GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Azospirillum sp. B510

Found 22 low-confidence and 64 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
alanine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) AZL_RS26820 AZL_RS31475
alanine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) AZL_RS31500 AZL_RS12750
alanine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) AZL_RS31495 AZL_RS29465
alanine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) AZL_RS31490 AZL_RS29470
arabinose xacC: L-arabinono-1,4-lactonase AZL_RS31975 AZL_RS15505
arabinose xacD: L-arabinonate dehydratase AZL_RS32010 AZL_RS27430
arginine braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) AZL_RS31500 AZL_RS12750
arginine braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) AZL_RS31495 AZL_RS29465
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component AZL_RS14970 AZL_RS23235
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 AZL_RS14985 AZL_RS23240
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 AZL_RS23245 AZL_RS14980
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component AZL_RS10935 AZL_RS14975
citrulline citrullinase: putative citrullinase AZL_RS07035
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase AZL_RS29760 AZL_RS07100
deoxyinosine deoB: phosphopentomutase AZL_RS27500 AZL_RS30730
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase AZL_RS28580 AZL_RS07850
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter AZL_RS20325 AZL_RS20305
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoP: deoxyribose transporter
fructose fba: fructose 1,6-bisphosphate aldolase AZL_RS05110
fucose fucD: L-fuconate dehydratase AZL_RS28035 AZL_RS18730
fucose fucDH: 2-keto-3-deoxy-L-fuconate 4-dehydrogenase AZL_RS18695 AZL_RS22050
fucose HSERO_RS05260: ABC transporter for L-fucose, substrate-binding component
galactose dgoD: D-galactonate dehydratase AZL_RS32010
galactose galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) AZL_RS31975 AZL_RS15505
galacturonate udh: D-galacturonate dehydrogenase
galacturonate uxuL: D-galactaro-1,5-lactonase (UxuL or UxuF) AZL_RS15505
gluconate eda: 2-keto-3-deoxygluconate 6-phosphate aldolase AZL_RS26835 AZL_RS32180
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) AZL_RS23875
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate eda: 2-keto-3-deoxygluconate 6-phosphate aldolase AZL_RS26835 AZL_RS32180
glucuronate uxaC: D-glucuronate isomerase AZL_RS28040
glutamate braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) AZL_RS31500 AZL_RS12750
glutamate braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) AZL_RS31495 AZL_RS29465
histidine braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) AZL_RS31500 AZL_RS12750
histidine braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) AZL_RS31495 AZL_RS29465
isoleucine livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) AZL_RS31500 AZL_RS12750
lactose dgoD: D-galactonate dehydratase AZL_RS32010
lactose galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) AZL_RS31975 AZL_RS15505
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric) AZL_RS30935 AZL_RS28435
leucine livH: L-leucine ABC transporter, permease component 1 (LivH/BraD) AZL_RS31500 AZL_RS16110
lysine cadA: lysine decarboxylase AZL_RS03275 AZL_RS30445
lysine davD: glutarate semialdehyde dehydrogenase AZL_RS24700 AZL_RS26205
lysine lysP: L-lysine:H+ symporter LysP
lysine patA: cadaverine aminotransferase AZL_RS24705 AZL_RS02205
lysine patD: 5-aminopentanal dehydrogenase AZL_RS20100 AZL_RS09525
maltose susB: alpha-glucosidase (maltase) AZL_RS18745 AZL_RS31835
mannitol mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) AZL_RS23780
mannose manA: mannose-6-phosphate isomerase AZL_RS33210
mannose manP: mannose PTS system, EII-CBA components AZL_RS25900
NAG nagEcb: N-acetylglucosamine phosphotransferase system, EII-CB components AZL_RS23875
phenylacetate ppa: phenylacetate permease ppa AZL_RS00815
phenylalanine iorAB: phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB AZL_RS09275
phenylalanine livH: L-phenylalanine ABC transporter, permease component 1 (LivH) AZL_RS31500 AZL_RS12750
propionate lctP: propionate permease AZL_RS32080
putrescine gabD: succinate semialdehyde dehydrogenase AZL_RS24700 AZL_RS26205
putrescine potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) AZL_RS24930
putrescine puuC: gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase AZL_RS28845 AZL_RS20100
putrescine puuD: gamma-glutamyl-gamma-aminobutyrate hydrolase AZL_RS13025 AZL_RS08465
rhamnose aldA: lactaldehyde dehydrogenase AZL_RS20100 AZL_RS28845
rhamnose LRA1: L-rhamnofuranose dehydrogenase AZL_RS22240 AZL_RS17875
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase AZL_RS28035 AZL_RS18730
rhamnose LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase AZL_RS17905
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsB: D-ribose ABC transporter, substrate-binding component RbsB AZL_RS23125 AZL_RS18715
ribose rbsC: D-ribose ABC transporter, permease component RbsC AZL_RS23130 AZL_RS21855
sucrose ams: sucrose hydrolase (invertase) AZL_RS18745 AZL_RS15640
threonine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) AZL_RS26820 AZL_RS31475
threonine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) AZL_RS31500 AZL_RS12750
threonine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) AZL_RS31495 AZL_RS29465
threonine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) AZL_RS31490 AZL_RS29470
thymidine deoB: phosphopentomutase AZL_RS27500 AZL_RS30730
thymidine nupG: thymidine permease NupG/XapB
trehalose treF: trehalase AZL_RS18745 AZL_RS15640
tryptophan andAa: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa AZL_RS22215 AZL_RS18930
tryptophan andAb: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin subunit AndAb AZL_RS18925 AZL_RS20230
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan kynB: kynurenine formamidase AZL_RS25650
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
valine livH: L-valine ABC transporter, permease component 1 (LivH/BraD) AZL_RS31500 AZL_RS16110
valine mmsA: methylmalonate-semialdehyde dehydrogenase AZL_RS19190 AZL_RS21870
xylitol PLT5: xylitol:H+ symporter PLT5
xylitol xdhA: xylitol dehydrogenase AZL_RS21500 AZL_RS04810

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