GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Alkalitalea saponilacus SC/BZ-SP2

Found 123 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
4-hydroxybenzoate adh: acetaldehyde dehydrogenase (not acylating) CDL62_RS06795
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
arginine put1: proline dehydrogenase CDL62_RS10620
arginine rocE: L-arginine permease
arginine rocF: arginase
asparagine glt: aspartate:proton symporter Glt CDL62_RS18030
aspartate glt: aspartate:proton symporter Glt CDL62_RS18030
citrate SLC13A5: citrate:Na+ symporter
citrulline arcC: carbamate kinase
citrulline PS417_17590: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline PS417_17595: ABC transporter for L-Citrulline, permease component 1
citrulline PS417_17600: ABC transporter for L-Citrulline, permease component 2
citrulline PS417_17605: ABC transporter for L-Citrulline, ATPase component CDL62_RS08575 CDL62_RS01045
citrulline put1: proline dehydrogenase CDL62_RS10620
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 CDL62_RS06025 CDL62_RS04670
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) CDL62_RS06795
deoxyinosine deoB: phosphopentomutase CDL62_RS17490
deoxyinosine nupC: deoxyinosine:H+ symporter NupC CDL62_RS07275
deoxyribonate atoB: acetyl-CoA C-acetyltransferase
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase CDL62_RS16365 CDL62_RS11830
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) CDL62_RS06795
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter CDL62_RS06355
ethanol adh: acetaldehyde dehydrogenase (not acylating) CDL62_RS06795
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) CDL62_RS16360 CDL62_RS14220
fructose 1pfk: 1-phosphofructokinase
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
fucose aldA: lactaldehyde dehydrogenase CDL62_RS06795 CDL62_RS11020
fucose fucA: L-fuculose-phosphate aldolase FucA
fucose fucI: L-fucose isomerase FucI
fucose fucK: L-fuculose kinase FucK
fumarate sdcL: fumarate:Na+ symporter SdcL CDL62_RS08880
galactose galK: galactokinase (-1-phosphate forming) CDL62_RS06460
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galacturonate exuT: D-galacturonate transporter ExuT CDL62_RS09555
gluconate gntK: D-gluconate kinase
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE)
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT CDL62_RS09555
glucuronate uxuB: D-mannonate dehydrogenase
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 LAT2: L-histidine transporter CDL62_RS00840
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase CDL62_RS00155 CDL62_RS14380
isoleucine Bap2: L-isoleucine permease Bap2
isoleucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit CDL62_RS16610
isoleucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component CDL62_RS16615 CDL62_RS13425
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase CDL62_RS12095
isoleucine fadA: 2-methylacetoacetyl-CoA thiolase CDL62_RS00365
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase CDL62_RS16365 CDL62_RS01185
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit CDL62_RS16100 CDL62_RS00145
L-lactate L-LDH: L-lactate dehydrogenase CDL62_RS03995
L-lactate SfMCT: L-lactate transporter SfMCT CDL62_RS09270
L-malate sdlC: L-malate:Na+ symporter SdlC CDL62_RS08880
lactose galK: galactokinase (-1-phosphate forming) CDL62_RS06460
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose lacP: lactose permease LacP
leucine atoB: acetyl-CoA C-acetyltransferase
leucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit CDL62_RS16610
leucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component CDL62_RS16615 CDL62_RS13425
leucine leuT: L-leucine:Na+ symporter LeuT
leucine liuA: isovaleryl-CoA dehydrogenase CDL62_RS00155 CDL62_RS14380
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit CDL62_RS16100 CDL62_RS00145
leucine liuC: 3-methylglutaconyl-CoA hydratase CDL62_RS00140 CDL62_RS12095
leucine liuE: hydroxymethylglutaryl-CoA lyase
lysine amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd)
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase CDL62_RS00260
lysine lysN: 2-aminoadipate transaminase CDL62_RS05340 CDL62_RS00260
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase CDL62_RS10685
mannitol mtlA: mannitol phosphotransferase system, EII-CBA components
mannose manA: mannose-6-phosphate isomerase CDL62_RS05240 CDL62_RS09745
mannose STP6: mannose:H+ symporter CDL62_RS00400 CDL62_RS11760
myoinositol iolG: myo-inositol 2-dehydrogenase
myoinositol iolM: 2-inosose 4-dehydrogenase
myoinositol iolN: 2,4-diketo-inositol hydratase
myoinositol iolO: 5-dehydro-L-gluconate epimerase
myoinositol iolT: myo-inositol:H+ symporter CDL62_RS00400 CDL62_RS11760
myoinositol uxaE: D-tagaturonate epimerase
myoinositol uxuB: D-mannonate dehydrogenase
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagP: N-acetylglucosamine transporter NagP CDL62_RS12465
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 CDL62_RS12095
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase CDL62_RS16320 CDL62_RS16365
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
phenylalanine hmgA: homogentisate dioxygenase
phenylalanine HPD: 4-hydroxyphenylpyruvate dioxygenase
phenylalanine maiA: maleylacetoacetate isomerase
phenylalanine PAH: phenylalanine 4-monooxygenase
phenylalanine QDPR: 6,7-dihydropteridine reductase CDL62_RS17595
proline ectP: proline transporter EctP CDL62_RS12440
proline put1: proline dehydrogenase CDL62_RS10620
propionate pccA: propionyl-CoA carboxylase, alpha subunit CDL62_RS16100 CDL62_RS00145
propionate prpE: propionyl-CoA synthetase CDL62_RS17710
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabT: gamma-aminobutyrate transaminase CDL62_RS05610 CDL62_RS00260
putrescine patA: putrescine aminotransferase (PatA/SpuC) CDL62_RS17645 CDL62_RS05610
putrescine patD: gamma-aminobutyraldehyde dehydrogenase CDL62_RS06795 CDL62_RS11020
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose aldA: lactaldehyde dehydrogenase CDL62_RS06795 CDL62_RS11020
rhamnose rhaD: rhamnulose 1-phosphate aldolase
ribose rbsK: ribokinase
ribose rbsU: probable D-ribose transporter RbsU
serine sdaB: L-serine ammonia-lyase CDL62_RS06025 CDL62_RS04670
serine serP: L-serine permease SerP
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase CDL62_RS02165 CDL62_RS16365
succinate sdc: succinate:Na+ symporter Sdc CDL62_RS08880
sucrose ams: sucrose hydrolase (invertase)
threonine adh: acetaldehyde dehydrogenase (not acylating) CDL62_RS06795
threonine tdcC: L-threonine:H+ symporter TdcC
thymidine adh: acetaldehyde dehydrogenase (not acylating) CDL62_RS06795
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase CDL62_RS17490
thymidine nupC: thymidine permease NupC CDL62_RS07275
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase CDL62_RS16620
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 CDL62_RS00155 CDL62_RS14380
valine Bap2: L-valine permease Bap2
valine bch: 3-hydroxyisobutyryl-CoA hydrolase
valine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit CDL62_RS16610
valine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component CDL62_RS16615 CDL62_RS13425
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase CDL62_RS12095
valine mmsA: methylmalonate-semialdehyde dehydrogenase CDL62_RS06795
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine pccA: propionyl-CoA carboxylase, alpha subunit CDL62_RS16100 CDL62_RS00145
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase CDL62_RS14220
xylose xylB: xylulokinase

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