Potential Gaps in catabolism of small carbon sources in Amycolatopsis xylanica CPCC 202699
Found 37 low-confidence and 69 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| alanine | cycA: L-alanine symporter CycA | BLV57_RS32970 | BLV57_RS20100 |
| arabinose | gguA: L-arabinose ABC transporter, ATPase component GguA | BLV57_RS00880 | BLV57_RS31835 |
| arginine | gbamidase: guanidinobutyramidase | BLV57_RS29695 | BLV57_RS21895 |
| arginine | rocE: L-arginine permease | BLV57_RS32970 | BLV57_RS20100 |
| aspartate | glt: aspartate:proton symporter Glt | BLV57_RS36115 | BLV57_RS38100 |
| cellobiose | cebE: cellobiose ABC transporter, substrate-binding component CebE | BLV57_RS03400 | BLV57_RS21080 |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | BLV57_RS30995 | BLV57_RS11975 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | BLV57_RS11980 | BLV57_RS31000 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | BLV57_RS11165 | BLV57_RS33985 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| citrulline | arcC: carbamate kinase | | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-serine | cycA: D-serine:H+ symporter CycA | BLV57_RS32970 | BLV57_RS35065 |
| D-serine | dsdA: D-serine ammonia-lyase | BLV57_RS41780 | BLV57_RS08730 |
| deoxyinosine | bmpA: deoxyinosine ABC transporter, substrate-binding component | BLV57_RS28605 | |
| deoxyinosine | deoB: phosphopentomutase | BLV57_RS28825 | BLV57_RS27890 |
| deoxyinosine | nupB: deoxyinosine ABC transporter, permease component 1 | BLV57_RS28615 | |
| deoxyinosine | nupC': deoxyinosine ABC transporter, permease component 2 | BLV57_RS28620 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | BLV57_RS37895 | BLV57_RS35695 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | BLV57_RS42095 | BLV57_RS01370 |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fructose | frcC: fructose ABC transporter, permease component FrcC | BLV57_RS11625 | BLV57_RS00495 |
| fructose | scrK: fructokinase | BLV57_RS07900 | BLV57_RS12630 |
| fucose | fucDH: 2-keto-3-deoxy-L-fuconate 4-dehydrogenase | BLV57_RS13760 | BLV57_RS33715 |
| fucose | fuconolactonase: L-fucono-1,5-lactonase | BLV57_RS35730 | |
| fucose | fucU: L-fucose mutarotase FucU | | |
| galactose | pgmA: alpha-phosphoglucomutase | BLV57_RS17235 | BLV57_RS28825 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | garD: meso-galactarate dehydratase (L-threo-forming) GarD | BLV57_RS02160 | BLV57_RS01345 |
| galacturonate | uxuL: D-galactaro-1,5-lactonase (UxuL or UxuF) | BLV57_RS30745 | |
| gluconate | gntT: gluconate:H+ symporter GntT | BLV57_RS38025 | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | BLV57_RS08745 | BLV57_RS27915 |
| glucosamine | nagX: transmembrane glucosamine N-acetyltransferase NagX | | |
| glucose | mglA: glucose ABC transporter, ATP-binding component (MglA) | BLV57_RS00880 | BLV57_RS01885 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | gudD: D-glucarate dehydratase | BLV57_RS00315 | |
| glucuronate | uxuL: D-glucaro-1,5-lactonase UxuL or UxuF | BLV57_RS30745 | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | BLV57_RS28955 | BLV57_RS07875 |
| histidine | Ga0059261_1577: L-histidine transporter | BLV57_RS24925 | BLV57_RS29690 |
| histidine | hutG': N-formylglutamate amidohydrolase | | |
| isoleucine | livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) | BLV57_RS38615 | BLV57_RS30170 |
| isoleucine | livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | BLV57_RS36495 | |
| isoleucine | livM: L-isoleucine ABC transporter, permease component 2 (LivM/BraE) | BLV57_RS38610 | BLV57_RS05265 |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | BLV57_RS28975 | BLV57_RS16770 |
| lactose | lacP: lactose permease LacP | | |
| lactose | pgmA: alpha-phosphoglucomutase | BLV57_RS17235 | BLV57_RS28825 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | BLV57_RS35310 | BLV57_RS22055 |
| leucine | livH: L-leucine ABC transporter, permease component 1 (LivH/BraD) | BLV57_RS38615 | BLV57_RS30170 |
| leucine | livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | BLV57_RS36495 | |
| leucine | livM: L-leucine ABC transporter, permease component 2 (LivM/BraE) | BLV57_RS38610 | BLV57_RS05265 |
