Multiple Alignments

A multiple alignment is an alignment of more than two nucleotide or amino acid sequences. Constructing a multiple alignment is a useful way to compare different genes. A multiple alignment can help you to identify important conserved positions. You can also use a multiple alignment to construct a phylogenetic tree of related proteins.

In this example, we will use our gene model for the D. ananassae Oct-TyrR gene as the starting point. Here is the predicted peptide:

>Oct-TyrR-PA_peptide [Drosophila ananassae]
MPSADQILFINVTTTVAAAALTAAASVGSVKSGGSNDAGSALERLEGTTPTSANVSGSLV
EGLTTVAAGLGTAQPDGDSGECGGAVEELHASILGIHLAVPEWEALLTALVLSVIIVLTI
IGNILVILSVFTYKPLRIVQNFFIVSLAVADLTVALLVLPFNVAYSILGRWEFGIHLCKL
WLTCDVLCCTSSILNLCAIALDRYWAITDPINYAQKRTVGRVLLLISGVWLLSLLISSPP
LIGWNDWPDEFTSATPCELTSQRGYVIYSSLGSFFIPLAIMTLVYIEIFVATRRRLRERA
RANKLNTIALKSTELEPINSSPAGASASASGSKSRLLTSWLCCGRDRAPFAAPMIQNDQE
SISSETHPPAQEASKTGPGSHISSDQQQHVVVLVKKSRRSKIKDSIKHGKARGVRKSQSS
STCEPHGEQQLLPATGGGQSAGGKSDAEISTESGSDPKGCIQVCVTQTDEQTSLKLTPPQ
SSTGAAVASATPLQKKPSGVNQFIEEKQKISLSKERRAARTLGIIMGVFVICWLPFFLMY
VILPFCQSCCPTNKFKNFITWLGYINSGLNPVIYTIFNLDYRRAFKRLLGLN

We use this peptide as the query sequence to search the nr protein database at NCBI using BLASTP. The results are shown below.

Oct-TyrR BLASTP


Notice at the top of the image that we have detected a conserved domain "7tm_1." Clicking on "7tm_1" gives us:

Oct-TyrR BLASTP conserved


Clicking the first link gives us:

Oct-TyrR BLASTP conserved 7 transmembrane receptor (rhodopsin family)
This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.

Our BLASTP output includes hits on very similar genes in related Drosophila species. We collect the sequences from the links in the alignments, gathering sequences in FASTA format to create the list below.

>Oct-TyrR-PA_peptide [Drosophila ananassae]
MPSADQILFINVTTTVAAAALTAAASVGSVKSGGSNDAGSALERLEGTTPTSANVSGSLV
EGLTTVAAGLGTAQPDGDSGECGGAVEELHASILGIHLAVPEWEALLTALVLSVIIVLTI
IGNILVILSVFTYKPLRIVQNFFIVSLAVADLTVALLVLPFNVAYSILGRWEFGIHLCKL
WLTCDVLCCTSSILNLCAIALDRYWAITDPINYAQKRTVGRVLLLISGVWLLSLLISSPP
LIGWNDWPDEFTSATPCELTSQRGYVIYSSLGSFFIPLAIMTLVYIEIFVATRRRLRERA
RANKLNTIALKSTELEPINSSPAGASASASGSKSRLLTSWLCCGRDRAPFAAPMIQNDQE
SISSETHPPAQEASKTGPGSHISSDQQQHVVVLVKKSRRSKIKDSIKHGKARGVRKSQSS
STCEPHGEQQLLPATGGGQSAGGKSDAEISTESGSDPKGCIQVCVTQTDEQTSLKLTPPQ
SSTGAAVASATPLQKKPSGVNQFIEEKQKISLSKERRAARTLGIIMGVFVICWLPFFLMY
VILPFCQSCCPTNKFKNFITWLGYINSGLNPVIYTIFNLDYRRAFKRLLGLN

>gi|24668474|ref|NP_524419.2| Octopamine-Tyramine receptor, isoform A [Drosophila melanogaster]
MPSADQILFVNVTTTVAAAALTAAAAVSTTKSGSGNAARGYTDSDDDAGMGTEAVANISGSLVEGLTTVT
AALSTAQADKDSAGECEGAVEELHASILGLQLAVPEWEALLTALVLSVIIVLTIIGNILVILSVFTYKPL
RIVQNFFIVSLAVADLTVALLVLPFNVAYSILGRWEFGIHLCKLWLTCDVLCCTSSILNLCAIALDRYWA
ITDPINYAQKRTVGRVLLLISGVWLLSLLISSPPLIGWNDWPDEFTSATPCELTSQRGYVIYSSLGSFFI
PLAIMTIVYIEIFVATRRRLRERARANKLNTIALKSTELEPMANSSPVAASNSGSKSRLLASWLCCGRDR
AQFATPMIQNDQESISSETHQPQDSSKAGPHGNSDPQQQHVVVLVKKSRRAKTKDSIKHGKTRGGRKSQS
SSTCEPHGEQQLLPAGGDGGSCQPGGGHSGGGKSDAEISTESGSDPKGCIQVCVTQADEQTSLKLTPPQS
STGVAAVSVTPLQKKTSGVNQFIEEKQKISLSKERRAARTLGIIMGVFVICWLPFFLMYVILPFCQTCCP
TNKFKNFITWLGYINSGLNPVIYTIFNLDYRRAFKRLLGLN

