Potential Gaps in catabolism of small carbon sources in Rhodopseudomonas pseudopalustris DSM 123
Found 101 low-confidence and 54 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | Ch1CoA: cyclohex-1-ene-1-carbonyl-CoA dehydrogenase | BMY71_RS08460 | BMY71_RS16335 |
| 4-hydroxybenzoate | fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase | BMY71_RS07945 | BMY71_RS13930 |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| alanine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | BMY71_RS09140 | |
| alanine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | BMY71_RS09160 | BMY71_RS17340 |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arabinose | xacB: L-arabinose 1-dehydrogenase | BMY71_RS14985 | BMY71_RS18395 |
| arabinose | xacC: L-arabinono-1,4-lactonase | | |
| arabinose | xacE: 2-dehydro-3-deoxy-L-arabinonate dehydratase | BMY71_RS16365 | |
| arginine | braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) | BMY71_RS09160 | BMY71_RS17340 |
| arginine | rocD: ornithine aminotransferase | BMY71_RS08020 | BMY71_RS13505 |
| asparagine | ans: asparaginase | BMY71_RS05350 | |
| asparagine | glt: aspartate:proton symporter Glt | BMY71_RS18500 | |
| aspartate | glt: aspartate:proton symporter Glt | BMY71_RS18500 | |
| cellobiose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | BMY71_RS23415 | BMY71_RS04195 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | BMY71_RS23410 | |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | BMY71_RS23410 | |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | BMY71_RS12985 | |
| citrulline | arcC: carbamate kinase | | |
| citrulline | rocD: ornithine aminotransferase | BMY71_RS08020 | BMY71_RS13505 |
| D-alanine | AZOBR_RS08240: D-alanine ABC transporter, permease component 2 | BMY71_RS09155 | BMY71_RS17335 |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | BMY71_RS15480 | |
| deoxyinosine | adh: acetaldehyde dehydrogenase (not acylating) | BMY71_RS03050 | BMY71_RS01975 |
| deoxyinosine | deoB: phosphopentomutase | BMY71_RS21220 | |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | BMY71_RS01840 | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | BMY71_RS18110 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | BMY71_RS22535 | BMY71_RS01625 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | BMY71_RS10960 | |
| deoxyribose | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | BMY71_RS22535 | BMY71_RS01625 |
| deoxyribose | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribose | drdehyd-alpha: 2-deoxy-D-ribose dehydrogenase, alpha subunit | BMY71_RS14905 | BMY71_RS13400 |
| deoxyribose | drdehyd-beta: 2-deoxy-D-ribose dehydrogenase, beta subunit | | |
| deoxyribose | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | BMY71_RS10960 | |
| ethanol | adh: acetaldehyde dehydrogenase (not acylating) | BMY71_RS03050 | BMY71_RS01975 |
| fructose | 1pfk: 1-phosphofructokinase | BMY71_RS24195 | |
| fructose | fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components | | |
| fucose | fdh: L-fucose 1-dehydrogenase | BMY71_RS07650 | BMY71_RS18155 |
| fucose | fucD: L-fuconate dehydratase | | |
| fucose | fuconolactonase: L-fucono-1,5-lactonase | | |
| fucose | fucP: L-fucose:H+ symporter FucP | | |
| fucose | fucU: L-fucose mutarotase FucU | | |
| galactose | galE: UDP-glucose 4-epimerase | BMY71_RS03975 | BMY71_RS15365 |
| galactose | galK: galactokinase (-1-phosphate forming) | | |
| galactose | galP: galactose:H+ symporter GalP | | |
| galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | gci: D-galactarolactone cycloisomerase | | |
| galacturonate | gli: D-galactarolactone isomerase | | |
| galacturonate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | BMY71_RS11510 | BMY71_RS23970 |
| galacturonate | udh: D-galacturonate dehydrogenase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | BMY71_RS11400 | |
| glucose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
| glucuronate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | BMY71_RS11510 | BMY71_RS23970 |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| glutamate | aspA: L-aspartate ammonia-lyase | BMY71_RS06995 | |
| glutamate | braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) | BMY71_RS09160 | BMY71_RS17340 |
| glycerol | glpF: glycerol facilitator glpF | BMY71_RS18630 | |
| histidine | braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) | BMY71_RS09160 | BMY71_RS17340 |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| isoleucine | livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) | BMY71_RS09160 | BMY71_RS17340 |
| lactose | galE: UDP-glucose 4-epimerase | BMY71_RS03975 | BMY71_RS15365 |
| lactose | galK: galactokinase (-1-phosphate forming) | | |
| lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| lactose | glk: glucokinase | | |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | BMY71_RS09460 | |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | BMY71_RS23280 | BMY71_RS09800 |
