An Example of Multiple Sequence Alignment with CLUSTAL W 
for OREXIN 1 Receptors 1 and 2 (mouse and human) 

10 20 30 40 50 60 
| | | | | | 
RatOX1R -------MEPSATPGAQPGVPTSSGEPFHLPPDYEDE-FLRYLWRDYLYPKQYEWVLIAA 
RatOX2R MSSTKLEDSLPRRNWSSASELNETQEPFLNPTDYDDEEFLRYLWREYLHPKEYEWVLIAG 
. . :... ..: *** *.**:** *******:**:**:*******. 

70 80 90 100 110 120 
| | | | | | 
RatOX1R YVAVFLIALVGNTLVCLAVWRNHHMRTVTNYFIVNLSLADVLVTAICLPASLLVDITESW 
RatOX2R YIIVFVVALIGNVLVCVAVWKNHHMRTVTNYFIVNLSLADVLVTITCLPATLVVDITETW 
*: **::**:**.***:***:*********************** ****:*:*****:* 

130 140 150 160 170 180 
| | | | | | 
RatOX1R LFGHALCKVIPYLQAVSVSVAVLTLSFIALDRWYAICHPLLFKSTARRARGSILGIWAVS 
RatOX2R FFGQSLCKVIPYLQTVSVSVSVLTLSCIALDRWYAICHPLMFKSTAKRARNSIVVIWIVS 
:**::*********:*****:***** *************:*****:***.**: ** ** 

190 200 210 220 230 240 
| | | | | | 
RatOX1R LAVMVPQAAVMECSSVLPELANRTRLFSVCDERWADELYPKIYHSCFFFVTYLAPLGLMG 
RatOX2R CIIMIPQAIVMERSSMLPGLANKTTLFTVCDERWGGEVYPKMYHICFFLVTYMAPLCLMV 
:*:*** *** **:** ***:* **:******..*:***:** ***:***:*** ** 

250 260 270 280 290 300 
| | | | | | 
RatOX1R MAYFQIFRKLWGPQIPGTTSALVRNWKRPSEQLEAQHQGLCTEPQPRARAFLAEVKQMRA 
RatOX2R LAYLQIFRKLWCRQIPGTSSVVQRKWKQP--QPVSQPRGSGQQSKARISAVAAEIKQIRA 
:**:******* *****:*.: *:**:* * :* :* :.:.* *. **:**:** 

310 320 330 340 350 360 
| | | | | | 
RatOX1R RRKTAKMLMVVLLVFALCYLPISVLNVLKRVFGMFRQASDREAVYACFTFSHWLVYANSA 
RatOX2R RRKTARMLMVVLLVFAICYLPISILNVLKRVFGMFTHTEDRETVYAWFTFSHWLVYANSA 
*****:**********:******:*********** ::.***:*** ************* 

370 380 390 400 410 420 
| | | | | | 
RatOX1R ANPIIYNFLSGKFREQFKAAFSCCLP---------GLGPSSSARHKSLSLQSRC--SVSK 
RatOX2R ANPIIYNFLSGKFREEFKAAFSCCLGVHRRQGDRLARGRTSTESRKSLTTQISNFDNVSK 
***************:********* . * :*: :***: * .*** 

430 440 450 460 
| | | | 
RatOX1R VSEHVVLTTVTTVLS--------------------------- 
RatOX2R LSEHVALTSISTLPAANGAGPLQNWYLQQGVPSSLLSTWLEV 
:****.**:::*: : 
Color code for secondary states h,g: Helix e: Sheet t: Turn c,s,b: Coil ?:
Ambigous

 1 RatOX1R      416 aa;  2 RatOX2R      460 aa

Number of perfect matches = * 282 => 61.04 % 
Number of high similarity = : 61 => 13.20 %
Number of low similarity = . 21 => 4.55 % 
Fast Pairwise Alignment Parameters 
Ktupl size =1; Window size =pam; Scoring method =Percentage
Number of top diagonals=5; Gap penalty= 3
Multiple Alignment Parameters 
Weight Matrix =pam; Gap opening penalty =10.0
Gap extension penalty =0.05; Hydophilic gaps =On
Hydrophilic residues-hgapresidues=GPSNDQERK; Residue-specific gap penalties =On

50912A