>gi|195348713|ref|XP_002040892.1| GM22427 [Drosophila sechellia]
MPSADQILFVNVTTTVAAAALTAAAAVNTTKSGSDNAARGYTDSDADAGMGTEAVANISGSLVEGLTTVT
AALSTAQADPDSAGECEGAVEELHASVLGLQLAVPEWEALLTALVLSVIIVLTIIGNILVILSVFTYKPL
RIVQNFFIVSLAVADLTVALLVLPFNVAYSILGRWEFGIHLCKLWLTCDVLCCTSSILNLCAIALDRYWA
ITDPINYAQKRTVGRVLLLISGVWLLSLLISSPPLIGWNDWPDEFTSATPCELTSQRGYVIYSSLGSFFI
PLAIMTIVYIEIFVATRRRLRERARANKLNTIALKSTELEPMANSSPVAASNSGSKSRLLASWLCCGRDR
AQFATPMIQNDQESISSETHQPQDSSKVGSHGNSDPQQQHVVVLVKKSRRAKIKDSIKHGKARGGRKSQS
SSTCEPHGEQQLLPAGGDGGRCQAGGGHSGGGKSDAEISTESGSDPKGCIQVCVTQAEEQTSLKLTPPQS
STGVAAVSVTPLQKKTSGVNQFIEEKQKISLSKERRAARTLGIIMGVFVICWLPFFLMYVILPFCQSCCP
TNKFKNFITWLGYINSGLNPVIYTIFNLDYRRAFKRLLGLN

>gi|195172881|ref|XP_002027224.1| GL25423 [Drosophila persimilis]
MPSADQILFINVTTTVAAAAFTAAAAVSTAPEAAAAAAAGGSTKSVTVVSAAAAAAAAAAAAATAASSSQ
ADEISGRGASATETAANISGSLVEGLTTVAAALTTTAGTSPGESEECGGGAVEELHASILGLQLAVPEWE
ALLTALVLSIIIVLTIIGNILVILSVFTYKPLRIVQNFFIVSLAVADLTVALLVLPFNVAYSILGRWEFG
IHLCKLWLTCDVLCCTSSILNLCAIALDRYWAITDPINYAQKRTVGRVLLLISGVWVLSLVISSPPLIGW
NDWPDEFTSATPCELTSQRGYVIYSSLGSFFIPLAIMTIVYIEIFVATRRRLRERAKATKLNTIALKSTE
LEPITNSSPAAASSSKSRALTNWLCCGRDRANFSTPMIQNDQESISSETHGQQEGSKTATTNDQQQHVVV
LVKKSRRSKIKDSIKHGKARGGRKSQSASTCEPHGEQQLLPAGGSGGGNAAGKSDAEISTESGSDPKGCI
QVCVTQAEEQTSLKLTPPQSSTGAGAVAAAPLQKKPSGVNQFIEEKQKISLSKERRAARTLGIIMGVFVI
CWLPFFLMYVILPFCQSCCPSDKFKNFITWLGYINSGLNPVIYTIFNLDYRRAFKRLLGMK

>gi|194876096|ref|XP_001973713.1| GG16242 [Drosophila erecta]
MPSADQILFVNVTTTVAAAALTAAAAVSTTNSGSDHAARGYADTDADAGMGTETVANISGSLVEGLTTVT
AALSTAQADPDSAGECDGAVDELHASVLGLQLAVPEWEALLTALVLSVIIVLTIIGNILVILSVFTYKPL
RIVQNFFIVSLAVADLTVALLVLPFNVAYSILGRWEFGIHLCKLWLTCDVLCCTSSILNLCAIALDRYWA
ITDPINYAQKRTVGRVLLLISGVWLLSLLISSPPLIGWNDWPDEFTSATPCELTSQRGYVIYSSLGSFFI
PLAIMTIVYIEIFVATRRRLRERARANKLNTIALKSTELEPMANSSPVAASNSGSKSRLLASWLCCGRDR
AQFATPMIQNDQESISSETHQPQDSSKAGSQGNSDSQQQHMVVLVKKSRRAKIKDSIKHGKARGGRKSQS
SSTCEPHGEQQLLPAGGDGGSCQAGGRHSGGGKSDAEISTESGSDPKGCIQVCVTQADEQTSLKLTPPQS
STGAAAVSATPLQKKTSGVNQFIEEKQKISLSKERRAARTLGIIMGVFVICWLPFFLMYVILPFCQSCCP
TNKFKNFITWLGYINSGLNPVIYTIFNLDYRRAFKRLLGLN

>gi|198463614|ref|XP_001352884.2| GA20386 [Drosophila pseudoobscura pseudoobscura]
MPSADQILFINVTTTVAAAAFTAAAAVSTAPEAAAAAAAGGSTKSVTVVSAAAAAAAAAAAAATATATGA
SSSQADEISGRGASATETAANISGSLVEGLTTVAAALTTTAGTSPGESEECGGGAVEELHASILGLQLAV
PEWEALLTALVLSIIIVLTIIGNILVILSVFTYKPLRIVQNFFIVSLAVADLTVALLVLPFNVAYSILGR
WEFGIHLCKLWLTCDVLCCTSSILNLCAIALDRYWAITDPINYAQKRTVGRVLLLISGVWVLSLVISSPP
LIGWNDWPDEFTSATPCELTSQRGYVIYSSLGSFFIPLAIMTIVYIEIFVATRRRLRERAKATKLNTIAL
KSTELEPITNSSPAAASSSKSRALTNWLCCGRDRANFSTPMIQNDQESISSETHGQQEGSKTATTNDQQQ
HVVVLVKKSRRSKIKDSIKHGKARGGRKSQSASTCEPHGEQQLLPAGGSGGGNAAGKSDAEISTESGSDP
KGCIQVCVTQAEEQTSLKLTPPQSSTGAGAVAAAPLQKKPSGVNQFIEEKQKISLSKERRAARTLGIIMG
VFVICWLPFFLMYVILPFCQSCCPSDKFKNFITWLGYINSGLNPVIYTIFNLDYRRAFKRLLGMK

