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: wise2-1-20c $ (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: IRK5_HUMAN
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence HSD134_3
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 1049.47 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.
IRK5_HUMAN 1 MAGDSRNAMNQDMEIGVTPWDPKKIPKQARDYVPIATDRTRLLAEGKKP
MAGDSRNAMNQDMEIGVTPWDPKKIPKQARDYVPIATDRTRLLAEGKKP
MAGDSRNAMNQDMEIGVTPWDPKKIPKQARDYVPIATDRTRLLAEGKKP
HSD134_3 1 agggtaagaacgagaggactgcaaacacgcgtgcagagcacccgggaac
tcgacgactaaatatgtccgacaatcaacgaatctccagcgttcagaac
gtcttgtcgcgcggtactcgccggtaagccttcctcactgcggcgcgga
IRK5_HUMAN 50 RQRYMEKSGKCNVHHGNVQETYRYLSDLFTTLVDLKWRFNLLVFTMVYT
RQRYMEKSGKCNVHHGNVQETYRYLSDLFTTLVDLKWRFNLLVFTMVYT
RQRYMEKSGKCNVHHGNVQETYRYLSDLFTTLVDLKWRFNLLVFTMVYT
HSD134_3 148 ccctagaagatagccgagcgatctcagctaacggcatctatcgtaagta
gagataaggagataagataacagatgattccttataggtattttcttac
cgccgggtcgccgcccccggccgcgtcccccggccggcccgccccgtct
IRK5_HUMAN 99 VTWLFFGFIWWLIAYIRGDLDHVGDQEWIPCVENLSGFVSAFLFSIETE
VTWLFFGFIWWLIAYIRGDLDHVGDQEWIPCVENLSGFVSAFLFSIETE
VTWLFFGFIWWLIAYIRGDLDHVGDQEWIPCVENLSGFVSAFLFSIETE
HSD134_3 295 gatcttgtattcagtacggcgcgggcgtactggacagtgtgtcttagag
tcgtttgttggttcatggataatgaaagtcgtaatggttcctttctaca
ccggcccctggctttcgtcgcttccaggttttacctccgctcgcctgca
IRK5_HUMAN 148 TTIGYGFRVITEKCPEGIILLLVQAILGSIVNAFMVGCMFVKISQPKKR
TTIGYGFRVITEKCPEGIILLLVQAILGSIVNAFMVGCMFVKISQPKKR
TTIGYGFRVITEKCPEGIILLLVQAILGSIVNAFMVGCMFVKISQPKKR
HSD134_3 442 aaagtgtcgaagatcggaacctgcgacgtagagtaggtatgaaaccaaa
cctgagtgttcaagcagttttttacttgcttactttggtttatgacaag
actgtccaccaggtaggtaccgcgccgcccctccgggcgtcgccgcgga
IRK5_HUMAN 197 AETLMFSNNAVISMRDEKLCLMFRVGDLRNSHIVEASIRAKLIKSRQTK
AETLMFSNNAVISMRDEKLCLMFRVGDLRNSHIVEASIRAKLIKSRQTK
AETLMFSNNAVISMRDEKLCLMFRVGDLRNSHIVEASIRAKLIKSRQTK
HSD134_3 589 ggacattaaggatacggactcatcgggccatcagggtacgacaatccaa
cactttcaacttctgaaatgtttgtgatgacattacctgcattacgaca
ggccgtcccacccggcgggccgcggccccccccggcccgcgccgcggca
IRK5_HUMAN 246 EGEFIPLNQTDINVGFDTGDDRLFLVSPLIISHEINEKSPFWEMSQAQL
EGEFIPLNQTDINVGFDTGDDRLFLVSPLIISHEINEKSPFWEMSQAQL
EGEFIPLNQTDINVGFDTGDDRLFLVSPLIISHEINEKSPFWEMSQAQL
HSD134_3 736 gggtaccacagaaggtgagggcctcgtccaatcgaagaacttgatcgcc
agattctaacatatgtacgaagttttcctttcaataaagctgatcacat
gggcccgcgacccgctcgcccccctgttgccctgccggctcgggtgtgg
IRK5_HUMAN 295 HQEEFEVVVILEGMVEATGMTCQARSSYMDTEVLWGHRFTPVLTLEKGF
HQEEFEVVVILEGMVEATGMTCQARSSYMDTEVLWGHRFTPVLTLEKGF
HQEEFEVVVILEGMVEATGMTCQARSSYMDTEVLWGHRFTPVLTLEKGF
HSD134_3 883 ccggtggggacggagggagaatcgcattagaggctgcctacgcatgagt
aaaatatttttagttaccgtcgacggcatacattggagtccttctaagt
tgagtatgctaagggacacgccacgcccgtaggcgccacaacccgagcc
IRK5_HUMAN 344 YEVDYNTFHDTYETNTPSCCAKELAEMKREGRLLQYLPSPPLLGGCAEA
YEVDYNTFHDTYETNTPSCCAKELAEMKREGRLLQYLPSPPLLGGCAEA
YEVDYNTFHDTYETNTPSCCAKELAEMKREGRLLQYLPSPPLLGGCAEA
HSD134_3 1030 tgggtaatcgatgaaacattgagcggaaaggcccctccaccccggtggg
aataaactaacaacaccgggcaatcatagaggttaatcgccttgggcac
tggcccccttctgccaccctcgggaagggacgccgcccccagggcttga
IRK5_HUMAN 393 GLDAEAEQNEEDEPKGLGGSREARGSV
GLDAEAEQNEEDEPKGLGGSREARGSV
GLDAEAEQNEEDEPKGLGGSREARGSV
HSD134_3 1177 gcgggggcaggggcagcggtaggagtg
gtacacaaaaaaacagtggcgacggct
ggtagtggtaatgcgggtgcggcgcgg
//
cmbi.ru.nl), 24-Jul-2003