SELENOPROTEÍNAS DE Meleagris gallopavo

PROTEIN REPORT FOR Selenoprotein I (Sel I)

DESCRIPCIÓN	Selenoproteína. 2(+):110474340...110479632.
SECISearch	Un elemento predicho en la cadena sense: 2:subseq(110479632,10000):[3973,4063]
SELENOPROFILES	Encontrada. Elección: exonerate. Elemento SECIS predicho (strand:+ positions:110483606-110483700).
COMENTARIOS	Elección: Genewise. Se trata de una de las Selenoproteínas I de Meleagris gallopavo. El alineamiento de las predicciones de Exonerate y Genewise obtuvieron el mismo score pero por defecto reportamos el alineamiento de Genewise. Analizando el multiple-alignment vemos que es mejor la predicción de Exonerate (predice la Selenocisteína, Genewise no) Los resultados de SECISearch y Selenoprofiles respaldan nuestro resultado.

1. ALINEAMIENTO MÚLTIPLE DE TODOS LOS HOMÓLOGOS DE SELENODB
2. BEST PAIRWISE ALIGNMENT
3. RESULTADOS DEL SECISearch
4. RESULTADOS DEL Selenoprofiles

ALINEAMIENTO MÚLTIPLE DE TODOS LOS HOMÓLOGOS DE SELENODB

 
     CLUSTAL FORMAT for T-COFFEE Version_7.54, SCORE=98, Nseq=9, Len=423 

SPP00000015_1.0              MAGYEYVSPEQLAGFDKYKYSAVDTNPLSLYVMHPFWNTIVK----VFPTWLAPNLITFS
SPP00000015_1.0.2.exonerate  -AGSQMASALQCARFWLGKYSAVDSNPLSVYVMHPFWNTIVK----IFPTWLAPNLITFS
SPP00000015_1.0.2.genewise   ------------------QYSAVDSNPLSVYVMHPFWNTIVK----IFPTWLAPNLITFS
SPP00000111_1.0              MAGYEYVSPEQLSGFDKYKYSALDTNPLSLYIMHPFWNTIVKKKKQVFPTWLAPNLITFS
SPP00000111_1.0.2.exonerate  -AGSQMASALQCARFWLGKYSAVDSNPLSVYVMHPFWNTIVKA-FPIFPTWLAPNLITFS
SPP00000111_1.0.2.genewise   ------------------QYSAVDSNPLSVYVMHPFWNTIVK----IFPTWLAPNLITFS
SPP00000088_1.0              MGCMRYLSEAHLRGFERYKYSSIDTSFLSVYVMHPFWNYCVK----FVPKWLAPNVLTFV
SPP00000088_1.0.2.exonerate  ------ISSAFLEGEDLFQYSAVDSNPLSVYVMHPFWNTIVK----IFPTWLAPNLITFS
SPP00000088_1.0.2.genewise   ------------------QYSAVDSNPLSVYVMHPFWNTIVK----IFPTWLAPNLITFS
                                               :**::*:. **:*:******  **    ..*.*****::** 

SPP00000015_1.0              GFLLVVFNFLLMAYFDPDFYAS-APGHKHVPDWVWIVVGILNFVAYTLDGVDGKQARRTN
SPP00000015_1.0.2.exonerate  GFLLLVFNFFLMAYFDPDFYAS-APDHQHVPNGVWVVVGLLNFIAYTLDGVDGKQARRTN
SPP00000015_1.0.2.genewise   GFLLLVFNFFLMAYFDPDFYAS-APDHQHVPNGVWVVVGLLNFIAYTLDGVDGKQARRTN
SPP00000111_1.0              GFMLLVFNFLLLTYFDPDFYAS-APGHKHVPDWVWIVVGILNFAAYTLDGVDGKQARRTN
SPP00000111_1.0.2.exonerate  GFLLLVFNFFLMAYFDPDFYAS-APDHQHVPNGVWVVVGLLNFIAYTLDGVDGKQARRTN
SPP00000111_1.0.2.genewise   GFLLLVFNFFLMAYFDPDFYAS-APDHQHVPNGVWVVVGLLNFIAYTLDGVDGKQARRTN
SPP00000088_1.0              GFLMTVVNFILIAYYDWGFEAANSETGNTVPAWVWTVAAINILIYYNLDGMDGKQARRTG
SPP00000088_1.0.2.exonerate  GFLLLVFNFFLMAYFDPDFYASAAPDHQHVPNGVWVVVGLLNFIAYTLDGVDGKQARRTN
SPP00000088_1.0.2.genewise   GFLLLVFNFFLMAYFDPDFYAS-APDHQHVPNGVWVVVGLLNFIAYTLDGVDGKQARRTN
                             **:: *.**:*::*:* .* *: :   : **  ** *..:  :  *.***:********.