>gi|195476747|ref|XP_002086227.1| GE23022 [Drosophila yakuba]
MPSADQILFVNVTTTVAAAALTAAAAVSTTEFGSDKDERGYVDTDADAGMGTESVANISGSLVEGLTTVT
AALSTAQADPDSAGECDGAVEELHASVLGLQLAVPEWEALLTALVLSVIIVLTIIGNILVILSVFTYKPL
RIVQNFFIVSLAVADLTVALLVLPFNVAYSILGRWEFGIHLCKLWLTCDVLCCTSSILNLCAIALDRYWA
ITDPINYAQKRTVGRVLLLISGVWLLSLLISSPPLIGWNDWPDEFTSATPCELTSQRGYVIYSSLGSFFI
PLAIMTIVYIEIFVATRRRLRERARANKLNTIALKSTELEPMANSSPVAASNSGSKSRLLASWLCCGRDR
AQFATPMIQNDQESISSEVHQPQDSSKAGSHGNSDPQQQHMVVLVKKSRRAKIKDSIKHGKARGGRRSQS
SSTCEPHGEQQLLPAGGDGVSCQAGGGHSGGGKSDAEISTESGSDPKGCIQVCVTQADEQTSLKLTPPQS
STGVAAVSATPLQKKTSGVNQFIEEKQKISLSKERRAARTLGIIMGVFVICWLPFFLMYVILPFCQSCCP
TNKFKNFITWLGYINSGLNPVIYTIFNLDYRRAFKRLLGLN

>gi|195379104|ref|XP_002048321.1| GJ13904 [Drosophila virilis]
MPSADQILFINVTTTVAAAALTAAAAVNSTPEASTAAAAAKAASAPATGNGRTALAANLSGSLVDSLTTA
TATATATATATAATIVETTHECGALAAEELQGSFLGVQLAVPEWEALLTALVLSIIIVLTIIGNILVILS
VFTYKPLRIVQNFFIVSLAVADLTVALLVLPFNVAYSILGRWEFGIHLCKLWLTCDVLCCTSSILNLCAI
ALDRYWAITDPINYAQKRTVGRVLLLISGVWLLSLLISSPPLIGWNDWPDEFTSATPCELTSQRGYVIYS
SLGSFFIPLIIMTIVYIEIFVATRRRLRERAKANKLNTIALKSTELEAINTSGAAAAGGSSTSSKARALG
SLCSSWLCCGRDRANFATPMIHNDQESLSSETHAQPEPNKEQQQQQQQQQQQHVVVLVKKSRRAKIKDSI
KHGKGRSGRRSQSSSSTCEPHGEQQLLPQANSNNASNAAKSDPEISTESGSDPKGCIQVCVTQAEEQTSL
KLTPPQSSSTGATAAAPALQKKPSTVNQFIEEKQKISLSKERRAARTLGIIMGVFVICWLPFFLMYVILP
FCQSCCPTNKFKNFITWLGYINSGLNPVIYTIFNLDYRRAFKRLLGIN

>gi|195128241|ref|XP_002008573.1| GI13571 [Drosophila mojavensis]
MPSADQILFINVTTTVAAAALTAAAAVNSTPEASTTAAAATAAAAASSGRSVETAAATATVASTTTAALA
ANLSGSLVDSLTTTATTTATATATAIVESTNDCSALAVEELHGSFLGVQLAVPEWEALLTALVLSIIIVL
TIIGNILVILSVFTYKPLRIVQNFFIVSLAVADLTVALLVLPLNVAYSILGRWEFGIHLCKLWLTCDVLC
CTSSILNLCAIALDRYWAITDPINYAQKRTVGRVLLLISGVWLLSLLISSPPLIGWNDWPDEFTSATPCE
LTSQRGYVIYSSLGSFFIPLIIMTIVYIEIFVATRRRLRERAKANKLNTIALKNTDLEAINASNVAVGGS
STSSKARALGSLCGSWLCCGRDRANFAAPMIHNDQESLSSETHAQPEGNNESQQQQQQHVVVLVKKSRRA
KIKDSIKHGKARGNRRSQSSSSACEPHGEQQLLPQGNSNNAAGKSDPEISTESGSDPKGCIQVCVTQTEE
QTSLKLTPPQSSSTGVAAASALQKKPSTVNQFIEEKQKISLSKERRAARTLGIIMGVFVICWLPFFLMYV
ILPFCQSCCPTNKFKNFITWLGYINSGLNPVIYTIFNLDYRRAFKRLLGIK

