GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Williamsia sterculiae CPCC 203464

Found 101 low-confidence and 53 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate kgtP: 2-oxoglutarate:H+ symporter KgtP BW971_RS16640 BW971_RS01235
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase BW971_RS01145
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK
4-hydroxybenzoate pobA: 4-hydroxybenzoate 3-monooxygenase
4-hydroxybenzoate praA: protocatechuate 2,3-dioxygenase
4-hydroxybenzoate praB: 2-hydroxymuconate 6-semialdehyde dehydrogenase BW971_RS05790 BW971_RS18685
4-hydroxybenzoate praD: 2-oxohex-3-enedioate decarboxylase BW971_RS01145
acetate dctA: organic acid/proton symporter DctA BW971_RS12205 BW971_RS13035
alanine snatA: L-alanine symporter SnatA BW971_RS05365
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter BW971_RS10475 BW971_RS11095
arginine arcC: carbamate kinase
arginine artP: L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA BW971_RS17350 BW971_RS05930
arginine bgtB: L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) BW971_RS15735 BW971_RS16650
asparagine ans: asparaginase BW971_RS17815
aspartate glt: aspartate:proton symporter Glt BW971_RS12205 BW971_RS13035
cellobiose bgl: cellobiase BW971_RS00885
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component BW971_RS17350 BW971_RS00080
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 BW971_RS15735 BW971_RS17355
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 BW971_RS17355 BW971_RS15735
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline arcC: carbamate kinase
D-alanine cycA: D-alanine:H+ symporter CycA BW971_RS07675 BW971_RS01220
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase BW971_RS14510 BW971_RS12250
D-lactate lctP: D-lactate:H+ symporter LctP or LidP
D-serine cycA: D-serine:H+ symporter CycA BW971_RS05740 BW971_RS09675
D-serine dsdA: D-serine ammonia-lyase BW971_RS15705 BW971_RS04190
deoxyinosine deoB: phosphopentomutase BW971_RS04935 BW971_RS04460
deoxyinosine nupC: deoxyinosine:H+ symporter NupC BW971_RS20870
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase BW971_RS03935 BW971_RS08115
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoP: deoxyribose transporter
fructose 1pfk: 1-phosphofructokinase BW971_RS05980
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 galP: galactose:H+ symporter GalP BW971_RS10475 BW971_RS11095
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase BW971_RS02200
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)
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) BW971_RS04495
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 BW971_RS05845
glucuronate garR: tartronate semialdehyde reductase BW971_RS14530
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate udh: D-glucuronate dehydrogenase
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) BW971_RS04980
glycerol glpF: glycerol facilitator glpF BW971_RS19525
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
histidine permease: L-histidine permease BW971_RS01220 BW971_RS07675
isoleucine livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
isoleucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused BW971_RS03235
L-lactate lctO: L-lactate oxidase or 2-monooxygenase
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase BW971_RS02200
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
leucine liuC: 3-methylglutaconyl-CoA hydratase BW971_RS12060 BW971_RS16050
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine livH: L-leucine ABC transporter, permease component 1 (LivH/BraD) BW971_RS17395
leucine livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) BW971_RS17400
leucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused BW971_RS03235
lysine bgtB: L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) BW971_RS15735 BW971_RS16650
lysine davD: glutarate semialdehyde dehydrogenase BW971_RS02050 BW971_RS04825
lysine gcdG: succinyl-CoA:glutarate CoA-transferase BW971_RS08680 BW971_RS09930
lysine hisP: L-lysine ABC transporter, ATPase component HisP BW971_RS05930 BW971_RS17350
mannitol mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE BW971_RS08975
mannitol mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) BW971_RS08980
mannitol mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) BW971_RS08985 BW971_RS05335
mannitol mtlK: polyol ABC transporter, ATP component MtlK/SmoG BW971_RS05340 BW971_RS08990
mannose manP: mannose PTS system, EII-CBA components BW971_RS05975
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 BW971_RS10475 BW971_RS11095
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) BW971_RS04495
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 BW971_RS14725
phenylacetate paaF: 2,3-dehydroadipyl-CoA hydratase BW971_RS12060 BW971_RS07840
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase BW971_RS12375 BW971_RS16050
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase BW971_RS00100 BW971_RS04170
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase BW971_RS00100 BW971_RS04170
phenylacetate paaK: phenylacetate-CoA ligase BW971_RS01900 BW971_RS16360
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase BW971_RS16050 BW971_RS12375
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP BW971_RS01220 BW971_RS07675
phenylalanine fahA: fumarylacetoacetate hydrolase BW971_RS12265
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 BW971_RS11065
phenylalanine QDPR: 6,7-dihydropteridine reductase
proline put1: proline dehydrogenase BW971_RS03110
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabT: gamma-aminobutyrate transaminase BW971_RS06015 BW971_RS04815
putrescine patA: putrescine aminotransferase (PatA/SpuC) BW971_RS06015 BW971_RS20655
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate ybdD: small subunit of pyruvate transporter (YbdD)
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
serine snatA: L-serine transporter BW971_RS05365
sorbitol mtlF: ABC transporter for polyols MtlEFGK, permease component MtlF BW971_RS08980
sorbitol mtlK: ABC transporter for polyols MtlEFGK, permease component MtlK BW971_RS05340 BW971_RS08990
sucrose 1pfk: 1-phosphofructokinase BW971_RS05980
sucrose ams: sucrose hydrolase (invertase) BW971_RS14260
threonine ltaE: L-threonine aldolase BW971_RS04300 BW971_RS05530
threonine snatA: L-threonine transporter snatA BW971_RS05365
thymidine deoB: phosphopentomutase BW971_RS04935 BW971_RS04460
thymidine nupG: thymidine permease NupG/XapB
tryptophan aroP: tryptophan:H+ symporter AroP BW971_RS01220 BW971_RS07675
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP) BW971_RS01220 BW971_RS07675
tyrosine fahA: fumarylacetoacetate hydrolase BW971_RS12265
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine bch: 3-hydroxyisobutyryl-CoA hydrolase BW971_RS03885 BW971_RS12060
valine livH: L-valine ABC transporter, permease component 1 (LivH/BraD) BW971_RS17395
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) BW971_RS17400
valine mmsA: methylmalonate-semialdehyde dehydrogenase BW971_RS07620 BW971_RS14520
valine mmsB: 3-hydroxyisobutyrate dehydrogenase BW971_RS14530
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused BW971_RS03235
xylitol PLT5: xylitol:H+ symporter PLT5
xylitol xdhA: xylitol dehydrogenase BW971_RS08965 BW971_RS11680
xylose xylA: xylose isomerase
xylose xylT: D-xylose transporter BW971_RS10475 BW971_RS11095

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