Potential Gaps in catabolism of small carbon sources in Saccharomonospora marina XMU15
Found 64 low-confidence and 73 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | SACMADRAFT_RS07795 | |
| alanine | alsT: L-alanine symporter AlsT/DagA | SACMADRAFT_RS27595 | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arabinose | xacB: L-arabinose 1-dehydrogenase | SACMADRAFT_RS08725 | SACMADRAFT_RS18785 |
| arabinose | xacC: L-arabinono-1,4-lactonase | | |
| arabinose | xacE: 2-dehydro-3-deoxy-L-arabinonate dehydratase | | |
| arginine | rocE: L-arginine permease | | |
| asparagine | glt: aspartate:proton symporter Glt | | |
| aspartate | glt: aspartate:proton symporter Glt | | |
| cellobiose | cebE: cellobiose ABC transporter, substrate-binding component CebE | SACMADRAFT_RS21985 | |
| citrate | tctB: citrate/Na+ symporter, small transmembrane component TctB | SACMADRAFT_RS12165 | |
| citrate | tctC: citrate/Na+ symporter, substrate-binding component TctC | SACMADRAFT_RS12160 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | SACMADRAFT_RS27815 | SACMADRAFT_RS15025 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | SACMADRAFT_RS20060 | |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | | |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| D-alanine | dadA: D-alanine dehydrogenase | SACMADRAFT_RS09640 | |
| D-lactate | glcE: D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) | SACMADRAFT_RS02290 | SACMADRAFT_RS27505 |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | SACMADRAFT_RS07355 | SACMADRAFT_RS21815 |
| deoxyinosine | deoB: phosphopentomutase | SACMADRAFT_RS04180 | SACMADRAFT_RS03620 |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | SACMADRAFT_RS07695 | SACMADRAFT_RS19480 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | garK: glycerate 2-kinase | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| ethanol | etoh-dh-nad: ethanol dehydrogenase (NAD(P)) | SACMADRAFT_RS27475 | SACMADRAFT_RS17975 |
| fructose | fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components | | |
| fucose | fucDH: 2-keto-3-deoxy-L-fuconate 4-dehydrogenase | SACMADRAFT_RS08725 | SACMADRAFT_RS07695 |
| fucose | fuconolactonase: L-fucono-1,5-lactonase | SACMADRAFT_RS07675 | |
| fucose | fucU: L-fucose mutarotase FucU | SACMADRAFT_RS25335 | |
| galactose | galP: galactose:H+ symporter GalP | | |
| galactose | pgmA: alpha-phosphoglucomutase | SACMADRAFT_RS21455 | SACMADRAFT_RS04180 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | uxaA: D-altronate dehydratase | | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | SACMADRAFT_RS23610 | SACMADRAFT_RS01970 |
| glucosamine | nagX: transmembrane glucosamine N-acetyltransferase NagX | | |
| glucose | MFS-glucose: glucose transporter, MFS superfamily | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | uxaC: D-glucuronate isomerase | | |
| glucuronate | uxuA: D-mannonate dehydratase | | |
| glucuronate | uxuB: D-mannonate dehydrogenase | | |
| glutamate | gluB: L-glutamate ABC transporter, substrate-binding component GluB | SACMADRAFT_RS18455 | |
| glutamate | gluC: L-glutamate ABC transporter, permease component 1 (GluC) | SACMADRAFT_RS18460 | |
| glutamate | gluD: L-glutamate ABC transporter, permease component 2 (GluD) | SACMADRAFT_RS18465 | SACMADRAFT_RS27820 |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | SACMADRAFT_RS04255 | SACMADRAFT_RS06590 |
| glycerol | glpF: glycerol facilitator glpF | SACMADRAFT_RS04250 | |
| histidine | Ga0059261_1577: L-histidine transporter | SACMADRAFT_RS11005 | |