>gi|195440432|ref|XP_002068046.1| GK10695 [Drosophila willistoni]
MPSADQILFINVTTTVAAAALTAAVAVNSSSSNSSSGGGSGNMALVDSLATTVAAAAAAATGSNGITTIA
TLSNDAGDCGNDGGVEEFQSSILGIQLAVPEWEALLTALVLSIIIVLTIIGNILVILSVFTYKPLRIVQN
FFIVSLAVADLTVALLVQPFNVAYSILGRWEFGIHLCKLWLTCDVLCCTSSILNLCAIALDRYWAITDPI
NYAQKRTVGRVLLLISGVWILSLLISSPPLIGWNDWPDEFTSATPCELTSQRGYVIYSALGSFFIPLAIM
TIVYIEIFIATRRRLRERAKANKLNTIALKSTELDTIHQNSSSSPVATSKSRQLANWLCCGRVAGERFQF
TTPMIQNDQESISSETHPHHHQQQQQQQHQQQQEGNDPQQQQQHVVVLVKKSRRSKIKDSIKHGKAKGGR
KSQSSSTCEPHGEQQLLPSSGRSGGPSSGAAKSDPEISTESGSDPKGCIQVCITQTDEQTSLKLTPPQSS
TGGTSIAIASLQKKPSGVNQFIEEKQKISLSKERRAARTLGIIMGVFVICWLPFFLMYVILPFCESCCPT
NKFKNFITWLGYINSGLNPVIYTIFNLDYRRAFKRLLGIK

>gi|195022359|ref|XP_001985558.1| GH14438 [Drosophila grimshawi]
MPSADQILFINVTTTVAAAALTAAVAVNGTPEASTGKASSPAAANGRSASAAAVAGAAASSTSTTTAALA
ANLSGSLVDSLTTATATATATATVTTATAIVESTQECGALAVEELHVSFLGLQLAVPEWEALLTALVLSI
IIVLTIIGNILVILSVFTYKPLRIVQNFFIVSLAVADLMVALLVLPFNVAYSILGRWEFGIHLCKLWLTC
DVLCCTSSILNLCAIALDRYWAITDPINYAQKRTVGRVLLLISGVWLLSLLISSPPLIGWNDWPDEFTSA
TPCELTSQRGYVIYSSLGSFFIPLVIMTIVYIEIFVATRRRLRERAKANKLNTIALKTTELEAINTSSAA
AGSSSTSSKARALGSLCGSWLCCGRDRANFATPMIHNDQESLSSETHAQPDTNTEQHQHQQQQQTVVVLV
KKSRRAKIKDSIKHGKGRSGRRSQSSSSGCEPHGEQQLLPQANSNNAATKSDQEISTESGSDPKGCIQVC
VTQADEQTSLKMTPPQSSMGTAATTVVQKKPSTVNQFIEEKQKISLSKERRAARTLGIIMGVFVICWLPF
FLMYVILPFCQSCCPTNKFKNFITWLGYINSGLNPVIYTIFNLDYRRAFKRLLGMKI


This list can be used as input to various multiple alignment programs. The first program that we will use is Clustal Omega. Here is the output.

CLUSTAL O(1.1.0) multiple sequence alignment


Oct-TyrR-PA_peptide                   MPSADQILFINVTTTVAAAALTAAASVGSVKSGGSNDAGSA-------------------
gi|24668474|ref|NP_524419.2|          MPSADQILFVNVTTTVAAAALTAAAAVSTTKSGSGNAARGY-------------------
gi|195348713|ref|XP_002040892.1|      MPSADQILFVNVTTTVAAAALTAAAAVNTTKSGSDNAARGY-------------------
gi|195172881|ref|XP_002027224.1|      MPSADQILFINVTTTVAAAAFTAAAAVSTAPEAAAAAAAGGSTKSVTVVSAAAAAAAAAA
gi|194876096|ref|XP_001973713.1|      MPSADQILFVNVTTTVAAAALTAAAAVSTTNSGSDHAARGY-------------------
gi|198463614|ref|XP_001352884.2|      MPSADQILFINVTTTVAAAAFTAAAAVSTAPEAAAAAAAGGSTKSVTVVSAAAAAAAAAA
gi|195476747|ref|XP_002086227.1|      MPSADQILFVNVTTTVAAAALTAAAAVSTTEFGSDKDERGY-------------------
gi|195379104|ref|XP_002048321.1|      MPSADQILFINVTTTVAAAALTAAAAVNSTPEASTAAAAAKAASAPATG-----------
gi|195128241|ref|XP_002008573.1|      MPSADQILFINVTTTVAAAALTAAAAVNSTPEASTTAAAATAAAAASSGRSVET--AAA-
gi|195440432|ref|XP_002068046.1|      MPSADQILFINVTTTVAAAALTAAVAVNSSSSNSSSGGGSGNM---ALVDSLATTVAAAA
gi|195022359|ref|XP_001985558.1|      MPSADQILFINVTTTVAAAALTAAVAVNGTPEASTGKASSPAAANGRSASAAAV--AGA-
                                      *********:**********:***.:*      .     .                    

