Potential Gaps in catabolism of small carbon sources in Microvirga lotononidis WSM3557
Found 31 low-confidence and 54 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 | MICLODRAFT_RS10820 | MICLODRAFT_RS27925 |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| alanine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | MICLODRAFT_RS30935 | MICLODRAFT_RS25195 |
| alanine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | MICLODRAFT_RS30910 | MICLODRAFT_RS11965 |
| alanine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | MICLODRAFT_RS30915 | MICLODRAFT_RS27010 |
| arabinose | xacC: L-arabinono-1,4-lactonase | MICLODRAFT_RS13840 | MICLODRAFT_RS17620 |
| asparagine | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | MICLODRAFT_RS19550 | MICLODRAFT_RS26255 |
| aspartate | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | MICLODRAFT_RS19550 | MICLODRAFT_RS26255 |
| cellobiose | glk: glucokinase | MICLODRAFT_RS05260 | MICLODRAFT_RS17985 |
| citrate | tctB: citrate/Na+ symporter, small transmembrane component TctB | | |
| citrate | tctC: citrate/Na+ symporter, substrate-binding component TctC | MICLODRAFT_RS08985 | MICLODRAFT_RS29780 |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | MICLODRAFT_RS20255 | MICLODRAFT_RS06870 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | MICLODRAFT_RS20260 | MICLODRAFT_RS11605 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | MICLODRAFT_RS20265 | MICLODRAFT_RS25060 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | MICLODRAFT_RS20275 | MICLODRAFT_RS24365 |
| citrulline | arcC: carbamate kinase | | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | MICLODRAFT_RS21385 | MICLODRAFT_RS10110 |
| deoxyinosine | bmpA: deoxyinosine ABC transporter, substrate-binding component | MICLODRAFT_RS31585 | |
| deoxyinosine | nupB: deoxyinosine ABC transporter, permease component 1 | MICLODRAFT_RS31600 | |
| deoxyinosine | nupC': deoxyinosine ABC transporter, permease component 2 | MICLODRAFT_RS12370 | MICLODRAFT_RS31605 |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | MICLODRAFT_RS19270 | MICLODRAFT_RS09215 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fucose | fucD: L-fuconate dehydratase | MICLODRAFT_RS26805 | |
| fucose | fucP: L-fucose:H+ symporter FucP | | |
| galactose | dgoD: D-galactonate dehydratase | MICLODRAFT_RS20855 | MICLODRAFT_RS07225 |
| galactose | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | MICLODRAFT_RS13840 | MICLODRAFT_RS17620 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | gci: D-galactarolactone cycloisomerase | MICLODRAFT_RS13870 | MICLODRAFT_RS20105 |
| galacturonate | gli: D-galactarolactone isomerase | | |
| gluconate | gntK: D-gluconate kinase | | |
| glucose | glk: glucokinase | MICLODRAFT_RS05260 | MICLODRAFT_RS17985 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | dctQ: D-glucuronate TRAP transporter, small permease component | MICLODRAFT_RS22590 | |
| glucuronate | uxaC: D-glucuronate isomerase | MICLODRAFT_RS26105 | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | MICLODRAFT_RS30480 | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | MICLODRAFT_RS17470 | MICLODRAFT_RS25365 |
| L-lactate | lctO: L-lactate oxidase or 2-monooxygenase | MICLODRAFT_RS20840 | MICLODRAFT_RS29700 |
| lactose | dgoD: D-galactonate dehydratase | MICLODRAFT_RS20855 | MICLODRAFT_RS07225 |
| lactose | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | MICLODRAFT_RS13840 | MICLODRAFT_RS17620 |
| lactose | glk: glucokinase | MICLODRAFT_RS05260 | MICLODRAFT_RS17985 |
| lactose | lacP: lactose permease LacP | | |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | MICLODRAFT_RS03885 | MICLODRAFT_RS07440 |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| lysine | hglS: D-2-hydroxyglutarate synthase | | |
| lysine | lysL: L-lysine transporter LysL | MICLODRAFT_RS23845 | |
| maltose | glk: glucokinase | MICLODRAFT_RS05260 | MICLODRAFT_RS17985 |
| maltose | susB: alpha-glucosidase (maltase) | MICLODRAFT_RS11150 | |
| mannitol | mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE | MICLODRAFT_RS23985 | MICLODRAFT_RS12700 |
| mannitol | mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) | MICLODRAFT_RS23990 | MICLODRAFT_RS12650 |
| myoinositol | PGA1_c07300: myo-inositol ABC transport, substrate-binding component | MICLODRAFT_RS17230 | |
| NAG | nagK: N-acetylglucosamine kinase | MICLODRAFT_RS27690 | MICLODRAFT_RS27800 |
| NAG | SMc02869: N-acetylglucosamine ABC transporter, ATPase component | MICLODRAFT_RS24000 | MICLODRAFT_RS24390 |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | MICLODRAFT_RS07440 | MICLODRAFT_RS27025 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | MICLODRAFT_RS30910 | MICLODRAFT_RS27015 |
| phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | MICLODRAFT_RS30935 | MICLODRAFT_RS25195 |
| phenylalanine | paaF: 2,3-dehydroadipyl-CoA hydratase | MICLODRAFT_RS07440 | MICLODRAFT_RS27025 |
| propionate | lctP: propionate permease | MICLODRAFT_RS17445 | |
| putrescine | gabD: succinate semialdehyde dehydrogenase | MICLODRAFT_RS20175 | MICLODRAFT_RS03140 |
| putrescine | gabT: gamma-aminobutyrate transaminase | MICLODRAFT_RS31980 | MICLODRAFT_RS13930 |
| putrescine | puuA: glutamate-putrescine ligase | | |
| putrescine | puuB: gamma-glutamylputrescine oxidase | MICLODRAFT_RS11195 | MICLODRAFT_RS19545 |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | MICLODRAFT_RS30935 | MICLODRAFT_RS25195 |
| serine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | MICLODRAFT_RS30910 | MICLODRAFT_RS11965 |
| serine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | MICLODRAFT_RS30915 | MICLODRAFT_RS27010 |
| sorbitol | sdh: sorbitol dehydrogenase | MICLODRAFT_RS24015 | MICLODRAFT_RS11945 |
| sucrose | SUS: sucrose synthase | | |
| sucrose | thuK: sucrose ABC transporter, ATPase component ThuK | MICLODRAFT_RS24390 | MICLODRAFT_RS24000 |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | MICLODRAFT_RS30935 | MICLODRAFT_RS25195 |
| threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | MICLODRAFT_RS30910 | MICLODRAFT_RS11965 |
| threonine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | MICLODRAFT_RS30915 | MICLODRAFT_RS27010 |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | glk: glucokinase | MICLODRAFT_RS05260 | MICLODRAFT_RS17985 |
| trehalose | treF: trehalase | MICLODRAFT_RS27805 | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | MICLODRAFT_RS25365 | MICLODRAFT_RS17470 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | MICLODRAFT_RS17490 | MICLODRAFT_RS27600 |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
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