GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Methanospirillum stamsii Pt1

Found 188 low-confidence and 39 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 adh: acetaldehyde dehydrogenase (not acylating) DLD82_RS12415 DLD82_RS16650
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase DLD82_RS00170
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
alanine snatA: L-alanine symporter SnatA DLD82_RS08715 DLD82_RS14930
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter
arginine aguA: agmatine deiminase DLD82_RS15840
arginine aguB: N-carbamoylputrescine hydrolase DLD82_RS15840
arginine gabD: succinate semialdehyde dehydrogenase DLD82_RS12415 DLD82_RS16650
arginine gabT: gamma-aminobutyrate transaminase DLD82_RS06180
arginine patA: putrescine aminotransferase (PatA/SpuC) DLD82_RS06180 DLD82_RS13760
arginine patD: gamma-aminobutyraldehyde dehydrogenase DLD82_RS12415 DLD82_RS16650
arginine rocE: L-arginine permease DLD82_RS12965
asparagine ans: asparaginase DLD82_RS02775
asparagine glt: aspartate:proton symporter Glt
aspartate glt: aspartate:proton symporter Glt
cellobiose bgl: cellobiase
cellobiose glk: glucokinase DLD82_RS03875
cellobiose SemiSWEET: Sugar transporter SemiSWEET DLD82_RS08180
citrate acn: aconitase
citrate icd: isocitrate dehydrogenase DLD82_RS12490 DLD82_RS09950
citrate SLC13A5: citrate:Na+ symporter DLD82_RS01570
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component DLD82_RS15815 DLD82_RS00895
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 DLD82_RS15810
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 DLD82_RS15810
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component DLD82_RS15830
citrulline citrullinase: putative citrullinase DLD82_RS15840
citrulline rocA: 1-pyrroline-5-carboxylate dehydrogenase DLD82_RS12415 DLD82_RS16650
citrulline rocD: ornithine aminotransferase DLD82_RS13760 DLD82_RS06180
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase DLD82_RS01305
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 DLD82_RS16935
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) DLD82_RS12415 DLD82_RS16650
deoxyinosine deoB: phosphopentomutase DLD82_RS10695 DLD82_RS03580
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase DLD82_RS07705
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase
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 adh: acetaldehyde dehydrogenase (not acylating) DLD82_RS12415 DLD82_RS16650
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
ethanol adh: acetaldehyde dehydrogenase (not acylating) DLD82_RS12415 DLD82_RS16650
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) DLD82_RS02330 DLD82_RS04745
fructose 1pfk: 1-phosphofructokinase
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
fucose aldA: lactaldehyde dehydrogenase DLD82_RS16650 DLD82_RS12415
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
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 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) DLD82_RS03565
glucose glk: glucokinase DLD82_RS03875
glucose SemiSWEET: Sugar transporter SemiSWEET DLD82_RS08180
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate dopDH: 2,5-dioxopentanonate dehydrogenase DLD82_RS12415 DLD82_RS16650
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate kdgD: 5-dehydro-4-deoxyglucarate dehydratase DLD82_RS08685
glucuronate udh: D-glucuronate dehydrogenase
glutamate gdhA: glutamate dehydrogenase, NAD-dependent DLD82_RS15940
glutamate gltS: L-glutamate:Na+ symporter GltS
glycerol dhaK': dihydroxyacetone kinase, ATP dependent (monomeric)
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
histidine permease: L-histidine permease DLD82_RS12965
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase
isoleucine Bap2: L-isoleucine permease Bap2
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase
isoleucine epi: methylmalonyl-CoA epimerase
isoleucine fadA: 2-methylacetoacetyl-CoA thiolase DLD82_RS06410
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase
isoleucine mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
isoleucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit DLD82_RS11815
isoleucine pccB: propionyl-CoA carboxylase, beta subunit
