Potential Gaps in catabolism of small carbon sources in Magnetospirillum magneticum AMB-1
Found 103 low-confidence and 66 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase | AMB_RS15050 | AMB_RS19750 |
| 4-hydroxybenzoate | pimB: 3-oxopimeloyl-CoA:CoA acetyltransferase | AMB_RS13850 | AMB_RS04295 |
| alanine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | AMB_RS15010 | |
| alanine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | AMB_RS09135 | AMB_RS08455 |
| alanine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | AMB_RS09125 | AMB_RS08465 |
| alanine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | AMB_RS09120 | AMB_RS10230 |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arginine | braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) | AMB_RS09135 | AMB_RS08455 |
| arginine | braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) | AMB_RS09130 | AMB_RS14460 |
| arginine | rocD: ornithine aminotransferase | AMB_RS04150 | AMB_RS08515 |
| arginine | rocF: arginase | | |
| asparagine | ans: asparaginase | AMB_RS00215 | AMB_RS00600 |
| cellobiose | SemiSWEET: Sugar transporter SemiSWEET | AMB_RS06675 | |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | AMB_RS10565 | AMB_RS06945 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | | |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | | |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| citrulline | arcC: carbamate kinase | | |
| citrulline | rocD: ornithine aminotransferase | AMB_RS04150 | AMB_RS08515 |
| D-alanine | AZOBR_RS08240: D-alanine ABC transporter, permease component 2 | AMB_RS09130 | AMB_RS14460 |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | | |
| deoxyinosine | deoB: phosphopentomutase | AMB_RS02965 | |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | AMB_RS20840 | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | AMB_RS20720 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | AMB_RS13470 | AMB_RS10625 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | AMB_RS16025 | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyribose | deoK: deoxyribokinase | AMB_RS16380 | |
| deoxyribose | deoP: deoxyribose transporter | | |
| ethanol | etoh-dh-nad: ethanol dehydrogenase (NAD(P)) | AMB_RS10835 | AMB_RS10625 |
| fructose | Slc2a5: fructose:H+ symporter | | |
| fucose | aldA: lactaldehyde dehydrogenase | AMB_RS01425 | AMB_RS06710 |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | | |
| fucose | fucI: L-fucose isomerase FucI | | |
| fucose | fucK: L-fuculose kinase FucK | | |
| fucose | fucP: L-fucose:H+ symporter FucP | | |
| fucose | fucU: L-fucose mutarotase FucU | | |
| galactose | galK: galactokinase (-1-phosphate forming) | | |
| galactose | galP: galactose:H+ symporter GalP | | |
| galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| galacturonate | dopDH: 2,5-dioxopentanonate dehydrogenase | AMB_RS06710 | AMB_RS04160 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | gci: D-galactarolactone cycloisomerase | | |
| galacturonate | gli: D-galactarolactone isomerase | | |
| galacturonate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | AMB_RS12805 | |
| galacturonate | udh: D-galacturonate dehydrogenase | | |
| gluconate | gnd: 6-phosphogluconate dehydrogenase, decarboxylating | | |
| gluconate | gntK: D-gluconate kinase | AMB_RS19870 | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | SLC2A2: glucosamine transporter SLC2A2 | | |
| glucose | SemiSWEET: Sugar transporter SemiSWEET | AMB_RS06675 | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | garL: 5-dehydro-4-deoxy-D-glucarate aldolase | AMB_RS04095 | AMB_RS12805 |
| glucuronate | garR: tartronate semialdehyde reductase | AMB_RS18155 | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| glutamate | braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) | AMB_RS09135 | AMB_RS08455 |
| glutamate | braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) | AMB_RS09130 | AMB_RS14460 |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | | |
| glycerol | glpF: glycerol facilitator glpF | | |
| glycerol | glpK: glycerol kinase | | |
| histidine | braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) | AMB_RS09135 | AMB_RS08455 |
| histidine | braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) | AMB_RS09130 | AMB_RS14460 |
| 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) | AMB_RS09135 | AMB_RS08455 |
| isoleucine | mcm-large: methylmalonyl-CoA mutase, large (catalytic) subunit | AMB_RS01570 | |
| isoleucine | mcm-small: methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit | AMB_RS01570 | |
| isoleucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| lactose | galK: galactokinase (-1-phosphate forming) | | |
| lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | AMB_RS11280 | AMB_RS01115 |
| leucine | livH: L-leucine ABC transporter, permease component 1 (LivH/BraD) | AMB_RS09135 | AMB_RS08455 |
| leucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| lysine | davA: 5-aminovaleramidase | AMB_RS08115 | |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | davT: 5-aminovalerate aminotransferase | AMB_RS01605 | AMB_RS04150 |