| histidine | hutG': N-formylglutamate amidohydrolase | | |
| histidine | hutH: histidine ammonia-lyase | SACMADRAFT_RS05350 | |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | SACMADRAFT_RS27880 | SACMADRAFT_RS07080 |
| isoleucine | natB: L-isoleucine ABC transporter, substrate-binding component NatB | SACMADRAFT_RS19825 | |
| isoleucine | natC: L-isoleucine ABC transporter, permease component 1 (NatC) | | |
| isoleucine | natD: L-isoleucine ABC transporter, permease component 2 (NatD) | SACMADRAFT_RS19805 | SACMADRAFT_RS11890 |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | SACMADRAFT_RS04285 | SACMADRAFT_RS21155 |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | SACMADRAFT_RS22000 | SACMADRAFT_RS01915 |
| lactose | pgmA: alpha-phosphoglucomutase | SACMADRAFT_RS21455 | SACMADRAFT_RS04180 |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | SACMADRAFT_RS27880 | SACMADRAFT_RS07080 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | SACMADRAFT_RS19140 | SACMADRAFT_RS08335 |
| leucine | natB: L-leucine ABC transporter, substrate-binding component NatB | SACMADRAFT_RS19825 | |
| leucine | natC: L-leucine ABC transporter, permease component 1 (NatC) | | |
| leucine | natD: L-leucine ABC transporter, permease component 2 (NatD) | SACMADRAFT_RS19805 | SACMADRAFT_RS11890 |
| lysine | cadA: lysine decarboxylase | SACMADRAFT_RS04570 | SACMADRAFT_RS10825 |
| lysine | davD: glutarate semialdehyde dehydrogenase | SACMADRAFT_RS21050 | SACMADRAFT_RS08720 |
| lysine | davT: 5-aminovalerate aminotransferase | SACMADRAFT_RS21055 | SACMADRAFT_RS17095 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | SACMADRAFT_RS17670 | SACMADRAFT_RS11800 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| lysine | patA: cadaverine aminotransferase | SACMADRAFT_RS17095 | SACMADRAFT_RS11300 |
| lysine | patD: 5-aminopentanal dehydrogenase | SACMADRAFT_RS08720 | SACMADRAFT_RS26445 |
| maltose | MAL11: maltose permease | | |
| mannitol | mt2d: mannitol 2-dehydrogenase | SACMADRAFT_RS22760 | SACMADRAFT_RS23995 |
| mannitol | mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE | SACMADRAFT_RS22755 | |
| mannitol | mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) | SACMADRAFT_RS22745 | SACMADRAFT_RS06540 |
| mannitol | mtlK: polyol ABC transporter, ATP component MtlK/SmoG | SACMADRAFT_RS04690 | SACMADRAFT_RS15515 |
| mannitol | scrK: fructokinase | SACMADRAFT_RS23105 | SACMADRAFT_RS29575 |
| mannose | manP: mannose PTS system, EII-CBA components | | |
| myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | SACMADRAFT_RS24185 | |
| myoinositol | iolE: scyllo-inosose 2-dehydratase | SACMADRAFT_RS24215 | |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | SACMADRAFT_RS24230 | SACMADRAFT_RS17600 |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | SACMADRAFT_RS24195 | |
| myoinositol | PGA1_c07300: myo-inositol ABC transport, substrate-binding component | SACMADRAFT_RS24210 | |
| myoinositol | PGA1_c07310: myo-inositol ABC transporter, permease component | SACMADRAFT_RS24205 | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | SACMADRAFT_RS23610 | SACMADRAFT_RS01970 |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | SACMADRAFT_RS19140 | SACMADRAFT_RS14875 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | SACMADRAFT_RS04595 | SACMADRAFT_RS23005 |
| phenylacetate | ppa: phenylacetate permease ppa | SACMADRAFT_RS08015 | SACMADRAFT_RS12530 |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | paaF: 2,3-dehydroadipyl-CoA hydratase | SACMADRAFT_RS19140 | SACMADRAFT_RS14875 |
