Potential Gaps in catabolism of small carbon sources in Azospirillum thiophilum BV-S
Found 38 low-confidence and 68 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| alanine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | AL072_RS29535 | AL072_RS15665 |
| alanine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | AL072_RS29560 | AL072_RS26405 |
| alanine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | AL072_RS29555 | AL072_RS26410 |
| alanine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | AL072_RS29550 | AL072_RS06650 |
| arabinose | xacC: L-arabinono-1,4-lactonase | AL072_RS30975 | AL072_RS26020 |
| arabinose | xacD: L-arabinonate dehydratase | AL072_RS30945 | AL072_RS23425 |
| arginine | braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) | AL072_RS26405 | AL072_RS29560 |
| arginine | braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) | AL072_RS29555 | AL072_RS26410 |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | AL072_RS05015 | AL072_RS30110 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | AL072_RS05000 | AL072_RS27395 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | AL072_RS05005 | AL072_RS17020 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | AL072_RS27370 | AL072_RS05010 |
| citrulline | citrullinase: putative citrullinase | AL072_RS13110 | |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | AL072_RS25885 | AL072_RS13045 |
| deoxyinosine | deoB: phosphopentomutase | AL072_RS23680 | AL072_RS28605 |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | AL072_RS28085 | AL072_RS25045 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fucose | fucD: L-fuconate dehydratase | AL072_RS24830 | |
| 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 | AL072_RS30945 | AL072_RS26825 |
| galactose | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | AL072_RS30975 | AL072_RS26020 |
| galacturonate | eda: 2-keto-3-deoxygluconate 6-phosphate aldolase | AL072_RS15650 | AL072_RS28850 |
| galacturonate | uxaA: D-altronate dehydratase | AL072_RS24830 | |
| galacturonate | uxaC: D-galacturonate isomerase | AL072_RS24835 | |
| gluconate | eda: 2-keto-3-deoxygluconate 6-phosphate aldolase | AL072_RS15650 | AL072_RS28850 |
| glucosamine | AO353_21710: glucosaminate ABC transporter, substrate-binding component | AL072_RS30105 | AL072_RS30380 |
| glucosamine | AO353_21715: glucosaminate ABC transporter, permease component 1 | AL072_RS30370 | AL072_RS30120 |
| glucosamine | AO353_21720: glucosaminate ABC transporter, permease component 2 | AL072_RS27395 | AL072_RS17020 |
| glucosamine | glucosaminate-lyase: glucosaminate ammonia-lyase | AL072_RS05820 | AL072_RS30125 |
| glucosamine | kdgA: 2-keto-3-deoxygluconate-6-phosphate aldolase EC:4.1.2.14 | AL072_RS15650 | AL072_RS28850 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | eda: 2-keto-3-deoxygluconate 6-phosphate aldolase | AL072_RS15650 | AL072_RS28850 |
| glucuronate | uxaC: D-glucuronate isomerase | AL072_RS24835 | |
| glutamate | braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) | AL072_RS26405 | AL072_RS29560 |
| glutamate | braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) | AL072_RS29555 | AL072_RS26410 |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | | |
| histidine | braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) | AL072_RS26405 | AL072_RS29560 |
| histidine | braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) | AL072_RS29555 | AL072_RS26410 |
| isoleucine | livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) | AL072_RS26405 | AL072_RS29560 |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| lactose | dgoD: D-galactonate dehydratase | AL072_RS30945 | AL072_RS26825 |
| lactose | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | AL072_RS30975 | AL072_RS26020 |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | AL072_RS30035 | AL072_RS15155 |
| leucine | livH: L-leucine ABC transporter, permease component 1 (LivH/BraD) | AL072_RS26405 | AL072_RS29560 |
| lysine | davA: 5-aminovaleramidase | AL072_RS13110 | AL072_RS30695 |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | hisM: L-lysine ABC transporter, permease component 1 (HisM) | AL072_RS05000 | AL072_RS17020 |