| lysine | davD: glutarate semialdehyde dehydrogenase | BLV57_RS16620 | BLV57_RS05155 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | BLV57_RS16500 | BLV57_RS02345 |
| lysine | lysP: L-lysine:H+ symporter LysP | BLV57_RS32970 | BLV57_RS20100 |
| maltose | mglA: glucose ABC transporter, ATP-binding component (MglA) | BLV57_RS00880 | BLV57_RS01885 |
| mannitol | cmtB: mannitol phosphotransferase system, EII-A component CmtB/MtlF | BLV57_RS21120 | |
| mannitol | mtlD: mannitol-1-phosphate 5-dehydrogenase | | |
| mannose | frcC: mannose ABC transporter, permease component FrcC | BLV57_RS11625 | BLV57_RS00495 |
| mannose | mannokinase: D-mannose kinase | BLV57_RS33615 | BLV57_RS30235 |
| myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | BLV57_RS35920 | |
| myoinositol | iolE: scyllo-inosose 2-dehydratase | BLV57_RS35950 | |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | BLV57_RS35965 | BLV57_RS33345 |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | BLV57_RS35930 | BLV57_RS37550 |
| myoinositol | PGA1_c07300: myo-inositol ABC transport, substrate-binding component | BLV57_RS35945 | |
| myoinositol | PGA1_c07310: myo-inositol ABC transporter, permease component | BLV57_RS35940 | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | BLV57_RS08745 | BLV57_RS27915 |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | BLV57_RS35310 | BLV57_RS23460 |
| phenylacetate | ppa: phenylacetate permease ppa | BLV57_RS35160 | BLV57_RS13565 |
| phenylalanine | livF: L-phenylalanine ABC transporter, ATPase component 1 (LivF) | BLV57_RS38600 | BLV57_RS30160 |
| phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | BLV57_RS38615 | BLV57_RS30170 |
| phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | BLV57_RS36495 | |
| phenylalanine | livM: L-phenylalanine ABC transporter, permease component 2 (LivM) | BLV57_RS38610 | BLV57_RS05265 |
| phenylalanine | paaF: 2,3-dehydroadipyl-CoA hydratase | BLV57_RS35310 | BLV57_RS23460 |
| phenylalanine | pad-dh: phenylacetaldehyde dehydrogenase | BLV57_RS05155 | BLV57_RS28715 |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | BLV57_RS28975 | BLV57_RS16770 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | BLV57_RS20525 | BLV57_RS16495 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| rhamnose | rhaM: L-rhamnose mutarotase | BLV57_RS35720 | |
| ribose | frcC: D-ribose ABC transporter, permease component FrcC | BLV57_RS11625 | BLV57_RS00495 |
| serine | serP: L-serine permease SerP | BLV57_RS32970 | BLV57_RS35065 |
| sorbitol | scrK: fructokinase | BLV57_RS07900 | BLV57_RS12630 |
| sorbitol | sdh: sorbitol dehydrogenase | BLV57_RS13760 | BLV57_RS13225 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
| sucrose | ams: sucrose hydrolase (invertase) | BLV57_RS22845 | BLV57_RS29545 |
| sucrose | mglA: glucose ABC transporter, ATP-binding component (MglA) | BLV57_RS00880 | BLV57_RS01885 |
| threonine | RR42_RS28305: L-threonine:H+ symporter | BLV57_RS32970 | BLV57_RS35065 |
| thymidine | deoB: phosphopentomutase | BLV57_RS28825 | BLV57_RS27890 |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | treF: trehalase | BLV57_RS22845 | BLV57_RS06775 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | BLV57_RS32970 | BLV57_RS20100 |
| tryptophan | tnaA: tryptophanase | BLV57_RS20635 | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | BLV57_RS32970 | BLV57_RS20100 |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | BLV57_RS29490 | BLV57_RS29875 |
| valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | BLV57_RS38615 | BLV57_RS30170 |
| valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | BLV57_RS36495 | |
| valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | BLV57_RS38610 | BLV57_RS05265 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | BLV57_RS35960 | BLV57_RS21830 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | BLV57_RS04465 | BLV57_RS02390 |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | BLV57_RS28975 | BLV57_RS16770 |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
| xylitol | xdhA: xylitol dehydrogenase | BLV57_RS21115 | BLV57_RS36750 |
| xylose | xylG: ABC transporter for xylose, ATP-binding component xylG | BLV57_RS00880 | BLV57_RS01885 |
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