Oct-TyrR-PA_peptide                   ---------------LER---LEGTTPTSANVSGSLVEGLTTVAAGLGTA-----QP-DG
gi|24668474|ref|NP_524419.2|          ---------------TDSDDDAGMGTEAVANISGSLVEGLTTVTAALSTA-----QA-DK
gi|195348713|ref|XP_002040892.1|      ---------------TDSDADAGMGTEAVANISGSLVEGLTTVTAALSTA-----QA-DP
gi|195172881|ref|XP_002027224.1|      ----AAATAASSSQADEISGRGASATETAANISGSLVEGLTTVAAALTTT-----AGTSP
gi|194876096|ref|XP_001973713.1|      ---------------ADTDADAGMGTETVANISGSLVEGLTTVTAALSTA-----QA-DP
gi|198463614|ref|XP_001352884.2|      AAATATATGASSSQADEISGRGASATETAANISGSLVEGLTTVAAALTTT-----AGTSP
gi|195476747|ref|XP_002086227.1|      ---------------VDTDADAGMGTESVANISGSLVEGLTTVTAALSTA-----QA-DP
gi|195379104|ref|XP_002048321.1|      ----------------------NGRTALAANLSGSLVDSLTTATATATATATA-TAATIV
gi|195128241|ref|XP_002008573.1|      ----------------TATVASTTTAALAANLSGSLVDSLTTT---ATTTATA-TATAIV
gi|195440432|ref|XP_002068046.1|      AA-------------------------------ATGSNGITTI-------------ATLS
gi|195022359|ref|XP_001985558.1|      ----------------AASSTSTTTAALAANLSGSLVDSLTTATATATATATVTTATAIV
                                                                       .:  :.:**                  

Oct-TyrR-PA_peptide                   D-SGEC--GGAVEELHASILGIHLAVPEWEALLTALVLSVIIVLTIIGNILVILSVFTYK
gi|24668474|ref|NP_524419.2|          DSAGEC--EGAVEELHASILGLQLAVPEWEALLTALVLSVIIVLTIIGNILVILSVFTYK
gi|195348713|ref|XP_002040892.1|      DSAGEC--EGAVEELHASVLGLQLAVPEWEALLTALVLSVIIVLTIIGNILVILSVFTYK
gi|195172881|ref|XP_002027224.1|      GESEECG-GGAVEELHASILGLQLAVPEWEALLTALVLSIIIVLTIIGNILVILSVFTYK
gi|194876096|ref|XP_001973713.1|      DSAGEC--DGAVDELHASVLGLQLAVPEWEALLTALVLSVIIVLTIIGNILVILSVFTYK
gi|198463614|ref|XP_001352884.2|      GESEECG-GGAVEELHASILGLQLAVPEWEALLTALVLSIIIVLTIIGNILVILSVFTYK
gi|195476747|ref|XP_002086227.1|      DSAGEC--DGAVEELHASVLGLQLAVPEWEALLTALVLSVIIVLTIIGNILVILSVFTYK
gi|195379104|ref|XP_002048321.1|      ETTHECG-ALAAEELQGSFLGVQLAVPEWEALLTALVLSIIIVLTIIGNILVILSVFTYK
gi|195128241|ref|XP_002008573.1|      ESTNDCS-ALAVEELHGSFLGVQLAVPEWEALLTALVLSIIIVLTIIGNILVILSVFTYK
gi|195440432|ref|XP_002068046.1|      NDAGDCGNDGGVEEFQSSILGIQLAVPEWEALLTALVLSIIIVLTIIGNILVILSVFTYK
gi|195022359|ref|XP_001985558.1|      ESTQECG-ALAVEELHVSFLGLQLAVPEWEALLTALVLSIIIVLTIIGNILVILSVFTYK
                                        : :*    ..:*:: *.**::****************:********************

Oct-TyrR-PA_peptide                   PLRIVQNFFIVSLAVADLTVALLVLPFNVAYSILGRWEFGIHLCKLWLTCDVLCCTSSIL
gi|24668474|ref|NP_524419.2|          PLRIVQNFFIVSLAVADLTVALLVLPFNVAYSILGRWEFGIHLCKLWLTCDVLCCTSSIL
gi|195348713|ref|XP_002040892.1|      PLRIVQNFFIVSLAVADLTVALLVLPFNVAYSILGRWEFGIHLCKLWLTCDVLCCTSSIL
gi|195172881|ref|XP_002027224.1|      PLRIVQNFFIVSLAVADLTVALLVLPFNVAYSILGRWEFGIHLCKLWLTCDVLCCTSSIL
gi|194876096|ref|XP_001973713.1|      PLRIVQNFFIVSLAVADLTVALLVLPFNVAYSILGRWEFGIHLCKLWLTCDVLCCTSSIL
gi|198463614|ref|XP_001352884.2|      PLRIVQNFFIVSLAVADLTVALLVLPFNVAYSILGRWEFGIHLCKLWLTCDVLCCTSSIL
gi|195476747|ref|XP_002086227.1|      PLRIVQNFFIVSLAVADLTVALLVLPFNVAYSILGRWEFGIHLCKLWLTCDVLCCTSSIL
gi|195379104|ref|XP_002048321.1|      PLRIVQNFFIVSLAVADLTVALLVLPFNVAYSILGRWEFGIHLCKLWLTCDVLCCTSSIL
gi|195128241|ref|XP_002008573.1|      PLRIVQNFFIVSLAVADLTVALLVLPLNVAYSILGRWEFGIHLCKLWLTCDVLCCTSSIL
gi|195440432|ref|XP_002068046.1|      PLRIVQNFFIVSLAVADLTVALLVQPFNVAYSILGRWEFGIHLCKLWLTCDVLCCTSSIL
gi|195022359|ref|XP_001985558.1|      PLRIVQNFFIVSLAVADLMVALLVLPFNVAYSILGRWEFGIHLCKLWLTCDVLCCTSSIL
                                      ****************** ***** *:*********************************

