GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Azospirillum brasilense Sp245

Found 70 low-confidence and 76 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
4-hydroxybenzoate ligA: protocatechuate 4,5-dioxygenase, alpha subunit AZOBR_RS26890
4-hydroxybenzoate pobA: 4-hydroxybenzoate 3-monooxygenase
alanine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) AZOBR_RS08260
alanine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) AZOBR_RS08235 AZOBR_RS03565
alanine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) AZOBR_RS08240 AZOBR_RS25635
alanine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) AZOBR_RS08250 AZOBR_RS29685
arabinose aldA: (glycol)aldehyde dehydrogenase AZOBR_RS19635 AZOBR_RS09720
arabinose KDG-aldolase: 2-dehydro-3-deoxy-L-arabinonate aldolase
arabinose xacC: L-arabinono-1,4-lactonase AZOBR_RS31230 AZOBR_RS22710
arabinose xacD: L-arabinonate dehydratase AZOBR_RS31260 AZOBR_RS25270
arginine braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) AZOBR_RS08235 AZOBR_RS03565
arginine braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) AZOBR_RS08240 AZOBR_RS32410
asparagine bztB: aspartate/asparagine ABC transporter, permease component 1 (BztB) AZOBR_RS08660
asparagine bztC: aspartate/asparagine ABC transporter, permease component 2 (BztC) AZOBR_RS08665
asparagine bztD: aspartate/asparagine ABC transporter, ATPase component (BztD) AZOBR_RS08670 AZOBR_RS15690
aspartate bztB: aspartate/asparagine ABC transporter, permease component 1 (BztB) AZOBR_RS08660
aspartate bztC: aspartate/asparagine ABC transporter, permease component 2 (BztC) AZOBR_RS08665
aspartate bztD: aspartate/asparagine ABC transporter, ATPase component (BztD) AZOBR_RS08670 AZOBR_RS15690
citrate tctB: citrate/Na+ symporter, small transmembrane component TctB AZOBR_RS31455
citrate tctC: citrate/Na+ symporter, substrate-binding component TctC AZOBR_RS31445
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component AZOBR_RS00690 AZOBR_RS23525
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 AZOBR_RS00675 AZOBR_RS18070
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 AZOBR_RS00680 AZOBR_RS23520
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component AZOBR_RS27130 AZOBR_RS00685
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase AZOBR_RS06795
deoxyinosine deoB: phosphopentomutase AZOBR_RS33725 AZOBR_RS07040
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate aacS: acetoacetyl-CoA synthetase AZOBR_RS31155 AZOBR_RS09405
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase AZOBR_RS25730 AZOBR_RS16640
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
fructose tpi: triose-phosphate isomerase AZOBR_RS03885 AZOBR_RS30960
fucose fucD: L-fuconate dehydratase AZOBR_RS31430
fucose fuconolactonase: L-fucono-1,5-lactonase
fucose fucP: L-fucose:H+ symporter FucP
fucose fucU: L-fucose mutarotase FucU
galactose dgoD: D-galactonate dehydratase AZOBR_RS31260 AZOBR_RS04900
galactose dgoK: 2-dehydro-3-deoxygalactonokinase AZOBR_RS29860
galacturonate uxaC: D-galacturonate isomerase AZOBR_RS31425
gluconate gntA: gluconate TRAP transporter, small permease component AZOBR_RS25410
glucosamine SLC2A2: glucosamine transporter SLC2A2
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate uxaC: D-glucuronate isomerase AZOBR_RS31425
glutamate braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) AZOBR_RS08235 AZOBR_RS03565
glutamate braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) AZOBR_RS08240 AZOBR_RS32410
glycerol tpi: triose-phosphate isomerase AZOBR_RS03885 AZOBR_RS30960
histidine Ac3H11_2555: L-histidine ABC transporter, substrate-binding component 2 AZOBR_RS18075 AZOBR_RS27130
histidine hutH: histidine ammonia-lyase
isoleucine livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) AZOBR_RS08235 AZOBR_RS03565
isoleucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
lactose dgoD: D-galactonate dehydratase AZOBR_RS31260 AZOBR_RS04900
lactose dgoK: 2-dehydro-3-deoxygalactonokinase AZOBR_RS29860
lactose lacP: lactose permease LacP
leucine aacS: acetoacetyl-CoA synthetase AZOBR_RS31155 AZOBR_RS09405
leucine livH: L-leucine ABC transporter, permease component 1 (LivH/BraD) AZOBR_RS08235 AZOBR_RS03565
leucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
lysine davB: L-lysine 2-monooxygenase
lysine fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase AZOBR_RS20225 AZOBR_RS29225
lysine hisM: L-lysine ABC transporter, permease component 1 (HisM) AZOBR_RS00675 AZOBR_RS23520
lysine hisQ: L-lysine ABC transporter, permease component 2 (HisQ) AZOBR_RS00680 AZOBR_RS23520
maltose susB: alpha-glucosidase (maltase) AZOBR_RS25735 AZOBR_RS04510
mannitol mt2d: mannitol 2-dehydrogenase AZOBR_RS31375 AZOBR_RS09410
mannitol PLT5: polyol transporter PLT5
mannitol scrK: fructokinase AZOBR_RS11685
