Exercice 1

>seq 1
MAASNHSSGKPGGVLSDALCRELWHACAGPLVTLPREGERVYYFPEGHMEQ
LEASMHQGLEQQMPSFNLPSKILCKVINIQRRAEPETDEVYAQITLLPEL
DQSEPTSPDAPVQEPEKCTVHSFCKTLTASDTSTHGGFSVLRRHADDCLP
PLDMSQQPPWQELVATDLHNSEWHFRHIFRGQPRRHLLTTGWSVFVSSKK
LVAGDAFIFLRGENEELRVGVRRHMRQQTNIPSSVISSHSMHIGVLATAA
HAITTGTIFSVFYKPRTSRSEFIVSVNRYLEAKTQKLSVGMRFKMRFEGE
EAPEKRFSGTIVGVQENKSSVWHDSEWRSLKVQWDEPSSVFRPERVSPWE
LEPLVANSTPSSQPQPPQRNKRPRPPGLPSPATGPSGPVTPDGVWKSPAD
TPSSVPLFSPPAKAATFGHGGNKSFGVSIGSAFWPTNADSAAESFASAFN
NESTEKKQTNGNVCRLFGFELVENVNVDECFSAASVSGAVAVDQPVPSNE
FDSGQQSEPLNINQSDIPSGSGDPEKSSLRSPQESQSRQIRSCTKVHMQG
SAVGRAIDLTRSECYEDLFKKLEEMFDIKGELLESTKKWQVVYTDDEDDM
MMVGDDPWNEFCGMVRKIFIYTPEEVKKLSPKNKLAVNARMQLKADAEEN
GNTEGRSSSMAGSR
1-. Go to PROSITE and scan for domains. Select "Prosite patterns" and "The Prosite profiles"
Do you get any clue of what this protein may do?

2-. Launch a PRODOM blast, parameters by derfault
What is the domain structure of the protein?

3-. Go to PFAM and do a search (default)
How many domains does PFAM find?
Are they related?, Any other protein in PFAM has similar domain structure?
How many A.thaliana proteins has the domain?

4- Go to SCOP and try to find a structure domain for tha protein
In wich structural superfamily can or protein be clasify?


Exercise 2

>seq
MPSKKKKYNA RFPPARIKKI MQTDEEIGKV AAAVPVIISR ALELFLESLL KKACQVTQSR
NAKTMTTSHL KQCIELEQQF DFLKDLVASV PDMQGDGEDN HMDGDKGARR GRKPGSGGRK
NGGMGTKSKD KKLSGTDSEQ EDESEDTDTD GEEETSQPPP QASHPSAHFQ SPPTPFLPFA
STLPLPPAPP GPSAPDEEDE EDYDS
1- Launch the query in INTERPROT
What is the domain structure?

2- Go to SCOP and try to find a structure domain for tha protein
In wich strucutural superfamily can or protein be clasify in?

3- Take a look at Kamada,K et al. Cell 106, 71-81