GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Calditerrivibrio nitroreducens DSM 19672

Found 166 low-confidence and 42 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate Psest_0084: 2-oxoglutarate TRAP transporter, fused 4TM/12TM components CALNI_RS02700 CALNI_RS01945
2-oxoglutarate Psest_0085: 2-oxoglutarate TRAP transporter, solute receptor component CALNI_RS02695 CALNI_RS01940
4-hydroxybenzoate adh: acetaldehyde dehydrogenase (not acylating) CALNI_RS00150
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase CALNI_RS02455 CALNI_RS03360
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
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter
arginine put1: proline dehydrogenase CALNI_RS04420
arginine rocD: ornithine aminotransferase CALNI_RS07435 CALNI_RS03705
arginine rocE: L-arginine permease
arginine rocF: arginase
asparagine ans: asparaginase
asparagine dauA: dicarboxylic acid transporter DauA CALNI_RS10365 CALNI_RS08970
aspartate dauA: dicarboxylic acid transporter DauA CALNI_RS10365 CALNI_RS08970
cellobiose cbp: cellobiose phosphorylase
cellobiose cdt: cellobiose transporter cdt-1/cdt-2
cellobiose glk: glucokinase CALNI_RS05430
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component CALNI_RS09160 CALNI_RS09555
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 CALNI_RS09165
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 CALNI_RS09165
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline citrullinase: putative citrullinase CALNI_RS07315
citrulline put1: proline dehydrogenase CALNI_RS04420
citrulline rocD: ornithine aminotransferase CALNI_RS07435 CALNI_RS03705
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase CALNI_RS06795 CALNI_RS05660
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 CALNI_RS00005
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) CALNI_RS00150
deoxyinosine deoB: phosphopentomutase CALNI_RS07265
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase CALNI_RS06140
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) CALNI_RS00150
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
ethanol adh: acetaldehyde dehydrogenase (not acylating) CALNI_RS00150
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) CALNI_RS06140 CALNI_RS06835
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 CALNI_RS07450
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 dauA: fumarate transporter DauA CALNI_RS10365 CALNI_RS08970
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) CALNI_RS02050
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
glucuronate garL: 5-dehydro-4-deoxy-D-glucarate aldolase
glucuronate garR: tartronate semialdehyde reductase
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate udh: D-glucuronate dehydrogenase
glutamate gdhA: glutamate dehydrogenase, NAD-dependent CALNI_RS03655
glutamate gltS: L-glutamate:Na+ symporter GltS
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric)
glycerol glpF: glycerol facilitator glpF
glycerol glpK: glycerol kinase
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
histidine permease: L-histidine permease
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase CALNI_RS01695 CALNI_RS01740
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase CALNI_RS06140 CALNI_RS07770
isoleucine livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) CALNI_RS03490
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit CALNI_RS02830 CALNI_RS01155
isoleucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC CALNI_RS01390
L-lactate L-LDH: L-lactate dehydrogenase CALNI_RS02315
L-lactate SfMCT: L-lactate transporter SfMCT CALNI_RS01295
L-malate dctQ: L-malate TRAP tranpsorter, small permease component DctQ CALNI_RS08605
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose glk: glucokinase CALNI_RS05430
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
leucine liuA: isovaleryl-CoA dehydrogenase CALNI_RS01695 CALNI_RS01740
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit CALNI_RS02830 CALNI_RS02480
leucine liuC: 3-methylglutaconyl-CoA hydratase CALNI_RS01690 CALNI_RS06640
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit CALNI_RS02825
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) CALNI_RS03490
leucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC CALNI_RS01390
lysine davA: 5-aminovaleramidase
lysine davB: L-lysine 2-monooxygenase
lysine davD: glutarate semialdehyde dehydrogenase CALNI_RS00150
lysine davT: 5-aminovalerate aminotransferase CALNI_RS03705 CALNI_RS07435
lysine gcdG: succinyl-CoA:glutarate CoA-transferase
lysine gcdH: glutaryl-CoA dehydrogenase CALNI_RS01695 CALNI_RS01740
lysine lysP: L-lysine:H+ symporter LysP
maltose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
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
myoinositol iolE: scyllo-inosose 2-dehydratase
myoinositol iolG: myo-inositol 2-dehydrogenase
myoinositol iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase CALNI_RS09785
myoinositol iolT: myo-inositol:H+ symporter
myoinositol mmsA: malonate-semialdehyde dehydrogenase CALNI_RS00150
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) CALNI_RS02050
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 CALNI_RS01690 CALNI_RS06640
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase CALNI_RS01690
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase CALNI_RS01735 CALNI_RS06825
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase CALNI_RS01735 CALNI_RS06825
phenylacetate paaZ1: oxepin-CoA hydrolase CALNI_RS01690
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylacetate ppa: phenylacetate permease ppa CALNI_RS03840
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
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 CALNI_RS01690 CALNI_RS06640
phenylalanine paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase CALNI_RS01690
phenylalanine paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase CALNI_RS01735 CALNI_RS06825
phenylalanine paaJ2: 3-oxoadipyl-CoA thiolase CALNI_RS01735 CALNI_RS06825
phenylalanine paaZ1: oxepin-CoA hydrolase CALNI_RS01690
phenylalanine paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
proline proY: proline:H+ symporter
proline put1: proline dehydrogenase CALNI_RS04420
propionate mctC: propionate:H+ symporter CALNI_RS03840
propionate pccA: propionyl-CoA carboxylase, alpha subunit CALNI_RS02830 CALNI_RS01155
propionate prpE: propionyl-CoA synthetase CALNI_RS01435 CALNI_RS04325
putrescine gabD: succinate semialdehyde dehydrogenase CALNI_RS00150
putrescine gabT: gamma-aminobutyrate transaminase CALNI_RS07435 CALNI_RS03705
putrescine patA: putrescine aminotransferase (PatA/SpuC) CALNI_RS07435 CALNI_RS03705
putrescine patD: gamma-aminobutyraldehyde dehydrogenase CALNI_RS00150
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate dctQ: pyruvate TRAP transporter, small permease component CALNI_RS00315 CALNI_RS06810
rhamnose LRA1: L-rhamnofuranose dehydrogenase CALNI_RS06140 CALNI_RS06835
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase
rhamnose LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsK: ribokinase
ribose rbsU: probable D-ribose transporter RbsU
serine serP: L-serine permease SerP
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase CALNI_RS06835 CALNI_RS07770
sucrose scrK: fructokinase
sucrose SUS: sucrose synthase
sucrose sut: sucrose:proton symporter SUT/SUC
threonine pccA: propionyl-CoA carboxylase, alpha subunit CALNI_RS02830 CALNI_RS01155
threonine phtA: L-threonine uptake permease PhtA CALNI_RS10225
threonine tdcE: 2-ketobutyrate formate-lyase
thymidine adh: acetaldehyde dehydrogenase (not acylating) CALNI_RS00150
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase CALNI_RS07265
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
trehalose glk: glucokinase CALNI_RS05430
trehalose PsTP: trehalose phosphorylase
trehalose TRET1: facilitated trehalose transporter Tret1
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine fahA: fumarylacetoacetate hydrolase CALNI_RS00220
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase CALNI_RS01695 CALNI_RS01740
valine bch: 3-hydroxyisobutyryl-CoA hydrolase
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) CALNI_RS03490
valine mmsA: methylmalonate-semialdehyde dehydrogenase CALNI_RS00150
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine pccA: propionyl-CoA carboxylase, alpha subunit CALNI_RS02830 CALNI_RS01155
valine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC CALNI_RS01390
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