2005, NucleaRDB.
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: NHR4_CAEEL
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence CEF32B6_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 1256.26 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.
NHR4_CAEEL 1 MNERGMLVDPRFDAFFKLEQIDDYKYDGADTSPSTSNGLPETSNGGRLI
MNERGMLVDPRFDAFFKLEQIDDYKYDGADTSPSTSNGLPETSNGGRLI
MNERGMLVDPRFDAFFKLEQIDDYKYDGADTSPSTSNGLPETSNGGRLI
CEF32B6_2 1 aagcgacggcatggttatgcaggtatggggatctatagccgataggcta
taaggtttacgtacttataataaaaaagcaccccccagtcaccagggtt
gtaaggagtgatcactagaaacccattatcttaagcctgaacacgtcgt
NHR4_CAEEL 50 CDVCGDVAFGKHYGINACNGCKGFFRRSVWSRRQYSCRFGGDCPVVKEH
CDVCGDVAFGKHYGINACNGCKGFFRRSVWSRRQYSCRFGGDCPVVKEH
CDVCGDVAFGKHYGINACNGCKGFFRRSVWSRRQYSCRFGGDCPVVKEH
CEF32B6_2 148 tggtggggtgactgaagtagtagttacagttaactttctgggtcggagc
gatggatctgaaagtacgaggagttgggtgcggaacggtggagcttaaa
tttttcggcaattgtttttgtattcaatggaggatttttaatcgtagat
NHR4_CAEEL 99 RNVCRSCRLKKCFEVGMNPDSVQNERDRNAKNGGMGGPMSSPTQSSLCK
RNVCRSCRLKKCFEVGMNPDSVQNERDRNAKNGGMGGPMSSPTQSSLCK
RNVCRSCRLKKCFEVGMNPDSVQNERDRNAKNGGMGGPMSSPTQSSLCK
CEF32B6_2 295 cagtattctaattgggaacgtgcagcgcagaaggaggcattcactttta
gatggcggtaagtatgtacactaaagagacaaggtggctccccacctga
atctattaggattatagtgttaatatttttataggtaagatatgttaca
NHR4_CAEEL 148 ELTISNGQIKRKRLRPETVEKTTQTDGKLEINDDFDFENMQQNPTPPGL
ELTISNGQIKRKRLRPETVEKTTQTDGKLEINDDFDFENMQQNPTPPGL
ELTISNGQIKRKRLRPETVEKTTQTDGKLEINDDFDFENMQQNPTPPGL
CEF32B6_2 442 gtaatagcaacaacacgaggaaacaggacgaaggtgtgaaccacaccgt
atctcagatagagtgcactaaccacagatataaatataataaaccccgt
agatttagtaagagagacaaagtgttaataactttttacgaacactaaa
NHR4_CAEEL 197 LPLKIERISTPPSDLPVPMDFSIHSAVLDIEQKVFYNCPVAVDNSINAT
LPLKIERISTPPSDLPVPMDFSIHSAVLDIEQKVFYNCPVAVDNSINAT
LPLKIERISTPPSDLPVPMDFSIHSAVLDIEQKVFYNCPVAVDNSINAT
CEF32B6_2 589 tccaagaatacctgtcgcagttactggcgagcagttatcggggataaga
tctatagtcccccatctctatctaccttataaattaagctctaactacc
gttataacaatactgtttgctatttattctgaaattttggttttattaa
NHR4_CAEEL 246 KTPITLPFEVVFRQPHLVCNRYPMRFSNTRVLTPEDLIDGWRRHFTYYS
KTPITLPFEVVFRQPHLVCNRYPMRFSNTRVLTPEDLIDGWRRHFTYYS
KTPITLPFEVVFRQPHLVCNRYPMRFSNTRVLTPEDLIDGWRRHFTYYS
CEF32B6_2 736 aacaatctgggtcccccgtactcacttaacgtacggcaggtccctattt
acctctctatttgacattgagactgtcacgttccaattaggggatcaac
atactgatgcactatttatcttagacgttaaataatttcagtttctttt
NHR4_CAEEL 295 DWCHAMDEFKALSPEDQIVLAKKKIILHGWLVHAYYSYKSGCNGICFAN
DWCHAMDEFKALSPEDQIVLAKKKIILHGWLVHAYYSYKSGCNGICFAN
DWCHAMDEFKALSPEDQIVLAKKKIILHGWLVHAYYSYKSGCNGICFAN
CEF32B6_2 883 gttcgaggtagttcggcagtgaaaaaccgtcgcgttttaagtagattga
aggactaatactccaaatttcaaatttaggttacaacaagggagtgtca
tgttagtacgagttatgttgagagtattagttttccacgttctatttat
NHR4_CAEEL 344 GAAHLPEGGHPSITEFYKECMPRYLNYVIYPMHNFQMDDAEMVLIKCIM
GAAHLPEGGHPSITEFYKECMPRYLNYVIYPMHNFQMDDAEMVLIKCIM
GAAHLPEGGHPSITEFYKECMPRYLNYVIYPMHNFQMDDAEMVLIKCIM
CEF32B6_2 1030 gggcccgggccaaagttagtacctcatgatcacatcaggggagcaataa
gccatcaggacgtcataaagtcgataattactaatataacattttagtt
acctttaattatcgaccaacgtttgctcttagttcagtttagatcatcg
NHR4_CAEEL 393 FFSSESGLSAAGRQIVSAAREKYLSALYNYGRANKCTTSAQATLRIAKF
FFSSESGLSAAGRQIVSAAREKYLSALYNYGRANKCTTSAQATLRIAKF
FFSSESGLSAAGRQIVSAAREKYLSALYNYGRANKCTTSAQATLRIAKF
CEF32B6_2 1177 tttagtgcagggccagtggcgatttgttatgcgaataatgcgaccagat
ttcgacgtgccggattcccgaaatcctaaaggcaagccccacctgtcat
ctgtacaatttagactggttaataatatttgtatatcaatgattacgat
NHR4_CAEEL 442 MIMLSAITSLTHLMNEGVHVTSLFNIIEFDELIQATHKTTPPQHSPPAP
MIMLSAITSLTHLMNEGVHVTSLFNIIEFDELIQATHKTTPPQHSPPAP
MIMLSAITSLTHLMNEGVHVTSLFNIIEFDELIQATHKTTPPQHSPPAP
CEF32B6_2 1324 aaactgaaatactaagggcgatctaaagtggcacgacaaacccctccgc
ttttcctcgtcattaagtatccttattataattaccaaccccaaccccc
gtgtcatgtgatagtaattggatctatatcaacaattggtatatttata
NHR4_CAEEL 491 MG
MG
MG
CEF32B6_2 1471 ag
tg
gt
//
cmbi.kun.nl), 18-Feb-2005