| lysine | hisQ: L-lysine ABC transporter, permease component 2 (HisQ) | AL072_RS05005 | AL072_RS17020 |
| maltose | susB: alpha-glucosidase (maltase) | AL072_RS19705 | AL072_RS08930 |
| mannitol | mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) | AL072_RS19180 | |
| mannose | manA: mannose-6-phosphate isomerase | AL072_RS32355 | |
| mannose | manP: mannose PTS system, EII-CBA components | AL072_RS14345 | |
| myoinositol | eda: 2-keto-3-deoxygluconate 6-phosphate aldolase | AL072_RS15650 | AL072_RS28850 |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | AL072_RS21170 | AL072_RS17590 |
| myoinositol | iolM: 2-inosose 4-dehydrogenase | AL072_RS00350 | |
| 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 | nagB: glucosamine 6-phosphate deaminase (isomerizing) | AL072_RS21320 | |
| NAG | nagEcb: N-acetylglucosamine phosphotransferase system, EII-CB components | AL072_RS17555 | |
| phenylacetate | ppa: phenylacetate permease ppa | AL072_RS03770 | AL072_RS03025 |
| phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | AL072_RS29560 | AL072_RS26405 |
| phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | AL072_RS15665 | AL072_RS27965 |
| propionate | mctC: propionate:H+ symporter | AL072_RS03770 | AL072_RS03025 |
| putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | AL072_RS15540 | |
| putrescine | puuC: gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase | AL072_RS26660 | AL072_RS23920 |
| putrescine | puuD: gamma-glutamyl-gamma-aminobutyrate hydrolase | AL072_RS06730 | AL072_RS11645 |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | AL072_RS18905 | AL072_RS26030 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | AL072_RS24830 | |
| rhamnose | LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase | | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsA: D-ribose ABC transporter, ATPase component RbsA | AL072_RS30960 | AL072_RS31000 |
| ribose | rbsB: D-ribose ABC transporter, substrate-binding component RbsB | AL072_RS17600 | AL072_RS30995 |
| ribose | rbsC: D-ribose ABC transporter, permease component RbsC | AL072_RS21990 | AL072_RS31005 |
| ribose | rbsK: ribokinase | AL072_RS27100 | |
| serine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | AL072_RS29535 | AL072_RS15665 |
| serine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | AL072_RS29560 | AL072_RS26405 |
| serine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | AL072_RS29555 | AL072_RS26410 |
| serine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | AL072_RS29550 | AL072_RS06650 |
| sucrose | ams: sucrose hydrolase (invertase) | AL072_RS19705 | AL072_RS08930 |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | AL072_RS29535 | AL072_RS15665 |
| threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | AL072_RS29560 | AL072_RS26405 |
| threonine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | AL072_RS29555 | AL072_RS26410 |
| threonine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | AL072_RS29550 | AL072_RS06650 |
| thymidine | deoB: phosphopentomutase | AL072_RS23680 | AL072_RS28605 |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | treF: trehalase | AL072_RS19705 | AL072_RS21415 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | Ac3H11_1693: L-tyrosine ABC transporter, ATPase component 1 | AL072_RS06650 | AL072_RS30275 |
| tyrosine | Ac3H11_1694: L-tyrosine ABC transporter, permease component 2 | AL072_RS29555 | AL072_RS26410 |
| tyrosine | Ac3H11_1695: L-tyrosine ABC transporter, permease component 1 | AL072_RS29560 | AL072_RS26405 |
| tyrosine | Ac3H11_2396: L-tyrosine ABC transporter, substrate-binding component component | AL072_RS29535 | AL072_RS15665 |
| valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | AL072_RS26405 | AL072_RS29560 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | AL072_RS20255 | AL072_RS23010 |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
| xylitol | xdhA: xylitol dehydrogenase | AL072_RS15245 | AL072_RS00350 |
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.
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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