GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Oscillibacter ruminantium GH1

Found 159 low-confidence and 48 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate Psest_0085: 2-oxoglutarate TRAP transporter, solute receptor component ON16_RS06350 ON16_RS08585
4-hydroxybenzoate adh: acetaldehyde dehydrogenase (not acylating)
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
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arginine rocA: 1-pyrroline-5-carboxylate dehydrogenase
arginine rocD: ornithine aminotransferase ON16_RS01580 ON16_RS10080
arginine rocE: L-arginine permease
aspartate dauA: dicarboxylic acid transporter DauA ON16_RS04725
cellobiose bgl: cellobiase
cellobiose glk: glucokinase ON16_RS08410 ON16_RS02730
citrate acn: aconitase
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component ON16_RS02565 ON16_RS02765
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 ON16_RS02570
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 ON16_RS02570
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline rocA: 1-pyrroline-5-carboxylate dehydrogenase
citrulline rocD: ornithine aminotransferase ON16_RS01580 ON16_RS10080
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase ON16_RS05670 ON16_RS05665
D-lactate lctP: D-lactate:H+ symporter LctP or LidP
D-serine cycA: D-serine:H+ symporter CycA
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating)
deoxyinosine bmpA: deoxyinosine ABC transporter, substrate-binding component ON16_RS02075
deoxyinosine deoB: phosphopentomutase ON16_RS11465 ON16_RS01800
deoxyinosine nupB: deoxyinosine ABC transporter, permease component 1 ON16_RS05575 ON16_RS14140
deoxyinosine nupC': deoxyinosine ABC transporter, permease component 2 ON16_RS14135 ON16_RS05580
deoxyribonate aacS: acetoacetyl-CoA synthetase
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase ON16_RS01385 ON16_RS13885
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose adh: acetaldehyde dehydrogenase (not acylating)
deoxyribose deoP: deoxyribose transporter
ethanol adh: acetaldehyde dehydrogenase (not acylating)
fructose Slc2a5: fructose:H+ symporter
fucose aldA: lactaldehyde dehydrogenase
fucose fucA: L-fuculose-phosphate aldolase FucA ON16_RS00635
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 dauA: fumarate transporter DauA ON16_RS04725
galactose galK: galactokinase (-1-phosphate forming) ON16_RS07545
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase ON16_RS07555
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate kdgK: 2-keto-3-deoxygluconate kinase ON16_RS14200 ON16_RS03880
galacturonate uxaA: D-altronate dehydratase ON16_RS00840
galacturonate uxaB: tagaturonate reductase
galacturonate uxaC: D-galacturonate isomerase
gluconate edd: phosphogluconate dehydratase
gluconate gntA: gluconate TRAP transporter, small permease component ON16_RS14510
gluconate gntB: gluconate TRAP transporter, large permease component ON16_RS02245 ON16_RS01180
gluconate gntC: gluconate TRAP transporter, periplasmic solute-binding component ON16_RS11725 ON16_RS01170
gluconate gntK: D-gluconate kinase ON16_RS04670 ON16_RS02710
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) ON16_RS08890
glucosamine SLC2A2: glucosamine transporter SLC2A2
glucose glk: glucokinase ON16_RS08410 ON16_RS02730
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate dctP: D-glucuronate TRAP transporter, solute receptor component ON16_RS14245 ON16_RS01170
glucuronate dctQ: D-glucuronate TRAP transporter, small permease component
glucuronate garL: 5-dehydro-4-deoxy-D-glucarate aldolase ON16_RS13930 ON16_RS01120
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate udh: D-glucuronate dehydrogenase
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric)
glycerol glpF: glycerol facilitator glpF
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine PA5503: L-histidine ABC transporter, ATPase component ON16_RS10455 ON16_RS09350
histidine PA5504: L-histidine ABC transporter, permease component ON16_RS10460
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase ON16_RS11550 ON16_RS10820
isoleucine acn: (2R,3S)-2-methylcitrate dehydratase
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase ON16_RS10830 ON16_RS05710
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase ON16_RS01680 ON16_RS09985
isoleucine livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) ON16_RS02795 ON16_RS01840
isoleucine livM: L-isoleucine ABC transporter, permease component 2 (LivM/BraE) ON16_RS01850 ON16_RS02805
isoleucine prpB: 2-methylisocitrate lyase
isoleucine prpC: 2-methylcitrate synthase ON16_RS03845
isoleucine prpD: 2-methylcitrate dehydratase
isoleucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
L-lactate L-LDH: L-lactate dehydrogenase ON16_RS03045
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
L-malate Dshi_1195: TRAP transporter for succinate, fumarate, L-malate, and 2-oxoglutarate, substrate-binding component
lactose galK: galactokinase (-1-phosphate forming) ON16_RS07545
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase ON16_RS07555
lactose glk: glucokinase ON16_RS08410 ON16_RS02730
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
leucine aacS: acetoacetyl-CoA synthetase
leucine liuA: isovaleryl-CoA dehydrogenase ON16_RS10820 ON16_RS15360
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit ON16_RS08580 ON16_RS01650