SPP00000015_1.0              SSTPLGELFDHGLDSWSCVYFVVTVYSIFGRGSTGVSVFVLYLLLWVVLFSFILSHWEKY
SPP00000015_1.0.2.exonerate  SSTPLGELFDHGLDSWACVYFVVTVYSTFGRGSTGVSVFVLYLLLWVVLFSFILSHWEKY
SPP00000015_1.0.2.genewise   SSTPLGELFDHGLDSWACVYFVVTVYSTFGRGSTGVSVFVLYLLLWVVLFSFILSHWEKY
SPP00000111_1.0              SSTPLGELFDHGLDSWSCVYFVVTVYSIFGRGPTGVSVFVLYLLLWVVLFSFILSHWEKY
SPP00000111_1.0.2.exonerate  SSTPLGELFDHGLDSWACVYFVVTVYSTFGRGSTGVSVFVLYLLLWVVLFSFILSHWEKY
SPP00000111_1.0.2.genewise   SSTPLGELFDHGLDSWACVYFVVTVYSTFGRGSTGVSVFVLYLLLWVVLFSFILSHWEKY
SPP00000088_1.0              TSGPLGELFDHGLDSYSAALIPIYLFSLFGT--HDLPPIRMFFVIWNVFLNFYLTHVEKY
SPP00000088_1.0.2.exonerate  SSTPLGELFDHGLDSWACVYFVVTVYSTFGRGSTGVSVFVLYLLLWVVLFSFILSHWEKY
SPP00000088_1.0.2.genewise   SSTPLGELFDHGLDSWACVYFVVTVYSTFGRGSTGVSVFVLYLLLWVVLFSFILSHWEKY
                             :* ************::.. : : ::* **    .:. : :::::* *::.* *:* ***

SPP00000015_1.0              NTGILFLPWGYDISQVTISFVYIVTAVVGVEAWYEPFLFNFLYRDLFTAMIIGCALCVTL
SPP00000015_1.0.2.exonerate  NTGILFLPWGYDISQVTISIVYIVTAIVGVEAWYAPFLFNFLYRDLFTTMIIACALTVTL
SPP00000015_1.0.2.genewise   NTGILFLPWGYDISQVTISIVYIVTAIVGVEAWYAPFLFNFLYRDLFTTMIIACALTVTL
SPP00000111_1.0              NTGVLFLPWGYDISQVTISFVYIVTAVVGVEAWYEPFLFNFLYRDLFTAMIIGCALCVTL
SPP00000111_1.0.2.exonerate  NTGILFLPWGYDISQVTISIVYIVTAIVGVEAWYAPFLFNFLYRDLFTTMIIACALTVTL
SPP00000111_1.0.2.genewise   NTGILFLPWGYDISQVTISIVYIVTAIVGVEAWYAPFLFNFLYRDLFTTMIIACALTVTL
SPP00000088_1.0              NTGVMFLPWGYDFTMWGVSGMLFVATVFGPEM-YRFSIYGFTMANMFEFVLIGSGMVSSH
SPP00000088_1.0.2.exonerate  NTGILFLPWGYDISQVTISIVYIVTAIVGVEAWYAPFLFNFLYRDLFTTMIIACALTVTL
SPP00000088_1.0.2.genewise   NTGILFLPWGYDISQVTISIVYIVTAIVGVEAWYAPFLFNFLYRDLFTTMIIACALTVTL
                             ***::*******::   :* : :*:::.* *  *   ::.*   ::*  ::*...:  : 

