GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Clostridium tyrobutyricum FAM22553

Found 142 low-confidence and 50 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) PN53_RS14860
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 dctA: organic acid/proton symporter DctA PN53_RS15075 PN53_RS12855
arabinose araE: L-arabinose:H+ symporter PN53_RS08915 PN53_RS09365
arginine davD: glutarate semialdehyde dehydrogenase
arginine gcdG: succinyl-CoA:glutarate CoA-transferase
arginine gcdH: glutaryl-CoA dehydrogenase PN53_RS07375 PN53_RS12270
arginine rocD: ornithine aminotransferase PN53_RS11750 PN53_RS10390
arginine rocE: L-arginine permease PN53_RS14530 PN53_RS11460
arginine rocF: arginase
asparagine ans: asparaginase PN53_RS07165
cellobiose bgl: cellobiase
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component PN53_RS11775 PN53_RS12180
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 PN53_RS12175 PN53_RS11785
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 PN53_RS09725
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component PN53_RS15160
citrulline arcC: carbamate kinase
citrulline davD: glutarate semialdehyde dehydrogenase
citrulline gcdG: succinyl-CoA:glutarate CoA-transferase
citrulline gcdH: glutaryl-CoA dehydrogenase PN53_RS07375 PN53_RS12270
citrulline rocD: ornithine aminotransferase PN53_RS11750 PN53_RS10390
D-alanine dadA: D-alanine dehydrogenase
D-lactate lctP: D-lactate:H+ symporter LctP or LidP PN53_RS11085
D-serine dsdA: D-serine ammonia-lyase PN53_RS07185
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) PN53_RS14860
deoxyinosine bmpA: deoxyinosine ABC transporter, substrate-binding component
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine nupB: deoxyinosine ABC transporter, permease component 1 PN53_RS09480
deoxyinosine nupC': deoxyinosine ABC transporter, permease component 2 PN53_RS09485
deoxyribonate aacS: acetoacetyl-CoA synthetase PN53_RS14470
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase PN53_RS02590 PN53_RS01450
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter PN53_RS12035
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose adh: acetaldehyde dehydrogenase (not acylating) PN53_RS14860
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoP: deoxyribose transporter
ethanol adh: acetaldehyde dehydrogenase (not acylating) PN53_RS14860
fucose aldA: lactaldehyde dehydrogenase
fucose fucA: L-fuculose-phosphate aldolase FucA PN53_RS04230
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 PN53_RS15075 PN53_RS12855
galactose galK: galactokinase (-1-phosphate forming)
galactose galP: galactose:H+ symporter GalP PN53_RS09365 PN53_RS08915
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 PN53_RS12045
gluconate gntT: gluconate:H+ symporter GntT PN53_RS01965
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) PN53_RS08955
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 PN53_RS03535
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate udh: D-glucuronate dehydrogenase
glycerol glpO: glycerol 3-phosphate oxidase PN53_RS01400 PN53_RS02695
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
histidine PA5503: L-histidine ABC transporter, ATPase component PN53_RS07200 PN53_RS01545
histidine PA5504: L-histidine ABC transporter, permease component PN53_RS07205 PN53_RS01540
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase PN53_RS02950 PN53_RS02775
isoleucine Bap2: L-isoleucine permease Bap2 PN53_RS14530 PN53_RS02235
isoleucine dddA: 3-hydroxypropionate dehydrogenase
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase PN53_RS14840 PN53_RS02770
isoleucine hpcD: 3-hydroxypropionyl-CoA dehydratase PN53_RS02770 PN53_RS14840
isoleucine iolA: malonate semialdehyde dehydrogenase (CoA-acylating)
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase PN53_RS09975
isoleucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
L-lactate lctP: L-lactate:H+ symporter LctP or LidP PN53_RS11085
L-malate dctA: L-malate:H+ symporter DctA PN53_RS15075 PN53_RS12855
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 PN53_RS14470
leucine leuT: L-leucine:Na+ symporter LeuT
leucine liuA: isovaleryl-CoA dehydrogenase PN53_RS02775 PN53_RS02950
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit PN53_RS02725 PN53_RS09955
leucine liuC: 3-methylglutaconyl-CoA hydratase PN53_RS14840 PN53_RS02770
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 davD: glutarate semialdehyde dehydrogenase
lysine gcdG: succinyl-CoA:glutarate CoA-transferase
lysine gcdH: glutaryl-CoA dehydrogenase PN53_RS07375 PN53_RS12270
maltose susB: alpha-glucosidase (maltase) PN53_RS09895
mannitol mtlD: mannitol-1-phosphate 5-dehydrogenase PN53_RS08975
