NucleaRDB: Pairwise Alignments

The pairwise alignment has been generated with the "genewise" program of the Wise2 package. The output shows the protein sequence on the first line, followed by a line indicating the similarity level of the match, followed by 4 lines representing the DNA sequence; The DNA sequence descending in triplets, each triplet being a codon. The translation of each codon is shown above it.
Between the two protein sequences a line indicating the similarity of the match is printed. "+" indicates a conservative mismatch while "- "indicates a dramatic one. Mismatches are indicated by "***" in the left column in addition to "!" at the relevant position(s).

genewise $Name: wise2-2-0 $ (unreleased release)
This program is freely distributed under a GPL. See source directory
Copyright (c) GRL limited: portions of the code are from separate copyright

Query protein:       Q92019_XENLA
Comp Matrix:         blosum62.bla
Gap open:            12
Gap extension:       2
Start/End            default
Target Sequence      XLRNARARA_2
Strand:              forward
Start/End (protein)  default
Gene Paras:          human.gf
Codon Table:         codon.table
Subs error:          1e-05
Indel error:         1e-05
Model splice?        model
Model codon bias?    flat
Model intron bias?   tied
Null model           syn
Algorithm            623

genewise output
Score 1125.31 bits over entire alignment
Scores as bits over a synchronous coding model

Warning: The bits scores is not probablistically correct for single seqs
See WWW help for more info.

Q92019_XENLA       1 MYENVDVSPTHYHMMDFYSHNRQCLWPEKRINPYGTPLGTQHWSSSNHS 
                     MYENVDVSPTHYHMMDFYSHNRQCLWPEKRINPYGTPLGTQHWSSSNHS 
                     MYENVDVSPTHYHMMDFYSHNRQCLWPEKRINPYGTPLGTQHWSSSNHS 
XLRNARARA_2        1 atgagggacactcaagttacacctctcgaaaactgaccgacctaatact 
                     taaatatgccaaattatagaagagtgcaagtacagcctgcaagggcaac 
                     gtgtgcccctcccggtcctccagctgagaatctcgaatgtacgctccca 


Q92019_XENLA      50 IETQSTSSEEIVPSPPSPPPLPRIYKPCFVCQDKSSGYHYGVSACEGCK 
                     IETQSTSSEEIVPSPPSPPPLPRIYKPCFVCQDKSSGYHYGVSACEGCK 
                     IETQSTSSEEIVPSPPSPPPLPRIYKPCFVCQDKSSGYHYGVSACEGCK 
XLRNARARA_2      148 agacaaatggagcacctcccccaatacttgtcgaatgtctggagtggta 
                     tacagcgcaattcgcccccctcgtaacgttgaaagcgaaagtgcgagga 
                     tgtgcctaggttgcctcaagccaccacctgtgcgtagtctaccttatcg 


Q92019_XENLA      99 GFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESV 
                     GFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESV 
                     GFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESV 
XLRNARARA_2      295 gttccaacaaagtatcagaataaaagacactcttctcattgggatagtg 
                     gttgggtaaattacgagaaagttaatcgaggaaggtaagtatgtcaact 
                     ctcgctcggcggtgtcacgtccatacgccccgtccggattgcagtaaca 


Q92019_XENLA     148 RNDRNKKKKEPPKVDVMESYVLSPETQDLIEKVRKAHKETFPALCQLGK 
                     RNDRNKKKKEPPKVDVMESYVLSPETQDLIEKVRKAHKETFPALCQLGK 
                     RNDRNKKKKEPPKVDVMESYVLSPETQDLIEKVRKAHKETFPALCQLGK 
XLRNARARA_2      442 cagcaaaaagccagggagatgcacgacgcagagcagcagatcgctccga 
                     gaagaaaaaaccatattagattgcacaattaatgacaaactcctgatga 
                     gccccggaggcaggcgggtcggccgtgtcagagcaccggactgccggca 


Q92019_XENLA     197 YTTNFSSEERVSLDIDLWDKFSELSTKCIIKTVEFAKQLPGFTTLTIAD 
                     YTTNFSSEERVSLDIDLWDKFSELSTKCIIKTVEFAKQLPGFTTLTIAD 
                     YTTNFSSEERVSLDIDLWDKFSELSTKCIIKTVEFAKQLPGFTTLTIAD 
XLRNARARA_2      589 taaatatggcgtcgagctgatagctaataaaaggtgacccgtaacaagg 
                     accatgcaagtctatatgaatgatccagttactatcaatcgtcctctca 
                     ctatccaggattgcttggcgctacctatccgggatcagggacctgcccc 


Q92019_XENLA     246 QITLLKSACLDILILRICTRYTPDQDTMTFSDGLTLNRTQMHNAGFGPL 
                     QITLLKSACLDILILRICTRYTPDQDTMTFSDGLTLNRTQMHNAGFGPL 
                     QITLLKSACLDILILRICTRYTPDQDTMTFSDGLTLNRTQMHNAGFGPL 
XLRNARARA_2      736 caaccatgtcgacaccatactacgcgaaattggcacacacacaggtgcc 
                     atcttaccgtattttgtgcgaccaaactctcagtctagcataacgtgct 
                     gcccgactcgtttcgatcatccccgccggctcagcacctggctgccacc 


Q92019_XENLA     295 TDLVFAFANQLLPLEMDDAETGLLSAICLICGDRQDLEQPDKVDKLQEP 
                     TDLVFAFANQLLPLEMDDAETGLLSAICLICGDRQDLEQPDKVDKLQEP 
                     TDLVFAFANQLLPLEMDDAETGLLSAICLICGDRQDLEQPDKVDKLQEP 
XLRNARARA_2      883 agcgtgtgacccccgaggggagccagatcatggccgcgccgaggaccgc 
                     catttctcaattctataacacgttgctgttggagaataacaataataac 
                     acggcccttggggaggcctgctagtccccctacggcgggatagcaggga 


Q92019_XENLA     344 LLEALKIYVRNRRPKKPHMFPKMLMKITDLRSISAKGAERVITLKMEIP 
                     LLEALKIYVRNRRPKKPHMFPKMLMKITDLRSISAKGAERVITLKMEIP 
                     LLEALKIYVRNRRPKKPHMFPKMLMKITDLRSISAKGAERVITLKMEIP 
XLRNARARA_2     1030 ctggtaatgaaaccaaccatcaacaaaagcaaaagagggcgaacaagac 
                     ttactatatgaggcaacattcatttatcatggtgcagcagttctatatc 
                     tgagggcccgcgacagacgccagcggcacggcctcgtggagctggggcg 


Q92019_XENLA     393 GSMPPLIQEMLENSEGLDTLGGGASSQTPVTPVAPGSCSPSLSPSSTHS 
                     GSMPPLIQEMLENSEGLDTLGGGASSQTPVTPVAPGSCSPSLSPSSTHS 
                     GSMPPLIQEMLENSEGLDTLGGGASSQTPVTPVAPGSCSPSLSPSSTHS 
XLRNARARA_2     1177 gtacccacgatgatggtgatggggtacacgacggcgatacactcataca 
                     gctccttaattaacagtactgggccgacctcctccggggcgtccgccag 
                     gcgccccgggggcggggcaggcgagtgaacaaaaaatctctgtcccccc 


Q92019_XENLA     442 SPSSHSP                                           
                     SPSSHSP                                           
                     SPSSHSP                                           
XLRNARARA_2     1324 acttctc                                           
                     gcccacc                                           
                     ccctcac                                           


//

F.Horn (nucleardbcmbi.kun.nl), 18-Feb-2005