GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Salinicoccus carnicancri Crm

Found 99 low-confidence and 51 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 C792_RS0112035 C792_RS0101755
2-oxoglutarate Psest_0085: 2-oxoglutarate TRAP transporter, solute receptor component C792_RS0101745 C792_RS0112040
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase C792_RS0112435 C792_RS0112125
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase C792_RS0112230
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 C792_RS0112465 C792_RS0112210
acetate actP: cation/acetate symporter ActP C792_RS0108705
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter
arginine rocE: L-arginine permease
citrate citM: citrate:cation:H+ symporter CitM C792_RS0113640
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component C792_RS0100130 C792_RS0112505
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 C792_RS0101010 C792_RS0103290
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 C792_RS0100120 C792_RS0112495
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline arcC: carbamate kinase
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase C792_RS0112670 C792_RS0112025
D-serine cycA: D-serine:H+ symporter CycA
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase C792_RS0100525 C792_RS0112530
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoP: deoxyribose transporter
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) C792_RS0110395 C792_RS0110710
fucose aldA: lactaldehyde dehydrogenase C792_RS0112615 C792_RS0108995
fucose fucA: L-fuculose-phosphate aldolase FucA
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 dgoA: 2-dehydro-3-deoxy-6-phosphogalactonate aldolase C792_RS0113060 C792_RS0112920
galactose dgoK: 2-dehydro-3-deoxygalactonokinase C792_RS0113065
galactose galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) C792_RS0104670
galactose galdh: D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) C792_RS0112530 C792_RS0106680
galactose galP: galactose:H+ symporter GalP
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate kdgK: 2-keto-3-deoxygluconate kinase C792_RS0113065 C792_RS0112925
galacturonate uxaA: D-altronate dehydratase
galacturonate uxaB: tagaturonate reductase
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) C792_RS0112000 C792_RS0110400
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate kdgK: 2-keto-3-deoxygluconate kinase C792_RS0113065 C792_RS0112925
glucuronate uxuB: D-mannonate dehydrogenase
histidine hutG: N-formiminoglutamate formiminohydrolase C792_RS0105170 C792_RS0111690
histidine PA5503: L-histidine ABC transporter, ATPase component C792_RS0102795 C792_RS0112050
histidine PA5505: L-histidine ABC transporter, substrate-binding component C792_RS0112060 C792_RS0102805
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase C792_RS0109335
isoleucine Bap2: L-isoleucine permease Bap2
isoleucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component C792_RS0107740 C792_RS0108920
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase C792_RS0109005 C792_RS0109330
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase C792_RS0100525 C792_RS0105790
isoleucine prpC: 2-methylcitrate synthase C792_RS0108700
L-lactate L-LDH: L-lactate dehydrogenase C792_RS0108690
lactose dgoA: 2-dehydro-3-deoxy-6-phosphogalactonate aldolase C792_RS0113060 C792_RS0112920
lactose dgoK: 2-dehydro-3-deoxygalactonokinase C792_RS0113065
lactose galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) C792_RS0104670
lactose galdh: D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) C792_RS0112530 C792_RS0106680
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric) C792_RS0109975
leucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component C792_RS0107740 C792_RS0108920
leucine leuT: L-leucine:Na+ symporter LeuT
leucine liuA: isovaleryl-CoA dehydrogenase C792_RS0109335
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit C792_RS0107655 C792_RS0110520
leucine liuC: 3-methylglutaconyl-CoA hydratase C792_RS0108985 C792_RS0109005
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit
leucine liuE: hydroxymethylglutaryl-CoA lyase
lysine davA: 5-aminovaleramidase C792_RS0110875
lysine davB: L-lysine 2-monooxygenase
lysine davD: glutarate semialdehyde dehydrogenase C792_RS0109240 C792_RS0112615
lysine davT: 5-aminovalerate aminotransferase C792_RS0103155 C792_RS0108435
lysine glaH: glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lysine lysP: L-lysine:H+ symporter LysP
myoinositol iolG: myo-inositol 2-dehydrogenase C792_RS0101270 C792_RS0101275
myoinositol iolM: 2-inosose 4-dehydrogenase C792_RS0112730
myoinositol iolN: 2,4-diketo-inositol hydratase
myoinositol iolO: 5-dehydro-L-gluconate epimerase
myoinositol iolT: myo-inositol:H+ symporter
myoinositol kdgK: 2-keto-3-deoxygluconate kinase C792_RS0113065 C792_RS0112925
myoinositol uxaE: D-tagaturonate epimerase
myoinositol uxuB: D-mannonate dehydrogenase
NAG nagEIIA: N-acetylglucosamine phosphotransferase system, EII-A component (PtsG/YpqE/GamP) C792_RS0112000 C792_RS0104345
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 C792_RS0109005 C792_RS0108985
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase C792_RS0109000 C792_RS0109005
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase C792_RS0109330 C792_RS0108990
phenylacetate paaK: phenylacetate-CoA ligase
phenylacetate paaZ1: oxepin-CoA hydrolase C792_RS0109000
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylacetate ppa: phenylacetate permease ppa C792_RS0108705
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine fahA: fumarylacetoacetate hydrolase C792_RS0112945 C792_RS0112305
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 C792_RS0100610
phenylalanine QDPR: 6,7-dihydropteridine reductase
propionate prpC: 2-methylcitrate synthase C792_RS0108700
propionate prpE: propionyl-CoA synthetase C792_RS0110000 C792_RS0109060
putrescine gabT: gamma-aminobutyrate transaminase C792_RS0103155 C792_RS0108435
putrescine patA: putrescine aminotransferase (PatA/SpuC) C792_RS0103155 C792_RS0109810
putrescine patD: gamma-aminobutyraldehyde dehydrogenase C792_RS0108995 C792_RS0112615
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate mctC: pyruvate symporter MctC C792_RS0108705
rhamnose LRA1: L-rhamnofuranose dehydrogenase C792_RS0110045 C792_RS0105790
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase C792_RS0112915
rhamnose LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase C792_RS0112730 C792_RS0100525
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
serine serP: L-serine permease SerP
sorbitol srlB: PTS system for sorbitol SrlABE, EII-A component SrlB C792_RS0113510
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase C792_RS0100470 C792_RS0110710
sucrose ams: sucrose hydrolase (invertase) C792_RS0111290 C792_RS0100025
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) C792_RS0107610 C792_RS0107605
threonine ltaE: L-threonine aldolase C792_RS0111580
threonine tdcC: L-threonine:H+ symporter TdcC
trehalose treC: trehalose-6-phosphate hydrolase C792_RS0100025
tryptophan antA: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA
tryptophan antB: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB
tryptophan antC: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC
tryptophan mhpD: 2-hydroxypentadienoate hydratase C792_RS0112435 C792_RS0112125
tryptophan mhpE: 4-hydroxy-2-oxovalerate aldolase C792_RS0112230
tryptophan trpP: energy-coupling factor transporter, tryptophan-specific (S) component TrpP
tryptophan xylF: 2-hydroxymuconate semialdehyde hydrolase C792_RS0112465 C792_RS0112210
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine fahA: fumarylacetoacetate hydrolase C792_RS0112945 C792_RS0112305
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase C792_RS0109335
valine Bap2: L-valine permease Bap2
valine bch: 3-hydroxyisobutyryl-CoA hydrolase C792_RS14900
valine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component C792_RS0107740 C792_RS0108920
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase C792_RS0109005 C792_RS0108985
valine mmsA: methylmalonate-semialdehyde dehydrogenase C792_RS0112845 C792_RS0108995
valine mmsB: 3-hydroxyisobutyrate dehydrogenase C792_RS0112970 C792_RS0110010
valine prpC: 2-methylcitrate synthase C792_RS0108700
xylitol fruI: xylitol PTS, enzyme IIABC (FruI) C792_RS0107295 C792_RS0112880
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase C792_RS0112730
xylose xylA: xylose isomerase
xylose xylB: xylulokinase C792_RS0112905
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