SPP00000015_1.0              PMSLLNFFRSYKNNTLKLNSVYEAMVPLFSPCLLFILSTAWILWSPSDILELHPRVFYFM
SPP00000015_1.0.2.exonerate  PMSLYNFYKAYKNNTLKHHSVYEIMLPLVSPVLLFALCTSWIFVSPMDILEVHPRLFYFM
SPP00000015_1.0.2.genewise   PMSLYNFYKAYKNNTLKHHSVYEIMLPLVSPVLLFALCTSWIFVSPMDILEVHPRLFYFM
SPP00000111_1.0              PMSLLNFFRSYKSNTLKHKSVYEAMVPFFSPCLLFTLCTVWILWSPSDILEIHPRIFYFM
SPP00000111_1.0.2.exonerate  PMSLYNFYKAYKNNTLKHHSVYEIMLPLVSPVLLFALCTSWIFVSPMDILEVHPRLFYFM
SPP00000111_1.0.2.genewise   PMSLYNFYKAYKNNTLKHHSVYEIMLPLVSPVLLFALCTSWIFVSPMDILEVHPRLFYFM
SPP00000088_1.0              PIIARNIYLSYKNKTGKMRPMWEMLRPFFAFVWLFVITVVWSFFSRNDVINKEPRILWIL
SPP00000088_1.0.2.exonerate  PMSLYNFYKAYKNNTLKHHSVYEIMLPLVSPVLLFALCTSWIFVSPMDILEVHPRLFYFM
SPP00000088_1.0.2.genewise   PMSLYNFYKAYKNNTLKHHSVYEIMLPLVSPVLLFALCTSWIFVSPMDILEVHPRLFYFM
                             *:   *:: :**.:* * ..::* : *:.:   ** : . * : *  *::: .**:::::

SPP00000015_1.0              VGTAFANSTCQLIVCQMSSTRCPTLNWLLVPLFLVVLVV---------NLGVASY-VESI
SPP00000015_1.0.2.exonerate  VGTAFANISCQLIVCQMSSTRCQPLNWMLLPIALVLFVV---------VSGFAPS-SETL
SPP00000015_1.0.2.genewise   VGTAFANISCQLIVCQMSSTRCQPLNWMLLPIALVLFVV---------VSGFAPS-SETL
SPP00000111_1.0              VGTAFANITCQLIVCQMSSTRCPTLNWLLLPLLLVVAAV---------IVGAATSRLESA
SPP00000111_1.0.2.exonerate  VGTAFANISCQLIVCQMSSTRCQPLNWMLLPIALVLFVV---------VSGFAPS-SETL
SPP00000111_1.0.2.genewise   VGTAFANISCQLIVCQMSSTRCQPLNWMLLPIALVLFVV---------VSGFAPS-SETL
SPP00000088_1.0              YGTIFSNIACRLIVAQMSDTRCDAFNVLMWPLAATVGVCCFPYYQQVFDSDLTSD-TERW
SPP00000088_1.0.2.exonerate  VGTAFANISCQLIVCQMSSTRCQPLNWMLLPIALVLFVV---------VSGFAPS-SETL
SPP00000088_1.0.2.genewise   VGTAFANISCQLIVCQMSSTRCQPLNWMLLPIALVLFVV---------VSGFAPS-SETL
                              ** *:* :*:***.***.*** .:* :: *:  .: .            . :.   *  

