GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Lacinutrix algicola AKS293

Found 115 low-confidence and 48 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate kgtP: 2-oxoglutarate:H+ symporter KgtP
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 actP: cation/acetate symporter ActP ASC41_RS11465
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
arginine rocF: arginase
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 ASC41_RS06935 ASC41_RS13385
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
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase ASC41_RS07450 ASC41_RS14145
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 ASC41_RS00030 ASC41_RS01620
deoxyinosine deoB: phosphopentomutase ASC41_RS15750
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase ASC41_RS13975 ASC41_RS04720
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)) ASC41_RS13670 ASC41_RS13975
fructose 1pfk: 1-phosphofructokinase
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
fucose aldA: lactaldehyde dehydrogenase ASC41_RS13180 ASC41_RS11440
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
fumarate SLC26dg: fumarate transporter SLC26dg ASC41_RS04540
galactose sglS: sodium/galactose cotransporter ASC41_RS12275
galacturonate exuT: D-galacturonate transporter ExuT ASC41_RS03335
galacturonate uxaA: D-altronate dehydratase
galacturonate uxaB: tagaturonate reductase
galacturonate uxaC: D-galacturonate isomerase
gluconate edd: phosphogluconate dehydratase ASC41_RS01600
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) ASC41_RS00425
glucose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT ASC41_RS03335
glucuronate uxaC: D-glucuronate isomerase
glucuronate uxuA: D-mannonate dehydratase
glucuronate uxuB: D-mannonate dehydrogenase ASC41_RS13445
glutamate gdhA: glutamate dehydrogenase, NAD-dependent ASC41_RS07795 ASC41_RS11310
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric)
glycerol glpF: glycerol facilitator glpF ASC41_RS05700
glycerol glpK: glycerol kinase
histidine hutG: N-formiminoglutamate formiminohydrolase ASC41_RS14350
histidine permease: L-histidine permease
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase ASC41_RS03630 ASC41_RS03050
isoleucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit ASC41_RS13240 ASC41_RS03545
isoleucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component ASC41_RS04735 ASC41_RS03540
isoleucine brnQ: L-isoleucine:cation symporter BrnQ/BraZ/BraB ASC41_RS09265
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase ASC41_RS02310 ASC41_RS09525
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase ASC41_RS13975 ASC41_RS03330
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit ASC41_RS11580 ASC41_RS08120
L-lactate lctO: L-lactate oxidase or 2-monooxygenase
L-malate sdlC: L-malate:Na+ symporter SdlC
lactose glk: glucokinase
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric) ASC41_RS12230
leucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit ASC41_RS13240 ASC41_RS03545
leucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component ASC41_RS04735 ASC41_RS03540
leucine brnQ: L-leucine:Na+ symporter BrnQ/BraB ASC41_RS09265
leucine liuA: isovaleryl-CoA dehydrogenase ASC41_RS03630 ASC41_RS03050
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit ASC41_RS11580 ASC41_RS08120
leucine liuC: 3-methylglutaconyl-CoA hydratase ASC41_RS09525 ASC41_RS02310
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit ASC41_RS14455 ASC41_RS11575
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase ASC41_RS11700
lysine lysN: 2-aminoadipate transaminase ASC41_RS05550 ASC41_RS04930
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase ASC41_RS13085
maltose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
maltose susB: alpha-glucosidase (maltase) ASC41_RS03410
mannitol PLT5: polyol transporter PLT5
mannitol scrK: fructokinase ASC41_RS13440
mannose manA: mannose-6-phosphate isomerase ASC41_RS14760 ASC41_RS01305
mannose manP: mannose PTS system, EII-CBA components
myoinositol iolG: myo-inositol 2-dehydrogenase
myoinositol iolM: 2-inosose 4-dehydrogenase
myoinositol iolN: 2,4-diketo-inositol hydratase
myoinositol iolO: 5-dehydro-L-gluconate epimerase
myoinositol iolT: myo-inositol:H+ symporter
myoinositol uxaE: D-tagaturonate epimerase
myoinositol uxuA: D-mannonate dehydratase
myoinositol uxuB: D-mannonate dehydrogenase ASC41_RS13445
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) ASC41_RS00425
NAG nagK: N-acetylglucosamine kinase
phenylacetate paaF: 2,3-dehydroadipyl-CoA hydratase ASC41_RS09525 ASC41_RS02310
phenylacetate paaK: phenylacetate-CoA ligase
phenylacetate paaT: phenylacetate transporter Paa
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine iorAB: phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB
phenylalanine paaF: 2,3-dehydroadipyl-CoA hydratase ASC41_RS09525 ASC41_RS02310
proline proY: proline:H+ symporter
propionate pccA: propionyl-CoA carboxylase, alpha subunit ASC41_RS11580 ASC41_RS08120
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabT: gamma-aminobutyrate transaminase ASC41_RS04930 ASC41_RS01645
putrescine patA: putrescine aminotransferase (PatA/SpuC) ASC41_RS04930 ASC41_RS11700
putrescine patD: gamma-aminobutyraldehyde dehydrogenase ASC41_RS13180 ASC41_RS05615
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate actP: large subunit of pyruvate transporter (actP-like) ASC41_RS11465
pyruvate yjcH: putative small subunit of pyruvate transporter (yjcH-like) ASC41_RS11460
rhamnose aldA: lactaldehyde dehydrogenase ASC41_RS13180 ASC41_RS11440
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 rbsA: D-ribose ABC transporter, ATPase component RbsA ASC41_RS13455
ribose rbsB: D-ribose ABC transporter, substrate-binding component RbsB ASC41_RS13460
ribose rbsC: D-ribose ABC transporter, permease component RbsC ASC41_RS13450
ribose rbsK: ribokinase
serine snatA: L-serine transporter ASC41_RS12525 ASC41_RS11570
sorbitol scrK: fructokinase ASC41_RS13440
sorbitol sdh: sorbitol dehydrogenase ASC41_RS13445 ASC41_RS13975
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
succinate sdc: succinate:Na+ symporter Sdc
sucrose scrK: fructokinase ASC41_RS13440
sucrose scrP: sucrose phosphorylase
sucrose sut: sucrose:proton symporter SUT/SUC
threonine snatA: L-threonine transporter snatA ASC41_RS12525 ASC41_RS11570
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase ASC41_RS15750
thymidine nupC: thymidine permease NupC ASC41_RS01910
trehalose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
trehalose treF: trehalase
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase ASC41_RS03630 ASC41_RS15620
valine bch: 3-hydroxyisobutyryl-CoA hydrolase ASC41_RS09525 ASC41_RS02310
valine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit ASC41_RS13240 ASC41_RS03545
valine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component ASC41_RS04735 ASC41_RS03540
valine brnQ: L-valine:cation symporter BrnQ/BraZ/BraB ASC41_RS09265
valine mmsA: methylmalonate-semialdehyde dehydrogenase ASC41_RS11440 ASC41_RS13180
valine mmsB: 3-hydroxyisobutyrate dehydrogenase ASC41_RS03990
valine pccA: propionyl-CoA carboxylase, alpha subunit ASC41_RS11580 ASC41_RS08120
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase
xylose Echvi_1871: sodium/xylose cotransporter ASC41_RS12275
xylose xylA: xylose isomerase
xylose xylB: xylulokinase

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