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: GNAO_DROME
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence DMGPAMA_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 854.30 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
GNAO_DROME 1 MGCAQSAEERAAAARSRLIERNLKEDGIQAAKDIKLLLLGAGESGKSTI
MGC--SAEERAA--RS+-IE+NLKEDGIQAAKDIKLLLLGAGESGKSTI
MGCTTSAEERAAIQRSKQIEKNLKEDGIQAAKDIKLLLLGAGESGKSTI
DMGPAMA_2 1 agtaatgggcggacctacagaacagggacggagaaccccggggtgaaaa
tggccccaagcctagcaataaataaagtaccaatattttgcgacgagct
gcccaccaaccccgacagcggtaggtacggcgccgcgggtctggcgcaa
*** !! !! !! !
GNAO_DROME 50 VKQMKIIHESGFTAEDFKQYRPVVYSNTIQSLVAILRAMPTLSIQYSNN
VKQMKIIHESGFTAEDFKQYRPVVYSNTIQSLVAILRAMPTLSIQYSNN
VKQMKIIHESGFTAEDFKQYRPVVYSNTIQSLVAILRAMPTLSIQYSNN
DMGPAMA_2 148 gacaaaacgagtagggtactccggtaaaacttggatcgacacaactaaa
taatattaaggtccaataaagcttagactacttcttgctcctgtaagaa
caggactcgccctggctaatagtccccaaaaataagcggacattacctc
GNAO_DROME 99 ERESDAKMVFDVCQRMHDTEPFSEELLAAMKRLWQDAGVQECFSRSNEY
ERESDAKMVFDVCQRMHDTEPFSEELLAAMKRLWQDAGVQECFSRSNEY
ERESDAKMVFDVCQRMHDTEPFSEELLAAMKRLWQDAGVQECFSRSNEY
DMGPAMA_2 295 gcgaggaagtggtccacgagcttggccggaacctcggggcgtttcaagt
agagacatttatgagtaacactcaattcctagtgaacgtaagtcggaaa
gggctcgggccacacgcccgccgggggccgaccggcctcggccgcccac
GNAO_DROME 148 QLNDSAKYFLDDLDRLGAKDYQPTEQDILRTRVKTTGIVEVHFSFKNLN
QLNDSAKYFLDDLDRLGAKDYQPTEQDILRTRVKTTGIVEVHFSFKNLN
QLNDSAKYFLDDLDRLGAKDYQPTEQDILRTRVKTTGIVEVHFSFKNLN
DMGPAMA_2 442 ccagtgattcggtgctggagtccagcgatcacgaaagagggctttaaca
ataaccaattaatagtgcaaaaccaaattgcgtaccgttatatctaata
aactcaatcgctgtgaccgtcgataatcgctccgctcctgaccccaccc
GNAO_DROME 197 FKLFDVGGQRSERKKWIHCFEDVTAIIFCVAMSEYDQVLHEDETTNRMQ
FKLFDVGGQRSERKKWIHCFEDVTAIIFCVAMSEYDQVLHEDETTNRMQ
FKLFDVGGQRSERKKWIHCFEDVTAIIFCVAMSEYDQVLHEDETTNRMQ
DMGPAMA_2 589 tattggggcctgcaatacttgggagaattggatgtgcgtcgggaaacac
tattatggagcagaagtagtaatcctttgtctcaaaattaaaaccagta
tagtcgctgcgatgagacccatcggctccgcgcgctacgtgtacgccga
GNAO_DROME 246 ESLKLFDSICNNKWFTDTSIILFLNKKDLFEEKIRKSPLTICFPEYTGG
ESLKLFDSICNNKWFTDTSIILFLNKKDLFEEKIRKSPLTICFPEYTGG
ESLKLFDSICNNKWFTDTSIILFLNKKDLFEEKIRKSPLTICFPEYTGG
DMGPAMA_2 736 gtcactgtataaattagataactcaaagttggaacaaccaattcgtagg
actattactgaaagtcacctttttaaaattaaatgagctctgtcaacgg
gggagtcgctccagcgccgttatgcggtgcgggtcgtcggtcccacata
GNAO_DROME 295 QEYGEAAAYIQAQFEAKNKSTSKEIYCHMTCATDTNNIQFVFDAVTDVI
QEYGEAAAYIQAQFEAKNKSTSKEIYCHMTCATDTNNIQFVFDAVTDVI
QEYGEAAAYIQAQFEAKNKSTSKEIYCHMTCATDTNNIQFVFDAVTDVI
DMGPAMA_2 883 cgtgggggtacgctggaaatatagattcaatgagaaaactgtgggagga
aaagacccatacatacaaacccaatagatcgccacaatatttactcatt
ggccggttctgtatagacaacaaaccccggtcatctctgtacttcctcc
GNAO_DROME 344 IANNLRGCGLY
IANNLRGCGLY
IANNLRGCGLY
DMGPAMA_2 1030 agaaccgtgct
tcaatggggta
aaccgcctagc
//
cmbi.kun.nl), 24-May-2005