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).
Strong and you can poor operon family genes centered on COG kinds. The graph boasts ribosomal family genes (Interpretation, ribosomal construction and you can biogenesis (J)).
Version from inside the evolutionary speed
From the phylogenetic research we checked-out the total evolutionary length predicated on most of the genes identified as chronic. not, there’ll obviously feel inter-gene version on the evolutionary speed. This is analysed by using partners-wise Blast piece scores normalised up against alignment length; come across Approaches for then facts.
Singleton versus duplicate genetics
Prior to analyses discovered a difference on evolutionary price from singletons and you may duplicates, however, it picture was highly influenced by new forty-five r-proteins inside our investigation put. Analyses conducted with roentgen-protein as part of the singletons group reveal that discover indeed a difference about your evolutionary speed. The brand new median of one’s average piece score (normalised more than alignment length) was 0.81 toward singletons and you can 0.73 to your copies (investigation perhaps not revealed), implying you to definitely genes into the clusters reigned over by the singletons are more the same as one another and you will evolve slower than copies. not, it is traditional to depart out r-protein when considering evolutionary rates since they’re highly shown and progress significantly more more sluggish than many other healthy protein. Without any r-healthy protein you will find zero significant difference between the singletons and you can duplicates (average out-of mediocre portion scores 0.71 and you can 0.72 correspondingly). Sure enough the fresh new roentgen-proteins evolve slower that have a median away from average section millions of 0.97. I in addition to tested if there clearly was any huge difference from proteins duration getting singletons and you will duplicates. When roentgen-proteins was indeed left out, so it research failed to render people significant difference.
Strong instead of poor operon genes
I then did a similar analyses because demonstrated above, however, comparing solid and you can weak operon protein. Brand new ribosomal and the fused/blended proteins was basically put aside of the studies. The result is shown inside the Contour nine. The brand new average from average portion results having strong and you can poor operon 
healthy protein is 0.65 and 0.79 respectively, therefore appearing that strong operon genetics progress faster compared to weak operon family genes (p-well worth step three.527 ? 10 -5 ). As mentioned previously brand new roentgen-healthy protein enjoys a median off average section an incredible number of 0.97. There is an improvement away from healthy protein length to have good and you will weakened operon proteins. The newest proteins out-of weak operon family genes (Contour 10) has actually the common length of amino acids compared to amino acids to have proteins out of good operon family genes (p-really worth step one.361 ? 10 -5 ).
Average proteins section rating getting good and weak operon gene clusters. A box spot demonstrating the various gene clusters rated based on average couple-wise bit rating of healthy protein sequences (BitScore) normalised facing alignment length (AliLen). The newest legend text reveals the fresh new average get of each and every classification (poor operon 0.79 bits, strong operon 0.65 parts). Ribosomal family genes aren’t included. While they are provided the amounts are 0.81 and 0.75, correspondingly.