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: KCNA5_MOUSE
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence MMKCHANN_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 1480.27 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.
KCNA5_MOUSE 1 MEISLVPTENGSAMTLRGGGEAVASCVQSPRGECGCPPTAGLNNQSKET
MEISLVPTENGSAMTLRGGGEAVASCVQSPRGECGCPPTAGLNNQSKET
MEISLVPTENGSAMTLRGGGEAVASCVQSPRGECGCPPTAGLNNQSKET
MMKCHANN_2 1 agatcgcagagagaacagggggggatgcacaggtgtccaggcaactaga
tatcttccaaggctctggggactcggtagcggagggccccgtaaacaac
ggccggcggcctcgccaaaggagactggccgagttctggtacttgcaaa
KCNA5_MOUSE 50 SPRRRATHEDAAQGGRPLPPMPQELPQPRRPSAEDEEGEGDPGLGTVEE
SPRRRATHEDAAQGGRPLPPMPQELPQPRRPSAEDEEGEGDPGLGTVEE
SPRRRATHEDAAQGGRPLPPMPQELPQPRRPSAEDEEGEGDPGLGTVEE
MMKCHANN_2 148 tcaacgacggggcggactccaccgccccaactgggggggggcgcgaggg
ccgggccaaaccagggctcctcaatcacggcccaaaagagacgtgctaa
agggccacgtgcgtggtgctgtgggagtagattgtggaaccttgcaggg
KCNA5_MOUSE 99 DQAPQDSGSLHHQRVLINISGLRFETQLDTLVQFPNNLLGDPVKRLRYF
DQAPQDSGSLHHQRVLINISGLRFETQLDTLVQFPNNLLGDPVKRLRYF
DQAPQDSGSLHHQRVLINISGLRFETQLDTLVQFPNNLLGDPVKRLRYF
MMKCHANN_2 295 gcgccgtgtcccccgcaaatgtctgaccgacgctcaaccggcgaccctt
aaccaacgctaaagtttatcgtgtacatacttatcaattgactagtgat
cgttgcaaactcggccaccgtgctggggccgggtccccggcacgcgccc
KCNA5_MOUSE 148 DPLRNEYFFDRNRPSFDGILYYYQSGGRLRRPVNVSLDVFADEIRFYQL
DPLRNEYFFDRNRPSFDGILYYYQSGGRLRRPVNVSLDVFADEIRFYQL
DPLRNEYFFDRNRPSFDGILYYYQSGGRLRRPVNVSLDVFADEIRFYQL
MMKCHANN_2 442 gctaagtttgcaccatggattttctggcccacgagtcggtgggacttcc
actgaaattagagcgtagttaaaacgggtggctatctattcaatgtaat
tcgatgccccccgtcctcagcccgtgccgcagctccgtgtatgcctcgg
KCNA5_MOUSE 197 GDEAMERFREDEGFIKEEEKPLPRNEFQRQVWLIFEYPESSGSARAIAI
GDEAMERFREDEGFIKEEEKPLPRNEFQRQVWLIFEYPESSGSARAIAI
GDEAMERFREDEGFIKEEEKPLPRNEFQRQVWLIFEYPESSGSARAIAI
MMKCHANN_2 589 ggggagctcggggtaagggaccccagtcccgtcatgtcgatgtgagaga
gaactagtgaaagttaaaaactcgaatagatgtttaacagcgccgctct
gcgcggccggtacccgagggcgcctgcgcgggtccacaactgaaactcc
KCNA5_MOUSE 246 VSVSVILISIITFCLETLPEFRVDRELLLHPPVPPQPPAPAPGTNASGS
VSVSVILISIITFCLETLPEFRVDRELLLHPPVPPQPPAPAPGTNASGS
VSVSVILISIITFCLETLPEFRVDRELLLHPPVPPQPPAPAPGTNASGS
MMKCHANN_2 736 gtgtgacataaattcgaccgtaggcgctccccgcccccgcgcgaagagt
tctcttttcttctgtactcatgtagatttacctccaccccccgcacggc