mannose manA: mannose-6-phosphate isomerase PN53_RS02025 PN53_RS12940
mannose manP: mannose PTS system, EII-CBA components PN53_RS13930
myoinositol iolB: 5-deoxy-D-glucuronate isomerase
myoinositol iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase PN53_RS07985 PN53_RS09000
myoinositol mmsA: malonate-semialdehyde dehydrogenase
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) PN53_RS08955
NAG nagPcb: N-acetylglucosamine phosphotransferase system, EII-CB component NagP PN53_RS12165
phenylacetate H281DRAFT_04042: phenylacetate:H+ symporter PN53_RS02235 PN53_RS11460
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 PN53_RS02770 PN53_RS14840
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase PN53_RS02770 PN53_RS14840
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase PN53_RS07740 PN53_RS14215
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase PN53_RS07740 PN53_RS14215
phenylacetate paaK: phenylacetate-CoA ligase
phenylacetate paaZ1: oxepin-CoA hydrolase
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP PN53_RS02235 PN53_RS11460
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 PN53_RS02770 PN53_RS14840
phenylalanine paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase PN53_RS02770 PN53_RS14840
phenylalanine paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase PN53_RS07740 PN53_RS14215
phenylalanine paaJ2: 3-oxoadipyl-CoA thiolase PN53_RS07740 PN53_RS14215
phenylalanine paaZ1: oxepin-CoA hydrolase
phenylalanine paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
proline davD: glutarate semialdehyde dehydrogenase
proline gcdG: succinyl-CoA:glutarate CoA-transferase
proline gcdH: glutaryl-CoA dehydrogenase PN53_RS07375 PN53_RS12270
proline opuBA: proline ABC transporter, ATPase component OpuBA/BusAA PN53_RS07140 PN53_RS07005
propionate dddA: 3-hydroxypropionate dehydrogenase
propionate hpcD: 3-hydroxypropionyl-CoA dehydratase PN53_RS02770 PN53_RS14840
propionate iolA: malonate semialdehyde dehydrogenase (CoA-acylating)
propionate prpE: propionyl-CoA synthetase
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabD: succinate semialdehyde dehydrogenase PN53_RS13140
putrescine gabT: gamma-aminobutyrate transaminase PN53_RS10390 PN53_RS11750
putrescine patA: putrescine aminotransferase (PatA/SpuC) PN53_RS06660 PN53_RS02345
putrescine patD: gamma-aminobutyraldehyde dehydrogenase
putrescine potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) PN53_RS11130 PN53_RS03190
pyruvate ybdD: small subunit of pyruvate transporter (YbdD)
rhamnose LRA1: L-rhamnofuranose dehydrogenase PN53_RS09975 PN53_RS01450
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase
rhamnose LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase PN53_RS14895 PN53_RS09975
rhamnose LRA6: 2,4-diketo-3-deoxyrhamnonate hydrolase PN53_RS06785
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsU: probable D-ribose transporter RbsU
serine serP: L-serine permease SerP PN53_RS02235 PN53_RS11460
sorbitol mtlA: PTS system for polyols, EII-CBA components PN53_RS08960
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase PN53_RS05335 PN53_RS09975
succinate dctA: succinate:H+ symporter DctA PN53_RS15075 PN53_RS12855
sucrose ams: sucrose hydrolase (invertase)
threonine dddA: 3-hydroxypropionate dehydrogenase
threonine hpcD: 3-hydroxypropionyl-CoA dehydratase PN53_RS02770 PN53_RS14840
threonine iolA: malonate semialdehyde dehydrogenase (CoA-acylating)
threonine RR42_RS28305: L-threonine:H+ symporter PN53_RS02235 PN53_RS11460
threonine tdcB: L-threonine dehydratase PN53_RS07185
thymidine adh: acetaldehyde dehydrogenase (not acylating) PN53_RS14860
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
trehalose treF: trehalase
tryptophan tnaA: tryptophanase
tyrosine aacS: acetoacetyl-CoA synthetase PN53_RS14470
tyrosine aroP: L-tyrosine transporter (AroP/FywP) PN53_RS02235 PN53_RS11460
tyrosine fahA: fumarylacetoacetate hydrolase PN53_RS06785
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase PN53_RS02950 PN53_RS07375
valine Bap2: L-valine permease Bap2 PN53_RS14530 PN53_RS02235
valine bch: 3-hydroxyisobutyryl-CoA hydrolase
valine dddA: 3-hydroxypropionate dehydrogenase
valine hpcD: 3-hydroxypropionyl-CoA dehydratase PN53_RS02770 PN53_RS14840
valine iolA: malonate semialdehyde dehydrogenase (CoA-acylating)
valine mmsA: methylmalonate-semialdehyde dehydrogenase
valine mmsB: 3-hydroxyisobutyrate dehydrogenase PN53_RS13140
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
xylitol EIIA-Axl: xylitol PTS, enzyme IIA (EIIA-Axl) PN53_RS11975
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase PN53_RS14895
xylose xylA: xylose isomerase

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