SPP00000015_1.0              LLYTLTTAFTLAHIHYGVRVVKQLSSHFQIYPFSLRKPNSDULGMEEKNI----------
SPP00000015_1.0.2.exonerate  LLYLLTAFLTLAHIHYGVVVVSQLSRHFNIRPFSLKKPTPDULGMEEEKI----------
SPP00000015_1.0.2.genewise   LLYLLTAFLTLAHIHYGVVVVSQLSRHFNIRPFSLKKPTP--------------------
SPP00000111_1.0              LLYTLTAAFTLAHIHYGVQVVKQLSRHFQIYPFSLRKPNSDULGMEEQNI----------
SPP00000111_1.0.2.exonerate  LLYLLTAFLTLAHIHYGVVVVSQLSRHFNIRPFSLKKPTPDULGMEEEKI----------
SPP00000111_1.0.2.genewise   LLYLLTAFLTLAHIHYGVVVVSQLSRHFNIRPFSLKKPTP--------------------
SPP00000088_1.0              ILYGLTIFSTLAHWHYGYGVVSEMCDHFHIRCFKVRKSSSQUSGSDITQLLQNNNKIKPL
SPP00000088_1.0.2.exonerate  LLYLLTAFLTLAHIHYGVVVVSQLSRHFNIRPFSLK------------------------
SPP00000088_1.0.2.genewise   LLYLLTAFLTLAHIHYGVVVVG--------------------------------------
                             :** **   **** ***  **                                       

SPP00000015_1.0              -GL
SPP00000015_1.0.2.exonerate  -SL
SPP00000015_1.0.2.genewise   --D
SPP00000111_1.0              -GL
SPP00000111_1.0.2.exonerate  -SL
SPP00000111_1.0.2.genewise   --D
SPP00000088_1.0              KSH
SPP00000088_1.0.2.exonerate  --K
SPP00000088_1.0.2.genewise   --E

......................................................................................................................................................................................................................................................

BEST PAIRWISE ALIGNMENT

 
CLUSTAL FORMAT for T-COFFEE Version_7.54, SCORE=99, Nseq=2, Len=402 

SPP00000111_1.0             MAGYEYVSPEQLSGFDKYKYSALDTNPLSLYIMHPFWNTIVKKKKQVFPTWLAPNLITFS
SPP00000111_1.0.2.genewise  ------------------QYSAVDSNPLSVYVMHPFWNTIVK----IFPTWLAPNLITFS
                                              :***:*:****:*:**********    :*************

SPP00000111_1.0             GFMLLVFNFLLLTYFDPDFYASAPGHKHVPDWVWIVVGILNFAAYTLDGVDGKQARRTNS
SPP00000111_1.0.2.genewise  GFLLLVFNFFLMAYFDPDFYASAPDHQHVPNGVWVVVGLLNFIAYTLDGVDGKQARRTNS
                            **:******:*::***********.*:***: **:***:*** *****************

SPP00000111_1.0             STPLGELFDHGLDSWSCVYFVVTVYSIFGRGPTGVSVFVLYLLLWVVLFSFILSHWEKYN
SPP00000111_1.0.2.genewise  STPLGELFDHGLDSWACVYFVVTVYSTFGRGSTGVSVFVLYLLLWVVLFSFILSHWEKYN
                            ***************:********** ****.****************************

SPP00000111_1.0             TGVLFLPWGYDISQVTISFVYIVTAVVGVEAWYEPFLFNFLYRDLFTAMIIGCALCVTLP
SPP00000111_1.0.2.genewise  TGILFLPWGYDISQVTISIVYIVTAIVGVEAWYAPFLFNFLYRDLFTTMIIACALTVTLP
                            **:***************:******:******* *************:***.*** ****

SPP00000111_1.0             MSLLNFFRSYKSNTLKHKSVYEAMVPFFSPCLLFTLCTVWILWSPSDILEIHPRIFYFMV
SPP00000111_1.0.2.genewise  MSLYNFYKAYKNNTLKHHSVYEIMLPLVSPVLLFALCTSWIFVSPMDILEVHPRLFYFMV
                            *** **:::**.*****:**** *:*:.** ***:*** **: ** ****:***:*****

SPP00000111_1.0             GTAFANITCQLIVCQMSSTRCPTLNWLLLPLLLVVAAVIVGAATSRLESALLYTLTAAFT
SPP00000111_1.0.2.genewise  GTAFANISCQLIVCQMSSTRCQPLNWMLLPIALVLFVVVSGFAPSS-ETLLLYLLTAFLT
                            *******:************* .***:***: **: .*: * *.*  *: *** *** :*

SPP00000111_1.0             LAHIHYGVQVVKQLSRHFQIYPFSLRKPNSDULGMEEQNIGL
SPP00000111_1.0.2.genewise  LAHIHYGVVVVSQLSRHFNIRPFSLKKPTP-----------D
                            ******** **.******:* ****:**..