Oct-TyrR-PA_peptide                   NLCAIALDRYWAITDPINYAQKRTVGRVLLLISGVWLLSLLISSPPLIGWNDWPDEFTSA
gi|24668474|ref|NP_524419.2|          NLCAIALDRYWAITDPINYAQKRTVGRVLLLISGVWLLSLLISSPPLIGWNDWPDEFTSA
gi|195348713|ref|XP_002040892.1|      NLCAIALDRYWAITDPINYAQKRTVGRVLLLISGVWLLSLLISSPPLIGWNDWPDEFTSA
gi|195172881|ref|XP_002027224.1|      NLCAIALDRYWAITDPINYAQKRTVGRVLLLISGVWVLSLVISSPPLIGWNDWPDEFTSA
gi|194876096|ref|XP_001973713.1|      NLCAIALDRYWAITDPINYAQKRTVGRVLLLISGVWLLSLLISSPPLIGWNDWPDEFTSA
gi|198463614|ref|XP_001352884.2|      NLCAIALDRYWAITDPINYAQKRTVGRVLLLISGVWVLSLVISSPPLIGWNDWPDEFTSA
gi|195476747|ref|XP_002086227.1|      NLCAIALDRYWAITDPINYAQKRTVGRVLLLISGVWLLSLLISSPPLIGWNDWPDEFTSA
gi|195379104|ref|XP_002048321.1|      NLCAIALDRYWAITDPINYAQKRTVGRVLLLISGVWLLSLLISSPPLIGWNDWPDEFTSA
gi|195128241|ref|XP_002008573.1|      NLCAIALDRYWAITDPINYAQKRTVGRVLLLISGVWLLSLLISSPPLIGWNDWPDEFTSA
gi|195440432|ref|XP_002068046.1|      NLCAIALDRYWAITDPINYAQKRTVGRVLLLISGVWILSLLISSPPLIGWNDWPDEFTSA
gi|195022359|ref|XP_001985558.1|      NLCAIALDRYWAITDPINYAQKRTVGRVLLLISGVWLLSLLISSPPLIGWNDWPDEFTSA
                                      ************************************:***:*******************

Oct-TyrR-PA_peptide                   TPCELTSQRGYVIYSSLGSFFIPLAIMTLVYIEIFVATRRRLRERARANKLNTIALKSTE
gi|24668474|ref|NP_524419.2|          TPCELTSQRGYVIYSSLGSFFIPLAIMTIVYIEIFVATRRRLRERARANKLNTIALKSTE
gi|195348713|ref|XP_002040892.1|      TPCELTSQRGYVIYSSLGSFFIPLAIMTIVYIEIFVATRRRLRERARANKLNTIALKSTE
gi|195172881|ref|XP_002027224.1|      TPCELTSQRGYVIYSSLGSFFIPLAIMTIVYIEIFVATRRRLRERAKATKLNTIALKSTE
gi|194876096|ref|XP_001973713.1|      TPCELTSQRGYVIYSSLGSFFIPLAIMTIVYIEIFVATRRRLRERARANKLNTIALKSTE
gi|198463614|ref|XP_001352884.2|      TPCELTSQRGYVIYSSLGSFFIPLAIMTIVYIEIFVATRRRLRERAKATKLNTIALKSTE
gi|195476747|ref|XP_002086227.1|      TPCELTSQRGYVIYSSLGSFFIPLAIMTIVYIEIFVATRRRLRERARANKLNTIALKSTE
gi|195379104|ref|XP_002048321.1|      TPCELTSQRGYVIYSSLGSFFIPLIIMTIVYIEIFVATRRRLRERAKANKLNTIALKSTE
gi|195128241|ref|XP_002008573.1|      TPCELTSQRGYVIYSSLGSFFIPLIIMTIVYIEIFVATRRRLRERAKANKLNTIALKNTD
gi|195440432|ref|XP_002068046.1|      TPCELTSQRGYVIYSALGSFFIPLAIMTIVYIEIFIATRRRLRERAKANKLNTIALKSTE
gi|195022359|ref|XP_001985558.1|      TPCELTSQRGYVIYSSLGSFFIPLVIMTIVYIEIFVATRRRLRERAKANKLNTIALKTTE
                                      ***************:******** ***:******:**********:*.********.*:

