corrected exercises

Using some functionalities of the MicroScope platform:
corrected exercises
Practice 1 Comparative genomics : Synteny/fusion
• Exercice 1 (AcinetoScope public)
A) Select “fusion/fission” item in the “Comparative genomics” Menu.
For ACIAD0380, the number of genomes which don’t have the same fusion is equal to
341.
B) Click on the icon glass
before ACIAD0380
+ change the selected genomes in the synteny map (“MaGe” menu/”Genome
browser options” item): add one strain of P. aeruginosa, Pseudomonas fluorescens, P.
putida, and P. syringae
+ modify the settings : begin= 366000 / Length(bp)=15000
• Move your mouse on the two corresponding genes in front of ACIAD0380 in the
Pseudomonas species synteny maps: hisE and hisI are encoded by two genes –
maxLrap is < to 1 because the protein in Acinetobacter in longer.
• Click on one synteny containing hisE and hisI genes, for example with P. syringae pv.
Tomato (use ‘Reverse’ to have the gene correctly organized in the synteny) :
PSTO5153 and 5154 are co-localized and highly similar to the Cterm part and the
Nterm of ACIAD0380 respectively. ACIAD0381 has no corresponding gene in the
synteny.
C) Open ACIAD0380 gene editor :
C1: Have a look in the Syntonome results, and filter using the “pseudo” keyword
Pseudomonas putida : hisI and ACIAD0380 are BBH (OrderQ=1 and OrderB=1). Exact
position of the hisI and hisE on the ACIAD0380 protein are given in column
BeginQ/EndQ and BeginB/EndB.
C2 : Have a look to the Syntonome refseq results (order by MaxLrap)
The simple way to get the complete list of genome having also this fusion is to order
the list by decreasing MaxLrap => this fusion is true in all the Acinetobacter species
and in Psychrobacter arcticum – that’s all for the bacterial genomes available in
PkGDB.
Look at the maxLrap value to find the name of complete bacterial genomes having the
same fusion: Acinetobacter species, Psychrobacter species, Clostridium difficile., and
Enhydrobacter aerosaccus.
Practice 2 : Keyword search
A) Change the selected genome :
B) Use de “Search by keywords” of the “Searches” Menu :
First part of the query :
48% of the annotated genes are of unknown function.
Second part of the query : the idea is to look at an updated results of Blast on Uniprot to use
new knowledge for the functional annotation of these proteins
Only 2 results in the Swissprot section and 13 in TrEMBL : following the PubMedId link, at least
four genes seems to be involved in the batI operon (Bacteroides aerotolerance).