GapMind for catabolism of small carbon sources


Potential Gaps in catabolism of small carbon sources in Dokdonella koreensis DS-123

Found 135 low-confidence and 19 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase I596_RS00605
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
alanine cycA: L-alanine symporter CycA
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter
arginine rocD: ornithine aminotransferase I596_RS12880 I596_RS03965
arginine rocE: L-arginine permease
asparagine ans: asparaginase I596_RS02180
cellobiose bgl: cellobiase
cellobiose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component I596_RS09325 I596_RS02480
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline citrullinase: putative citrullinase I596_RS08295
citrulline rocD: ornithine aminotransferase I596_RS12880 I596_RS03965
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase I596_RS04610
D-lactate D-LDH: D-lactate dehydrogenase I596_RS07265 I596_RS02995
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 I596_RS16215 I596_RS17335
deoxyinosine deoB: phosphopentomutase I596_RS17115 I596_RS06125
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase I596_RS02340
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase I596_RS02455 I596_RS09390
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 deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoP: deoxyribose transporter
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
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 galE: UDP-glucose 4-epimerase I596_RS05190 I596_RS05165
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) I596_RS14265
glucose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate dopDH: 2,5-dioxopentanonate dehydrogenase I596_RS02225 I596_RS04570
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate kdgD: 5-dehydro-4-deoxyglucarate dehydratase I596_RS12675
glucuronate udh: D-glucuronate dehydrogenase
glutamate gltP: L-glutamate:cation symporter GltP/GltT I596_RS02910
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric)
glycerol glpF: glycerol facilitator glpF I596_RS00815
glycerol glpK: glycerol kinase
histidine hutH: histidine ammonia-lyase I596_RS15860 I596_RS08810
isoleucine Bap2: L-isoleucine permease Bap2
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
L-malate sdlC: L-malate:Na+ symporter SdlC
lactose galE: UDP-glucose 4-epimerase I596_RS05190 I596_RS05165
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose glk: glucokinase
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
leucine leuT: L-leucine:Na+ symporter LeuT
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase I596_RS03960
lysine lysN: 2-aminoadipate transaminase I596_RS14430 I596_RS03960
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase I596_RS07265 I596_RS02995
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 manA: mannose-6-phosphate isomerase I596_RS14730
mannose manP: mannose PTS system, EII-CBA components
myoinositol iolB: 5-deoxy-D-glucuronate isomerase
myoinositol iolC: 5-dehydro-2-deoxy-D-gluconate kinase I596_RS05395
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 I596_RS11670
myoinositol iolT: myo-inositol:H+ symporter
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) I596_RS14265
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 I596_RS12940 I596_RS04715
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase I596_RS12940 I596_RS08905
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase I596_RS06325 I596_RS05370
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase I596_RS06325 I596_RS05370
phenylacetate paaK: phenylacetate-CoA ligase I596_RS07565
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase I596_RS04715 I596_RS08905
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase I596_RS12135
phenylalanine QDPR: 6,7-dihydropteridine reductase I596_RS11280
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabD: succinate semialdehyde dehydrogenase I596_RS04570 I596_RS02225
putrescine gabT: gamma-aminobutyrate transaminase I596_RS12880 I596_RS03960
putrescine patA: putrescine aminotransferase (PatA/SpuC) I596_RS12880 I596_RS03960
putrescine patD: gamma-aminobutyraldehyde dehydrogenase I596_RS04570 I596_RS02225
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
rhamnose rhaA: L-rhamnose isomerase
rhamnose rhaB: L-rhamnulokinase
rhamnose rhaD: rhamnulose 1-phosphate aldolase
rhamnose rhaM: L-rhamnose mutarotase
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
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 I596_RS10645 I596_RS08880
sucrose scrK: fructokinase I596_RS05395
sucrose SUS: sucrose synthase
sucrose sut: sucrose:proton symporter SUT/SUC
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) I596_RS15740 I596_RS03290
threonine tdcC: L-threonine:H+ symporter TdcC
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase I596_RS17115 I596_RS06125
thymidine deoC: deoxyribose-5-phosphate aldolase
trehalose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
trehalose treF: trehalase I596_RS13870
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
valine Bap2: L-valine permease Bap2
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase I596_RS12940 I596_RS02240
valine mmsB: 3-hydroxyisobutyrate dehydrogenase I596_RS04725 I596_RS16190
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