GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Corynebacterium deserti GIMN1.010

Found 118 low-confidence and 33 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate csbX: 2-oxoglutarate permease csbX CDES_RS00700
4-hydroxybenzoate pcaB: 3-carboxymuconate cycloisomerase CDES_RS10485 CDES_RS08875
4-hydroxybenzoate pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase CDES_RS10465 CDES_RS13435
4-hydroxybenzoate pcaI: 3-oxoadipate CoA-transferase subunit A (PcaI) CDES_RS10455 CDES_RS05470
4-hydroxybenzoate pcaJ: 3-oxoadipate CoA-transferase subunit B (PcaJ) CDES_RS05475 CDES_RS10450
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK CDES_RS10430 CDES_RS05005
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter CDES_RS01040 CDES_RS13335
arginine odc: L-ornithine decarboxylase
arginine patA: putrescine aminotransferase (PatA/SpuC) CDES_RS06515 CDES_RS06150
arginine patD: gamma-aminobutyraldehyde dehydrogenase CDES_RS12085 CDES_RS04150
arginine rocE: L-arginine permease CDES_RS09325 CDES_RS05420
arginine rocF: arginase
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component CDES_RS06245 CDES_RS08400
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 CDES_RS06250
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 CDES_RS06250 CDES_RS08415
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline arcC: carbamate kinase
citrulline odc: L-ornithine decarboxylase
citrulline patA: putrescine aminotransferase (PatA/SpuC) CDES_RS06515 CDES_RS06150
citrulline patD: gamma-aminobutyraldehyde dehydrogenase CDES_RS12085 CDES_RS04150
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase CDES_RS05950 CDES_RS10310
D-lactate lctP: D-lactate:H+ symporter LctP or LidP
D-serine dsdA: D-serine ammonia-lyase CDES_RS09220
deoxyinosine deoB: phosphopentomutase CDES_RS03380
deoxyinosine deoD: deoxyinosine phosphorylase
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase CDES_RS13670 CDES_RS11670
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoP: deoxyribose transporter
fructose 1pfk: 1-phosphofructokinase CDES_RS08325
fucose fdh: L-fucose 1-dehydrogenase CDES_RS12400
fucose fucDH: 2-keto-3-deoxy-L-fuconate 4-dehydrogenase CDES_RS13670 CDES_RS10875
fucose fuconolactonase: L-fucono-1,5-lactonase
fucose fucU: L-fucose mutarotase FucU
fucose HSERO_RS05255: ABC transporter for L-fucose, permease component CDES_RS05840
fucose HSERO_RS05260: ABC transporter for L-fucose, substrate-binding component
galactose galK: galactokinase (-1-phosphate forming)
galactose galP: galactose:H+ symporter GalP CDES_RS01040 CDES_RS13335
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate gci: D-galactarolactone cycloisomerase CDES_RS13690
galacturonate gli: D-galactarolactone isomerase
galacturonate kdgD: 5-dehydro-4-deoxyglucarate dehydratase CDES_RS08495 CDES_RS11570
galacturonate udh: D-galacturonate dehydrogenase
gluconate gntT: gluconate:H+ symporter GntT CDES_RS12675
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
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase CDES_RS13690
glucuronate kdgD: 5-dehydro-4-deoxyglucarate dehydratase CDES_RS08495 CDES_RS11570
glucuronate udh: D-glucuronate dehydrogenase
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) CDES_RS07920
glycerol glpF: glycerol facilitator glpF
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase
isoleucine brnQ: L-isoleucine:cation symporter BrnQ/BraZ/BraB CDES_RS10075
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase CDES_RS04395
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase CDES_RS13425 CDES_RS13030
isoleucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
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) CDES_RS12300
leucine brnQ: L-leucine:Na+ symporter BrnQ/BraB CDES_RS10075
leucine liuA: isovaleryl-CoA dehydrogenase
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit CDES_RS03415 CDES_RS03395
leucine liuC: 3-methylglutaconyl-CoA hydratase
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit CDES_RS03450 CDES_RS03455
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 CDES_RS04150 CDES_RS02480
lysine glaH: glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lysine lhgD: L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
maltose susB: alpha-glucosidase (maltase) CDES_RS10040
mannitol PLT5: polyol transporter PLT5 CDES_RS13335 CDES_RS01040
mannitol scrK: fructokinase CDES_RS00950
mannose manP: mannose PTS system, EII-CBA components CDES_RS08330 CDES_RS13065
myoinositol iolB: 5-deoxy-D-glucuronate isomerase CDES_RS00965
myoinositol iolE: scyllo-inosose 2-dehydratase CDES_RS00975
myoinositol iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase CDES_RS00950
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase CDES_RS11565
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 CDES_RS04395
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase CDES_RS13425 CDES_RS11670
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase CDES_RS10465 CDES_RS13435
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase CDES_RS10465 CDES_RS13435
phenylacetate paaK: phenylacetate-CoA ligase CDES_RS02115
phenylacetate paaZ1: oxepin-CoA hydrolase
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylacetate ppa: phenylacetate permease ppa CDES_RS04050
phenylalanine fahA: fumarylacetoacetate hydrolase CDES_RS09080
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 CDES_RS02375
phenylalanine QDPR: 6,7-dihydropteridine reductase
proline put1: proline dehydrogenase
proline putA: L-glutamate 5-semialdeyde dehydrogenase CDES_RS00655 CDES_RS12085
propionate prpE: propionyl-CoA synthetase CDES_RS02115
putrescine patA: putrescine aminotransferase (PatA/SpuC) CDES_RS06515 CDES_RS06150
putrescine patD: gamma-aminobutyraldehyde dehydrogenase CDES_RS12085 CDES_RS04150
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
rhamnose LRA1: L-rhamnofuranose dehydrogenase CDES_RS09270 CDES_RS11670
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase
rhamnose LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase CDES_RS13030 CDES_RS10875
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
serine serP: L-serine permease SerP CDES_RS02405 CDES_RS05420
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase CDES_RS13425 CDES_RS11670
threonine RR42_RS28305: L-threonine:H+ symporter CDES_RS02405 CDES_RS12695
threonine tdcE: 2-ketobutyrate formate-lyase
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase CDES_RS03380
thymidine nupG: thymidine permease NupG/XapB
trehalose PsTP: trehalose phosphorylase
trehalose thuE: trehalose ABC transporter, substrate-binding component ThuE CDES_RS03580
trehalose thuF: trehalose ABC transporter, permease component 1 (ThuF) CDES_RS03570 CDES_RS06445
trehalose thuK: trehalose ABC transporter, ATPase component ThuK CDES_RS06460 CDES_RS03585
tryptophan tnaA: tryptophanase
tyrosine fahA: fumarylacetoacetate hydrolase CDES_RS09080
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase
valine bch: 3-hydroxyisobutyryl-CoA hydrolase CDES_RS04395
valine brnQ: L-valine:cation symporter BrnQ/BraZ/BraB CDES_RS10075
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase CDES_RS04395
valine mmsA: methylmalonate-semialdehyde dehydrogenase CDES_RS00960 CDES_RS06155
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
xylitol PLT5: xylitol:H+ symporter PLT5 CDES_RS13335 CDES_RS01040
xylitol xdhA: xylitol dehydrogenase CDES_RS13820 CDES_RS00555
xylose xylA: xylose isomerase
xylose xylT: D-xylose transporter CDES_RS01040 CDES_RS13335

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