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: GNAI2_MOUSE
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence MMGI_3
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 866.80 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.
Warning: mismatch(es) found
GNAI2_MOUSE 1 GCTVSAEDKAAAERSKMIDKNLREDGEKAAREVKLLLLGAGESGKSTIV
GCTVSAEDKAAAERSKMIDKNLREDGEKAAREVKLLLLGAGESGKSTIV
GCTVSAEDKAAAERSKMIDKNLREDGEKAAREVKLLLLGAGESGKSTIV
MMGI_3 4 gtagagggaggggctaaagaaccggggaggcggatcctggggtgaaaag
ggctgcaaacccagcattaaatgaagaaccgatattttgcgacgagctt
cccgccgcggacgctagccgcgggccgggggggggtgattaaaggcccc
GNAI2_MOUSE 50 KQMKIIHEDGYSEEECRQYRAVVYSNTIQSILAIVKAMGNLQIDFADPQ
KQMKIIHEDGYSEEECRQYRAVVYSNTIQSILAIVK-MGNLQIDFADPQ
KQMKIIHEDGYSEEECRQYRAVVYSNTIQSILAIVKRMGNLQIDFADPQ
MMGI_3 151 acaaaacgggttgggtcctcgggtaaaactacgagacagaccagtggcc
aatattaaagacaaaggaagcttagactacttcttagtgatatatcaca
ggggcctatccaaggcggctcgccccccgtagccggcgccggccttccg
*** !
GNAI2_MOUSE 99 RADDARQLFALSCAAEEQGMLPEDLSGVIRRLWADHGVQACFGRSREYQ
RADDARQLFALSCAAEEQGMLPEDLSGVIRRLWADHGVQACFGRSREYQ
RADDARQLFALSCAAEEQGMLPEDLSGVIRRLWADHGVQACFGRSREYQ
MMGI_3 298 cggggacctgcttggggcgaccggctggacactggcggcgttgctcgtc
gcaacgattctcgccaaagttcaatcgttggtgcaagtacgtggcgaaa
tgttcgggccgcttagaaggttacgctccggcgtcctgacctccaaacg
GNAI2_MOUSE 148 LNDSAAYYLNDLERIAQSDYIPTQQDVLRTRVKTTGIVETHFTFKDLHF
LNDSAAYYLNDLERIAQSDYIPTQQDVLRTRVKTTGIVETHFTFKDLHF
LNDSAAYYLNDLERIAQSDYIPTQQDVLRTRVKTTGIVETHFTFKDLHF
MMGI_3 445 cagtggttcagcgcagcagtacaccggccacgaaagaggactatagtct
taacccaataatagtcagaatccaaattgcgtaccgttacatctaatat
ctcactccgttggctagtccctaggtgggctggcgccgaaccccgcacc
GNAI2_MOUSE 197 KMFDVGGQRSERKKWIHCFEGVTAIIFCVALSAYDLVLAEDEEMNRMHE
KMFDVGGQRSERKKWIHCFEGVTAIIFCVALSAYDLVLAEDEEMNRMHE
KMFDVGGQRSERKKWIHCFEGVTAIIFCVALSAYDLVLAEDEEMNRMHE
MMGI_3 592 aatggggcctgcaatacttgggagaattggtagtgtgcgggggaacacg
attatggagcagaagtagtagtcctttgtctgcaatttcaaaatagtaa
ggttgttggtgcgggccctgccgcccctccgcctcgggtgtgggccgtg
GNAI2_MOUSE 246 SMKLFDSICNNKWFTDTSIILFLNKKDLFEEKITQSSLTICFPEYTGAN
SMKLFDSICNNKWFTDTSIILFLNKKDLFEEKITQSSLTICFPEYTGAN
SMKLFDSICNNKWFTDTSIILFLNKKDLFEEKITQSSLTICFPEYTGAN
MMGI_3 739 aaactgaataaattagataactcaaagctggaaacatcaattcgtagga
gtattagtgaaagtcacctttttaaaattaaatcagctctgtcaacgca
cgggtccccccggcacccccccccggcgtaagcagccgcctctgcggcc
GNAI2_MOUSE 295 KYDEAASYIQSKFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVI
KYDEAASYIQSKFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVI
KYDEAASYIQSKFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVI
MMGI_3 886 atggggatacaatggcaacagaagatactatgagaaagctgtgggagga
aaaaccgatagataataagaacaatacatcgccacaatatttactcatt
gccgaccccgcgtgtatgcaccggccgccacccccgcggtgctcctccc
GNAI2_MOUSE 344 IKNNLKDCGLF
IKNNLKDCGLF
IKNNLKDCGLF
MMGI_3 1033 aaaacagtgct
taaataaggtt
cgccggctccc
//
cmbi.kun.nl), 24-May-2005