GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Ardenticatena maritima 110S

Found 104 low-confidence and 83 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 SE16_RS07345 SE16_RS13645
acetate actP: cation/acetate symporter ActP SE16_RS01385
alanine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) SE16_RS12950 SE16_RS15150
alanine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) SE16_RS12935 SE16_RS14790
alanine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) SE16_RS12945 SE16_RS14780
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 arcC: carbamate kinase SE16_RS11340
arginine rocE: L-arginine permease
asparagine ans: asparaginase SE16_RS01260 SE16_RS12730
asparagine bgtA: aspartate ABC transporter, ATPase component BgtA SE16_RS15010 SE16_RS11275
asparagine bgtB': aspartate ABC transporter, permease component 1 (BgtB) SE16_RS15000
aspartate bgtA: aspartate ABC transporter, ATPase component BgtA SE16_RS15010 SE16_RS11275
aspartate bgtB': aspartate ABC transporter, permease component 1 (BgtB) SE16_RS15000
cellobiose aglE': glucose ABC transporter, substrate-binding component (AglE) SE16_RS03550
cellobiose aglF': glucose ABC transporter, permease component 1 (AglF) SE16_RS03545
cellobiose aglG': glucose ABC transporter, permease component 2 (AglG) SE16_RS03540 SE16_RS12350
cellobiose aglK': glucose ABC transporter, ATPase component (AglK) SE16_RS08755 SE16_RS02415
cellobiose bgl: cellobiase SE16_RS08470 SE16_RS08495
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component SE16_RS15010 SE16_RS11275
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 SE16_RS09375
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 SE16_RS09375
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component SE16_RS09565
citrulline arcC: carbamate kinase SE16_RS11340
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate larD: D,L-lactic acid transporter SE16_RS13535
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase SE16_RS15125
deoxyinosine deoB: phosphopentomutase
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate aacS: acetoacetyl-CoA synthetase SE16_RS01120 SE16_RS04000
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase SE16_RS13660 SE16_RS11575
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoP: deoxyribose transporter
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) SE16_RS11160 SE16_RS02095
fructose Slc2a5: fructose:H+ symporter
fucose aldA: lactaldehyde dehydrogenase SE16_RS08700 SE16_RS04050
fucose fucA: L-fuculose-phosphate aldolase FucA SE16_RS06160
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
galactose pgmA: alpha-phosphoglucomutase SE16_RS06805 SE16_RS14175
galacturonate eda: 2-keto-3-deoxygluconate 6-phosphate aldolase
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate kdgK: 2-keto-3-deoxygluconate kinase SE16_RS09225
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) SE16_RS13090
glucose aglE': glucose ABC transporter, substrate-binding component (AglE) SE16_RS03550
glucose aglF': glucose ABC transporter, permease component 1 (AglF) SE16_RS03545
glucose aglG': glucose ABC transporter, permease component 2 (AglG) SE16_RS03540 SE16_RS12350
glucose aglK': glucose ABC transporter, ATPase component (AglK) SE16_RS08755 SE16_RS02415
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
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate udh: D-glucuronate dehydrogenase
glutamate dmeA: L-glutamate transporter DmeA SE16_RS09185
glutamate gdhA: glutamate dehydrogenase, NAD-dependent SE16_RS13830 SE16_RS00355
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) SE16_RS13555
histidine aapJ: L-histidine ABC transporter, substrate-binding component AapJ SE16_RS14995
histidine aapM: L-histidine ABC transporter, permease component 2 (AapM) SE16_RS15005 SE16_RS09375
histidine aapP: L-histidine ABC transporter, ATPase component AapP SE16_RS15010 SE16_RS11275
histidine hutG: N-formiminoglutamate formiminohydrolase
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase SE16_RS08930 SE16_RS05905
isoleucine livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) SE16_RS12950 SE16_RS15150
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit SE16_RS08915 SE16_RS03415
L-lactate Shew_2732: L-lactate:Na+ symporter, small component SE16_RS01390
L-malate sdlC: L-malate:Na+ symporter SdlC
lactose lacP: lactose permease LacP
lactose pgmA: alpha-phosphoglucomutase SE16_RS06805 SE16_RS14175
leucine aacS: acetoacetyl-CoA synthetase SE16_RS01120 SE16_RS04000
leucine liuA: isovaleryl-CoA dehydrogenase SE16_RS05905 SE16_RS08930
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit SE16_RS03415 SE16_RS08915
leucine liuC: 3-methylglutaconyl-CoA hydratase SE16_RS08740 SE16_RS14460
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit SE16_RS03395 SE16_RS08920
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) SE16_RS12950 SE16_RS15150
lysine hglS: D-2-hydroxyglutarate synthase
lysine lysN: 2-aminoadipate transaminase SE16_RS11185 SE16_RS07105
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase SE16_RS11695
maltose aglE: maltose ABC transporter, substrate-binding component AglK SE16_RS03550
maltose aglF: maltose ABC transporter, permease component 1 (AglF) SE16_RS03545 SE16_RS12355
maltose aglK: maltose ABC transporter, ATPase component AglK SE16_RS08755 SE16_RS02415
mannitol mt2d: mannitol 2-dehydrogenase SE16_RS00340 SE16_RS11575