ggcgctcctcccccggtgtgcgttgagacccaggagcactcagatctct
KCNA5_MOUSE 295 GVLSSGTTVAPLLPRTLADPFFIVETTCVIWFTFELLVRFFACPSKAEF
GVLSSGTTVAPLLPRTLADPFFIVETTCVIWFTFELLVRFFACPSKAEF
GVLSSGTTVAPLLPRTLADPFFIVETTCVIWFTFELLVRFFACPSKAEF
MMKCHANN_2 883 ggcttgaaggccccaacggcttaggaatgattatgccgcttgtcaaggt
gttccgcctccttcgctcacttttaccgttgtctatttgttcgcgacat
tctctccagtgcgtgagtcacccggcatgcgcttggtgtcttcccgaac
KCNA5_MOUSE 344 SRNIMNIIDIVAIFPYFITLGTELAEQQPGGGGQNGQQAMSLAILRVIR
SRNIMNIIDIVAIFPYFITLGTELAEQQPGGGGQNGQQAMSLAILRVIR
SRNIMNIIDIVAIFPYFITLGTELAEQQPGGGGQNGQQAMSLAILRVIR
MMKCHANN_2 1030 tcaaaaaagaggatcttaacgagcggcccggggcagccgatcgacagac
cgattattattcttcattctgcatcaaacggggaagaactctcttgttg
tgttgcctttgccccctccgccggagaaagtttgtgggcgcacccggcc
KCNA5_MOUSE 393 LVRVFRIFKLSRHSKGLQILGKTLQASMRELGLLIFFLFIGVILFSSAV
LVRVFRIFKLSRHSKGLQILGKTLQASMRELGLLIFFLFIGVILFSSAV
LVRVFRIFKLSRHSKGLQILGKTLQASMRELGLLIFFLFIGVILFSSAV
MMKCHANN_2 1177 cgcgtcatactcctagccacgaatcgtacgcgccattctaggacttagg
ttgttgttatcgacagtattgactacctgatgttttttttgttttcgct
gcggcaccgcccccgaggcgtgcaggcgggcggcccccccacccccctc
KCNA5_MOUSE 442 YFAEADNQGSQLSSIPDAFWWAVVTMTTVGYGDMRPITVGGKIVGSLCA
YFAEADNQGSQLSSIPDAFWWAVVTMTTVGYGDMRPITVGGKIVGSLCA
YFAEADNQGSQLSSIPDAFWWAVVTMTTVGYGDMRPITVGGKIVGSLCA
MMKCHANN_2 1324 ttggggacgtcctaacggtttgggaaaaggtggaacaagggaaggtctg
atcacaaagcatcgtcactggcttctcctgagatgctctggattgctgc
ccagactgggacctcgtacggaactgctaccgcggcctagcgtgcagcc
KCNA5_MOUSE 491 IAGVLTIALPVPVIVSNFNYFYHRETDHEEQAALKEEQGIQRRESGLDT
IAGVLTIALPVPVIVSNFNYFYHRETDHEEQAALKEEQGIQRRESGLDT
IAGVLTIALPVPVIVSNFNYFYHRETDHEEQAALKEEQGIQRRESGLDT
MMKCHANN_2 1471 agggcaagccgcgagtatatttccgagcggcggcaggcgacacgtgcga
tcgttctctctctttcataataagacaaaaacctaaaagtaggacgtac
atgcccttgtgccccctttccttggaccgggtcggagaccggggtggca
KCNA5_MOUSE 540 GGQRKVSCSKASFHKTGGPLESTDSIRRGSCPLEKCHLKAKSNVDLRRS
GGQRKVSCSKASFHKTGGPLESTDSIRRGSCPLEKCHLKAKSNVDLRRS
GGQRKVSCSKASFHKTGGPLESTDSIRRGSCPLEKCHLKAKSNVDLRRS
MMKCHANN_2 1618 ggccagataagttcaaggccgaagaaaagatccgatccagaaaggccat
ggagatgggacctaacggctagcagtgggggctaagatacagatatggc
ataggccccgccccgtgacggttctcagtcttaagtcagcgccgcgagt
KCNA5_MOUSE 589 LYALCLDTSRETDL
LYALCLDTSRETDL
LYALCLDTSRETDL
MMKCHANN_2 1765 ctgctcgaacgagt
tactgtacggacat
gtcctgctcgaatg
//
cmbi.kun.nl), 28-Jun-2005