Process of turning raw genome data into knowledge for making new drugs

1.

 Where is it ?

BLAST search the human genome

2.

Translate to Protein Sequence

ORF (Open Reading Frame) Finder

>lcl|Sequence 1 ORF:164..4447 Frame +2

MDLSGLPETAVDSEDDDDEEDIERASDPLMSRDIVRDCLEKDPIDRTDDDIEQLLEFMHQLPAFANMTMS
VRRELCAVMVFAVVERAGTIVLNDGEELDSWSVILNGSVEVTYPDGKAEILCMGNSFGVSPTMDKEYMKG
VMRTKVDDCQFVCIAQQDYCRILNQVEKNMQKVEEEGEIVMVKEHRELDRTGTRKGHIVIKGTSERLTMH
LVEEHSVVDPTFIEDFLLTYRTFLSSPMEVGKKLLEWFNDPSLRDKVTRVVLLWVNNHFNDFEGDPAMTR
FLEEFENNLEREKMGGHLRLLNIACAAKAKRRLMTLTKPSREAPLPFILLGGSEKGFGIFVDSVDSGSKA
TEAGLKRGDQILEVNGQNFENIQLSKAMEILRNNTHLSITVKTNLFVFKELLTRLSEEKRNGAPHLPKIG
DIKKASRYSIPDLAVDVEQVIGLEKVNKKSKANTVGGRNKLKKILDKTRISILPQKPYNDIGIGQSQDDS
IVGLRQTKHIPTALPVSGTLSSSNPDLLQSHHRILDFSATPDLPDQVLRVFKADQQSRYIMISKDTTAKE
VVIQAIREFAVTATPDQYSLCEVSVTPEGVIKQRRLPDQLSKLADRIQLSGRYYLKNNMETETLCSDEDA
QELLRESQISLLQLSTVEVATQLSMRNFELFRNIEPTEYIDDLFKLRSKTSCANLKRFEEVINQETFWVA
SEILRETNQLKRMKIIKHFIKIALHCRECKNFNSMFAIISGLNLAPVARLRTTWEKLPNKYEKLFQDLQD
LFDPSRNMAKYRNVLNSQNLQPPIIPLFPVIKKDLTFLHEGNDSKVDGLVNFEKLRMIAKEIRHVGRMAS
VNMDPALMFRTRKKKWRSLGSLSQGSTNATVLDVAQTGGHKKRVRRSSFLNAKKLYEDAQMARKVKQYLS
NLELEMDEESLQTLSLQCEPATNTLPKNPGDKKPVKSETSPVAPRAGSQQKAQSLPQPQQQPPPAHKINQ
GLQVPAVSLYPSRKKVPVKDLPPFGINSPQALKKILSLSEEGSLERHKKQAEDTISNASSQLSSPPTSPQ
SSPRKGYTLAPSGTVDNFSDSGHSEISSRSSIVSNSSFDSVPVSLHDERRQRHSVSIVETNLGMGRMERR
TMIEPDQYSLGSYAPMSEGRGLYATATVISSPSTEELSQDQGDRASLDAADSGRGSWTSCSSGSHDNIQT
IQHQRSWETLPFGHTHFDYSGDPAGLWASSSHMDQIMFSDHSTKYNRQNQSRESLEQAQSRASWASSTGY
WGEDSEGDTGTIKRRGGKDVSIEAESSSLTSVTTEETKPVPMPAHIAVASSTTKGLIARKEGRYREPPPT
PPGYIGIPITDFPEGHSHPARKPPDYNVALQRSRMVARSSDTAGPSSVQQPHGHPTSSRPVNKPQWHKPN
ESDPRLAPYQSQGFSTEEDEDEQVSAV*

3.

Identify the protein

NP_055062    PDZ domain containing guanine nucleotide exchange factor(GEF)1;
             RA(Ras/Rap1A-associating)-GEF; PDZ domain containing guanine nucleotide
             exchange factor(GEF)1; RA(Ras/Rap1A-associating)-GEF [Homosapiens]

   Search the Conserved Domain Database

This protein has 5 conserved domain
cNMP      - Cyclic nucleotide-monophosphate binding domain
RasGEFN - Guanine nucleotide exchange factor for Ras-like GTPases
PDZ         - PDZ domain
RA           - Ras association domain
RasGEF    - RasGEF domain
 
  PSSMs producing significant alignments: Score
(bits)		 E
value
 
gnl|Smart|RasGEF Guanine nucleotide exchange factor for Ras-like small GTPases 239 7e-64
  gnl|Pfam|pfam00617 RasGEF, RasGEF domain 167 3e-42
  gnl|Smart|RasGEFN Guanine nucleotide exchange factor for Ras-like GTPases; N-ter... 87.0 5e-18
gnl|Smart|RA Ras association (RalGDS/AF-6) domain; RasGTP effectors (in cas... 66.2 1e-11
gnl|Smart|PDZ Domain present in PSD-95, Dlg, and ZO-1/2.; Also called DHR (D... 64.3 4e-11
gnl|Smart|cNMP Cyclic nucleotide-monophosphate binding domain; Catabolite gen... 59.3 1e-09
gnl|Pfam|pfam00595 PDZ, PDZ domain (Also known as DHR or GLGF) 54.3 4e-08
gnl|Pfam|pfam00788 RA, Ras association (RalGDS/AF-6) domain 50.8 4e-07
  gnl|Pfam|pfam00618 RasGEFN, Guanine nucleotide exchange factor for Ras-like GTPas... 38.9 0.002
gnl|Pfam|pfam00027 cNMP_binding, Cyclic nucleotide-binding domain 37.0 0.006

4.

 Structure Information

5.

(a)

 
  
 PDB C D
 
RMSD
 
NRES
 
%Id
 
Description
 
1KWA A 
 1.6 78 21.8 Human CaskLIN-2 Pdz Domain 
1B8Q A 1
 2.3 81 24.7 Solution Structure Of The Extended Neuronal Nitric Oxide Synthase Pdz Domain Complexed With An Associated Peptide 
  
(b)