mannitol PLT5: polyol transporter PLT5
mannose manA: mannose-6-phosphate isomerase SE16_RS11915 SE16_RS05930
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
myoinositol iolT: myo-inositol:H+ symporter
myoinositol mmsA: malonate-semialdehyde dehydrogenase SE16_RS08700 SE16_RS04050
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) SE16_RS13090
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components
phenylacetate paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C SE16_RS13330
phenylacetate paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E
phenylacetate paaK: phenylacetate-CoA ligase SE16_RS07830 SE16_RS13575
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase SE16_RS08735 SE16_RS14460
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine livF: L-phenylalanine ABC transporter, ATPase component 1 (LivF) SE16_RS12945 SE16_RS14780
phenylalanine livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK SE16_RS12950 SE16_RS15160
phenylalanine paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C SE16_RS13330
phenylalanine paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E
phenylalanine paaK: phenylacetate-CoA ligase SE16_RS07830 SE16_RS13575
phenylalanine paaZ1: oxepin-CoA hydrolase SE16_RS08735 SE16_RS14460
phenylalanine paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine pfor: phenylacetaldeyde:ferredoxin oxidoreductase SE16_RS04100
phenylalanine PPDCalpha: phenylpyruvate decarboxylase, alpha subunit SE16_RS05650 SE16_RS03115
phenylalanine PPDCbeta: phenylpyruvate decarboxylase, beta subunit SE16_RS03110 SE16_RS05650
proline HSERO_RS00870: proline ABC transporter, substrate-binding component SE16_RS12950 SE16_RS15160
proline HSERO_RS00885: proline ABC transporter, permease component 1 SE16_RS12930 SE16_RS14795
proline HSERO_RS00900: proline ABC transporter, ATPase component 2 SE16_RS12945 SE16_RS14780
propionate pccA: propionyl-CoA carboxylase, alpha subunit SE16_RS08915 SE16_RS03415
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabT: gamma-aminobutyrate transaminase SE16_RS01285 SE16_RS14690
putrescine patA: putrescine aminotransferase (PatA/SpuC) SE16_RS01285 SE16_RS14690
putrescine patD: gamma-aminobutyraldehyde dehydrogenase SE16_RS04050 SE16_RS08700
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate dctM: pyruvate TRAP transporter, large permease component SE16_RS04130
rhamnose LRA1: L-rhamnofuranose dehydrogenase SE16_RS00340 SE16_RS13660
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase
rhamnose LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase SE16_RS13660 SE16_RS00340
rhamnose LRA6: 2,4-diketo-3-deoxyrhamnonate hydrolase SE16_RS14345 SE16_RS03810
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsU: probable D-ribose transporter RbsU
serine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) SE16_RS12950 SE16_RS15150
serine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) SE16_RS12935 SE16_RS14790
serine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) SE16_RS12945 SE16_RS14780
serine sdaB: L-serine ammonia-lyase SE16_RS15125
sorbitol sdh: sorbitol dehydrogenase SE16_RS13660 SE16_RS11575
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
succinate sdc: succinate:Na+ symporter Sdc
sucrose aglE: sucrose ABC transporter, substrate-binding component AglK SE16_RS03550
sucrose aglF: sucrose ABC transporter, permease component 1 (AglF) SE16_RS03545 SE16_RS12355
sucrose aglK: sucrose ABC transporter, ATPase component AglK SE16_RS08755 SE16_RS02415
sucrose ams: sucrose hydrolase (invertase) SE16_RS01195 SE16_RS04190
threonine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) SE16_RS12950 SE16_RS15150
threonine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) SE16_RS12935 SE16_RS14790
threonine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) SE16_RS12945 SE16_RS14780
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) SE16_RS08075 SE16_RS08085
thymidine deoB: phosphopentomutase
thymidine nupG: thymidine permease NupG/XapB
trehalose aglF: trehalose ABC transporter, permease component 1 (AglF) SE16_RS03545 SE16_RS12355
trehalose aglK: trehalose ABC trehalose, ATPase component AglK SE16_RS08755 SE16_RS02415
trehalose treF: trehalase SE16_RS04190 SE16_RS14730
tryptophan aroP: tryptophan:H+ symporter AroP
tyrosine aacS: acetoacetyl-CoA synthetase SE16_RS01120 SE16_RS04000
tyrosine Ac3H11_1692: L-tyrosine ABC transporter, ATPase component 2 SE16_RS12945 SE16_RS14780
tyrosine Ac3H11_1695: L-tyrosine ABC transporter, permease component 1 SE16_RS12930 SE16_RS14795
tyrosine Ac3H11_2396: L-tyrosine ABC transporter, substrate-binding component component SE16_RS12950 SE16_RS15160
tyrosine fahA: fumarylacetoacetate hydrolase SE16_RS14345
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase SE16_RS08930 SE16_RS05905
valine bch: 3-hydroxyisobutyryl-CoA hydrolase SE16_RS14460 SE16_RS08740
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) SE16_RS12950 SE16_RS15150
valine mmsA: methylmalonate-semialdehyde dehydrogenase SE16_RS04050 SE16_RS08700
valine mmsB: 3-hydroxyisobutyrate dehydrogenase SE16_RS09795
valine pccA: propionyl-CoA carboxylase, alpha subunit SE16_RS08915 SE16_RS03415
xylitol PLT5: xylitol:H+ symporter PLT5
xylitol xdhA: xylitol dehydrogenase SE16_RS01205 SE16_RS11160
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.

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