GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Flavobacterium ummariense DS-12

Found 136 low-confidence and 45 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate kgtP: 2-oxoglutarate:H+ symporter KgtP BM253_RS07155
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 dctA: organic acid/proton symporter DctA BM253_RS01970
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter
arginine rocA: 1-pyrroline-5-carboxylate dehydrogenase BM253_RS09455 BM253_RS15450
arginine rocE: L-arginine permease BM253_RS06410
arginine rocF: arginase
asparagine glt: aspartate:proton symporter Glt BM253_RS01970
aspartate glt: aspartate:proton symporter Glt BM253_RS01970
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 BM253_RS02520 BM253_RS12820
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 rocA: 1-pyrroline-5-carboxylate dehydrogenase BM253_RS09455 BM253_RS15450
D-alanine cycA: D-alanine:H+ symporter CycA BM253_RS06410
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase BM253_RS15700 BM253_RS10205
D-lactate lctP: D-lactate:H+ symporter LctP or LidP
D-serine cycA: D-serine:H+ symporter CycA BM253_RS06410
D-serine dsdA: D-serine ammonia-lyase BM253_RS08980
deoxyinosine deoB: phosphopentomutase BM253_RS07440
deoxyinosine deoD: deoxyinosine phosphorylase
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase BM253_RS10910 BM253_RS15945
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
deoxyribose deoP: deoxyribose transporter
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) BM253_RS12600 BM253_RS16945
fructose 1pfk: 1-phosphofructokinase
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
fucose aldA: lactaldehyde dehydrogenase BM253_RS15450 BM253_RS02660
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 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) BM253_RS06520
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 BM253_RS15450 BM253_RS02660
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate kdgD: 5-dehydro-4-deoxyglucarate dehydratase
glucuronate udh: D-glucuronate dehydrogenase
glutamate gltP: L-glutamate:cation symporter GltP/GltT BM253_RS01970
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric)
glycerol glpF: glycerol facilitator glpF BM253_RS02445
glycerol glpK: glycerol kinase
histidine hutG: N-formiminoglutamate formiminohydrolase BM253_RS03960 BM253_RS14275
histidine permease: L-histidine permease BM253_RS06410
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase BM253_RS07875 BM253_RS09155
isoleucine Bap2: L-isoleucine permease Bap2
isoleucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BM253_RS04080 BM253_RS09270
isoleucine bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit BM253_RS07735 BM253_RS04080
isoleucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component BM253_RS03970 BM253_RS09510
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase BM253_RS01100 BM253_RS15650
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase BM253_RS10910 BM253_RS15945
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit BM253_RS02595 BM253_RS08790
L-lactate lctO: L-lactate oxidase or 2-monooxygenase
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
L-malate dctA: L-malate:H+ symporter DctA BM253_RS01970
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 bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BM253_RS04080 BM253_RS09270
leucine bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit BM253_RS07735 BM253_RS04080
leucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component BM253_RS03970 BM253_RS09510
leucine leuT: L-leucine:Na+ symporter LeuT
leucine liuA: isovaleryl-CoA dehydrogenase BM253_RS09155 BM253_RS07875
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit BM253_RS02595 BM253_RS08790
leucine liuC: 3-methylglutaconyl-CoA hydratase BM253_RS01100
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit BM253_RS13550 BM253_RS02600
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase BM253_RS04065 BM253_RS04610
lysine lysN: 2-aminoadipate transaminase BM253_RS07965 BM253_RS04065
lysine lysP: L-lysine:H+ symporter LysP BM253_RS06410
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase BM253_RS15700
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 BM253_RS06875 BM253_RS03920
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
myoinositol mmsA: malonate-semialdehyde dehydrogenase BM253_RS15450
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) BM253_RS06520
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components
phenylacetate H281DRAFT_04042: phenylacetate:H+ symporter BM253_RS06410
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 BM253_RS05925
phenylacetate paaF: 2,3-dehydroadipyl-CoA hydratase BM253_RS01100
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase BM253_RS01100
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase BM253_RS15640 BM253_RS12775
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase BM253_RS15640 BM253_RS12775
phenylacetate paaK: phenylacetate-CoA ligase
phenylacetate paaZ1: oxepin-CoA hydrolase
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine maiA: maleylacetoacetate isomerase
phenylalanine PAH: phenylalanine 4-monooxygenase
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase
phenylalanine QDPR: 6,7-dihydropteridine reductase BM253_RS14025 BM253_RS11395
propionate pccA: propionyl-CoA carboxylase, alpha subunit BM253_RS02595 BM253_RS08790
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabT: gamma-aminobutyrate transaminase BM253_RS04610 BM253_RS08990
putrescine patA: putrescine aminotransferase (PatA/SpuC) BM253_RS04610 BM253_RS04065
putrescine patD: gamma-aminobutyraldehyde dehydrogenase BM253_RS15450 BM253_RS02660
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose aldA: lactaldehyde dehydrogenase BM253_RS15450 BM253_RS02660
rhamnose LRA1: L-rhamnofuranose dehydrogenase BM253_RS10910 BM253_RS10560
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase
rhamnose LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsK: ribokinase
ribose rbsU: probable D-ribose transporter RbsU
serine serP: L-serine permease SerP BM253_RS06410
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase BM253_RS11700 BM253_RS15945
succinate dctA: succinate:H+ symporter DctA BM253_RS01970
sucrose 1pfk: 1-phosphofructokinase
sucrose ams: sucrose hydrolase (invertase)
sucrose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
threonine RR42_RS28305: L-threonine:H+ symporter BM253_RS06410
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase BM253_RS07440
trehalose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
trehalose treF: trehalase
tryptophan tnaA: tryptophanase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase BM253_RS07875 BM253_RS09155
valine Bap2: L-valine permease Bap2
valine bch: 3-hydroxyisobutyryl-CoA hydrolase BM253_RS01100
valine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BM253_RS04080 BM253_RS09270
valine bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit BM253_RS07735 BM253_RS04080
valine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component BM253_RS03970 BM253_RS09510
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase BM253_RS01100 BM253_RS15650
valine mmsA: methylmalonate-semialdehyde dehydrogenase BM253_RS15450
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine pccA: propionyl-CoA carboxylase, alpha subunit BM253_RS02595 BM253_RS08790
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