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 (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