L-lactate lctO: L-lactate oxidase or 2-monooxygenase
L-lactate SfMCT: L-lactate transporter SfMCT DLD82_RS15130
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose glk: glucokinase DLD82_RS03875
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
leucine leuT: L-leucine:Na+ symporter LeuT
leucine liuA: isovaleryl-CoA dehydrogenase
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit DLD82_RS11815
leucine liuC: 3-methylglutaconyl-CoA hydratase
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) DLD82_RS12415
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase DLD82_RS06180
lysine lysN: 2-aminoadipate transaminase DLD82_RS06230 DLD82_RS14280
lysine lysP: L-lysine:H+ symporter LysP DLD82_RS12965
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase
maltose glk: glucokinase DLD82_RS03875
maltose SemiSWEET: Sugar transporter SemiSWEET DLD82_RS08180
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 DLD82_RS00165
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 DLD82_RS12415 DLD82_RS16650
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) DLD82_RS03565
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
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase
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 DLD82_RS12965
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 proY: proline:H+ symporter DLD82_RS12965
proline put1: proline dehydrogenase
proline putA: L-glutamate 5-semialdeyde dehydrogenase DLD82_RS12415 DLD82_RS16650
propionate epi: methylmalonyl-CoA epimerase
propionate mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
propionate pccA: propionyl-CoA carboxylase, alpha subunit DLD82_RS11815
propionate pccB: propionyl-CoA carboxylase, beta subunit
propionate prpE: propionyl-CoA synthetase DLD82_RS02360 DLD82_RS15135
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabD: succinate semialdehyde dehydrogenase DLD82_RS12415 DLD82_RS16650
putrescine gabT: gamma-aminobutyrate transaminase DLD82_RS06180
putrescine patA: putrescine aminotransferase (PatA/SpuC) DLD82_RS06180 DLD82_RS13760
putrescine patD: gamma-aminobutyraldehyde dehydrogenase DLD82_RS12415 DLD82_RS16650
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate ybdD: small subunit of pyruvate transporter (YbdD)
rhamnose aldA: lactaldehyde dehydrogenase DLD82_RS16650 DLD82_RS12415
rhamnose rhaA: L-rhamnose isomerase
rhamnose rhaB: L-rhamnulokinase
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 snatA: L-serine transporter DLD82_RS08715 DLD82_RS14930
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase
sucrose ams: sucrose hydrolase (invertase)
sucrose glk: glucokinase DLD82_RS03875
sucrose SemiSWEET: Sugar transporter SemiSWEET DLD82_RS08180
threonine aldA: lactaldehyde dehydrogenase DLD82_RS16650 DLD82_RS12415
threonine lctO: L-lactate oxidase or 2-monooxygenase
threonine snatA: L-threonine transporter snatA DLD82_RS08715 DLD82_RS14930
threonine tdh: L-threonine 3-dehydrogenase DLD82_RS02330
threonine tynA: aminoacetone oxidase
threonine yvgN: methylglyoxal reductase (NADPH-dependent)
thymidine adh: acetaldehyde dehydrogenase (not acylating) DLD82_RS12415 DLD82_RS16650
thymidine deoA: thymidine phosphorylase DeoA DLD82_RS10000
thymidine deoB: phosphopentomutase DLD82_RS10695 DLD82_RS03580
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
trehalose glk: glucokinase DLD82_RS03875
trehalose SemiSWEET: Sugar transporter SemiSWEET DLD82_RS08180
trehalose treF: trehalase
tryptophan aroP: tryptophan:H+ symporter AroP DLD82_RS12965
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP) DLD82_RS12965
tyrosine fahA: fumarylacetoacetate hydrolase
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase
valine Bap2: L-valine permease Bap2
valine bch: 3-hydroxyisobutyryl-CoA hydrolase
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase
valine epi: methylmalonyl-CoA epimerase
valine mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
valine mmsA: methylmalonate-semialdehyde dehydrogenase DLD82_RS12415 DLD82_RS16650
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
valine pccA: propionyl-CoA carboxylase, alpha subunit DLD82_RS11815
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 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