RESULTADOS DEL SECISearch

 
>2:subseq(110479632,10000):[3973,4063] [3973 - 4063] - Free Energy: -23.53
AUUUAAUGAAGAUCUGUGCUUGAAUGAAGAGUGUAGCUUAAACCCAGGCUCUGGAAAGGCUGCAUCCGGAAGCGAACAAGCACAGCAGAUU

RESULTADOS DEL Selenoprofiles

 
Output_id:  SelI.1.selenocysteine
----------  ---------------------
-Species        Meleagris gallopavo                          -Taxid 9103
-Target         /homes/users/U63748/gallopavo.fa
-Chromosome (+) 2
-Program        exonerate
-Query name     gi|144925919|ref|NP_001026699.2| ethanolaminephosphotransferase 1 [Gallus gallus]
-Query range    13-400     length:400   coverage: 0.97
-Profile range  16-411     length:411   coverage: 0.96    sec_position: [395]
-Average sequence identity with profile: 0.7508   (ignoring gaps: 0.7901)
-State          kept

------- alignment -------
Query   SKYKYSAVDSNPLSLYVMHPFWNTIVK <---Intron---> IFPTWLAPNLITFSGFLLLVFNFFLMAYFDPDFYASA <---Intron---> PDHQ
        |  /||||||||||/|||||||||||| <   305bp    > ||||||||||||||||||||||||||||||||||||| <   1262bp   > ||||
Target  SHSQYSAVDSNPLSVYVMHPFWNTIVK                IFPTWLAPNLITFSGFLLLVFNFFLMAYFDPDFYASA                PDHQ
        tctctagggaacctgtgaccttaaaga                atcatcgcacaattgtcccgtattcagttgcgttgtg                cgcc
        cacaagctagactctattactgactta                ttccgtccattctcgttttttattttcatacatacc                ccaaa
        ttagctcgccctgtgccgtccgcgagg                ccttggcatcaattccggtccccccgaccctctctt                ttccg
                                                                                                            

Query   HVPNGVWVVVGLLNFIAYTLD <---Intron---> GVDGKQARRTNSSTPLGELFDHGLDSWACVYFVVTVYSTFGRGSTGVSVFVLYLLLWVVLFSF
        ||||||||||||||||||||| <   487bp    > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Target  HVPNGVWVVVGLLNFIAYTLD                GVDGKQARRTNSSTPLGELFDHGLDSWACVYFVVTVYSTFGRGSTGVSVFVLYLLLWVVLFSF
        cgcaggtggggccatagtatg                ggggacgcaaataactggctgcgcgatgtgttggagttatgcgtaggagtgctccttggtttt
        atcagtgtttgttattcact                agtagaacggcacgcctgattaagtaggcgtatttctacctgggccgtgttttatttgttttct
        ctatatgctgtcccctccga                ttttcaatcgccccacaagttctcgccgttgcctgacccctcgccgtctcctcccgaggggtac
                                                                                                            

Query   ILSHWEKYNTGILFLPWGYDISQV <---Intron---> TISIVYIVTAIVGVEAWYAPFLFNFLYRDLFTTMIIA <---Intron---> CALTVTL
        |||||||||||||||||||||||| <   1087bp   > ||||||||||||||||||||||||||||||||||||| <   1001bp   > |||||||
Target  ILSHWEKYNTGILFLPWGYDISQV                TISIVYIVTAIVGVEAWYAPFLFNFLYRDLFTTMIIA                CALTVTL
        actctgataagactcctgtgaacg                aatagtagagagggggttgctctatttagctaaaaag                tgcagac
        ttcagaaaacgttttcggaatgat                ctcttattccttgtacgacctttattagattccttt                cgctctct
        ccctgggtcagtccgcgatcccgg                ctatccagactgaagcgtatcgttcatacactagtt                ttcctggg
                                                                                                            

