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: GNAT1_HUMAN
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence AF493908_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 856.44 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.
GNAT1_HUMAN 1 GAGASAEEKHSRELEKKLKEDAEKDARTVKLLLLGAGESGKSTIVKQMK
GAGASAEEKHSRELEKKLKEDAEKDARTVKLLLLGAGESGKSTIVKQMK
GAGASAEEKHSRELEKKLKEDAEKDARTVKLLLLGAGESGKSTIVKQMK
AF493908_2 4 ggggagggactagcgaacaggggaggcagaccccggggtgaaaagacaa
gcgcgcaaaacgataaataaacaaacgctattttgcgacgagcttaata
gtgcttgggccgggagggagctggttacggggtgtctgcggccccgggg
GNAT1_HUMAN 50 IIHQDGYSLEECLEFIAIIYGNTLQSILAIVRAMTTLNIQYGDSARQDD
IIHQDGYSLEECLEFIAIIYGNTLQSILAIVRAMTTLNIQYGDSARQDD
IIHQDGYSLEECLEFIAIIYGNTLQSILAIVRAMTTLNIQYGDSARQDD
AF493908_2 151 aaccggttcggtcgtagaatgaatctacgagcgaaacaactggtgccgg
ttaaagactaagtattcttagactacttcttgctcctataagaccgaaa
tccgcgcggagccgtcccccccgggccgccaccgcacccgcactacgcc
GNAT1_HUMAN 99 ARKLMHMADTIEEGTMPKEMSDIIQRLWKDSGIQACFERASEYQLNDSA
ARKLMHMADTIEEGTMPKEMSDIIQRLWKDSGIQACFERASEYQLNDSA
ARKLMHMADTIEEGTMPKEMSDIIQRLWKDSGIQACFERASEYQLNDSA
AF493908_2 298 gcacacaggaagggaacagatgaaccctagtgacgttgcgtgtccagtg
cgattatcactaagctcaatcattagtgaacgtacgtagccaaataacc
cggggcgactcggcggcggggcccgggggcctcgcttgccggcgcccgg
GNAT1_HUMAN 148 GYYLSDLERLVTPGYVPTEQDVLRSRVKTTGIIETQFSFKDLNFRMFDV
GYYLSDLERLVTPGYVPTEQDVLRSRVKTTGIIETQFSFKDLNFRMFDV
GYYLSDLERLVTPGYVPTEQDVLRSRVKTTGIIETQFSFKDLNFRMFDV
AF493908_2 445 gttctgcgccgacgtgcagcggcctcgaaagaagactttagcatcatgg
gaatcatagttccgatccaaattgcgtaccgttacatctaatatgttat
ccccccggcgacgccgccggcggcgacgctcccgggcccgtcccggctg
GNAT1_HUMAN 197 GGQRSERKKWIHCFEGVTCIIFIAALSAYDMVLVEDDEVNRMHESLHLF
GGQRSERKKWIHCFEGVTCIIFIAALSAYDMVLVEDDEVNRMHESLHLF
GGQRSERKKWIHCFEGVTCIIFIAALSAYDMVLVEDDEVNRMHESLHLF
AF493908_2 592 ggcctgcaatacttgggataataggcagtgagcggggggacacgaccct
ggagcagaagtagtagtcgttttcctgcaattttaaaatagtaagtatt
cggcggcgggccccgcgccccccgggccccggaggccagccgcgcgcgc
GNAT1_HUMAN 246 NSICNHRYFATTSIVLFLNKKDVFFEKIKKAHLSICFPDYDGPNTYEDA
NSICNHRYFATTSIVLFLNKKDVFFEKIKKAHLSICFPDYDGPNTYEDA
NSICNHRYFATTSIVLFLNKKDVFFEKIKKAHLSICFPDYDGPNTYEDA
AF493908_2 739 aaataccttgaatagctcaaaggttgaaaagccaattcgtggcaatggg
agtgaagatcccctttttaaaatttaataacatgtgtcaaagcacaaac
ccccccccccggccgcctcggccccggcgggcccctcgcctaccccgcc
GNAT1_HUMAN 295 GNYIKVQFLELNMRRDVKEIYSHMTCATDTQNVKFVFDAVTDIIIKENL
GNYIKVQFLELNMRRDVKEIYSHMTCATDTQNVKFVFDAVTDIIIKENL
GNYIKVQFLELNMRRDVKEIYSHMTCATDTQNVKFVFDAVTDIIIKENL
AF493908_2 886 gataagctcgcaaccggagattcaatgagacagatgtgggagaaaagac
gaatatattatatggataatacatcgccacaatatttactcatttaaat
ccccgggccgccggccgggctccggccccggccatccctccccccggcc
GNAT1_HUMAN 344 KDCGLF
KDCGLF
KDCGLF
AF493908_2 1033 agtgct
aaggtt
actccc
//
cmbi.kun.nl), 24-May-2005