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: KCNK2_HUMAN
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence AF129399_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 978.37 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.
Warning: mismatch(es) found
KCNK2_HUMAN 16 VAAPDLLDPKSAAQNSKPRLSFSTKPTVLASRVESDTTINVMKWKTVST
+AAPDLLDPKSAAQNSKPRLSFSTKPTVLASRVESDTTINVMKWKTVST
MAAPDLLDPKSAAQNSKPRLSFSTKPTVLASRVESDTTINVMKWKTVST
AF129399_2 1 aggcgtcgcatggcatacactttaacagcgtcggagaaaagaataagta
tcccattacacccaacacgtctccaccttccgtagacctattagactcc
ggctcggttatctgccaggcgtcgacagttcgggtcgctttgagggccg
*** !
KCNK2_HUMAN 65 IFLVVVLYLIIGATVFKALEQPHEISQRTTIVIQKQTFISQHSCVNSTE
IFLVVVLYLIIGATVFKALEQPHEISQRTTIVIQKQTFISQHSCVNSTE
IFLVVVLYLIIGATVFKALEQPHEISQRTTIVIQKQTFISQHSCVNSTE
AF129399_2 148 atcgggctcaaggagtagtgcccgatcaaaagacacatatccttgatag
tttttttatttgccttactaacaatcagcctttaaacttcaacgtacca
acggtcctgccaccgcaagggttgtaggcctgcggaacacatctctggg
KCNK2_HUMAN 114 LDELIQQIVAAINAGIIPLGNTSNQISHWDLGSSFFFAGTVITTIGFGN
LDELIQQIVAAINAGIIPLGNTSNQISHWDLGSSFFFAGTVITTIGFGN
LDELIQQIVAAINAGIIPLGNTSNQISHWDLGSSFFFAGTVITTIGFGN
AF129399_2 295 cggcaccagggaaggaactgaatacaactgtgattttggagaaaagtga
taattaattcctacgttctgaccaatgagatggctttcgcttcctgtga
gtactgaagaaatagtagaaccctactcgtgatcccttctttacaatac
KCNK2_HUMAN 163 ISPRTEGGKIFCIIYALLGIPLFGFLLAGVGDQLGTIFGKGIAKVEDTF
ISPRTEGGKIFCIIYALLGIPLFGFLLAGVGDQLGTIFGKGIAKVEDTF
ISPRTEGGKIFCIIYALLGIPLFGFLLAGVGDQLGTIFGKGIAKVEDTF
AF129399_2 442 atccagggaattaatgtcgacctgtctgggggccgaatgagagagggat
tccgcaggattgttacttgtcttgtttcgtgaatgcttgagtcataact
caacaaccaactcctcagatcctttcgtatatgaccataaatcagatgt
KCNK2_HUMAN 212 IKWNVSQTKIRIISTIIFILFGCVLFVALPAIIFKHIEGWSALDAIYFV
IKWNVSQTKIRIISTIIFILFGCVLFVALPAIIFKHIEGWSALDAIYFV
IKWNVSQTKIRIISTIIFILFGCVLFVALPAIIFKHIEGWSALDAIYFV
AF129399_2 589 aatagacaaacaataaatactgtgctggccgaatacaggtagcggattg
tagatgacatgttccttttttggttttctcctttaatagggctactatt
tggtttgcgtcccaacataatctactgtgtgcacacaacgtcgcctttg
KCNK2_HUMAN 261 VITLTTIGFGDYVAGGSDIEYLDFYKPVVWFWILVGLAYFAAVLSMIGR
VITLTTIGFGDYVAGGSDIEYLDFYKPVVWFWILVGLAYFAAVLSMIG
VITLTTIGFGDYVAGGSDIEYLDFYKPVVWFWILVGLAYFAAVLSMIGD
AF129399_2 736 gaacaaagtggtggggtgagtcgttacggtttacggcgttgggcaaagg
ttctcctgtgaatcggcataatataacttgtgtttgtcatccttgttga
tctaattattcctatacttatgcctgtcggcgctagttctttcgcgtat
***
KCNK2_HUMAN 310 LVRVISKKTKEEVGEFRAHAAEWTANVTAEFKETRRRLSVEIYDKFQRA
-+RVISKKTKEEVGEFRAHAAEWTANVTAEFKETRRRLSVEIYDKFQRA
WLRVISKKTKEEVGEFRAHAAEWTANVTAEFKETRRRLSVEIYDKFQRA
AF129399_2 883 tccgataaaagggggtagcgggtagagaggtagaaaccaggatgatccg
gtgttcaacaaatgatgcaccagccatccataacgggtgtataaatagc
gcagatagaaaggagcaacttggacccacacaacggagtggttcgcggc
*** !!
KCNK2_HUMAN 359 TSIKRKLSAELAGNHNQELTPCRRTLSVNHLTSERDVLPPLLKTESIYL
TSIKRKLSAELAGNHNQELTPCRRTLSVNHLT+ERDVLPPLLKTESIYL
TSIKRKLSAELAGNHNQELTPCRRTLSVNHLTNERDVLPPLLKTESIYL
AF129399_2 1030 ataacactggcggacacgcactaaactgaccaagaggtcctcaagaatc
cctagatccatcgaaaaatccgggctctaatcaagattccttacagtat
cccgggcgaagtacctgggtttggcgagccgccggtcgtcaggtgtctg
*** !
KCNK2_HUMAN 408 NGLAPHCAGEEIAVIENIK
NGL-PHCAGEEIAVIENIK
NGLTPHCAGEEIAVIENIK
AF129399_2 1177 agtacctggggaggagaaa
agtccagcgaatcttaata
ttggactttagttgtgcca
*** !
//
cmbi.kun.nl), 28-Jun-2005