GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Pseudarthrobacter sulfonivorans Ar51

Found 41 low-confidence and 72 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
4-hydroxybenzoate pcaB: 3-carboxymuconate cycloisomerase AU252_RS10750
4-hydroxybenzoate pcaD: 3-oxoadipate enol-lactone hydrolase AU252_RS16275 AU252_RS10755
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK AU252_RS04970 AU252_RS22885
arginine gabT: gamma-aminobutyrate transaminase AU252_RS16125 AU252_RS02890
arginine gbamidase: guanidinobutyramidase AU252_RS04565 AU252_RS09230
arginine kauB: 4-guanidinobutyraldehyde dehydrogenase AU252_RS01555 AU252_RS22410
arginine rocE: L-arginine permease AU252_RS04790 AU252_RS08100
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component AU252_RS13905 AU252_RS15210
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 AU252_RS09255 AU252_RS15205
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 AU252_RS13390 AU252_RS09255
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline citrullinase: putative citrullinase AU252_RS13110 AU252_RS06335
citrulline gabT: gamma-aminobutyrate transaminase AU252_RS16125 AU252_RS02890
citrulline odc: L-ornithine decarboxylase
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase AU252_RS06485 AU252_RS16225
D-lactate larD: D,L-lactic acid transporter AU252_RS21085
D-serine dsdA: D-serine ammonia-lyase AU252_RS04295 AU252_RS13625
deoxyinosine bmpA: deoxyinosine ABC transporter, substrate-binding component AU252_RS04435
deoxyinosine deoB: phosphopentomutase AU252_RS03935 AU252_RS06775
deoxyinosine nupB: deoxyinosine ABC transporter, permease component 1 AU252_RS04425
deoxyinosine nupC': deoxyinosine ABC transporter, permease component 2 AU252_RS04420
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase AU252_RS13405 AU252_RS01350
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter AU252_RS05895 AU252_RS20980
deoxyribose deoP: deoxyribose transporter
fructose scrK: fructokinase AU252_RS09170 AU252_RS08575
fucose fucA: L-fuculose-phosphate aldolase FucA
fucose fucI: L-fucose isomerase FucI
fucose fucP: L-fucose:H+ symporter FucP
fucose fucU: L-fucose mutarotase FucU AU252_RS14775
galacturonate PS417_04205: D-galacturonate transporter AU252_RS13435
galacturonate udh: D-galacturonate dehydrogenase
galacturonate uxuL: D-galactaro-1,5-lactonase (UxuL or UxuF)
gluconate gntT: gluconate:H+ symporter GntT AU252_RS04805 AU252_RS08420
glucosamine crr: N-acetylglucosamine phosphotransferase system, EII-A component Crr AU252_RS11915
glucosamine nagX: transmembrane glucosamine N-acetyltransferase NagX
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate eda: 2-keto-3-deoxygluconate 6-phosphate aldolase AU252_RS16240 AU252_RS14180
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate uxaC: D-glucuronate isomerase AU252_RS07655
glucuronate uxuA: D-mannonate dehydratase AU252_RS07640 AU252_RS14175
glucuronate uxuB: D-mannonate dehydrogenase AU252_RS07650
glutamate gltP: L-glutamate:cation symporter GltP/GltT AU252_RS03850 AU252_RS13765
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) AU252_RS17445 AU252_RS21080
histidine hutH: histidine ammonia-lyase AU252_RS08055 AU252_RS12375
isoleucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component AU252_RS15600 AU252_RS02340
isoleucine lpd: branched-chain alpha-ketoacid dehydrogenase, E3 component AU252_RS02335 AU252_RS03920
isoleucine natB: L-isoleucine ABC transporter, substrate-binding component NatB AU252_RS04345
isoleucine natC: L-isoleucine ABC transporter, permease component 1 (NatC) AU252_RS04330
isoleucine natD: L-isoleucine ABC transporter, permease component 2 (NatD) AU252_RS04325
L-lactate larD: D,L-lactic acid transporter LarD AU252_RS21085
lactose lacP: lactose permease LacP
leucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component AU252_RS15600 AU252_RS02340
leucine liuC: 3-methylglutaconyl-CoA hydratase AU252_RS00745 AU252_RS00825
leucine liuE: hydroxymethylglutaryl-CoA lyase AU252_RS01445 AU252_RS01285
leucine lpd: branched-chain alpha-ketoacid dehydrogenase, E3 component AU252_RS02335 AU252_RS03920
leucine natB: L-leucine ABC transporter, substrate-binding component NatB AU252_RS04345
