Potential Gaps in catabolism of small carbon sources in Planktomarina temperata RCA23
Found 57 low-confidence and 72 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase | RCA23_RS10475 | RCA23_RS00115 |
| 4-hydroxybenzoate | pcaI: 3-oxoadipate CoA-transferase subunit A (PcaI) | RCA23_RS09585 | |
| 4-hydroxybenzoate | pcaJ: 3-oxoadipate CoA-transferase subunit B (PcaJ) | RCA23_RS09580 | |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arabinose | xacC: L-arabinono-1,4-lactonase | RCA23_RS00700 | |
| arginine | artJ: L-arginine ABC transporter, periplasmic substrate-binding component ArtJ/HisJ/ArtI/AotJ/ArgT | RCA23_RS14170 | |
| arginine | artM: L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) | RCA23_RS14180 | RCA23_RS12185 |
| arginine | artP: L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA | RCA23_RS14165 | RCA23_RS12180 |
| arginine | artQ: L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) | RCA23_RS14175 | RCA23_RS05745 |
| citrate | tctB: citrate/Na+ symporter, small transmembrane component TctB | RCA23_RS13480 | |
| citrulline | arcC: carbamate kinase | | |
| citrulline | PS417_17590: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| citrulline | PS417_17595: ABC transporter for L-Citrulline, permease component 1 | RCA23_RS05745 | RCA23_RS14175 |
| citrulline | PS417_17600: ABC transporter for L-Citrulline, permease component 2 | RCA23_RS14180 | |
| citrulline | PS417_17605: ABC transporter for L-Citrulline, ATPase component | RCA23_RS14165 | RCA23_RS05740 |
| D-alanine | cycA: D-alanine:H+ symporter CycA | | |
| D-alanine | dadA: D-alanine dehydrogenase | RCA23_RS03485 | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | RCA23_RS12505 | RCA23_RS10315 |
| deoxyinosine | bmpA: deoxyinosine ABC transporter, substrate-binding component | RCA23_RS10930 | |
| deoxyinosine | nupB: deoxyinosine ABC transporter, permease component 1 | RCA23_RS10920 | |
| deoxyinosine | nupC': deoxyinosine ABC transporter, permease component 2 | RCA23_RS10825 | RCA23_RS10915 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | garK: glycerate 2-kinase | RCA23_RS09545 | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | RCA23_RS11270 | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fructose | scrK: fructokinase | RCA23_RS14820 | RCA23_RS09975 |
| fucose | fucP: L-fucose:H+ symporter FucP | | |
| fucose | fucU: L-fucose mutarotase FucU | RCA23_RS12570 | |
| galactose | dgoD: D-galactonate dehydratase | RCA23_RS09025 | RCA23_RS13770 |
| galactose | dgoK: 2-dehydro-3-deoxygalactonokinase | RCA23_RS01450 | RCA23_RS00710 |
| galactose | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | RCA23_RS00700 | |
| galactose | galP: galactose:H+ symporter GalP | | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | uxaA: D-altronate dehydratase | RCA23_RS01430 | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | RCA23_RS01460 | |
| gluconate | gntK: D-gluconate kinase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | RCA23_RS06835 | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | uxaC: D-glucuronate isomerase | RCA23_RS01460 | |
| glucuronate | uxuB: D-mannonate dehydrogenase | RCA23_RS01455 | RCA23_RS14965 |
| glycerol | glpF: glycerol facilitator glpF | | |
| histidine | aapJ: L-histidine ABC transporter, substrate-binding component AapJ | RCA23_RS12195 | |
| histidine | aapM: L-histidine ABC transporter, permease component 2 (AapM) | RCA23_RS12185 | |
| histidine | aapP: L-histidine ABC transporter, ATPase component AapP | RCA23_RS12180 | RCA23_RS05740 |
| histidine | aapQ: L-histidine ABC transporter, permease component 1 (AapQ) | RCA23_RS12190 | |
| 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) | RCA23_RS06060 | RCA23_RS05710 |
| isoleucine | livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | | |
| isoleucine | livM: L-isoleucine ABC transporter, permease component 2 (LivM/BraE) | RCA23_RS14585 | RCA23_RS05715 |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| lactose | dgoD: D-galactonate dehydratase | RCA23_RS09025 | RCA23_RS13770 |
| lactose | dgoK: 2-dehydro-3-deoxygalactonokinase | RCA23_RS01450 | RCA23_RS00710 |
| lactose | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | RCA23_RS00700 | |
| lactose | lacP: lactose permease LacP | | |
| leucine | livH: L-leucine ABC transporter, permease component 1 (LivH/BraD) | RCA23_RS06060 | RCA23_RS05710 |
| leucine | livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | | |
| leucine | livM: L-leucine ABC transporter, permease component 2 (LivM/BraE) | RCA23_RS14585 | RCA23_RS05715 |
