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: NHR5_CAEEL
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence CEY73F8A_22
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 1737.41 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.
NHR5_CAEEL 1 MSSGGNSSNVNRNSGSSNVITLNDSDEETEDSNLGSSSSTNLCKVCGAE
MSSGGNSSNVNRNSGSSNVITLNDSDEETEDSNLGSSSSTNLCKVCGAE
MSSGGNSSNVNRNSGSSNVITLNDSDEETEDSNLGSSSSTNLCKVCGAE
CEY73F8A_22 1 attggaatagaaatgaaagaatagtgggaggaatgaattaactagtggg
tccggagcatagacgggattctaacaaacaagatgggcccatgatggca
gttctctatgtattgtctgttgtttcaacgcctgcccgcattcaacaca
NHR5_CAEEL 50 KAALHYGALSCVGCKGFFRRALLKADQLECAANGECTVSVLQKTQCRSC
KAALHYGALSCVGCKGFFRRALLKADQLECAANGECTVSVLQKTQCRSC
KAALHYGALSCVGCKGFFRRALLKADQLECAANGECTVSVLQKTQCRSC
CEY73F8A_22 148 aggcctggcatggtagttccgccaggccgtggaggtagagtcaactaat
acctaagctggtggagttggcttacaatagccagagctgttaacagggg
atttccaagctcataccctgttggttagattatagtatttggacacact
NHR5_CAEEL 99 RFNKCLREGMNPAYVRPNRDAPPKPRKPTTTVATCDQTDRGRTTKSREE
RFNKCLREGMNPAYVRPNRDAPPKPRKPTTTVATCDQTDRGRTTKSREE
RFNKCLREGMNPAYVRPNRDAPPKPRKPTTTVATCDQTDRGRTTKSREE
CEY73F8A_22 295 ataatccggaacgtgccacggccaccacaaaggatgcagcgaaaaacgg
gtaagtgagtaccatgcagacccacgacccctccgaacagggccaggaa
actgcacaagttttccacacatagatggataacgctattttgcaaccgg
NHR5_CAEEL 148 WMKKMTVEMRTILMTLLNIETKVMKGDTQQEASKLYPLKGIDKLSDIIE
WMKKMTVEMRTILMTLLNIETKVMKGDTQQEASKLYPLKGIDKLSDIIE
WMKKMTVEMRTILMTLLNIETKVMKGDTQQEASKLYPLKGIDKLSDIIE
CEY73F8A_22 442 taaaaaggaaaataactaagaagaaggaccggtactccagagacagaag
gtaatctatgctttcttatacattagacaaaccatactagtaatgatta
ggagggtggaaaagaggttgaaagaataaaaaaagcggaattgcttcta
NHR5_CAEEL 197 TPIQLKGKRTEMRYEAYRMAGNDELCAIAYRRLIAAIDWVESLSPLLGH
TPIQLKGKRTEMRYEAYRMAGNDELCAIAYRRLIAAIDWVESLSPLLGH
TPIQLKGKRTEMRYEAYRMAGNDELCAIAYRRLIAAIDWVESLSPLLGH
CEY73F8A_22 589 acactagacagaatggtaaggaggttgagtcataggagtggtctcctgc
cctatagagcatgaacagtcgaaatgctcaggttcctagtactccttga
agtaaaaaaaagataacagtattgatatctgggttattgtaggaaggac
NHR5_CAEEL 246 LTPQDKVINILCKIALVKSSFAPLMVFNFCARTAEACQDENVLCLCNFA
LTPQDKVINILCKIALVKSSFAPLMVFNFCARTAEACQDENVLCLCNFA
LTPQDKVINILCKIALVKSSFAPLMVFNFCARTAEACQDENVLCLCNFA
CEY73F8A_22 736 caccgagaaactaagcgatttgccagtattgaagggtcggagctctatg
tccaaattattgatcttacctccttttatgcgccacgaaaattgtgatc
agtgtgaatttcaaagcataccatgcctttgaaaattgtgttactttta
NHR5_CAEEL 295 YVPRNISKMYEDTYHLGNGLVERALNELVAVYREYGMREEEIVCVNAMI
YVPRNISKMYEDTYHLGNGLVERALNELVAVYREYGMREEEIVCVNAMI
YVPRNISKMYEDTYHLGNGLVERALNELVAVYREYGMREEEIVCVNAMI
CEY73F8A_22 883 tgccaataatggatccgagcggcgcagcgggtcgtgaagggagtgagaa
atcgatcataaacaatgagttagctaattctagaagtgaaattgtactt
