information

Whoever comes in this website may find a hint

Phage therapy is influenced by:

Phage therapy is influenced by:

Country :
the epidemiological situation is different from country to country in terms of circulating bacteria and bacteriophages. Example: a lytic phages from Italy may be no active on the same bacteria (genus and species) isolated from another country and vice versa.
Chronolability
Mutation rate
Phenotypical delay
Phage cocktail
My point of view

From Wikipedia


If the target host* of a phage therapy treatment is not
an animal the term "
biocontrol" (as in phage-mediated biocontrol of bacteria) is usually employed, rather than "phage therapy".

"In silico"

From:"Genomics,Proteomics and Clinical Bacteriology", N.Woodford and Alan P.Johnson

Phrase that emphasizes the fact that many molecular biologists spend increasing amounts of their time in front of a computer screen, generating hypotheses that can subsequently be tested and (hopefully) confirmed in the laboratory.

Thursday, 28 August 2014

D29 phage integrase, Prophage and prophage integrase of M.ulcerans


My working hypotesis

"If before phiMU01 and phiMU02 prophages were active mycobacteriophages probably
Phage integrase of  D29 mycobacteri0phage (or  L5) could have some common features with these prophages and with  the prophage integrase inside  the genome  of Mycobacterium ulcerans ".
This analysis could give strength to my conviction about the presence
of a new specific and  unknown
mycobateriophage usable  in Buruli disease but at moment this phage  has not been isolated in the soil or in fresch water or in other sources  .


Mycobacteriophage D29 

    D29p32

predicted 40.0 kD protein; integrase                      
                                                         

Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582




Phage integrase family; Region: Phage_integrase; pfam00589


Phage integrase, N-terminal SAM-like domain; Region: Phage_int_SAM_3; pfam14659


Statistics on the protein properties:
                                

Distinguishing markVAL is present 27 times                            



  Prophage integrase sequences from Mycobacterium ulcerans genome.



I have chosen  MUL 0529:

 MUL 0529





Site-specific recombinase XerC [DNA replication, recombination, and repair]; Region: XerC; COG4973





DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213



Statistics on the protein properties:




Distinguishing markVAL is present 27 times


Comparison:


MUL 0529 Protein / D29p32 Protein Dot plot





D29p32 and MUL 0529 alignment



In this first part of the  analysis  is not  clear if my working hypotesis is confirmed but if I  use the observation: VAL is present 27 times, I can obtain my goal after 1 h0urs of work .


1-by Jemboss and by Wordcount software I select the word with 3 Aa  but I chose only the words that contain Val Aa.
2- in the protein sequence I write all positions of VAL Aa,the start and the end  of the  main miscellaneous features.
3- in the protein sequence I check the positions of the words with the  Val Aa.









In Position 91 in both the sequences is present VAL Aa .
In position 167 and 166 there is a VAL Aa.
LDV and TVP words are present in both the sequences and my working hypotesis is  in part confirmed.

phiMU01 prophage

In the alignment with phiMU01 prophage  and D29 phage  integrase 
I have the confirmation  of my working hypotesis.




By Swiss-Model there is  also the confirmation:




The  reference Model :



My contribution by Discovery Studio 4.0: