GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Succinatimonas hippei YIT 12066

Found 149 low-confidence and 46 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate kgtP: 2-oxoglutarate:H+ symporter KgtP HMPREF9444_RS00900
4-hydroxybenzoate adh: acetaldehyde dehydrogenase (not acylating) HMPREF9444_RS04280
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase HMPREF9444_RS08050
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 alsT: L-alanine symporter AlsT/DagA HMPREF9444_RS06920
arabinose araA: L-arabinose isomerase
arginine artP: L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA HMPREF9444_RS05610 HMPREF9444_RS09575
arginine rocA: 1-pyrroline-5-carboxylate dehydrogenase HMPREF9444_RS04280
arginine rocD: ornithine aminotransferase HMPREF9444_RS01560 HMPREF9444_RS05885
arginine rocF: arginase
asparagine dauA: dicarboxylic acid transporter DauA HMPREF9444_RS05735
aspartate dauA: dicarboxylic acid transporter DauA HMPREF9444_RS05735
cellobiose bgl: cellobiase
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component HMPREF9444_RS05610 HMPREF9444_RS09575
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 HMPREF9444_RS05615
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 HMPREF9444_RS05615
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component HMPREF9444_RS06990 HMPREF9444_RS00360
citrulline arcC: carbamate kinase
citrulline rocA: 1-pyrroline-5-carboxylate dehydrogenase HMPREF9444_RS04280
citrulline rocD: ornithine aminotransferase HMPREF9444_RS01560 HMPREF9444_RS05885
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
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 HMPREF9444_RS02320
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) HMPREF9444_RS04280
deoxyinosine deoB: phosphopentomutase HMPREF9444_RS09920
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate aacS: acetoacetyl-CoA synthetase
deoxyribonate atoB: acetyl-CoA C-acetyltransferase
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 HMPREF9444_RS08105
deoxyribose adh: acetaldehyde dehydrogenase (not acylating) HMPREF9444_RS04280
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoK: deoxyribokinase HMPREF9444_RS04775 HMPREF9444_RS09200
deoxyribose deoP: deoxyribose transporter
ethanol adh: acetaldehyde dehydrogenase (not acylating) HMPREF9444_RS04280
fructose frcA: fructose ABC transporter, ATPase component FrcA HMPREF9444_RS09995 HMPREF9444_RS00045
fructose frcB: fructose ABC transporter, substrate-binding component FrcB HMPREF9444_RS10000
fructose frcC: fructose ABC transporter, permease component FrcC HMPREF9444_RS09990 HMPREF9444_RS00040
fructose scrK: fructokinase HMPREF9444_RS06235 HMPREF9444_RS05040
fucose aldA: lactaldehyde dehydrogenase HMPREF9444_RS04280
fucose fucA: L-fuculose-phosphate aldolase FucA HMPREF9444_RS02415
fucose fucK: L-fuculose kinase FucK
fucose fucP: L-fucose:H+ symporter FucP
fumarate dauA: fumarate transporter DauA HMPREF9444_RS05735
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate uxaB: tagaturonate reductase HMPREF9444_RS05175 HMPREF9444_RS08550
gluconate gntT: gluconate:H+ symporter GntT HMPREF9444_RS08505
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) HMPREF9444_RS00535
glucosamine SLC2A2: glucosamine transporter SLC2A2
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate dctP: D-glucuronate TRAP transporter, solute receptor component HMPREF9444_RS09330 HMPREF9444_RS02450
glucuronate dctQ: D-glucuronate TRAP transporter, small permease component
glutamate gdhA: glutamate dehydrogenase, NAD-dependent HMPREF9444_RS08875
glycerol dhaD: glycerol dehydrogenase HMPREF9444_RS04070 HMPREF9444_RS08900
glycerol dhaK': dihydroxyacetone kinase, ATP dependent (monomeric)
glycerol glpF: glycerol facilitator glpF
histidine bgtA: L-histidine ABC transporter, ATPase component BgtA HMPREF9444_RS05610 HMPREF9444_RS08825
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase HMPREF9444_RS03550
isoleucine fadA: 2-methylacetoacetyl-CoA thiolase
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase HMPREF9444_RS01835 HMPREF9444_RS08900
isoleucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
isoleucine prpB: 2-methylisocitrate lyase
isoleucine prpC: 2-methylcitrate synthase HMPREF9444_RS02200
isoleucine prpD: 2-methylcitrate dehydratase
L-lactate lctO: L-lactate oxidase or 2-monooxygenase
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
L-malate sdlC: L-malate:Na+ symporter SdlC
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
leucine aacS: acetoacetyl-CoA synthetase
leucine atoB: acetyl-CoA C-acetyltransferase
leucine brnQ: L-leucine:Na+ symporter BrnQ/BraB HMPREF9444_RS03585 HMPREF9444_RS00380
leucine liuA: isovaleryl-CoA dehydrogenase
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit HMPREF9444_RS06410
leucine liuC: 3-methylglutaconyl-CoA hydratase HMPREF9444_RS03550
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