mannose manA: mannose-6-phosphate isomerase AZOBR_RS33830
mannose manP: mannose PTS system, EII-CBA components AZOBR_RS32335
myoinositol iolG: myo-inositol 2-dehydrogenase AZOBR_RS22955
myoinositol iolM: 2-inosose 4-dehydrogenase AZOBR_RS13230
myoinositol iolN: 2,4-diketo-inositol hydratase
myoinositol iolO: 5-dehydro-L-gluconate epimerase
myoinositol iolT: myo-inositol:H+ symporter
myoinositol uxaE: D-tagaturonate epimerase
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 paaH: 3-hydroxyadipyl-CoA dehydrogenase AZOBR_RS20225 AZOBR_RS29225
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase AZOBR_RS30610 AZOBR_RS20220
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase AZOBR_RS30610 AZOBR_RS20220
phenylacetate paaK: phenylacetate-CoA ligase AZOBR_RS31155
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylacetate ppa: phenylacetate permease ppa AZOBR_RS02940 AZOBR_RS19235
phenylalanine livH: L-phenylalanine ABC transporter, permease component 1 (LivH) AZOBR_RS08235 AZOBR_RS03565
phenylalanine livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK AZOBR_RS08260 AZOBR_RS25645
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 paaH: 3-hydroxyadipyl-CoA dehydrogenase AZOBR_RS20225 AZOBR_RS29225
phenylalanine paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase AZOBR_RS30610 AZOBR_RS20220
phenylalanine paaJ2: 3-oxoadipyl-CoA thiolase AZOBR_RS30610 AZOBR_RS20220
phenylalanine paaK: phenylacetate-CoA ligase AZOBR_RS31155
phenylalanine paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine pad-dh: phenylacetaldehyde dehydrogenase AZOBR_RS26825 AZOBR_RS22315
propionate lctP: propionate permease AZOBR_RS25125
putrescine patA: putrescine aminotransferase (PatA/SpuC) AZOBR_RS03635 AZOBR_RS22505
putrescine patD: gamma-aminobutyraldehyde dehydrogenase AZOBR_RS22315 AZOBR_RS19635
putrescine potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) AZOBR_RS08845
rhamnose LRA1: L-rhamnofuranose dehydrogenase AZOBR_RS09410 AZOBR_RS02035
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase AZOBR_RS31430 AZOBR_RS26635
rhamnose LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase AZOBR_RS08390 AZOBR_RS24695
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsK: ribokinase
ribose rbsU: probable D-ribose transporter RbsU
serine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) AZOBR_RS08260
serine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) AZOBR_RS08235 AZOBR_RS03565
serine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) AZOBR_RS08240 AZOBR_RS25635
serine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) AZOBR_RS08250 AZOBR_RS29685
serine sdaB: L-serine ammonia-lyase AZOBR_RS06795
sorbitol scrK: fructokinase AZOBR_RS11685
sorbitol sdh: sorbitol dehydrogenase AZOBR_RS04810 AZOBR_RS24695
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
sucrose ams: sucrose hydrolase (invertase) AZOBR_RS25735
threonine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) AZOBR_RS08260
threonine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) AZOBR_RS08235 AZOBR_RS03565
threonine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) AZOBR_RS08240 AZOBR_RS25635
threonine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) AZOBR_RS08250 AZOBR_RS29685
threonine tdcB: L-threonine dehydratase AZOBR_RS06795
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase AZOBR_RS33725 AZOBR_RS07040
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
trehalose treF: trehalase AZOBR_RS25735 AZOBR_RS22875
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aacS: acetoacetyl-CoA synthetase AZOBR_RS31155 AZOBR_RS09405
tyrosine Ac3H11_1692: L-tyrosine ABC transporter, ATPase component 2 AZOBR_RS29685 AZOBR_RS20990
tyrosine Ac3H11_1693: L-tyrosine ABC transporter, ATPase component 1 AZOBR_RS28565 AZOBR_RS32405
tyrosine Ac3H11_1694: L-tyrosine ABC transporter, permease component 2 AZOBR_RS08240 AZOBR_RS25635
tyrosine Ac3H11_1695: L-tyrosine ABC transporter, permease component 1 AZOBR_RS08235 AZOBR_RS29670
tyrosine Ac3H11_2396: L-tyrosine ABC transporter, substrate-binding component component AZOBR_RS25645 AZOBR_RS08260
tyrosine fahA: fumarylacetoacetate hydrolase AZOBR_RS15905 AZOBR_RS26375
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase AZOBR_RS27895 AZOBR_RS07405
valine livH: L-valine ABC transporter, permease component 1 (LivH/BraD) AZOBR_RS08235 AZOBR_RS03565
valine mmsA: methylmalonate-semialdehyde dehydrogenase AZOBR_RS22500 AZOBR_RS29750
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
xylitol fruI: xylitol PTS, enzyme IIABC (FruI) AZOBR_RS32335
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase

Confidence: high confidence medium confidence low confidence

This GapMind analysis is from Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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