leucine liuC: 3-methylglutaconyl-CoA hydratase ON16_RS05710 ON16_RS10830
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) ON16_RS02795 ON16_RS01840
leucine livM: L-leucine ABC transporter, permease component 2 (LivM/BraE) ON16_RS01850 ON16_RS02805
leucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
lysine amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd)
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase ON16_RS10080 ON16_RS01580
lysine lysN: 2-aminoadipate transaminase ON16_RS13900 ON16_RS05675
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase
maltose glk: glucokinase ON16_RS08410 ON16_RS02730
maltose susB: alpha-glucosidase (maltase) ON16_RS06835
mannitol mt2d: mannitol 2-dehydrogenase ON16_RS09985 ON16_RS01680
mannitol PLT5: polyol transporter PLT5
mannose man-isomerase: D-mannose isomerase
mannose STP6: mannose:H+ symporter
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 ON16_RS09320
myoinositol iolT: myo-inositol:H+ symporter
myoinositol mmsA: malonate-semialdehyde dehydrogenase
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) ON16_RS08890
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 ON16_RS10830 ON16_RS05710
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase ON16_RS05710 ON16_RS10830
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase ON16_RS05715 ON16_RS04985
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase ON16_RS05715 ON16_RS04985
phenylacetate paaK: phenylacetate-CoA ligase
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine iorAB: phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB
phenylalanine paaA: phenylacetyl-CoA 1,2-epoxidase, subunit A
phenylalanine paaB: phenylacetyl-CoA 1,2-epoxidase, subunit B
phenylalanine paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C
phenylalanine paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E
phenylalanine paaF: 2,3-dehydroadipyl-CoA hydratase ON16_RS10830 ON16_RS05710
phenylalanine paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase ON16_RS05710 ON16_RS10830
phenylalanine paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase ON16_RS05715 ON16_RS04985
phenylalanine paaJ2: 3-oxoadipyl-CoA thiolase ON16_RS05715 ON16_RS04985
phenylalanine paaZ1: oxepin-CoA hydrolase
phenylalanine paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
proline put1: proline dehydrogenase
proline putA: L-glutamate 5-semialdeyde dehydrogenase
propionate acn: (2R,3S)-2-methylcitrate dehydratase
propionate prpB: 2-methylisocitrate lyase
propionate prpC: 2-methylcitrate synthase ON16_RS03845
propionate prpD: 2-methylcitrate dehydratase
propionate prpE: propionyl-CoA synthetase
propionate putP: propionate transporter; proline:Na+ symporter ON16_RS13915
putrescine gabD: succinate semialdehyde dehydrogenase ON16_RS01115
putrescine gabT: gamma-aminobutyrate transaminase ON16_RS10080 ON16_RS01580
putrescine patA: putrescine aminotransferase (PatA/SpuC) ON16_RS01580 ON16_RS10080
putrescine patD: gamma-aminobutyraldehyde dehydrogenase
putrescine potB: putrescine ABC transporter, permease component 1 (PotB/PotH) ON16_RS08360
putrescine potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) ON16_RS08350
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose LRA1: L-rhamnofuranose dehydrogenase ON16_RS01385 ON16_RS09985
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase ON16_RS00840
rhamnose LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase ON16_RS01680 ON16_RS13885
rhamnose LRA6: 2,4-diketo-3-deoxyrhamnonate hydrolase
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsU: probable D-ribose transporter RbsU
serine serP: L-serine permease SerP
sorbitol sdh: sorbitol dehydrogenase ON16_RS01680 ON16_RS09985
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
succinate dauA: succinate:H+ symporter DauA ON16_RS04725
sucrose ams: sucrose hydrolase (invertase)
sucrose glk: glucokinase ON16_RS08410 ON16_RS02730
threonine adh: acetaldehyde dehydrogenase (not acylating)
threonine ltaE: L-threonine aldolase ON16_RS09800 ON16_RS04170
threonine tdcC: L-threonine:H+ symporter TdcC
thymidine adh: acetaldehyde dehydrogenase (not acylating)
thymidine deoB: phosphopentomutase ON16_RS11465 ON16_RS01800
thymidine nupG: thymidine permease NupG/XapB
trehalose glk: glucokinase ON16_RS08410 ON16_RS02730
trehalose treF: trehalase
tryptophan tnaA: tryptophanase
tryptophan trpP: energy-coupling factor transporter, tryptophan-specific (S) component TrpP
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 ON16_RS11550 ON16_RS15360
valine acn: (2R,3S)-2-methylcitrate dehydratase
valine bch: 3-hydroxyisobutyryl-CoA hydrolase ON16_RS05710 ON16_RS09920
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) ON16_RS02795 ON16_RS01840
valine livM: L-valine ABC transporter, permease component 2 (LivM/BraE) ON16_RS01850 ON16_RS02805
valine mmsA: methylmalonate-semialdehyde dehydrogenase
valine mmsB: 3-hydroxyisobutyrate dehydrogenase ON16_RS01115
valine prpB: 2-methylisocitrate lyase
valine prpC: 2-methylcitrate synthase ON16_RS03845
valine prpD: 2-methylcitrate dehydratase
valine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
xylitol PLT5: xylitol:H+ symporter PLT5
xylitol xdhA: xylitol dehydrogenase ON16_RS15695 ON16_RS04320
xylose xylA: xylose isomerase

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