Oct-TyrR-PA_peptide                   LEPINSSPAGASASA-SGSK----SRLLTSWLCCGR---DRAPFAAPMIQNDQESISSET
gi|24668474|ref|NP_524419.2|          LEPMANSSP-VAASN-SGSK----SRLLASWLCCGR---DRAQFATPMIQNDQESISSET
gi|195348713|ref|XP_002040892.1|      LEPMANSSP-VAASN-SGSK----SRLLASWLCCGR---DRAQFATPMIQNDQESISSET
gi|195172881|ref|XP_002027224.1|      LEPITNSSPAA---A-SSSK----SRALTNWLCCGR---DRANFSTPMIQNDQESISSET
gi|194876096|ref|XP_001973713.1|      LEPMANSSP-VAASN-SGSK----SRLLASWLCCGR---DRAQFATPMIQNDQESISSET
gi|198463614|ref|XP_001352884.2|      LEPITNSSPAA---A-SSSK----SRALTNWLCCGR---DRANFSTPMIQNDQESISSET
gi|195476747|ref|XP_002086227.1|      LEPMANSSP-VAASN-SGSK----SRLLASWLCCGR---DRAQFATPMIQNDQESISSEV
gi|195379104|ref|XP_002048321.1|      LEAINTSGAAAAGGSSTSSKARALGSLCSSWLCCGR---DRANFATPMIHNDQESLSSET
gi|195128241|ref|XP_002008573.1|      LEAINASNV-AVGGSSTSSKARALGSLCGSWLCCGR---DRANFAAPMIHNDQESLSSET
gi|195440432|ref|XP_002068046.1|      LDTIHQNSSSS--PV-ATSK----SRQLANWLCCGRVAGERFQFTTPMIQNDQESISSET
gi|195022359|ref|XP_001985558.1|      LEAINTSSA-AAGSSSTSSKARALGSLCGSWLCCGR---DRANFATPMIHNDQESLSSET
                                      *: :  .         : **    .    .******   :*  *::***:*****:***.

Oct-TyrR-PA_peptide                   HPPAQEASK-----TGPGSHISSDQQQHVVVLVKKSRRSKIKDSIKHGKARGVRKSQS-S
gi|24668474|ref|NP_524419.2|          HQPQDS-SK-----AGPHG-NSDPQQQHVVVLVKKSRRAKTKDSIKHGKTRGGRKSQS-S
gi|195348713|ref|XP_002040892.1|      HQPQDS-SK-----VGSHG-NSDPQQQHVVVLVKKSRRAKIKDSIKHGKARGGRKSQS-S
gi|195172881|ref|XP_002027224.1|      HGQQEG----------SKTATTNDQQQHVVVLVKKSRRSKIKDSIKHGKARGGRKSQS-A
gi|194876096|ref|XP_001973713.1|      HQPQDS-SK-----AGSQG-NSDSQQQHMVVLVKKSRRAKIKDSIKHGKARGGRKSQS-S
gi|198463614|ref|XP_001352884.2|      HGQQEG----------SKTATTNDQQQHVVVLVKKSRRSKIKDSIKHGKARGGRKSQS-A
gi|195476747|ref|XP_002086227.1|      HQPQDS-SK-----AGSHG-NSDPQQQHMVVLVKKSRRAKIKDSIKHGKARGGRRSQS-S
gi|195379104|ref|XP_002048321.1|      HAQPEPNKEQQQ-------QQQQQQQQHVVVLVKKSRRAKIKDSIKHGKGRSGRRSQSSS
gi|195128241|ref|XP_002008573.1|      HAQPEGNNESQ-----------QQQQQHVVVLVKKSRRAKIKDSIKHGKARGNRRSQSSS
gi|195440432|ref|XP_002068046.1|      HPHHHQQQQQQQHQQQQEGNDPQQQQQHVVVLVKKSRRSKIKDSIKHGKAKGGRKSQS-S
gi|195022359|ref|XP_001985558.1|      HAQPDTNTEQHQ-------H--QQQQQTVVVLVKKSRRAKIKDSIKHGKGRSGRRSQSSS
                                      *   .                 . *** :*********:* ******** :. *:*** :

Oct-TyrR-PA_peptide                   STCEPHGEQQLLPATG--------GGQSAGGKSDAEISTESGSDPKGCIQVCVTQTDEQT
gi|24668474|ref|NP_524419.2|          STCEPHGEQQLLPAGGDGGSCQPGGGHSGGGKSDAEISTESGSDPKGCIQVCVTQADEQT
gi|195348713|ref|XP_002040892.1|      STCEPHGEQQLLPAGGDGGRCQAGGGHSGGGKSDAEISTESGSDPKGCIQVCVTQAEEQT
gi|195172881|ref|XP_002027224.1|      STCEPHGEQQLLPAGGSGG-------GNAAGKSDAEISTESGSDPKGCIQVCVTQAEEQT
gi|194876096|ref|XP_001973713.1|      STCEPHGEQQLLPAGGDGGSCQAGGRHSGGGKSDAEISTESGSDPKGCIQVCVTQADEQT
gi|198463614|ref|XP_001352884.2|      STCEPHGEQQLLPAGGSGG-------GNAAGKSDAEISTESGSDPKGCIQVCVTQAEEQT
gi|195476747|ref|XP_002086227.1|      STCEPHGEQQLLPAGGDGVSCQAGGGHSGGGKSDAEISTESGSDPKGCIQVCVTQADEQT
gi|195379104|ref|XP_002048321.1|      STCEPHGEQQLLPQANSNN-------ASNAAKSDPEISTESGSDPKGCIQVCVTQAEEQT
gi|195128241|ref|XP_002008573.1|      SACEPHGEQQLLPQGNSNN-------A--AGKSDPEISTESGSDPKGCIQVCVTQTEEQT
gi|195440432|ref|XP_002068046.1|      STCEPHGEQQLLPSSGRSG-----GPSSGAAKSDPEISTESGSDPKGCIQVCITQTDEQT
gi|195022359|ref|XP_001985558.1|      SGCEPHGEQQLLPQANSNN-------A--ATKSDQEISTESGSDPKGCIQVCVTQADEQT
                                      * ***********                . *** *****************:**::***

