GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Caldicellulosiruptor kronotskyensis 2002

Found 162 low-confidence and 33 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)
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 actP: cation/acetate symporter ActP
alanine cycA: L-alanine symporter CycA
arabinose araA: L-arabinose isomerase
arabinose araE: L-arabinose:H+ symporter
arginine gabD: succinate semialdehyde dehydrogenase
arginine gabT: gamma-aminobutyrate transaminase CALKRO_RS04390
arginine patA: putrescine aminotransferase (PatA/SpuC) CALKRO_RS04390 CALKRO_RS07580
arginine patD: gamma-aminobutyraldehyde dehydrogenase
arginine rocE: L-arginine permease
asparagine ans: asparaginase
asparagine glt: aspartate:proton symporter Glt
aspartate glt: aspartate:proton symporter Glt
cellobiose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component CALKRO_RS03800 CALKRO_RS01370
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 CALKRO_RS03795
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 CALKRO_RS03795
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 CALKRO_RS07580 CALKRO_RS04390
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase CALKRO_RS02590 CALKRO_RS00720
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
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating)
deoxyinosine bmpA: deoxyinosine ABC transporter, substrate-binding component CALKRO_RS04655
deoxyinosine nupB: deoxyinosine ABC transporter, permease component 1 CALKRO_RS04670
deoxyinosine nupC': deoxyinosine ABC transporter, permease component 2 CALKRO_RS04675
deoxyribonate atoB: acetyl-CoA C-acetyltransferase
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase CALKRO_RS09770 CALKRO_RS07790
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose adh: acetaldehyde dehydrogenase (not acylating)
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
ethanol adh: acetaldehyde dehydrogenase (not acylating)
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) CALKRO_RS02845 CALKRO_RS02020
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components CALKRO_RS12210
fucose aldA: lactaldehyde dehydrogenase
fucose fucA: L-fuculose-phosphate aldolase FucA CALKRO_RS01405 CALKRO_RS02110
fucose fucI: L-fucose isomerase FucI
fucose fucP: L-fucose:H+ symporter FucP
fucose fucU: L-fucose mutarotase FucU
fumarate dctA: fumarate:H+ symporter DctA
galactose galP: galactose:H+ symporter GalP
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase CALKRO_RS08760
galactose pgmA: alpha-phosphoglucomutase CALKRO_RS00500 CALKRO_RS04810
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate uxaA: D-altronate dehydratase
galacturonate uxaB: tagaturonate reductase
gluconate edd: phosphogluconate dehydratase CALKRO_RS09920
gluconate gntK: D-gluconate kinase CALKRO_RS10450
gluconate gntT: gluconate:H+ symporter GntT
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) CALKRO_RS00485 CALKRO_RS01130
glucosamine SLC2A2: glucosamine transporter SLC2A2
glucose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glutamate gltS: L-glutamate:Na+ symporter GltS
glycerol glpF: glycerol facilitator glpF
glycerol glpK: glycerol kinase CALKRO_RS00705 CALKRO_RS10450
glycerol glpO: glycerol 3-phosphate oxidase CALKRO_RS08800
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
histidine LAT2: L-histidine transporter CALKRO_RS09790
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase CALKRO_RS07430
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase
isoleucine fadA: 2-methylacetoacetyl-CoA thiolase
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase CALKRO_RS07790 CALKRO_RS00745
isoleucine livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) CALKRO_RS06675 CALKRO_RS10675
isoleucine mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit
isoleucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
L-lactate SfMCT: L-lactate transporter SfMCT CALKRO_RS07675
L-malate mleP: malate permease MleP CALKRO_RS01110
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase CALKRO_RS08760
lactose glk: glucokinase CALKRO_RS10530 CALKRO_RS10160
lactose lacP: lactose permease LacP
lactose pgmA: alpha-phosphoglucomutase CALKRO_RS00500 CALKRO_RS04810
