GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Frankia alni ACN14a

Found 112 low-confidence and 66 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 FRAAL_RS14880
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 FRAAL_RS02485
acetate dctA: organic acid/proton symporter DctA FRAAL_RS06065
alanine cycA: L-alanine symporter CycA
arabinose araE: L-arabinose:H+ symporter
arabinose xacB: L-arabinose 1-dehydrogenase FRAAL_RS26370 FRAAL_RS10545
arabinose xacC: L-arabinono-1,4-lactonase
arabinose xacD: L-arabinonate dehydratase FRAAL_RS29895
arabinose xacE: 2-dehydro-3-deoxy-L-arabinonate dehydratase
arginine adiA: arginine decarboxylase (AdiA/SpeA)
arginine aguB: N-carbamoylputrescine hydrolase FRAAL_RS06160 FRAAL_RS00760
arginine gabT: gamma-aminobutyrate transaminase FRAAL_RS26530 FRAAL_RS06200
arginine patA: putrescine aminotransferase (PatA/SpuC) FRAAL_RS22695 FRAAL_RS06200
arginine rocE: L-arginine permease
asparagine glt: aspartate:proton symporter Glt FRAAL_RS06065
aspartate glt: aspartate:proton symporter Glt FRAAL_RS06065
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 FRAAL_RS26090 FRAAL_RS24880
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 FRAAL_RS26085
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 FRAAL_RS26085
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline arcC: carbamate kinase
citrulline put1: proline dehydrogenase FRAAL_RS18995 FRAAL_RS08175
citrulline rocD: ornithine aminotransferase FRAAL_RS26530 FRAAL_RS06200
D-alanine dadA: D-alanine dehydrogenase FRAAL_RS24620
D-lactate D-LDH: D-lactate dehydrogenase FRAAL_RS16885 FRAAL_RS23870
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase FRAAL_RS19290 FRAAL_RS05015
deoxyinosine deoB: phosphopentomutase FRAAL_RS05230 FRAAL_RS04860
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase FRAAL_RS19180 FRAAL_RS25580
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
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
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
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate gci: D-galactarolactone cycloisomerase
galacturonate gli: D-galactarolactone isomerase
galacturonate kdgD: 5-dehydro-4-deoxyglucarate dehydratase FRAAL_RS24990
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) FRAAL_RS04865 FRAAL_RS20020
glucose MFS-glucose: glucose transporter, MFS superfamily
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 FRAAL_RS14885 FRAAL_RS24990
glucuronate garR: tartronate semialdehyde reductase FRAAL_RS35065 FRAAL_RS26490
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glutamate yveA: L-glutamate:H+ symporter YveA FRAAL_RS13090
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) FRAAL_RS06805 FRAAL_RS31395
glycerol glpF: glycerol facilitator glpF FRAAL_RS06150
histidine Ga0059261_1577: L-histidine transporter FRAAL_RS16235
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
isoleucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit FRAAL_RS14120 FRAAL_RS00345
isoleucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component FRAAL_RS14110 FRAAL_RS22465
isoleucine livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) FRAAL_RS03125 FRAAL_RS11430
isoleucine livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) FRAAL_RS03120 FRAAL_RS20185
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit FRAAL_RS05280 FRAAL_RS13800
L-lactate lctO: L-lactate oxidase or 2-monooxygenase FRAAL_RS16695 FRAAL_RS15640
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
leucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit FRAAL_RS14120 FRAAL_RS00345
leucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component FRAAL_RS14110 FRAAL_RS22465
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit FRAAL_RS13800 FRAAL_RS07215
leucine liuC: 3-methylglutaconyl-CoA hydratase FRAAL_RS25610 FRAAL_RS13585
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine livH: L-leucine ABC transporter, permease component 1 (LivH/BraD) FRAAL_RS03125
leucine livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) FRAAL_RS03120 FRAAL_RS20185
lysine cadA: lysine decarboxylase FRAAL_RS26605 FRAAL_RS28025
lysine davD: glutarate semialdehyde dehydrogenase FRAAL_RS14890 FRAAL_RS18340
lysine gcdG: succinyl-CoA:glutarate CoA-transferase FRAAL_RS20775 FRAAL_RS14895
lysine gcdH: glutaryl-CoA dehydrogenase FRAAL_RS13805 FRAAL_RS12160
lysine lysP: L-lysine:H+ symporter LysP
lysine patA: cadaverine aminotransferase FRAAL_RS22695 FRAAL_RS28020
maltose MAL11: maltose permease
mannitol mtlA: mannitol phosphotransferase system, EII-CBA components
mannitol mtlD: mannitol-1-phosphate 5-dehydrogenase
mannose manA: mannose-6-phosphate isomerase FRAAL_RS05545
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 FRAAL_RS08930 FRAAL_RS13170
