GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Lactobacillus silagei IWT126

Found 135 low-confidence and 26 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 CES79_RS03435
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase CES79_RS04090
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 ybhL: acetate uptake transporter YbhL CES79_RS06240
arabinose araA: L-arabinose isomerase CES79_RS12380
arginine rocA: 1-pyrroline-5-carboxylate dehydrogenase CES79_RS01180
arginine rocD: ornithine aminotransferase CES79_RS03125 CES79_RS03360
arginine rocE: L-arginine permease CES79_RS06570 CES79_RS01340
asparagine ans: asparaginase
cellobiose bgl: cellobiase CES79_RS11520
citrate cit1: citrate:H+ symporter Cit1 CES79_RS04110
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component CES79_RS03450 CES79_RS09760
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 CES79_RS06000
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 CES79_RS03760
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline rocA: 1-pyrroline-5-carboxylate dehydrogenase CES79_RS01180
citrulline rocD: ornithine aminotransferase CES79_RS03125 CES79_RS03360
D-alanine dadA: D-alanine dehydrogenase
D-serine dsdA: D-serine ammonia-lyase
deoxyribonate aacS: acetoacetyl-CoA synthetase
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase CES79_RS05900 CES79_RS02380
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoP: deoxyribose transporter
fructose Slc2a5: fructose:H+ symporter CES79_RS07910 CES79_RS11430
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 dctA: fumarate:H+ symporter DctA CES79_RS07870
galactose galP: galactose:H+ symporter GalP CES79_RS07910 CES79_RS11430
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
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 garL: 5-dehydro-4-deoxy-D-glucarate aldolase
glucuronate garR: tartronate semialdehyde reductase CES79_RS00720
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate udh: D-glucuronate dehydrogenase
glutamate gdhA: glutamate dehydrogenase, NAD-dependent
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric)
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 ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase CES79_RS05900 CES79_RS00985
isoleucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
isoleucine prpB: 2-methylisocitrate lyase
isoleucine prpC: 2-methylcitrate synthase CES79_RS02950
isoleucine prpD: 2-methylcitrate dehydratase
L-malate dctA: L-malate:H+ symporter DctA CES79_RS07870
lactose lacS: lactose permease LacS CES79_RS03135 CES79_RS08005
leucine aacS: acetoacetyl-CoA synthetase
leucine liuA: isovaleryl-CoA dehydrogenase
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit CES79_RS05880 CES79_RS03295
leucine liuC: 3-methylglutaconyl-CoA hydratase
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
lysine amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) CES79_RS01180
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase CES79_RS03125 CES79_RS03360
lysine lysN: 2-aminoadipate transaminase CES79_RS10750 CES79_RS08185
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase
maltose malI: maltose transporter CES79_RS07405
mannitol PLT5: polyol transporter PLT5 CES79_RS11430 CES79_RS12280
mannose man-isomerase: D-mannose isomerase
mannose STP6: mannose:H+ symporter CES79_RS07910 CES79_RS12280
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 CES79_RS12280 CES79_RS07910
myoinositol mmsA: malonate-semialdehyde dehydrogenase CES79_RS01180
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components
phenylacetate H281DRAFT_04042: phenylacetate:H+ symporter CES79_RS03490 CES79_RS11280
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
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase CES79_RS00960 CES79_RS10690
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase CES79_RS08555
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase CES79_RS08555
phenylacetate paaK: phenylacetate-CoA ligase
phenylacetate paaZ1: oxepin-CoA hydrolase
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aacS: acetoacetyl-CoA synthetase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP CES79_RS01925 CES79_RS11280
phenylalanine fahA: fumarylacetoacetate hydrolase
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
phenylalanine QDPR: 6,7-dihydropteridine reductase
proline opuBA: proline ABC transporter, ATPase component OpuBA/BusAA CES79_RS04320 CES79_RS11440
proline put1: proline dehydrogenase
proline putA: L-glutamate 5-semialdeyde dehydrogenase CES79_RS01180
propionate prpB: 2-methylisocitrate lyase
propionate prpC: 2-methylcitrate synthase CES79_RS02950
propionate prpD: 2-methylcitrate dehydratase
propionate prpE: propionyl-CoA synthetase
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabD: succinate semialdehyde dehydrogenase CES79_RS01180 CES79_RS07645
putrescine gabT: gamma-aminobutyrate transaminase CES79_RS03125 CES79_RS03360
putrescine patA: putrescine aminotransferase (PatA/SpuC) CES79_RS03125 CES79_RS03360
putrescine patD: gamma-aminobutyraldehyde dehydrogenase CES79_RS01180
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate SLC5A8: sodium-coupled pyruvate transporter
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 CES79_RS12100 CES79_RS05170
serine sdaB: L-serine ammonia-lyase
sorbitol sdh: sorbitol dehydrogenase CES79_RS08015 CES79_RS11460
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2 CES79_RS11430 CES79_RS12280
succinate dctA: succinate:H+ symporter DctA CES79_RS07870
sucrose ams: sucrose hydrolase (invertase) CES79_RS11370
threonine serP1: L-threonine uptake transporter SerP1 CES79_RS01015 CES79_RS04050
threonine tdh: L-threonine 3-dehydrogenase CES79_RS07670 CES79_RS02635
threonine tynA: aminoacetone oxidase
threonine yvgN: methylglyoxal reductase (NADPH-dependent) CES79_RS10880 CES79_RS01880
thymidine nupG: thymidine permease NupG/XapB
trehalose treF: trehalase CES79_RS11370
tryptophan aroP: tryptophan:H+ symporter AroP CES79_RS01925 CES79_RS03490
tryptophan tnaA: tryptophanase
tyrosine aacS: acetoacetyl-CoA synthetase
tyrosine aroP: L-tyrosine transporter (AroP/FywP) CES79_RS01925 CES79_RS03490
tyrosine fahA: fumarylacetoacetate hydrolase
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase
valine bch: 3-hydroxyisobutyryl-CoA hydrolase
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase
valine mmsA: methylmalonate-semialdehyde dehydrogenase CES79_RS01180
valine mmsB: 3-hydroxyisobutyrate dehydrogenase CES79_RS00720
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
valine prpB: 2-methylisocitrate lyase
valine prpC: 2-methylcitrate synthase CES79_RS02950
valine prpD: 2-methylcitrate dehydratase
xylitol PLT5: xylitol:H+ symporter PLT5 CES79_RS11430 CES79_RS12280
xylitol xdhA: xylitol dehydrogenase CES79_RS06470 CES79_RS01690

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