GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Weissella oryzae SG25

Found 152 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
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 ybhL: acetate uptake transporter YbhL TT13_RS05825
arginine rocA: 1-pyrroline-5-carboxylate dehydrogenase
arginine rocD: ornithine aminotransferase TT13_RS00935
arginine rocE: L-arginine permease TT13_RS08760 TT13_RS01405
asparagine ansP: L-asparagine permease AnsP TT13_RS01405 TT13_RS00995
aspartate glt: aspartate:proton symporter Glt
cellobiose bgl: cellobiase
cellobiose manY: glucose PTS, enzyme EIIC TT13_RS09610
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component TT13_RS07590 TT13_RS01035
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 TT13_RS01030
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 TT13_RS07595 TT13_RS01030
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline rocA: 1-pyrroline-5-carboxylate dehydrogenase
citrulline rocD: ornithine aminotransferase TT13_RS00935
D-alanine dadA: D-alanine dehydrogenase
D-serine dsdA: D-serine ammonia-lyase
deoxyinosine deoB: phosphopentomutase TT13_RS03255
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase
deoxyribonate aacS: acetoacetyl-CoA synthetase
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase TT13_RS08720
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 levF: fructose PTS system (fructose 6-phosphate forming), EII-C component TT13_RS09610
fructose levG: fructose PTS system (fructose 6-phosphate forming), EII-D component TT13_RS09605
fucose aldA: lactaldehyde dehydrogenase
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
galactose galP: galactose:H+ symporter GalP TT13_RS07120 TT13_RS06920
galacturonate eda: 2-keto-3-deoxygluconate 6-phosphate aldolase
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate uxaA: D-altronate dehydratase
galacturonate uxaB: tagaturonate reductase
galacturonate uxaC: D-galacturonate isomerase
glucosamine manX: glucosamine PTS system, EII-AB component ManX TT13_RS09615
glucosamine manY: glucosamine PTS system, EII-C component ManY TT13_RS09610
glucosamine manZ: glucosamine PTS system, EII-D component ManZ TT13_RS09605
glucose manY: glucose PTS, enzyme EIIC TT13_RS09610
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate eda: 2-keto-3-deoxygluconate 6-phosphate aldolase
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate uxaC: D-glucuronate isomerase
glucuronate uxuA: D-mannonate dehydratase
glucuronate uxuB: D-mannonate dehydrogenase
glutamate gdhA: glutamate dehydrogenase, NAD-dependent
glutamate glnP: L-glutamate ABC transporter, fused permease and substrate-binding components GlnP
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 epi: methylmalonyl-CoA epimerase
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase TT13_RS08720
isoleucine mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
isoleucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit TT13_RS08740
isoleucine pccB: propionyl-CoA carboxylase, beta subunit
L-lactate lctO: L-lactate oxidase or 2-monooxygenase
lactose lacS: lactose permease LacS TT13_RS08900
leucine aacS: acetoacetyl-CoA synthetase
leucine ilvE: L-leucine transaminase TT13_RS06065
leucine liuA: isovaleryl-CoA dehydrogenase
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit TT13_RS08740
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)
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase TT13_RS00935
lysine lysN: 2-aminoadipate transaminase TT13_RS06065
lysine lysP: L-lysine:H+ symporter LysP TT13_RS08760 TT13_RS01405
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase
maltose malI: maltose transporter TT13_RS01885
mannitol mt2d: mannitol 2-dehydrogenase TT13_RS08720 TT13_RS05830
mannitol PLT5: polyol transporter PLT5 TT13_RS07120 TT13_RS06920
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 TT13_RS08845
myoinositol iolT: myo-inositol:H+ symporter TT13_RS06920 TT13_RS07120
myoinositol mmsA: malonate-semialdehyde dehydrogenase
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components
phenylacetate H281DRAFT_04042: phenylacetate:H+ symporter TT13_RS00995 TT13_RS01405
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 TT13_RS08720
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase TT13_RS02270
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase TT13_RS02270
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 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 put1: proline dehydrogenase
proline putA: L-glutamate 5-semialdeyde dehydrogenase
propionate epi: methylmalonyl-CoA epimerase
propionate mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
propionate pccA: propionyl-CoA carboxylase, alpha subunit TT13_RS08740
propionate pccB: propionyl-CoA carboxylase, beta subunit
propionate prpE: propionyl-CoA synthetase
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabD: succinate semialdehyde dehydrogenase TT13_RS05060
putrescine gabT: gamma-aminobutyrate transaminase TT13_RS00935
putrescine patA: putrescine aminotransferase (PatA/SpuC) TT13_RS00935
putrescine patD: gamma-aminobutyraldehyde dehydrogenase
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose aldA: lactaldehyde dehydrogenase
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
serine sdaB: L-serine ammonia-lyase
serine serP: L-serine permease SerP TT13_RS00995 TT13_RS01405
sorbitol sdh: sorbitol dehydrogenase TT13_RS08680 TT13_RS08720
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2 TT13_RS07120 TT13_RS06920
succinate sdc: succinate:Na+ symporter Sdc
sucrose ams: sucrose hydrolase (invertase)
sucrose manY: glucose PTS, enzyme EIIC TT13_RS09610
threonine gcvH: glycine cleavage system, H component (lipoyl protein)
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase)
threonine gcvT: glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase)
threonine ltaE: L-threonine aldolase TT13_RS00625
threonine serP1: L-threonine uptake transporter SerP1 TT13_RS00995 TT13_RS01405
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase TT13_RS03255
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
trehalose manY: glucose PTS, enzyme EIIC TT13_RS09610
trehalose treF: trehalase
tryptophan tnaA: tryptophanase
tyrosine aacS: acetoacetyl-CoA synthetase
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 epi: methylmalonyl-CoA epimerase
valine mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
valine mmsA: methylmalonate-semialdehyde dehydrogenase
valine mmsB: 3-hydroxyisobutyrate dehydrogenase TT13_RS05300
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
valine pccA: propionyl-CoA carboxylase, alpha subunit TT13_RS08740
valine pccB: propionyl-CoA carboxylase, beta subunit
xylitol PLT5: xylitol:H+ symporter PLT5 TT13_RS07120 TT13_RS06920
xylitol xdhA: xylitol dehydrogenase TT13_RS08545 TT13_RS05830

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.

Links

Downloads

Related tools

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