GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Methylohalobius crimeensis 10Ki

Found 180 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 actP: cation/acetate symporter ActP
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter
arginine gabT: gamma-aminobutyrate transaminase H035_RS0106595 H035_RS0111080
arginine patA: putrescine aminotransferase (PatA/SpuC) H035_RS0111080 H035_RS0104615
arginine patD: gamma-aminobutyraldehyde dehydrogenase H035_RS0111795 H035_RS0106590
arginine rocE: L-arginine permease
asparagine ans: asparaginase
cellobiose cbp: cellobiose phosphorylase
cellobiose cdt: cellobiose transporter cdt-1/cdt-2
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component H035_RS0117200 H035_RS0115485
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
citrulline arcC: carbamate kinase
citrulline rocD: ornithine aminotransferase H035_RS0111080 H035_RS0106595
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
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 H035_RS0114785
deoxyinosine deoB: phosphopentomutase H035_RS0115785
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase H035_RS0115905
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate aacS: acetoacetyl-CoA synthetase
deoxyribonate atoB: acetyl-CoA C-acetyltransferase H035_RS0116515
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase H035_RS0114820 H035_RS0104415
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 deoK: deoxyribokinase H035_RS17985
deoxyribose deoP: deoxyribose transporter
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) H035_RS0115435 H035_RS0114775
fructose Slc2a5: fructose:H+ symporter
fucose aldA: lactaldehyde dehydrogenase H035_RS0111795 H035_RS0106590
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 galK: galactokinase (-1-phosphate forming)
galactose galP: galactose:H+ symporter GalP
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galacturonate dopDH: 2,5-dioxopentanonate dehydrogenase H035_RS0106590 H035_RS0111795
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate gci: D-galactarolactone cycloisomerase
galacturonate gli: D-galactarolactone isomerase
galacturonate kdgD: 5-dehydro-4-deoxyglucarate dehydratase H035_RS0112360
galacturonate udh: D-galacturonate dehydrogenase
gluconate gnd: 6-phosphogluconate dehydrogenase, decarboxylating
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) H035_RS0117040
glucose MFS-glucose: glucose transporter, MFS superfamily
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate dopDH: 2,5-dioxopentanonate dehydrogenase H035_RS0106590 H035_RS0111795
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate kdgD: 5-dehydro-4-deoxyglucarate dehydratase H035_RS0112360
glucuronate udh: D-glucuronate dehydrogenase
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) H035_RS20290
glycerol glpF: glycerol facilitator glpF
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
histidine permease: L-histidine permease
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase H035_RS17865
isoleucine Bap2: L-isoleucine permease Bap2
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase H035_RS0116520
isoleucine fadA: 2-methylacetoacetyl-CoA thiolase H035_RS0116515
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase H035_RS0109625 H035_RS0114820
isoleucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
isoleucine prpB: 2-methylisocitrate lyase
isoleucine prpC: 2-methylcitrate synthase H035_RS0111545 H035_RS19370
isoleucine prpD: 2-methylcitrate dehydratase
L-lactate lctO: L-lactate oxidase or 2-monooxygenase H035_RS0114640
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
L-malate sdlC: L-malate:Na+ symporter SdlC
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
leucine aacS: acetoacetyl-CoA synthetase
leucine atoB: acetyl-CoA C-acetyltransferase H035_RS0116515
leucine leuT: L-leucine:Na+ symporter LeuT H035_RS0109575
leucine liuA: isovaleryl-CoA dehydrogenase H035_RS17865
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit H035_RS0103075 H035_RS0104445
leucine liuC: 3-methylglutaconyl-CoA hydratase H035_RS0116520
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
lysine davT: 5-aminovalerate aminotransferase H035_RS0106595 H035_RS0111080
lysine glaH: glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lysine lhgD: L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
lysine lysP: L-lysine:H+ symporter LysP
lysine patA: cadaverine aminotransferase H035_RS0111080 H035_RS0104615
lysine patD: 5-aminopentanal dehydrogenase H035_RS0111795 H035_RS0106590
maltose MAL11: maltose permease
mannitol mt2d: mannitol 2-dehydrogenase H035_RS0114820 H035_RS0109625
mannitol PLT5: polyol transporter PLT5
mannose manP: mannose PTS system, EII-CBA components
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 H035_RS0110995 H035_RS0110990
myoinositol iolT: myo-inositol:H+ symporter
myoinositol mmsA: malonate-semialdehyde dehydrogenase H035_RS0106590 H035_RS0111795
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) H035_RS0117040
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 H035_RS0116520
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase H035_RS0116520 H035_RS0114820
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase H035_RS0116515
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase H035_RS0116515
phenylacetate paaK: phenylacetate-CoA ligase H035_RS0106275
phenylacetate paaT: phenylacetate transporter Paa
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
phenylalanine atoB: acetyl-CoA C-acetyltransferase H035_RS0116515
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 H035_RS0107865
phenylalanine QDPR: 6,7-dihydropteridine reductase
proline ectP: proline transporter EctP H035_RS0112280
propionate prpB: 2-methylisocitrate lyase
propionate prpC: 2-methylcitrate synthase H035_RS0111545 H035_RS19370
propionate prpD: 2-methylcitrate dehydratase
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabT: gamma-aminobutyrate transaminase H035_RS0106595 H035_RS0111080
putrescine patA: putrescine aminotransferase (PatA/SpuC) H035_RS0111080 H035_RS0104615
putrescine patD: gamma-aminobutyraldehyde dehydrogenase H035_RS0111795 H035_RS0106590
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate dctM: pyruvate TRAP transporter, large permease component H035_RS0111955 H035_RS0106485
pyruvate dctQ: pyruvate TRAP transporter, small permease component H035_RS0111960
rhamnose aldA: lactaldehyde dehydrogenase H035_RS0111795 H035_RS0106590
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 rbsK: ribokinase H035_RS17985
ribose rbsU: probable D-ribose transporter RbsU
serine snatA: L-serine transporter H035_RS0111395
sorbitol sdh: sorbitol dehydrogenase H035_RS0114820 H035_RS0109625
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
succinate sdc: succinate:Na+ symporter Sdc
sucrose sut: sucrose:proton symporter SUT/SUC
threonine snatA: L-threonine transporter snatA H035_RS0111395
threonine tdh: L-threonine 3-dehydrogenase
threonine tynA: aminoacetone oxidase
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase H035_RS0115785
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
trehalose PsTP: trehalose phosphorylase
trehalose thuE: trehalose ABC transporter, substrate-binding component ThuE H035_RS0104700
tryptophan tnaA: tryptophanase
tryptophan tnaT: tryptophan:Na+ symporter TnaT H035_RS0109575
tyrosine aacS: acetoacetyl-CoA synthetase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine atoB: acetyl-CoA C-acetyltransferase H035_RS0116515
tyrosine fahA: fumarylacetoacetate hydrolase
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase H035_RS17865
valine Bap2: L-valine permease Bap2
valine bch: 3-hydroxyisobutyryl-CoA hydrolase
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase H035_RS0116520
valine mmsA: methylmalonate-semialdehyde dehydrogenase H035_RS0106590 H035_RS0111795
valine mmsB: 3-hydroxyisobutyrate dehydrogenase H035_RS0104575
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
valine prpB: 2-methylisocitrate lyase
valine prpC: 2-methylcitrate synthase H035_RS0111545 H035_RS19370
valine prpD: 2-methylcitrate dehydratase
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase
xylose xylA: xylose isomerase
xylose xylB: xylulokinase
xylose xylT: D-xylose transporter

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