| lysine | fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase | AMB_RS15050 | AMB_RS19750 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| maltose | SemiSWEET: Sugar transporter SemiSWEET | AMB_RS06675 | |
| maltose | susB: alpha-glucosidase (maltase) | AMB_RS13755 | |
| mannitol | mt2d: mannitol 2-dehydrogenase | AMB_RS04300 | AMB_RS08070 |
| mannitol | PLT5: polyol transporter PLT5 | | |
| mannose | manA: mannose-6-phosphate isomerase | AMB_RS00190 | |
| mannose | STP6: mannose:H+ symporter | | |
| 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 | AMB_RS00635 | AMB_RS00695 |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | AMB_RS06985 | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| myoinositol | mmsA: malonate-semialdehyde dehydrogenase | AMB_RS04115 | AMB_RS06710 |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| phenylacetate | fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase | AMB_RS15050 | AMB_RS19750 |
| phenylacetate | pimB: 3-oxopimeloyl-CoA:CoA acetyltransferase | AMB_RS13850 | AMB_RS04295 |
| phenylalanine | fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase | AMB_RS15050 | AMB_RS19750 |
| phenylalanine | iorB: phenylpyruvate:ferredoxin oxidoreductase, IorB subunit | AMB_RS16330 | |
| phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | AMB_RS09135 | AMB_RS08455 |
| phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | AMB_RS15010 | |
| phenylalanine | pimB: 3-oxopimeloyl-CoA:CoA acetyltransferase | AMB_RS13850 | AMB_RS04295 |
| proline | AZOBR_RS08240: proline ABC transporter, permease component 2 | AMB_RS09130 | AMB_RS14460 |
| propionate | lctP: propionate permease | AMB_RS20875 | |
| propionate | mcm-large: methylmalonyl-CoA mutase, large (catalytic) subunit | AMB_RS01570 | |
| propionate | mcm-small: methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit | AMB_RS01570 | |
| putrescine | gabD: succinate semialdehyde dehydrogenase | AMB_RS06710 | AMB_RS04160 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | AMB_RS08515 | AMB_RS04150 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | AMB_RS06710 | AMB_RS04115 |
| rhamnose | aldA: lactaldehyde dehydrogenase | AMB_RS01425 | AMB_RS06710 |
| rhamnose | rhaA: L-rhamnose isomerase | | |
| rhamnose | rhaB: L-rhamnulokinase | | |
| rhamnose | rhaD: rhamnulose 1-phosphate aldolase | AMB_RS01425 | |
| rhamnose | rhaM: L-rhamnose mutarotase | | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsK: ribokinase | AMB_RS16380 | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | AMB_RS15010 | |
| serine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | AMB_RS09135 | AMB_RS08455 |
| serine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | AMB_RS09125 | AMB_RS08465 |
| serine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | AMB_RS09120 | AMB_RS10230 |
| serine | sdaB: L-serine ammonia-lyase | | |
| sorbitol | sdh: sorbitol dehydrogenase | AMB_RS13035 | AMB_RS10625 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
| sucrose | SUS: sucrose synthase | | |
| sucrose | sut: sucrose:proton symporter SUT/SUC | | |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | AMB_RS15010 | |
| threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | AMB_RS09135 | AMB_RS08455 |
| threonine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | AMB_RS09125 | AMB_RS08465 |
| threonine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | AMB_RS09120 | AMB_RS10230 |
| threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | AMB_RS03940 | AMB_RS03935 |
| threonine | ltaE: L-threonine aldolase | AMB_RS11815 | |
| thymidine | deoA: thymidine phosphorylase DeoA | | |
| thymidine | deoB: phosphopentomutase | AMB_RS02965 | |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| thymidine | nupC: thymidine permease NupC | AMB_RS20720 | |
| trehalose | SemiSWEET: Sugar transporter SemiSWEET | AMB_RS06675 | |
| trehalose | treF: trehalase | | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | Ac3H11_1693: L-tyrosine ABC transporter, ATPase component 1 | AMB_RS08465 | AMB_RS09125 |
| tyrosine | Ac3H11_1694: L-tyrosine ABC transporter, permease component 2 | AMB_RS09130 | AMB_RS08460 |
| tyrosine | Ac3H11_1695: L-tyrosine ABC transporter, permease component 1 | AMB_RS09135 | AMB_RS08455 |
| tyrosine | Ac3H11_2396: L-tyrosine ABC transporter, substrate-binding component component | AMB_RS15010 | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | AMB_RS14215 | AMB_RS04120 |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | AMB_RS19950 | AMB_RS20760 |
| valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | AMB_RS09135 | AMB_RS08455 |
| valine | mcm-large: methylmalonyl-CoA mutase, large (catalytic) subunit | AMB_RS01570 | |
| valine | mcm-small: methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit | AMB_RS01570 | |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | AMB_RS04115 | AMB_RS06710 |
| valine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | | |
| xylose | xylA: xylose isomerase | | |
| xylose | xylB: xylulokinase | | |
| xylose | xylT: D-xylose transporter | | |
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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