leucine natC: L-leucine ABC transporter, permease component 1 (NatC) AU252_RS04330
leucine natD: L-leucine ABC transporter, permease component 2 (NatD) AU252_RS04325
lysine davD: glutarate semialdehyde dehydrogenase AU252_RS01005 AU252_RS04095
lysine fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase AU252_RS02130 AU252_RS07090
lysine gcdG: succinyl-CoA:glutarate CoA-transferase AU252_RS00300 AU252_RS01440
lysine lysP: L-lysine:H+ symporter LysP AU252_RS04790 AU252_RS13875
lysine patA: cadaverine aminotransferase AU252_RS02890 AU252_RS16125
mannose manP: mannose PTS system, EII-CBA components AU252_RS08305
myoinositol iolB: 5-deoxy-D-glucuronate isomerase AU252_RS05915
myoinositol iolE: scyllo-inosose 2-dehydratase AU252_RS06000
myoinositol iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase AU252_RS06020 AU252_RS08415
NAG crr: N-acetylglucosamine phosphotransferase system, EII-A component Crr AU252_RS11915
phenylacetate paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E AU252_RS15440
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase AU252_RS07800 AU252_RS00885
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase AU252_RS02130 AU252_RS07090
phenylacetate ppa: phenylacetate permease ppa AU252_RS03465 AU252_RS03490
phenylalanine paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E AU252_RS15440
phenylalanine paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase AU252_RS07800 AU252_RS00885
phenylalanine paaH: 3-hydroxyadipyl-CoA dehydrogenase AU252_RS02130 AU252_RS07090
phenylalanine pad-dh: phenylacetaldehyde dehydrogenase AU252_RS01160 AU252_RS01555
proline put1: proline dehydrogenase AU252_RS11615 AU252_RS09435
proline putA: L-glutamate 5-semialdeyde dehydrogenase AU252_RS22410 AU252_RS01555
putrescine gabT: gamma-aminobutyrate transaminase AU252_RS16125 AU252_RS02890
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
rhamnose rhaM: L-rhamnose mutarotase AU252_RS14775
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
serine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) AU252_RS04345
serine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) AU252_RS04325 AU252_RS00670
serine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) AU252_RS04330 AU252_RS00900
sorbitol mtlK: ABC transporter for polyols MtlEFGK, permease component MtlK AU252_RS06475 AU252_RS13340
sorbitol scrK: fructokinase AU252_RS09170 AU252_RS08575
threonine lpd: dihydrolipoyl dehydrogenase AU252_RS02335 AU252_RS03920
threonine RR42_RS28305: L-threonine:H+ symporter AU252_RS15260 AU252_RS08100
thymidine deoB: phosphopentomutase AU252_RS03935 AU252_RS06775
thymidine nupG: thymidine permease NupG/XapB
trehalose treF: trehalase AU252_RS06490 AU252_RS14285
tryptophan antA: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA AU252_RS22725
tryptophan antB: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB AU252_RS22720
tryptophan antC: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC AU252_RS22715
tryptophan kyn: kynureninase AU252_RS03235
tryptophan kynB: kynurenine formamidase AU252_RS09345
tryptophan xylE: catechol 2,3-dioxygenase AU252_RS19380 AU252_RS22415
tryptophan xylF: 2-hydroxymuconate semialdehyde hydrolase AU252_RS17320 AU252_RS22250
tyrosine fahA: fumarylacetoacetate hydrolase AU252_RS19175
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine bch: 3-hydroxyisobutyryl-CoA hydrolase AU252_RS07810 AU252_RS00745
valine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component AU252_RS15600 AU252_RS02340
valine lpd: branched-chain alpha-ketoacid dehydrogenase, E3 component AU252_RS02335 AU252_RS03920
valine mmsA: methylmalonate-semialdehyde dehydrogenase AU252_RS07815 AU252_RS22410
valine mmsB: 3-hydroxyisobutyrate dehydrogenase AU252_RS07805 AU252_RS13575
valine natB: L-valine ABC transporter, substrate-binding component NatB AU252_RS04345
valine natC: L-valine ABC transporter, permease component 1 (NatC) AU252_RS04330
valine natD: L-valine ABC transporter, permease component 2 (NatD) AU252_RS04325
xylitol PLT5: xylitol:H+ symporter PLT5 AU252_RS05985

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