| phenylalanine | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | SACMADRAFT_RS04595 | SACMADRAFT_RS23005 |
| phenylalanine | PPDCalpha: phenylpyruvate decarboxylase, alpha subunit | SACMADRAFT_RS27870 | SACMADRAFT_RS18020 |
| proline | ectP: proline transporter EctP | SACMADRAFT_RS01470 | SACMADRAFT_RS09130 |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | SACMADRAFT_RS04285 | SACMADRAFT_RS21155 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | SACMADRAFT_RS17095 | SACMADRAFT_RS11300 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | SACMADRAFT_RS26445 | SACMADRAFT_RS27255 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| rhamnose | rhaM: L-rhamnose mutarotase | SACMADRAFT_RS25335 | |
| rhamnose | rhaP: L-rhamnose ABC transporter, permease component 1 (RhaP) | SACMADRAFT_RS25350 | SACMADRAFT_RS25345 |
| rhamnose | rhaQ: L-rhamnose ABC transporter, permease component 2 (RhaQ) | SACMADRAFT_RS25345 | SACMADRAFT_RS25350 |
| rhamnose | rhaT': L-rhamnose ABC transporter, ATPase component RhaT | SACMADRAFT_RS25355 | SACMADRAFT_RS07390 |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | SACMADRAFT_RS19825 | |
| serine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | SACMADRAFT_RS19805 | SACMADRAFT_RS27850 |
| serine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | SACMADRAFT_RS27855 | SACMADRAFT_RS19810 |
| sorbitol | mtlK: ABC transporter for polyols MtlEFGK, permease component MtlK | SACMADRAFT_RS04690 | SACMADRAFT_RS15515 |
| sorbitol | scrK: fructokinase | SACMADRAFT_RS23105 | SACMADRAFT_RS29575 |
| sorbitol | sdh: sorbitol dehydrogenase | SACMADRAFT_RS27250 | SACMADRAFT_RS08725 |
| sucrose | ams: sucrose hydrolase (invertase) | SACMADRAFT_RS26825 | |
| sucrose | fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components | | |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | SACMADRAFT_RS19825 | |
| threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | SACMADRAFT_RS19805 | SACMADRAFT_RS27850 |
| threonine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | SACMADRAFT_RS27855 | SACMADRAFT_RS19810 |
| thymidine | deoB: phosphopentomutase | SACMADRAFT_RS04180 | SACMADRAFT_RS03620 |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | thuE: trehalose ABC transporter, substrate-binding component ThuE | | |
| trehalose | treF: trehalase | SACMADRAFT_RS26825 | SACMADRAFT_RS05335 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | SACMADRAFT_RS10990 | SACMADRAFT_RS04595 |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | SACMADRAFT_RS27880 | SACMADRAFT_RS07080 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | SACMADRAFT_RS24225 | SACMADRAFT_RS26775 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | SACMADRAFT_RS06510 | SACMADRAFT_RS27165 |
| valine | natB: L-valine ABC transporter, substrate-binding component NatB | SACMADRAFT_RS19825 | |
| valine | natC: L-valine ABC transporter, permease component 1 (NatC) | | |
| valine | natD: L-valine ABC transporter, permease component 2 (NatD) | SACMADRAFT_RS19805 | SACMADRAFT_RS11890 |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | SACMADRAFT_RS04285 | SACMADRAFT_RS21155 |
| xylitol | PS417_12055: xylitol ABC transporter, substrate-binding component | | |
| xylitol | PS417_12065: xylitol ABC transporter, ATPase component | SACMADRAFT_RS25355 | SACMADRAFT_RS07670 |
| xylitol | xdhA: xylitol dehydrogenase | SACMADRAFT_RS17725 | SACMADRAFT_RS17480 |
| 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.
Links
Downloads
Related tools
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