lysine amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) HMPREF9444_RS04280
lysine hglS: D-2-hydroxyglutarate synthase
lysine hisP: L-lysine ABC transporter, ATPase component HisP HMPREF9444_RS05610 HMPREF9444_RS08825
lysine lat: L-lysine 6-aminotransferase HMPREF9444_RS05885
lysine lysN: 2-aminoadipate transaminase
maltose susB: alpha-glucosidase (maltase) HMPREF9444_RS02175
mannitol mtlA: mannitol phosphotransferase system, EII-CBA components
mannitol mtlD: mannitol-1-phosphate 5-dehydrogenase
mannose HSERO_RS03635: mannose ABC transporter, substrate-binding component HMPREF9444_RS10000
mannose HSERO_RS03640: mannose ABC transporter, ATPase component HMPREF9444_RS09995 HMPREF9444_RS07215
mannose HSERO_RS03645: mannose ABC transporter, permease component HMPREF9444_RS09990 HMPREF9444_RS00040
mannose manA: mannose-6-phosphate isomerase
mannose mannokinase: D-mannose kinase HMPREF9444_RS06235
myoinositol iolG: myo-inositol 2-dehydrogenase
myoinositol iolM: 2-inosose 4-dehydrogenase HMPREF9444_RS01410 HMPREF9444_RS07535
myoinositol iolN: 2,4-diketo-inositol hydratase
myoinositol iolO: 5-dehydro-L-gluconate epimerase
myoinositol iolT: myo-inositol:H+ symporter HMPREF9444_RS05050
myoinositol uxaE: D-tagaturonate epimerase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) HMPREF9444_RS00535
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 HMPREF9444_RS03550
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase HMPREF9444_RS03550
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase
phenylacetate paaK: phenylacetate-CoA ligase HMPREF9444_RS07915
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aacS: acetoacetyl-CoA synthetase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine atoB: acetyl-CoA C-acetyltransferase
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 HMPREF9444_RS03535
proline put1: proline dehydrogenase
proline putA: L-glutamate 5-semialdeyde dehydrogenase HMPREF9444_RS04280
propionate prpB: 2-methylisocitrate lyase
propionate prpC: 2-methylcitrate synthase HMPREF9444_RS02200
propionate prpD: 2-methylcitrate dehydratase
propionate prpE: propionyl-CoA synthetase HMPREF9444_RS07915
propionate putP: propionate transporter; proline:Na+ symporter HMPREF9444_RS09045
putrescine gabD: succinate semialdehyde dehydrogenase HMPREF9444_RS04280
putrescine gabT: gamma-aminobutyrate transaminase HMPREF9444_RS01560 HMPREF9444_RS05885
putrescine patA: putrescine aminotransferase (PatA/SpuC) HMPREF9444_RS05885 HMPREF9444_RS01560
putrescine patD: gamma-aminobutyraldehyde dehydrogenase HMPREF9444_RS04280
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose aldA: lactaldehyde dehydrogenase HMPREF9444_RS04280
rhamnose LRA1: L-rhamnofuranose dehydrogenase HMPREF9444_RS01835 HMPREF9444_RS08900
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase HMPREF9444_RS08150 HMPREF9444_RS08545
rhamnose LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase HMPREF9444_RS08050
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsA: D-ribose ABC transporter, ATPase component RbsA HMPREF9444_RS09995 HMPREF9444_RS07215
ribose rbsB: D-ribose ABC transporter, substrate-binding component RbsB HMPREF9444_RS10000
ribose rbsC: D-ribose ABC transporter, permease component RbsC HMPREF9444_RS09990 HMPREF9444_RS00040
ribose rbsK: ribokinase HMPREF9444_RS04775 HMPREF9444_RS09200
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase HMPREF9444_RS01835
succinate dauA: succinate:H+ symporter DauA HMPREF9444_RS05735
sucrose ams: sucrose hydrolase (invertase)
threonine gloA: glyoxylase I HMPREF9444_RS04395
threonine tdh: L-threonine 3-dehydrogenase HMPREF9444_RS01410 HMPREF9444_RS10010
threonine tynA: aminoacetone oxidase
thymidine adh: acetaldehyde dehydrogenase (not acylating) HMPREF9444_RS04280
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase HMPREF9444_RS09920
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
trehalose treF: trehalase
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aacS: acetoacetyl-CoA synthetase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine atoB: acetyl-CoA C-acetyltransferase
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 HMPREF9444_RS03550
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase HMPREF9444_RS03550
valine mmsA: methylmalonate-semialdehyde dehydrogenase HMPREF9444_RS04280
valine mmsB: 3-hydroxyisobutyrate dehydrogenase HMPREF9444_RS09120
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
valine prpB: 2-methylisocitrate lyase
valine prpC: 2-methylcitrate synthase HMPREF9444_RS02200
valine prpD: 2-methylcitrate dehydratase
xylitol PLT5: xylitol:H+ symporter PLT5 HMPREF9444_RS05050
xylitol xylB: xylulokinase HMPREF9444_RS02410 HMPREF9444_RS01400
xylose xylB: xylulokinase HMPREF9444_RS02410 HMPREF9444_RS01400
xylose xyrA: xylitol reductase HMPREF9444_RS00145 HMPREF9444_RS02630

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