myoinositol iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase
myoinositol iolT: myo-inositol:H+ symporter
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) FRAAL_RS04865 FRAAL_RS20020
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 FRAAL_RS25610 FRAAL_RS13585
phenylacetate paaK: phenylacetate-CoA ligase FRAAL_RS11395 FRAAL_RS13580
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase FRAAL_RS20785 FRAAL_RS20780
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine livF: L-phenylalanine ABC transporter, ATPase component 1 (LivF) FRAAL_RS03140 FRAAL_RS21210
phenylalanine livG: L-phenylalanine ABC transporter, ATPase component 2 (LivG) FRAAL_RS03135 FRAAL_RS13665
phenylalanine livH: L-phenylalanine ABC transporter, permease component 1 (LivH) FRAAL_RS03125 FRAAL_RS11430
phenylalanine livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK FRAAL_RS03120 FRAAL_RS20185
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 FRAAL_RS25610 FRAAL_RS13585
phenylalanine paaK: phenylacetate-CoA ligase FRAAL_RS11395 FRAAL_RS13580
phenylalanine paaZ1: oxepin-CoA hydrolase FRAAL_RS20785 FRAAL_RS20780
phenylalanine paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine pad-dh: phenylacetaldehyde dehydrogenase FRAAL_RS00920 FRAAL_RS14890
proline HSERO_RS00870: proline ABC transporter, substrate-binding component FRAAL_RS03120 FRAAL_RS20185
proline HSERO_RS00900: proline ABC transporter, ATPase component 2 FRAAL_RS03140 FRAAL_RS21210
proline put1: proline dehydrogenase FRAAL_RS18995 FRAAL_RS08175
propionate pccA: propionyl-CoA carboxylase, alpha subunit FRAAL_RS05280 FRAAL_RS13800
putrescine gabT: gamma-aminobutyrate transaminase FRAAL_RS26530 FRAAL_RS06200
putrescine patA: putrescine aminotransferase (PatA/SpuC) FRAAL_RS22695 FRAAL_RS06200
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
rhamnose LRA1: L-rhamnofuranose dehydrogenase FRAAL_RS11520 FRAAL_RS03280
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase
rhamnose LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase FRAAL_RS14885
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsU: probable D-ribose transporter RbsU
serine Ac3H11_1692: L-tyrosine ABC transporter, ATPase component 2 FRAAL_RS03140 FRAAL_RS21210
serine Ac3H11_1693: L-tyrosine ABC transporter, ATPase component 1 FRAAL_RS03135 FRAAL_RS13665
serine Ac3H11_1695: L-tyrosine ABC transporter, permease component 1 FRAAL_RS03125
serine Ac3H11_2396: L-tyrosine ABC transporter, substrate-binding component component FRAAL_RS03120 FRAAL_RS20185
serine sdaB: L-serine ammonia-lyase FRAAL_RS05015 FRAAL_RS19290
sorbitol scrK: fructokinase FRAAL_RS17365 FRAAL_RS22205
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
sucrose ams: sucrose hydrolase (invertase) FRAAL_RS07960 FRAAL_RS25690
sucrose MFS-glucose: glucose transporter, MFS superfamily
threonine tdcC: L-threonine:H+ symporter TdcC
thymidine deoB: phosphopentomutase FRAAL_RS05230 FRAAL_RS04860
thymidine nupG: thymidine permease NupG/XapB
trehalose lpqY: trehalose ABC transporter, substrate-binding lipoprotein component LpqY FRAAL_RS16475
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine Ac3H11_1692: L-tyrosine ABC transporter, ATPase component 2 FRAAL_RS03140 FRAAL_RS21210
tyrosine Ac3H11_1693: L-tyrosine ABC transporter, ATPase component 1 FRAAL_RS03135 FRAAL_RS13665
tyrosine Ac3H11_1695: L-tyrosine ABC transporter, permease component 1 FRAAL_RS03125
tyrosine Ac3H11_2396: L-tyrosine ABC transporter, substrate-binding component component FRAAL_RS03120 FRAAL_RS20185
tyrosine fahA: fumarylacetoacetate hydrolase FRAAL_RS25420
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine bch: 3-hydroxyisobutyryl-CoA hydrolase FRAAL_RS12225 FRAAL_RS07100
valine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit FRAAL_RS14120 FRAAL_RS00345
valine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component FRAAL_RS14110 FRAAL_RS22465
valine livH: L-valine ABC transporter, permease component 1 (LivH/BraD) FRAAL_RS03125
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) FRAAL_RS03120 FRAAL_RS20185
valine livM: L-valine ABC transporter, permease component 2 (LivM/BraE) FRAAL_RS03130 FRAAL_RS03425
valine mmsA: methylmalonate-semialdehyde dehydrogenase FRAAL_RS06170 FRAAL_RS13635
valine mmsB: 3-hydroxyisobutyrate dehydrogenase FRAAL_RS26490 FRAAL_RS06570
valine pccA: propionyl-CoA carboxylase, alpha subunit FRAAL_RS05280 FRAAL_RS13800
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase FRAAL_RS23810
xylose xylA: xylose isomerase
xylose xylB: xylulokinase FRAAL_RS19965
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.

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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