Now let's use the profile we just created to align xlrhodop.pep to our opsin2 sequences.
unix % prophet
Gapped alignment for profiles
Input sequence(s): xlrhodop.pep
Profile or matrix file: OPS2_*.prophecy
Gap opening coefficient [1.0]:
Gap extension coefficient [0.1]:
Output file [OPS2_*.prophet]:
unix % more OPS2_*.prophet
Local: Consensus vs OPSD_XENLA Score: 2189.00 Consensus 1 M.ERS.HLPEG.PFAAALSGARFAAQSSGN.ASVL..DWNVLP.E 38 | : : : || : ::::: : |: | ::|: : | : OPSD_XENLA 1 MNG.GTE..EGPN.NFYVP.PMS...SN.NKTGVVRSP.P..PFD 33 Consensus 39 MAPLVHPHWSRF.APMNPMWHKILGLFTLILGII.SCLG.NGLVI 80 ::: ::: : : :|: :::|: ::::|::: |: | ::: OPSD_XENLA 34 YPQ.Q.QYYL.LAE..EPWQYSALAAYMFLLILLGL.LPINFMTL 72 Consensus 81 YI.FA.GTKSLRTPANLLVLNLAFSD..FCMMASMSPV.MAINCF 120 :: :: :: |||| |:::|||:|:: : |:: :::| | :::: OPSD_XENLA 73 FVTIQHKKL.LRTPLNYILLNLVFANHFM.MVLCGFTVTMYTSMH 115 Consensus 121 YGETWVLGPLGC..D.IYAAL.GSLFGCVSIWSMCMIAFDRYNVI 161 : :::|| || : ::|:| | | |::||::::|::|| |: OPSD_XENLA 116 G.GYFIFGPTGCYIEGFFATLGG...GEVALWSLVVLAVERYIVV 156 Consensus 162 VKGINGTPLTIKTAILKALFIWMM.AVFW.TIMPLFGWSRYVPEG 204 :|:::: ::::: ||: ::|:|:| : :: : :||||||||:||| OPSD_XENLA 157 CKPMANFRFGENHAIMGVAFTWIMAL.LSCAAPPLFGWSRYIPEG 200 Consensus 205 NLTSCSIDYLT.R.DWNPRSYL.ITYFLFV.YFFPLFIICYSY.W 244 : :||::||:| : : |: |:: |:::| : :||::|:::| : OPSD_XENLA 201 MQCSCGVDYYTLKPEVNNESFVIY.YMFIVHFTIPLIVIFFCYGR 244 Consensus 245 FIIAAVAAHEKAMRDQAKKMNVKSLRSNEDCDKQSAEI.R.LAKV 287 ::::: :|:|:::|:: : :::::::: : |: | :: | OPSD_XENLA 245 LLCTVK..KEAAAQQQESLT..TTQKAEKE..E...EVTRMVV.V 279 Consensus 288 ALTTISLWFMAWTPYAIIAY.FGLFGIDGA.LTP.LTT.IWGALF 328 :::: :::::|:|||::|: : :|: :|: ::| ::| :|:| OPSD_XENLA 280 IMVVF.FFLICWVPYAYVAFYI.IFTHQGSNFGPVFMTVP.PAFF 321 Consensus 329 AKASSCYNPIVYAISHPKYRA.ALKEKCPMCVCGETD.EPSPDAP 371 ||:|::|||::| : ::::| :: :: ::||::: ::::::: OPSD_XENLA 322 AKSSAIYNPVIYIVLNKQFRNCLI...ITTLCCGKNPFGDEDGSS 363 Consensus 372 QSDATTTSEAAS..KAPAAI.EFPD 393 |:||:::||:| ::: :: : |: OPSD_XENLA 364 .SAATSKTEASSVSSSQ.QVSP.PA 385
The vertical bars (|) represent residues that are identical between the OPS2_* consensus and our rhodopsin, while the colons (:) represent conservative substitutions. We hope you can see that aligning members of a family can reveal conserved regions that may be important for structure and/or function.