leucine atoB: acetyl-CoA C-acetyltransferase
leucine liuA: isovaleryl-CoA dehydrogenase CALKRO_RS07430
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit
leucine liuC: 3-methylglutaconyl-CoA hydratase
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit CALKRO_RS07010
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) CALKRO_RS06675 CALKRO_RS10675
leucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
lysine amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd)
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase
lysine lysN: 2-aminoadipate transaminase CALKRO_RS07930 CALKRO_RS06575
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase
maltose glk: glucokinase CALKRO_RS10530 CALKRO_RS10160
mannitol PLT5: polyol transporter PLT5
mannitol scrK: fructokinase CALKRO_RS02610 CALKRO_RS10530
mannose manA: mannose-6-phosphate isomerase CALKRO_RS10150 CALKRO_RS06290
mannose manP: mannose PTS system, EII-CBA components CALKRO_RS12210
myoinositol iolG: myo-inositol 2-dehydrogenase
myoinositol iolM: 2-inosose 4-dehydrogenase CALKRO_RS10605 CALKRO_RS02950
myoinositol iolN: 2,4-diketo-inositol hydratase
myoinositol iolO: 5-dehydro-L-gluconate epimerase
myoinositol iolT: myo-inositol:H+ symporter
myoinositol uxaE: D-tagaturonate epimerase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) CALKRO_RS00485 CALKRO_RS01130
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 CALKRO_RS07790 CALKRO_RS09770
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
phenylalanine atoB: acetyl-CoA C-acetyltransferase
phenylalanine fahA: fumarylacetoacetate hydrolase CALKRO_RS09245
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
proline put1: proline dehydrogenase CALKRO_RS08795
proline putA: L-glutamate 5-semialdeyde dehydrogenase
propionate mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
propionate pccA: propionyl-CoA carboxylase, alpha subunit
propionate prpE: propionyl-CoA synthetase CALKRO_RS09395
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabD: succinate semialdehyde dehydrogenase
putrescine gabT: gamma-aminobutyrate transaminase CALKRO_RS04390
putrescine patA: putrescine aminotransferase (PatA/SpuC) CALKRO_RS04390 CALKRO_RS07580
putrescine patD: gamma-aminobutyraldehyde dehydrogenase
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate ybdD: small subunit of pyruvate transporter (YbdD)
rhamnose aldA: lactaldehyde dehydrogenase
rhamnose rhaB: L-rhamnulokinase CALKRO_RS09135
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 sdaB: L-serine ammonia-lyase
serine serP: L-serine permease SerP
sorbitol mtlA: PTS system for polyols, EII-CBA components
succinate sdc: succinate:Na+ symporter Sdc
sucrose ams: sucrose hydrolase (invertase) CALKRO_RS12150
sucrose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components CALKRO_RS12210
threonine adh: acetaldehyde dehydrogenase (not acylating)
threonine gcvH: glycine cleavage system, H component (lipoyl protein) CALKRO_RS04120
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase)
threonine gcvT: glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase)
threonine ltaE: L-threonine aldolase CALKRO_RS08255
threonine tdcC: L-threonine:H+ symporter TdcC
thymidine adh: acetaldehyde dehydrogenase (not acylating)
thymidine nupG: thymidine permease NupG/XapB
trehalose glk: glucokinase CALKRO_RS10530 CALKRO_RS10160
trehalose thuE: trehalose ABC transporter, substrate-binding component ThuE CALKRO_RS01635
trehalose thuK: trehalose ABC transporter, ATPase component ThuK CALKRO_RS04555 CALKRO_RS07665
tryptophan tnaA: tryptophanase
tryptophan trpP: energy-coupling factor transporter, tryptophan-specific (S) component TrpP
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine atoB: acetyl-CoA C-acetyltransferase
tyrosine fahA: fumarylacetoacetate hydrolase CALKRO_RS09245
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase CALKRO_RS07430
valine bch: 3-hydroxyisobutyryl-CoA hydrolase
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) CALKRO_RS06675 CALKRO_RS10675
valine mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
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
xylitol PLT5: xylitol:H+ symporter PLT5

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