS22655 DHAF_RS14270
valine brnQ: L-valine:cation symporter BrnQ/BraZ/BraB DHAF_RS11265
valine epi: methylmalonyl-CoA epimerase
valine mcm-small: methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit DHAF_RS13505 DHAF_RS14625
valine mmsA: methylmalonate-semialdehyde dehydrogenase DHAF_RS13220
valine mmsB: 3-hydroxyisobutyrate dehydrogenase DHAF_RS05885 DHAF_RS09785
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
valine pccA: propionyl-CoA carboxylase, alpha subunit DHAF_RS17500
valine pccB: propionyl-CoA carboxylase, beta subunit
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 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