Query   PMSLYNFYK <---Intron---> AYKNNTLKHHSVYEIMLPLVSPVLLFALCTTWIFVSPMDILEVHPRLFYFMVGTAFANIS <---Intron--->
        ||||||||| <   293bp    > ||||||||||||||||||||||||||||||/||||||||||||||||||||||||||||| <   596bp    >
Target  PMSLYNFYK                AYKNNTLKHHSVYEIMLPLVSPVLLFALCTSWIFVSPMDILEVHPRLFYFMVGTAFANIS               
        caactatta                gtaaaatacctgtgaacccgtcgtctgctaatatgtcagacggccactttaggagtgaat               
        ctgtaataa                caaaactaaactaatttcttccttttctgcggtttcctattatacgttatttgcctcatc               
        ggcgcccc                gctatccggcctttgcggaggcaggtttccctgcttatgccggctcgccccgtaccttctt               
                                                                                                            

Query    CQLIVCQMSSTRCQPLNWMLLPIALVLFMVMSGFAPSSETLLLYLLTAFLTLAHIHYGVVV <---Intron---> VSQLSRHFNIRPFSLKKPTPDUU
         ||||||||||||||||||||||||||||/|/|||||||||||||||||||||||||||||| <   1892bp   > ||||||||||||||||||||||
Target   CQLIVCQMSSTRCQPLNWMLLPIALVLFVVVSGFAPSSETLLLYLLTAFLTLAHIHYGVVV                VSQLSRHFNIRPFSLKKPTPDUU
         tccagtcaaaactcccatacccagcgctgggtgtgcaagaccctccagtcacgcactgggg                gaccaactaaccttcaacacgt
         gatttgatggcggactagtttctctttttttcgtccggactttattccttctcataagttt                tgatggatatgctctaacccag
         cggcctggcctccgtgcggggcacggccgggtttacccaatcccgatacccggccctagcg                gcggcgtctaaccaagacggta
                                                                                                           *

Query   LGMEEEKISLRSAEVL
        ||||||||||||||||
Target  LGMEEEKISLRSAEVL
        cgagggaaatctgggc
        tgtaaaatgtgccatt
        aagaagaccggtaaag
                        
------- positions -------
Exon 1    110474331    110474411
Exon 2    110474717    110474825
Exon 3    110476088    110476162
Exon 4    110476650    110476912
Exon 5    110478000    110478108
Exon 6    110479110    110479158
Exon 7    110479452    110479632
Exon 8    110480229    110480411
Exon 9    110482304    110482417

--------- SECIS ---------
>SelI.1.selenocysteine.esecis:str.1 chromosome:2 strand:+ positions:110483606-110483700 species:"Meleagris gallopavo" 
target:/homes/users/U63748/gallopavo.fa distance_from_sec_uga:1236 distance_from_cds:1188
UUUAAUGAAG AUCUGUGC UUGA AUGAA GAGUGUAGCUU AA ACCCAGGCUCUGGAA AGGCUGCAUCC GGAA GCGAACAA GCACAGC AGAUUGUGCA
.......... ...((((( (((. .(((( (.((((((((( .. ..((((...)))).. ))))))))).) )))) .....))) )))))(( (.....))).

--------- 3' seq --------
Total sequence length available downstream >= 3000
Sequence until first stop codon: 
TAA
 *

REFERENCIAS AGRADECIMIENTOS CONTACTO

© All Rights Reserved. Página web diseñada para soporte Mozilla FireFox. Grupo 7 de Bioinformática. 4º curso de Biología Humana. Curso 2012-2013. Facultad de Ciencias de la Salud y de la Vida | Universidad Pompeu Fabra (www.upf.edu)

Grupo7:
Jolita Jancyte, Lidia Mateo, Aina Ollé, Marta Perera, Clara Pérez