| leucine | livH: L-leucine ABC transporter, permease component 1 (LivH/BraD) | BMY71_RS09160 | BMY71_RS17340 |
| lysine | davA: 5-aminovaleramidase | BMY71_RS02305 | |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | davT: 5-aminovalerate aminotransferase | BMY71_RS13505 | BMY71_RS17635 |
| lysine | fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase | BMY71_RS07945 | BMY71_RS13930 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | BMY71_RS02720 | BMY71_RS10410 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| maltose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
| maltose | susB: alpha-glucosidase (maltase) | BMY71_RS07590 | |
| mannitol | mtlA: mannitol phosphotransferase system, EII-CBA components | | |
| mannitol | mtlD: mannitol-1-phosphate 5-dehydrogenase | | |
| mannose | manA: mannose-6-phosphate isomerase | BMY71_RS15410 | |
| mannose | manP: mannose PTS system, EII-CBA components | | |
| myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | | |
| myoinositol | iolC: 5-dehydro-2-deoxy-D-gluconate kinase | | |
| myoinositol | iolD: 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase | | |
| myoinositol | iolE: scyllo-inosose 2-dehydratase | | |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | | |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | BMY71_RS03670 | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | BMY71_RS11400 | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| phenylacetate | Ch1CoA: cyclohex-1-ene-1-carbonyl-CoA dehydrogenase | BMY71_RS08460 | BMY71_RS16335 |
| phenylacetate | fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase | BMY71_RS07945 | BMY71_RS13930 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylalanine | Ch1CoA: cyclohex-1-ene-1-carbonyl-CoA dehydrogenase | BMY71_RS08460 | BMY71_RS16335 |
| phenylalanine | fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase | BMY71_RS07945 | BMY71_RS13930 |
| phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | BMY71_RS09160 | BMY71_RS17340 |
| phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | BMY71_RS09140 | |
| phenylalanine | pad-dh: phenylacetaldehyde dehydrogenase | BMY71_RS01975 | BMY71_RS08135 |
| proline | AZOBR_RS08240: proline ABC transporter, permease component 2 | BMY71_RS09155 | BMY71_RS17335 |
| propionate | lctP: propionate permease | BMY71_RS00200 | |
| putrescine | gabD: succinate semialdehyde dehydrogenase | BMY71_RS03050 | BMY71_RS01975 |
| putrescine | gabT: gamma-aminobutyrate transaminase | BMY71_RS04880 | BMY71_RS13505 |
| putrescine | puuA: glutamate-putrescine ligase | BMY71_RS12845 | |
| putrescine | puuB: gamma-glutamylputrescine oxidase | BMY71_RS04140 | |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | BMY71_RS18155 | BMY71_RS14985 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsK: ribokinase | BMY71_RS24195 | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | BMY71_RS09140 | |
| serine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | BMY71_RS09160 | BMY71_RS17340 |
| serine | sdaB: L-serine ammonia-lyase | BMY71_RS15480 | |
| sorbitol | mtlA: PTS system for polyols, EII-CBA components | | |
| sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | BMY71_RS00335 | BMY71_RS16325 |
| sucrose | scrK: fructokinase | | |
| sucrose | SUS: sucrose synthase | | |
| sucrose | sut: sucrose:proton symporter SUT/SUC | | |
| threonine | adh: acetaldehyde dehydrogenase (not acylating) | BMY71_RS03050 | BMY71_RS01975 |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | BMY71_RS09140 | |
| threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | BMY71_RS09160 | BMY71_RS17340 |
| thymidine | adh: acetaldehyde dehydrogenase (not acylating) | BMY71_RS03050 | BMY71_RS01975 |
| thymidine | deoB: phosphopentomutase | BMY71_RS21220 | |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| thymidine | nupC: thymidine permease NupC | BMY71_RS18110 | |
| trehalose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
| trehalose | treF: trehalase | BMY71_RS07575 | BMY71_RS07590 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | BMY71_RS07310 | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | BMY71_RS06675 | BMY71_RS09800 |
| valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | BMY71_RS09160 | BMY71_RS17340 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | BMY71_RS06685 | BMY71_RS03050 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | | |
| xylose | DKDP-dehydrog: D-2-keto-3-deoxypentoate dehydrogenase | BMY71_RS06805 | BMY71_RS00650 |
| xylose | HDOP-hydrol: 5-hydroxy-2,4-dioxopentanonate hydrolase | BMY71_RS21950 | BMY71_RS08145 |
| xylose | xdh: D-xylose dehydrogenase | BMY71_RS00650 | BMY71_RS06805 |
| xylose | xylC: xylonolactonase | | |
| xylose | xylT: D-xylose transporter | | |
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