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).
Good and weakened operon genes predicated on COG groups. The fresh chart is sold with ribosomal genetics (Interpretation, ribosomal design and biogenesis (J)).
Version within the evolutionary price
Regarding phylogenetic analysis i checked out the evolutionary length based on the genetics identified as persistent. But not, there may of course feel inter-gene variation on evolutionary rate. It was analysed by using couples-wise Great time piece results normalised up against positioning length; come across Suggestions for next info.
Singleton as opposed to backup genetics
Before analyses have discovered a difference in the evolutionary rate off singletons and you will duplicates, but it image is highly determined by the new 45 roentgen-necessary protein within studies set. Analyses presented that have r-healthy protein included in the singletons category show that you will find in fact a difference regarding your evolutionary rate. This new average of one’s average piece score (normalised over positioning length) is actually 0.81 toward singletons and you may 0.73 towards the duplicates (study not shown), implying you to definitely genetics when you look at the groups ruled because of the singletons tend to be much more like both and you will evolve slower than simply copies. However, it’s old-fashioned to depart out r-healthy protein when looking at evolutionary price because they are extremely indicated and you can develop significantly more slowly than many other healthy protein. With no roentgen-healthy protein there can be no significant difference involving the singletons and you can duplicates (average off average bit results 0.71 and you may 0.72 correspondingly). Sure-enough brand new roentgen-necessary protein develop more sluggish with a median away from average section many 0.97. We plus examined whether or not there was one improvement regarding proteins size to own singletons and you can copies. When roentgen-protein have been put aside, which analysis don’t bring any factor.
Strong instead of poor operon family genes
I up coming did an equivalent analyses because the revealed over, but comparing good and poor operon proteins. New ribosomal and the fused/blended necessary protein have been left out of study. As a result, revealed from inside the Profile nine. The newest median off mediocre portion results to have good and poor operon necessary protein was 0.65 and you may 0.79 respectively, ergo exhibiting your solid operon genes develop smaller versus poor operon genetics (p-worth step three.527 ? ten -5 ). As stated previously the new roentgen-protein keeps an average out of average bit countless 0.97. There is also a big difference from protein length to possess strong and weakened operon healthy protein. The brand new proteins off weak operon genetics (Contour 10) enjoys an average length of amino acids than the proteins to possess necessary protein regarding strong operon genetics (p-worth 1.361 ? ten -5 ).
Mediocre proteins portion score having solid and you can poor operon gene clusters. A package patch demonstrating the various gene groups rated considering average few-wise section rating of proteins sequences (BitScore) normalised up against positioning size (AliLen). The legend text message shows the latest median get of every classification (weakened operon 0.79 bits, strong operon 0.65 bits). Ribosomal family genes commonly provided. When they are provided the fresh wide variety try 0.81 and you will 0.75, correspondingly.