Oct-TyrR-PA_peptide                   SLKLTPPQSSTGAAVASATPLQKKPSGVNQFIEEKQKISLSKERRAARTLGIIMGVFVIC
gi|24668474|ref|NP_524419.2|          SLKLTPPQSSTGVAAVSVTPLQKKTSGVNQFIEEKQKISLSKERRAARTLGIIMGVFVIC
gi|195348713|ref|XP_002040892.1|      SLKLTPPQSSTGVAAVSVTPLQKKTSGVNQFIEEKQKISLSKERRAARTLGIIMGVFVIC
gi|195172881|ref|XP_002027224.1|      SLKLTPPQSSTGAGAVAAAPLQKKPSGVNQFIEEKQKISLSKERRAARTLGIIMGVFVIC
gi|194876096|ref|XP_001973713.1|      SLKLTPPQSSTGAAAVSATPLQKKTSGVNQFIEEKQKISLSKERRAARTLGIIMGVFVIC
gi|198463614|ref|XP_001352884.2|      SLKLTPPQSSTGAGAVAAAPLQKKPSGVNQFIEEKQKISLSKERRAARTLGIIMGVFVIC
gi|195476747|ref|XP_002086227.1|      SLKLTPPQSSTGVAAVSATPLQKKTSGVNQFIEEKQKISLSKERRAARTLGIIMGVFVIC
gi|195379104|ref|XP_002048321.1|      SLKLTPPQSSSTGATAAAPALQKKPSTVNQFIEEKQKISLSKERRAARTLGIIMGVFVIC
gi|195128241|ref|XP_002008573.1|      SLKLTPPQSSSTGVA-AASALQKKPSTVNQFIEEKQKISLSKERRAARTLGIIMGVFVIC
gi|195440432|ref|XP_002068046.1|      SLKLTPPQSSTGGTSIAIASLQKKPSGVNQFIEEKQKISLSKERRAARTLGIIMGVFVIC
gi|195022359|ref|XP_001985558.1|      SLKMTPPQSSMGT--AATTVVQKKPSTVNQFIEEKQKISLSKERRAARTLGIIMGVFVIC
                                      ***:******      :   :*** * *********************************

Oct-TyrR-PA_peptide                   WLPFFLMYVILPFCQSCCPTNKFKNFITWLGYINSGLNPVIYTIFNLDYRRAFKRLLGLN
gi|24668474|ref|NP_524419.2|          WLPFFLMYVILPFCQTCCPTNKFKNFITWLGYINSGLNPVIYTIFNLDYRRAFKRLLGLN
gi|195348713|ref|XP_002040892.1|      WLPFFLMYVILPFCQSCCPTNKFKNFITWLGYINSGLNPVIYTIFNLDYRRAFKRLLGLN
gi|195172881|ref|XP_002027224.1|      WLPFFLMYVILPFCQSCCPSDKFKNFITWLGYINSGLNPVIYTIFNLDYRRAFKRLLGMK
gi|194876096|ref|XP_001973713.1|      WLPFFLMYVILPFCQSCCPTNKFKNFITWLGYINSGLNPVIYTIFNLDYRRAFKRLLGLN
gi|198463614|ref|XP_001352884.2|      WLPFFLMYVILPFCQSCCPSDKFKNFITWLGYINSGLNPVIYTIFNLDYRRAFKRLLGMK
gi|195476747|ref|XP_002086227.1|      WLPFFLMYVILPFCQSCCPTNKFKNFITWLGYINSGLNPVIYTIFNLDYRRAFKRLLGLN
gi|195379104|ref|XP_002048321.1|      WLPFFLMYVILPFCQSCCPTNKFKNFITWLGYINSGLNPVIYTIFNLDYRRAFKRLLGIN
gi|195128241|ref|XP_002008573.1|      WLPFFLMYVILPFCQSCCPTNKFKNFITWLGYINSGLNPVIYTIFNLDYRRAFKRLLGIK
gi|195440432|ref|XP_002068046.1|      WLPFFLMYVILPFCESCCPTNKFKNFITWLGYINSGLNPVIYTIFNLDYRRAFKRLLGIK
gi|195022359|ref|XP_001985558.1|      WLPFFLMYVILPFCQSCCPTNKFKNFITWLGYINSGLNPVIYTIFNLDYRRAFKRLLGMK
                                      **************::***::*************************************::

Oct-TyrR-PA_peptide                   -
gi|24668474|ref|NP_524419.2|          -
gi|195348713|ref|XP_002040892.1|      -
gi|195172881|ref|XP_002027224.1|      -
gi|194876096|ref|XP_001973713.1|      -
gi|198463614|ref|XP_001352884.2|      -
gi|195476747|ref|XP_002086227.1|      -
gi|195379104|ref|XP_002048321.1|      -
gi|195128241|ref|XP_002008573.1|      -
gi|195440432|ref|XP_002068046.1|      -
gi|195022359|ref|XP_001985558.1|      I
                                       


We also use the COBALT program at NCBI. The output is shown below.

COBALT Oct-TyrR


We also use the MUSCLE program. The output is shown below.

COBALT Oct-TyrR


The proteins that we have used are all closely related. All three programs have given us similar results. The portion of the protein identified as a conserved transmembrane domain common to G-protein-coupled receptors (around 120-300 and 500-575) are highly conserved in the group of proteins that we have analyzed. Notice that the sequences near the amino terminus are highly divergent.

You may find these programs useful in the analysis of your gene models.