Potential Gaps in catabolism of small carbon sources in Azospirillum humicireducens SgZ-5
Found 31 low-confidence and 62 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) | A6A40_RS30135 | A6A40_RS13365 |
| alanine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | A6A40_RS13390 | A6A40_RS09880 |
| alanine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | A6A40_RS13380 | A6A40_RS10200 |
| arabinose | xacC: L-arabinono-1,4-lactonase | A6A40_RS14345 | A6A40_RS19440 |
| arabinose | xacD: L-arabinonate dehydratase | A6A40_RS14375 | A6A40_RS28560 |
| arginine | braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) | A6A40_RS13390 | A6A40_RS09880 |
| arginine | braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) | A6A40_RS13385 | A6A40_RS22595 |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | A6A40_RS12685 | A6A40_RS17545 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | A6A40_RS12670 | A6A40_RS29325 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | A6A40_RS12675 | A6A40_RS29325 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | A6A40_RS12680 | A6A40_RS15265 |
| citrulline | citrullinase: putative citrullinase | A6A40_RS05810 | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | A6A40_RS25680 | A6A40_RS24665 |
| deoxyinosine | deoB: phosphopentomutase | A6A40_RS26190 | A6A40_RS13045 |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | A6A40_RS28835 | A6A40_RS27210 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | A6A40_RS15710 | A6A40_RS14875 |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fucose | fucD: L-fuconate dehydratase | A6A40_RS24745 | A6A40_RS22165 |
| fucose | fucDH: 2-keto-3-deoxy-L-fuconate 4-dehydrogenase | A6A40_RS29505 | A6A40_RS05080 |
| fucose | fuconolactonase: L-fucono-1,5-lactonase | | |
| fucose | fucU: L-fucose mutarotase FucU | | |
| fucose | HSERO_RS05255: ABC transporter for L-fucose, permease component | A6A40_RS23005 | A6A40_RS15550 |
| fucose | HSERO_RS05260: ABC transporter for L-fucose, substrate-binding component | A6A40_RS23010 | |
| galactose | dgoD: D-galactonate dehydratase | A6A40_RS14375 | A6A40_RS29870 |
| galactose | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | A6A40_RS14345 | A6A40_RS19440 |
| galacturonate | eda: 2-keto-3-deoxygluconate 6-phosphate aldolase | A6A40_RS30150 | A6A40_RS13325 |
| galacturonate | uxaA: D-altronate dehydratase | A6A40_RS24745 | A6A40_RS22165 |
| galacturonate | uxaC: D-galacturonate isomerase | A6A40_RS24740 | |
| gluconate | eda: 2-keto-3-deoxygluconate 6-phosphate aldolase | A6A40_RS30150 | A6A40_RS13325 |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | A6A40_RS15480 | A6A40_RS15510 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | eda: 2-keto-3-deoxygluconate 6-phosphate aldolase | A6A40_RS30150 | A6A40_RS13325 |
| glucuronate | uxaC: D-glucuronate isomerase | A6A40_RS24740 | |
| glutamate | braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) | A6A40_RS13390 | A6A40_RS09880 |
| glutamate | braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) | A6A40_RS13385 | A6A40_RS22595 |
| histidine | braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) | A6A40_RS13390 | A6A40_RS09880 |
| histidine | braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) | A6A40_RS13385 | A6A40_RS22595 |
| lactose | dgoD: D-galactonate dehydratase | A6A40_RS14375 | A6A40_RS29870 |
| lactose | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | A6A40_RS14345 | A6A40_RS19440 |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | A6A40_RS14025 | A6A40_RS27845 |
| lysine | bgtB: L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) | | |
| lysine | cadA: lysine decarboxylase | A6A40_RS02045 | A6A40_RS20000 |
| lysine | patA: cadaverine aminotransferase | A6A40_RS27690 | A6A40_RS01095 |
| lysine | patD: 5-aminopentanal dehydrogenase | A6A40_RS29725 | A6A40_RS13560 |
| maltose | susB: alpha-glucosidase (maltase) | A6A40_RS20300 | A6A40_RS22700 |
| mannitol | mt2d: mannitol 2-dehydrogenase | A6A40_RS13240 | A6A40_RS16630 |
| mannitol | PLT5: polyol transporter PLT5 | | |
| mannose | manA: mannose-6-phosphate isomerase | A6A40_RS24030 | |
| mannose | manP: mannose PTS system, EII-CBA components | A6A40_RS28450 | |
| myoinositol | eda: 2-keto-3-deoxygluconate 6-phosphate aldolase | A6A40_RS30150 | A6A40_RS13325 |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | A6A40_RS21125 | A6A40_RS15565 |
| myoinositol | iolM: 2-inosose 4-dehydrogenase | A6A40_RS03045 | |
| 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 | | |
| phenylacetate | ppa: phenylacetate permease ppa | A6A40_RS11400 | A6A40_RS00325 |
| phenylalanine | iorAB: phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB | A6A40_RS06170 | |
| phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | A6A40_RS13390 | A6A40_RS09880 |
| phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | A6A40_RS30135 | A6A40_RS13365 |
| propionate | lctP: propionate permease | A6A40_RS13760 | |
| putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | A6A40_RS27475 | |
| putrescine | puuC: gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase | A6A40_RS26775 | A6A40_RS13560 |
| putrescine | puuD: gamma-glutamyl-gamma-aminobutyrate hydrolase | A6A40_RS10125 | A6A40_RS04675 |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | A6A40_RS21865 | A6A40_RS20625 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsB: D-ribose ABC transporter, substrate-binding component RbsB | A6A40_RS23010 | A6A40_RS15555 |
| ribose | rbsC: D-ribose ABC transporter, permease component RbsC | A6A40_RS23005 | A6A40_RS22790 |
| sorbitol | sdh: sorbitol dehydrogenase | A6A40_RS03050 | A6A40_RS07150 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
| sucrose | ams: sucrose hydrolase (invertase) | A6A40_RS20300 | A6A40_RS19285 |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | A6A40_RS30135 | A6A40_RS13365 |
| threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | A6A40_RS13390 | A6A40_RS09880 |
| threonine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | A6A40_RS13380 | A6A40_RS10200 |
| thymidine | deoB: phosphopentomutase | A6A40_RS26190 | A6A40_RS13045 |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | treF: trehalase | A6A40_RS20300 | A6A40_RS19285 |
| tryptophan | andAa: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa | A6A40_RS16035 | A6A40_RS17335 |
| tryptophan | andAb: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin subunit AndAb | A6A40_RS16040 | A6A40_RS17320 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | kynB: kynurenine formamidase | A6A40_RS16005 | A6A40_RS16705 |
| tyrosine | Ac3H11_1693: L-tyrosine ABC transporter, ATPase component 1 | A6A40_RS29810 | A6A40_RS10200 |
| tyrosine | Ac3H11_1694: L-tyrosine ABC transporter, permease component 2 | A6A40_RS13385 | A6A40_RS22595 |
| tyrosine | Ac3H11_1695: L-tyrosine ABC transporter, permease component 1 | A6A40_RS13390 | A6A40_RS18700 |
| tyrosine | Ac3H11_2396: L-tyrosine ABC transporter, substrate-binding component component | A6A40_RS13365 | A6A40_RS30135 |
| valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | A6A40_RS13390 | A6A40_RS09880 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | A6A40_RS18190 | A6A40_RS25750 |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
| xylitol | xdhA: xylitol dehydrogenase | A6A40_RS24185 | A6A40_RS29865 |
Confidence: high confidence medium confidence low confidence
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Links
Downloads
Related tools
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