GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Corynebacterium lactis RW2-5

Found 122 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 CLAC_RS01150
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
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter CLAC_RS02995
arginine gabT: gamma-aminobutyrate transaminase CLAC_RS11005 CLAC_RS06935
arginine odc: L-ornithine decarboxylase
arginine patA: putrescine aminotransferase (PatA/SpuC) CLAC_RS06935 CLAC_RS11005
arginine patD: gamma-aminobutyraldehyde dehydrogenase CLAC_RS11495 CLAC_RS08280
arginine rocE: L-arginine permease CLAC_RS06165 CLAC_RS11000
arginine rocF: arginase
asparagine ans: asparaginase CLAC_RS07665 CLAC_RS08555
aspartate glt: aspartate:proton symporter Glt CLAC_RS04310 CLAC_RS08200
cellobiose MFS-glucose: glucose transporter, MFS superfamily CLAC_RS02995
citrate SLC13A5: citrate:Na+ symporter CLAC_RS05595
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component CLAC_RS07365 CLAC_RS10250
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 CLAC_RS07360
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 CLAC_RS07360
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline arcC: carbamate kinase
citrulline gabT: gamma-aminobutyrate transaminase CLAC_RS11005 CLAC_RS06935
citrulline odc: L-ornithine decarboxylase
citrulline patA: putrescine aminotransferase (PatA/SpuC) CLAC_RS06935 CLAC_RS11005
citrulline patD: gamma-aminobutyraldehyde dehydrogenase CLAC_RS11495 CLAC_RS08280
D-alanine cycA: D-alanine:H+ symporter CycA CLAC_RS03880 CLAC_RS06165
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase CLAC_RS08550 CLAC_RS04725
D-lactate lctP: D-lactate:H+ symporter LctP or LidP CLAC_RS00055
D-serine cycA: D-serine:H+ symporter CycA CLAC_RS03880 CLAC_RS06165
D-serine dsdA: D-serine ammonia-lyase CLAC_RS07615
deoxyinosine deoB: phosphopentomutase CLAC_RS00435 CLAC_RS02175
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase CLAC_RS04775 CLAC_RS11150
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 deoK: deoxyribokinase CLAC_RS09755 CLAC_RS08220
deoxyribose deoP: deoxyribose transporter
fructose 1pfk: 1-phosphofructokinase CLAC_RS05470
fructose fba: fructose 1,6-bisphosphate aldolase CLAC_RS10975
fucose aldA: lactaldehyde dehydrogenase CLAC_RS11495 CLAC_RS08280
fucose fucA: L-fuculose-phosphate aldolase FucA CLAC_RS08545
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 galP: galactose:H+ symporter GalP CLAC_RS02995
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate gci: D-galactarolactone cycloisomerase
galacturonate gli: D-galactarolactone isomerase
galacturonate kdgD: 5-dehydro-4-deoxyglucarate dehydratase CLAC_RS05330
galacturonate udh: D-galacturonate dehydrogenase CLAC_RS01160
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) CLAC_RS02230
glucose MFS-glucose: glucose transporter, MFS superfamily CLAC_RS02995
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate kdgD: 5-dehydro-4-deoxyglucarate dehydratase CLAC_RS05330
glucuronate udh: D-glucuronate dehydrogenase CLAC_RS01160
glutamate gltP: L-glutamate:cation symporter GltP/GltT CLAC_RS08200 CLAC_RS04310
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) CLAC_RS11745 CLAC_RS08475
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
isoleucine brnQ: L-isoleucine:cation symporter BrnQ/BraZ/BraB CLAC_RS08055
isoleucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit CLAC_RS09420 CLAC_RS02580
L-lactate lctP: L-lactate:H+ symporter LctP or LidP CLAC_RS00055
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric) CLAC_RS06770
leucine brnQ: L-leucine:Na+ symporter BrnQ/BraB CLAC_RS08055
leucine liuC: 3-methylglutaconyl-CoA hydratase CLAC_RS09725 CLAC_RS11130
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 CLAC_RS02530 CLAC_RS11495
