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:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
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:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
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:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
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