Potential Gaps in catabolism of small carbon sources in Mycolicibacterium vanbaalenii PYR-1
Found 92 low-confidence and 64 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | Psest_0084: 2-oxoglutarate TRAP transporter, fused 4TM/12TM components | MVAN_RS09730 | |
| 2-oxoglutarate | Psest_0085: 2-oxoglutarate TRAP transporter, solute receptor component | MVAN_RS09735 | |
| 4-hydroxybenzoate | pcaB: 3-carboxymuconate cycloisomerase | MVAN_RS02855 | |
| 4-hydroxybenzoate | pcaD: 3-oxoadipate enol-lactone hydrolase | MVAN_RS02860 | MVAN_RS02735 |
| 4-hydroxybenzoate | pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase | MVAN_RS25465 | MVAN_RS04625 |
| 4-hydroxybenzoate | pcaH: protocatechuate 3,4-dioxygenase, alpha subunit | MVAN_RS02845 | |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| 4-hydroxybenzoate | pobA: 4-hydroxybenzoate 3-monooxygenase | MVAN_RS05250 | MVAN_RS03415 |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | MVAN_RS17435 | |
| arginine | artP: L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA | MVAN_RS23630 | MVAN_RS14240 |
| arginine | bgtB: L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) | MVAN_RS31485 | MVAN_RS23625 |
| arginine | rocA: 1-pyrroline-5-carboxylate dehydrogenase | MVAN_RS22735 | MVAN_RS09340 |
| asparagine | ans: asparaginase | MVAN_RS13920 | |
| asparagine | glt: aspartate:proton symporter Glt | MVAN_RS23590 | |
| aspartate | glt: aspartate:proton symporter Glt | MVAN_RS23590 | |
| cellobiose | bgl: cellobiase | MVAN_RS25280 | |
| citrate | tctB: citrate/Na+ symporter, small transmembrane component TctB | | |
| citrate | tctC: citrate/Na+ symporter, substrate-binding component TctC | MVAN_RS17590 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | MVAN_RS14240 | MVAN_RS23630 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | MVAN_RS31485 | MVAN_RS14235 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | MVAN_RS23625 | MVAN_RS14235 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | MVAN_RS30415 | |
| citrulline | rocA: 1-pyrroline-5-carboxylate dehydrogenase | MVAN_RS22735 | MVAN_RS09340 |
| D-alanine | cycA: D-alanine:H+ symporter CycA | | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | D-LDH: D-lactate dehydrogenase | MVAN_RS22430 | MVAN_RS22475 |
| 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 | MVAN_RS15175 | MVAN_RS13975 |
| deoxyinosine | deoB: phosphopentomutase | MVAN_RS08095 | MVAN_RS07420 |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | MVAN_RS20025 | MVAN_RS09365 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoK: deoxyribokinase | MVAN_RS19720 | MVAN_RS20120 |
| deoxyribose | deoP: deoxyribose transporter | | |
| 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 | galE: UDP-glucose 4-epimerase | MVAN_RS27095 | MVAN_RS04455 |
| galactose | galK: galactokinase (-1-phosphate forming) | | |
| galactose | galP: galactose:H+ symporter GalP | MVAN_RS17435 | |
| 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 | udh: D-galacturonate dehydrogenase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | MVAN_RS29745 | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | MVAN_RS07460 | MVAN_RS13640 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| glucuronate | uxuL: D-glucaro-1,5-lactonase UxuL or UxuF | | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | MVAN_RS08160 | MVAN_RS18820 |
| glycerol | glpF: glycerol facilitator glpF | MVAN_RS11035 | |
| histidine | bgtA: L-histidine ABC transporter, ATPase component BgtA | MVAN_RS23630 | MVAN_RS14240 |
| histidine | bgtB: L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) | MVAN_RS31485 | MVAN_RS23625 |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | MVAN_RS15185 | MVAN_RS00255 |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | MVAN_RS15810 | |
| histidine | hutU: urocanase | | |
| isoleucine | livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | | |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | MVAN_RS08390 | MVAN_RS20500 |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| lactose | galE: UDP-glucose 4-epimerase | MVAN_RS27095 | MVAN_RS04455 |
| 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) | MVAN_RS25280 | |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | MVAN_RS23045 | MVAN_RS23515 |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | MVAN_RS09530 | |
| leucine | livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | | |
| lysine | cadA: lysine decarboxylase | MVAN_RS22660 | |
| lysine | davD: glutarate semialdehyde dehydrogenase | MVAN_RS24505 | MVAN_RS00090 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | MVAN_RS09335 | MVAN_RS09955 |
