GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Methylosarcina fibrata AML-C10

Found 152 low-confidence and 34 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 adh: acetaldehyde dehydrogenase (not acylating) A3OW_RS0110015 A3OW_RS0103305
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase
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 arcA: arginine deiminase
arginine rocE: L-arginine permease
asparagine ans: asparaginase A3OW_RS0120000
aspartate glt: aspartate:proton symporter Glt A3OW_RS0110865 A3OW_RS0104325
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component A3OW_RS0114160 A3OW_RS0113235
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
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 A3OW_RS0103355
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) A3OW_RS0110015 A3OW_RS0103305
deoxyinosine deoB: phosphopentomutase
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate atoB: acetyl-CoA C-acetyltransferase A3OW_RS0123290
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase A3OW_RS0122110 A3OW_RS0115980
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter A3OW_RS0117810
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose adh: acetaldehyde dehydrogenase (not acylating) A3OW_RS0110015 A3OW_RS0103305
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
ethanol adh: acetaldehyde dehydrogenase (not acylating) A3OW_RS0110015 A3OW_RS0103305
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) A3OW_RS0103345 A3OW_RS0119655
fructose fruP: fructose porter FruP A3OW_RS23845
fucose aldA: lactaldehyde dehydrogenase A3OW_RS0110015 A3OW_RS0102820
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 A3OW_RS23845
fucose fucU: L-fucose mutarotase FucU
fumarate dctA: fumarate:H+ symporter DctA A3OW_RS0110865
galactose galK: galactokinase (-1-phosphate forming)
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
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
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) A3OW_RS0118920
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 A3OW_RS0107135
glucuronate garR: tartronate semialdehyde reductase A3OW_RS0118330 A3OW_RS0103075
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate udh: D-glucuronate dehydrogenase
glutamate aspA: L-aspartate ammonia-lyase A3OW_RS0103975
glutamate gltP: L-glutamate:cation symporter GltP/GltT A3OW_RS0110865
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) A3OW_RS0122820
glycerol glpF: glycerol facilitator glpF A3OW_RS0104855
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 A3OW_RS0123280
isoleucine Bap2: L-isoleucine permease Bap2
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase A3OW_RS0109870 A3OW_RS0107185
isoleucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
isoleucine prpB: 2-methylisocitrate lyase
isoleucine prpC: 2-methylcitrate synthase A3OW_RS0112990
isoleucine prpD: 2-methylcitrate dehydratase
L-lactate L-LDH: L-lactate dehydrogenase A3OW_RS0103515
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) A3OW_RS0102400
leucine atoB: acetyl-CoA C-acetyltransferase A3OW_RS0123290
leucine leuT: L-leucine:Na+ symporter LeuT A3OW_RS27485
leucine liuA: isovaleryl-CoA dehydrogenase
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit A3OW_RS0110545 A3OW_RS0114705
leucine liuC: 3-methylglutaconyl-CoA hydratase A3OW_RS0123285
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) A3OW_RS0110015 A3OW_RS0112455
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase A3OW_RS0104890
lysine lysN: 2-aminoadipate transaminase A3OW_RS0107000 A3OW_RS0104890
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase
maltose susB: alpha-glucosidase (maltase)
mannitol mt2d: mannitol 2-dehydrogenase A3OW_RS0112260 A3OW_RS0115045
mannitol PLT5: polyol transporter PLT5
mannose gluP: mannose:Na+ symporter A3OW_RS23845
mannose man-isomerase: D-mannose isomerase
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
myoinositol mmsA: malonate-semialdehyde dehydrogenase A3OW_RS0110015
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) A3OW_RS0118920
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
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase A3OW_RS0123285 A3OW_RS0109870
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase A3OW_RS0123290
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase A3OW_RS0123290
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 atoB: acetyl-CoA C-acetyltransferase A3OW_RS0123290
phenylalanine PAH: phenylalanine 4-monooxygenase
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase A3OW_RS0110380
phenylalanine QDPR: 6,7-dihydropteridine reductase
proline proY: proline:H+ symporter
propionate prpB: 2-methylisocitrate lyase
propionate prpC: 2-methylcitrate synthase A3OW_RS0112990
propionate prpD: 2-methylcitrate dehydratase
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabD: succinate semialdehyde dehydrogenase A3OW_RS0110015 A3OW_RS0102820
putrescine gabT: gamma-aminobutyrate transaminase A3OW_RS0104890 A3OW_RS0110530
putrescine patA: putrescine aminotransferase (PatA/SpuC) A3OW_RS0104890 A3OW_RS0107650
putrescine patD: gamma-aminobutyraldehyde dehydrogenase A3OW_RS0110015 A3OW_RS0102820
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
rhamnose aldA: lactaldehyde dehydrogenase A3OW_RS0110015 A3OW_RS0102820
rhamnose LRA1: L-rhamnofuranose dehydrogenase A3OW_RS0107185 A3OW_RS0115045
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase
rhamnose LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsK: ribokinase
ribose rbsU: probable D-ribose transporter RbsU
serine snatA: L-serine transporter A3OW_RS0101915
sorbitol sdh: sorbitol dehydrogenase A3OW_RS0112260 A3OW_RS0115045
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
succinate sdc: succinate:Na+ symporter Sdc
threonine adh: acetaldehyde dehydrogenase (not acylating) A3OW_RS0110015 A3OW_RS0103305
threonine snatA: L-threonine transporter snatA A3OW_RS0101915
thymidine adh: acetaldehyde dehydrogenase (not acylating) A3OW_RS0110015 A3OW_RS0103305
thymidine deoB: phosphopentomutase
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
trehalose lpqY: trehalose ABC transporter, substrate-binding lipoprotein component LpqY A3OW_RS0109815
trehalose PsTP: trehalose phosphorylase
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine atoB: acetyl-CoA C-acetyltransferase A3OW_RS0123290
valine acdH: isobutyryl-CoA dehydrogenase
valine Bap2: L-valine permease Bap2
valine bch: 3-hydroxyisobutyryl-CoA hydrolase
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase
valine mmsA: methylmalonate-semialdehyde dehydrogenase A3OW_RS0110015
valine mmsB: 3-hydroxyisobutyrate dehydrogenase A3OW_RS0118330 A3OW_RS0103075
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
valine prpB: 2-methylisocitrate lyase
valine prpC: 2-methylcitrate synthase A3OW_RS0112990
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 Apr 09 2024. 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