ttagtaaagtgcatccccacgattatgtaaatgattgaagattcgtagt
NHR5_CAEEL 344 CLNPLAKDVSDSLFEKIVELRNRIADCLFSIVKEVRLSPTPNVCYGHIL
CLNPLAKDVSDSLFEKIVELRNRIADCLFSIVKEVRLSPTPNVCYGHIL
CLNPLAKDVSDSLFEKIVELRNRIADCLFSIVKEVRLSPTPNVCYGHIL
CEY73F8A_22 1030 tcaccgaggtgtttgaaggcaacaggtcttagaggctacacagttgcac
gtactcaatcacttaattatgagtcagttcttaatgtgcccatgagatt
tgttgaatagttgtagttggatattttttattggtaatgagtatcatat
NHR5_CAEEL 393 LSLATVTELANAMSENLQFAQTFSNQGEIPLLTDLFGCFTVEPFFKEVD
LSLATVTELANAMSENLQFAQTFSNQGEIPLLTDLFGCFTVEPFFKEVD
LSLATVTELANAMSENLQFAQTFSNQGEIPLLTDLFGCFTVEPFFKEVD
CEY73F8A_22 1177 cttgagagcgagaagacctgcattacggacccagttgttaggcttaggg
tctcctcatcactgaatatcactcaagatcttcattggtctacttaata
tagtttaaaatggtatcattaatataaatatctcacctcataatcaacc
NHR5_CAEEL 442 ELAAMSLEKAKAEKKKEMSTQTDRLPPPRALLKRQATIDEDSEEPARQN
ELAAMSLEKAKAEKKKEMSTQTDRLPPPRALLKRQATIDEDSEEPARQN
ELAAMSLEKAKAEKKKEMSTQTDRLPPPRALLKRQATIDEDSEEPARQN
CEY73F8A_22 1324 gcggaatgagaggaaagaaacagatcccagttaccgaagggaggcgcca
atcctgtaacacaaaaatgcacagtcccgcttagacctaaagaaccgaa
gggagtgaggatagggagtaattggttaaaagaaaatctgccaattagt
NHR5_CAEEL 491 FRLLQPPNNFYITEMLDDLRNNHAENHLISLNFDASNVSNAIASRPSFE
FRLLQPPNNFYITEMLDDLRNNHAENHLISLNFDASNVSNAIASRPSFE
FRLLQPPNNFYITEMLDDLRNNHAENHLISLNFDASNVSNAIASRPSFE
CEY73F8A_22 1471 tcctcccaattaagatggtaaacggactaacatggtagtagagtacatg
tgttaccaatatcattaatgaaacaaattgtataccatcactccgcgta
tatggtactccttaggttggctccgttgatcctctactgtactgacttg
NHR5_CAEEL 540 DLGTVPSGSTVTRRIGSNIQGPSHLPQCGSTVTQRPTVPSSTTSSTFYN
DLGTVPSGSTVTRRIGSNIQGPSHLPQCGSTVTQRPTVPSSTTSSTFYN
DLGTVPSGSTVTRRIGSNIQGPSHLPQCGSTVTQRPTVPSSTTSSTFYN
CEY73F8A_22 1618 gtgagcagtagaccagaaacgctcccctgtagacacagcttaattatta
atgctcggcctcggtggatagccatcaggcctcagcctcccccccctaa
tgttaattaaaaaatgtttaaaccctatttaacaataacccaaccacct
NHR5_CAEEL 589 FPPPPGYPPLNAGYTPNVNYPNLYQQPQYFQNFQQNNYPSQVMEQQNYG
FPPPPGYPPLNAGYTPNVNYPNLYQQPQYFQNFQQNNYPSQVMEQQNYG
FPPPPGYPPLNAGYTPNVNYPNLYQQPQYFQNFQQNNYPSQVMEQQNYG
CEY73F8A_22 1765 tccccgtcctaggtacagatcattccccttcatccaatctcgagccatg
tccccgacctacgaccataacataaacaataataaaaaccattaaaaag
ctaatttaaattacagtcctgtgtaaagtcgttgattcatacgagatta
NHR5_CAEEL 638 NVESTSYPFPRNDENVKQSIHFSRHLNLTKTDFEIREVHDSPACSQADM
NVESTSYPFPRNDENVKQSIHFSRHLNLTKTDFEIREVHDSPACSQADM
NVESTSYPFPRNDENVKQSIHFSRHLNLTKTDFEIREVHDSPACSQADM
CEY73F8A_22 1912 aggaaatctccaggagacaacttcctacaaagtgacggcgacgttcgga
atagcgactcgaaaataagtatcgatatcacatatgataagccgcacat
ttatctcataattatgagcacttccgctaaattatagcctcgtccggcg
NHR5_CAEEL 687 PTVPTLFFIISQILELI
PTVPTLFFIISQILELI
PTVPTLFFIISQILELI
CEY73F8A_22 2059 cagcatttaatcatgca
cctcctttttcattatt
tcgtcattttgatagta
//
cmbi.kun.nl), 18-Feb-2005