We looked at the distribution of strong and weak operon genes according to COG category and compared this to the overall distribution of COG categories in E. coli (Figure 8). Here r-protein genes were included. The strong operon genes are overrepresented in several of the COG categories compared to the weak operon genes; Translation, ribosomal structure and biogenesis (J), Transcription (K), Cell wall/membrane/envelope biogenesis (M), Energy production and conversion (C), Lipid transport and metabolism (I) and Secondary metabolites biosynthesis, transport and catabolism (Q). On the other hand, the weak operon genes are mainly overrepresented in Replication, recombination and repair (L), Posttranslational modification, protein turnover, chaperones (O) and Nucleotide transport and metabolism (F). This difference between strong and weak operon genes was confirmed with DAVID (excluding r-proteins), showing that whereas gene ontology terms like cell wall biogenesis and ATP metabolic process are overrepresented in strong operon genes, terms like DNA replication, response to stress and nucleotide binding are overrepresented in weak operon genes (p-values < 0.05 after Benjamini and Hochberg correction).
Solid and you may weak operon genes predicated on COG categories. The newest chart boasts ribosomal genes (Interpretation, ribosomal construction and you will biogenesis (J)).
Variation into the evolutionary rate
Throughout the phylogenetic research we checked-out the full evolutionary point according to most of the family genes recognized as chronic. However, there will definitely be inter-gene adaptation about evolutionary speed. This is analysed by using couples-smart Blast bit scores normalised facing positioning size; pick Tricks for after that facts.
Singleton in the place of content family genes
Earlier analyses have found a positive change regarding the evolutionary price from singletons and you will copies, however, that it visualize try firmly dependent on the fresh forty-five roentgen-necessary protein in our research place. Analyses held that have roentgen-necessary protein within the singletons class show that discover indeed an improvement regarding your evolutionary rate. The average of one’s average bit score (normalised more than alignment length) are 0.81 into the singletons and you will 0.73 to the copies (studies not found), implying you to definitely genes when you look at the groups controlled because of the singletons are a lot more similar to both and evolve slowly than simply duplicates. not, it’s conventional to go out of aside roentgen-protein when looking at evolutionary price as they are extremely indicated and you may develop a great deal more more sluggish than many other healthy protein. Without the roentgen-proteins there can be no significant difference between your singletons and you will copies (average off average piece ratings 0.71 and you can 0.72 correspondingly). Affirmed new r-proteins develop slower that have an average away from mediocre section millions of 0.97. I also checked whether or not there’s any difference out of necessary protein length getting singletons and you will copies. Whenever r-proteins was basically put aside, so it data didn’t give people factor.
Good instead of poor operon genetics
I then did an identical analyses because described significantly more than, however, evaluating good and you will poor operon necessary protein. Brand new ribosomal together with bonded/combined healthy protein was overlooked of your own studies. The result is revealed in Shape nine. The brand new average off average piece scores to own strong and you can weakened operon necessary protein was 0.65 and 0.79 correspondingly, ergo exhibiting that the good operon family genes develop smaller compared to weakened operon family genes (p-really worth 3.527 ? 10 -5 ). As mentioned previously the newest roentgen-necessary protein features a median regarding average section many 0.97. Addititionally there is a big difference out-of proteins size for solid and you can poor operon healthy protein. The healthy protein from weakened operon family genes (Contour 10) has actually the average amount of amino acids compared to amino acids getting protein regarding solid operon genes (p-really worth step one.361 ? 10 -5 ).
Mediocre protein piece score for good and poor operon gene clusters. A package spot profil down dating proving the many gene groups ranked based on average partners-wise section get of one’s protein sequences (BitScore) normalised against positioning length (AliLen). The brand new legend text message reveals the newest average rating of every group (poor operon 0.79 parts, solid operon 0.65 parts). Ribosomal genetics aren’t provided. If they are integrated brand new amounts is actually 0.81 and you will 0.75, respectively.