Demystifying sequence number four

1
Demystifying sequence number four

• Post-genomics and bio-informatics
• Pawel, Salvo, Supat
• 2006-02-13

2
DNA analysis

• SUP (SUPERMAN)floral defective 10
• e-val 2.1e-135
• match 100.00
• length 240
• chromosome 3 (8242691-8242930)
• Function
• DNA binding
• nucleic acid binding
• transcription factor
• zinc ion binding

GCACTTGGTGGCCACATGAATGTTCACAGAAGAGACAGAGCAAGACTCAG
ATTACAACAGTCTCCATCATCATCTTCAACACCTTCTCCTCCTTACCCTA
ACCCTAATTACTCTTACTCAACCATGGCAAACTCTCCTCCTCCTCATCAT
TCTCCTCTAACCCTATTTCCAACCCTTTCTCCTCCATCCTCACCAAGATA
TAGGGCAGGTTTGATCCGTTCCTTGAGCCCCAAGTCAAAA
3
Protein analysis

• Domain
• zf-C2H2
• classical zinc finger domain
• Prediction (Ginzu)
• Parent 213iA (1-88)
• DNA binding protein
• Aart, a six finger zinc finger designed to
  recognize ann triplets
• PSIBLAST
• Zebra fish (danio rerio) - similar to Zinc finger
  protein
• 13.33, e-val 5E-85

MERSNSIELRNSFYGRARTSPWSYGDYDNCQQDHDYLLGFSWPPRSYTCS
FCKREFRSAQALGGHMNVHRRDRARLRLQQSPSSSSTPSPPYPNPNYSYS
TMANSPPPHHSPLTLFPTLSPPSSPRYRAGLIRSLSPKSKHTPENACKTK
KSSLLVEAGEATRFTSKDACKILRNDEIISLELEIGLINESEQDLDLELR
LGFA
4
Structure prediction

• CPH templates
• 1NJQA
• score79, e-val3e-15
• 2CSHA
• score28, e-val4.7
• Visualization
• SPDB
• Chimera

5
Phylogenetic tree

• Method
• Blastx
• Blastp
• ClustalW
• Phylogenetic tree
• Neighbour joining