| lysine | davA: 5-aminovaleramidase | | |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | davT: 5-aminovalerate aminotransferase | RCA23_RS00940 | RCA23_RS00055 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| maltose | susB: alpha-glucosidase (maltase) | RCA23_RS08400 | RCA23_RS03765 |
| mannitol | mt2d: mannitol 2-dehydrogenase | RCA23_RS14965 | RCA23_RS01455 |
| mannitol | mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE | RCA23_RS14985 | |
| mannitol | mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) | RCA23_RS14980 | |
| mannitol | mtlK: polyol ABC transporter, ATP component MtlK/SmoG | RCA23_RS00745 | RCA23_RS14960 |
| mannitol | scrK: fructokinase | RCA23_RS14820 | RCA23_RS09975 |
| mannose | man-isomerase: D-mannose isomerase | | |
| mannose | scrK: fructokinase | RCA23_RS14820 | RCA23_RS09975 |
| myoinositol | PS417_11890: myo-inositol ABC transporter, ATPase component | RCA23_RS11900 | RCA23_RS06210 |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | RCA23_RS06835 | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | RCA23_RS15830 | RCA23_RS14850 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylalanine | iorAB: phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB | RCA23_RS07555 | |
| phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | RCA23_RS06060 | RCA23_RS05710 |
| phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | | |
| phenylalanine | livM: L-phenylalanine ABC transporter, permease component 2 (LivM) | RCA23_RS14585 | RCA23_RS05715 |
| phenylalanine | paaF: 2,3-dehydroadipyl-CoA hydratase | RCA23_RS15830 | RCA23_RS14850 |
| proline | natB: proline ABC transporter, substrate-binding component NatB | RCA23_RS08225 | |
| proline | natC: proline ABC transporter, permease component 1 (NatC) | | |
| proline | natD: proline ABC transporter, permease component 2 (NatD) | RCA23_RS08240 | RCA23_RS05710 |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | gabT: gamma-aminobutyrate transaminase | RCA23_RS14205 | RCA23_RS10360 |
| putrescine | potB: putrescine ABC transporter, permease component 1 (PotB/PotH) | RCA23_RS10400 | RCA23_RS11980 |
| putrescine | potC: putrescine ABC transporter, permease component 2 (PotC/PotI) | RCA23_RS10395 | RCA23_RS11975 |
| putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | | |
| putrescine | puuD: gamma-glutamyl-gamma-aminobutyrate hydrolase | RCA23_RS05440 | |
| pyruvate | dctM: pyruvate TRAP transporter, large permease component | RCA23_RS08940 | RCA23_RS13795 |
| pyruvate | dctP: pyruvate TRAP transporter, substrate-binding component | RCA23_RS08715 | RCA23_RS13805 |
| pyruvate | dctQ: pyruvate TRAP transporter, small permease component | RCA23_RS13800 | RCA23_RS08945 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | rhaP: L-rhamnose ABC transporter, permease component 1 (RhaP) | RCA23_RS11895 | RCA23_RS12375 |
| rhamnose | rhaQ: L-rhamnose ABC transporter, permease component 2 (RhaQ) | RCA23_RS11890 | RCA23_RS12375 |
| rhamnose | rhaS: L-rhamnose ABC transporter, substrate-binding component RhaS | RCA23_RS11905 | |
| rhamnose | rhaT': L-rhamnose ABC transporter, ATPase component RhaT | RCA23_RS11900 | RCA23_RS06210 |
| serine | snatA: L-serine transporter | RCA23_RS09060 | |
| sorbitol | mtlK: ABC transporter for polyols MtlEFGK, permease component MtlK | RCA23_RS14960 | RCA23_RS00745 |
| sorbitol | scrK: fructokinase | RCA23_RS14820 | RCA23_RS09975 |
| sucrose | ams: sucrose hydrolase (invertase) | RCA23_RS03765 | RCA23_RS08400 |
| threonine | ltaE: L-threonine aldolase | RCA23_RS10660 | RCA23_RS00995 |
| threonine | snatA: L-threonine transporter snatA | RCA23_RS09060 | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | treF: trehalase | RCA23_RS03765 | RCA23_RS08400 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | RCA23_RS11855 | RCA23_RS09030 |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | RCA23_RS12535 | |
| tyrosine | maiA: maleylacetoacetate isomerase | RCA23_RS05670 | RCA23_RS02210 |
| valine | acdH: isobutyryl-CoA dehydrogenase | RCA23_RS06860 | RCA23_RS07485 |
| valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | RCA23_RS06060 | RCA23_RS05710 |
| valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | | |
| valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | RCA23_RS14585 | RCA23_RS05715 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | RCA23_RS07490 | RCA23_RS14405 |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
| xylitol | xdhA: xylitol dehydrogenase | RCA23_RS01310 | RCA23_RS12000 |
| 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