lysine gcdG: succinyl-CoA:glutarate CoA-transferase CLAC_RS11020
maltose musI: maltose ABC transporter, uncharacterized membrane component MusI CLAC_RS08225
maltose susB: alpha-glucosidase (maltase) CLAC_RS08450
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
myoinositol iolT: myo-inositol:H+ symporter CLAC_RS02995
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) CLAC_RS02230
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 CLAC_RS11130 CLAC_RS08700
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase CLAC_RS08700 CLAC_RS11130
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase CLAC_RS11430 CLAC_RS02615
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase CLAC_RS11430 CLAC_RS02615
phenylacetate paaK: phenylacetate-CoA ligase CLAC_RS03050 CLAC_RS01335
phenylacetate paaZ1: oxepin-CoA hydrolase CLAC_RS11130 CLAC_RS08700
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylacetate ppa: phenylacetate permease ppa CLAC_RS09710
phenylalanine fahA: fumarylacetoacetate hydrolase CLAC_RS04765
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 davD: glutarate semialdehyde dehydrogenase CLAC_RS02530 CLAC_RS11495
proline gcdG: succinyl-CoA:glutarate CoA-transferase CLAC_RS11020
proline prdA: D-proline reductase, prdA component
proline prdB: D-proline reductase, prdB component
proline prdC: D-proline reductase, electron transfer component PrdC
proline prdF: proline racemase
propionate pccA: propionyl-CoA carboxylase, alpha subunit CLAC_RS09420 CLAC_RS02580
propionate prpE: propionyl-CoA synthetase CLAC_RS11135 CLAC_RS10685
putrescine gabT: gamma-aminobutyrate transaminase CLAC_RS11005 CLAC_RS06935
putrescine patA: putrescine aminotransferase (PatA/SpuC) CLAC_RS06935 CLAC_RS11005
putrescine patD: gamma-aminobutyraldehyde dehydrogenase CLAC_RS11495 CLAC_RS08280
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
rhamnose LRA1: L-rhamnofuranose dehydrogenase CLAC_RS11150 CLAC_RS12425
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase
rhamnose LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase
rhamnose LRA6: 2,4-diketo-3-deoxyrhamnonate hydrolase CLAC_RS11960 CLAC_RS04765
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsK: ribokinase CLAC_RS09755 CLAC_RS08220
ribose rbsU: probable D-ribose transporter RbsU
serine sdaC: L-serine transporter:H+ symporter sdaC CLAC_RS11180
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase CLAC_RS11150
sucrose 1pfk: 1-phosphofructokinase CLAC_RS05470
sucrose ams: sucrose hydrolase (invertase) CLAC_RS08450
sucrose fba: fructose 1,6-bisphosphate aldolase CLAC_RS10975
threonine pccA: propionyl-CoA carboxylase, alpha subunit CLAC_RS09420 CLAC_RS02580
threonine RR42_RS28305: L-threonine:H+ symporter CLAC_RS03880 CLAC_RS06165
threonine tdcE: 2-ketobutyrate formate-lyase
thymidine deoB: phosphopentomutase CLAC_RS00435 CLAC_RS02175
trehalose pgmB: beta-phosphoglucomutase CLAC_RS01270
trehalose thuE: trehalose ABC transporter, substrate-binding component ThuE
trehalose treP: trehalose phosphorylase, inverting CLAC_RS01275
tryptophan tnaA: tryptophanase
tyrosine fahA: fumarylacetoacetate hydrolase CLAC_RS04765
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine bch: 3-hydroxyisobutyryl-CoA hydrolase CLAC_RS08910 CLAC_RS11130
valine brnQ: L-valine:cation symporter BrnQ/BraZ/BraB CLAC_RS08055
valine mmsA: methylmalonate-semialdehyde dehydrogenase CLAC_RS11165 CLAC_RS08280
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
valine pccA: propionyl-CoA carboxylase, alpha subunit CLAC_RS09420 CLAC_RS02580
xylitol fruI: xylitol PTS, enzyme IIABC (FruI) CLAC_RS05465
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase
xylose xylA: xylose isomerase
xylose xylB: xylulokinase
xylose xylT: D-xylose transporter CLAC_RS02995

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