| lysine | lysL: L-lysine transporter LysL | MVAN_RS07035 | |
| lysine | patA: cadaverine aminotransferase | MVAN_RS16610 | MVAN_RS15790 |
| mannitol | mtlD: mannitol-1-phosphate 5-dehydrogenase | | |
| mannose | manP: mannose PTS system, EII-CBA components | MVAN_RS00500 | |
| myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | MVAN_RS20130 | |
| myoinositol | iolE: scyllo-inosose 2-dehydratase | MVAN_RS01965 | MVAN_RS19890 |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | MVAN_RS19885 | MVAN_RS20140 |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | MVAN_RS20120 | |
| myoinositol | PGA1_c07300: myo-inositol ABC transport, substrate-binding component | | |
| myoinositol | PGA1_c07310: myo-inositol ABC transporter, permease component | MVAN_RS20090 | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | MVAN_RS07460 | MVAN_RS13640 |
| 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 | MVAN_RS14540 | MVAN_RS20990 |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | MVAN_RS23515 | MVAN_RS23045 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | MVAN_RS25465 | MVAN_RS09940 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | MVAN_RS25465 | MVAN_RS09940 |
| phenylacetate | paaK: phenylacetate-CoA ligase | MVAN_RS10580 | MVAN_RS04760 |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | MVAN_RS23045 | MVAN_RS09415 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylacetate | ppa: phenylacetate permease ppa | MVAN_RS22925 | |
| phenylalanine | fahA: fumarylacetoacetate hydrolase | MVAN_RS10690 | |
| phenylalanine | hmgA: homogentisate dioxygenase | MVAN_RS09545 | |
| phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| phenylalanine | livF: L-phenylalanine ABC transporter, ATPase component 1 (LivF) | MVAN_RS14300 | MVAN_RS13020 |
| phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | | |
| phenylalanine | maiA: maleylacetoacetate isomerase | | |
| phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
| phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | MVAN_RS22850 | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | MVAN_RS07765 | |
| proline | put1: proline dehydrogenase | MVAN_RS11480 | |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | MVAN_RS08390 | MVAN_RS20500 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | MVAN_RS16610 | MVAN_RS07905 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | MVAN_RS15070 | MVAN_RS09935 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | | |
| rhamnose | LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase | MVAN_RS30280 | MVAN_RS11235 |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsK: ribokinase | MVAN_RS19720 | MVAN_RS20120 |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | | |
| serine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | MVAN_RS14290 | |
| serine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | MVAN_RS14295 | MVAN_RS13025 |
| serine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | MVAN_RS14300 | MVAN_RS13020 |
| sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | MVAN_RS13160 | MVAN_RS09365 |
| sucrose | ams: sucrose hydrolase (invertase) | MVAN_RS12780 | |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | | |
| threonine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | MVAN_RS14290 | |
| threonine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | MVAN_RS14295 | MVAN_RS13025 |
| threonine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | MVAN_RS14300 | MVAN_RS13020 |
| threonine | ltaE: L-threonine aldolase | MVAN_RS05945 | MVAN_RS23385 |
| thymidine | deoB: phosphopentomutase | MVAN_RS08095 | MVAN_RS07420 |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | MVAN_RS10690 | |
| tyrosine | hmgA: homogentisate dioxygenase | MVAN_RS09545 | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | MVAN_RS23510 | MVAN_RS23045 |
| valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | | |
| valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | MVAN_RS14290 | |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | MVAN_RS09180 | MVAN_RS06885 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | MVAN_RS24230 | MVAN_RS06875 |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | MVAN_RS08390 | MVAN_RS20500 |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
| xylitol | xdhA: xylitol dehydrogenase | MVAN_RS28105 | MVAN_RS02680 |
| xylitol | xylB: xylulokinase | MVAN_RS13185 | MVAN_RS26630 |
| xylose | xylB: xylulokinase | MVAN_RS13185 | MVAN_RS26630 |
| xylose | xylT: D-xylose transporter | MVAN_RS17435 | |
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