KChannelDB: Pairwise Alignments

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:       IRK16_HUMAN
Comp Matrix:         blosum62.bla
Gap open:            12
Gap extension:       2
Start/End            default
Target Sequence      AF153817_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 1046.71 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.

IRK16_HUMAN        1 MSYYGSSYHIINADAKYPGYPPEHIIAEKRRARRRLLHKDGSCNVYFKH 
                     MSYYGSSYHIINADAKYPGYPPEHIIAEKRRARRRLLHKDGSCNVYFKH 
                     MSYYGSSYHIINADAKYPGYPPEHIIAEKRRARRRLLHKDGSCNVYFKH 
AF153817_2         1 aattgaatcaaagggatcgtccgcaaggaaagaactccaggatagttac 
                     tgaagggaattacacaacgaccaattcaaggcgggttaaagggatataa 
                     gctcccctttctgcaacaccgagctatggaaaaaaatcatccttcccgc 


IRK16_HUMAN       50 IFGEWGSYVVDIFTTLVDTKWRHMFVIFSLSYILSWLIFGSVFWLIAFH 
                     IFGEWGSYVVDIFTTLVDTKWRHMFVIFSLSYILSWLIFGSVFWLIAFH 
                     IFGEWGSYVVDIFTTLVDTKWRHMFVIFSLSYILSWLIFGSVFWLIAFH 
AF153817_2       148 atggtgatgggataacggaatccatgatttttactttatgtgttcagtc 
                     ttgagggattattccttacaggatttttctcattcgtttgcttgttcta 
                     ttaagactgtccccttgccggctgtgattatttcgggatctctgcactt 


IRK16_HUMAN       99 HGDLLNDPDITPCVDNVHSFTGAFLFSLETQTTIGYGYRCVTEECSVAV 
                     HGDLLNDPDITPCVDNVHSFTGAFLFSLETQTTIGYGYRCVTEECSVAV 
                     HGDLLNDPDITPCVDNVHSFTGAFLFSLETQTTIGYGYRCVTEECSVAV 
AF153817_2       295 cggctagcgaactggagcttaggttttcgacaaagtgtctgaggttggg 
                     agattaacatccgtaatactcgctttctacacctgagaggtcaagctct 
                     tctaattaccatttcccttcagctgccagcaccaatttctttaattgcg 


IRK16_HUMAN      148 LMVILQSILSCIINTFIIGAALAKMATARKRAQTIRFSYFALIGMRDGK 
                     LMVILQSILSCIINTFIIGAALAKMATARKRAQTIRFSYFALIGMRDGK 
                     LMVILQSILSCIINTFIIGAALAKMATARKRAQTIRFSYFALIGMRDGK 
AF153817_2       442 cagacctatataaaataagggtgaagagcaagcaactattgcagaagga 
                     tttttacttggttactttgcctcatcccgagcactgtgatcttgtgaga 
                     cggccgccatccatctctatcgcagattagacacttccctatatgatgg 


IRK16_HUMAN      197 LCLMWRIGDFRPNHVVEGTVRAQLLRYTEDSEGRMTMAFKDLKLVNDQI 
                     LCLMWRIGDFRPNHVVEGTVRAQLLRYTEDSEGRMTMAFKDLKLVNDQI 
                     LCLMWRIGDFRPNHVVEGTVRAQLLRYTEDSEGRMTMAFKDLKLVNDQI 
AF153817_2       589 ctcatcaggtccacggggagagcccctaggaggaaaagtagcatgagca 
                     tgttggtgatgcaattagctgcattgacaagaggtctctaatattaaat 
                     tccggcttttgaccgaaaatacatcctaactagggggataccaacccac 


IRK16_HUMAN      246 ILVTPVTIVHEIDHESPLYALDRKAVAKDNFEILVTFIYTGDSTGTSHQ 
                     ILVTPVTIVHEIDHESPLYALDRKAVAKDNFEILVTFIYTGDSTGTSHQ 
                     ILVTPVTIVHEIDHESPLYALDRKAVAKDNFEILVTFIYTGDSTGTSHQ 
AF153817_2       736 acgacgaagcgagcgacctgcgcagggagatgatgatataggtagatcc 
                     tttcctcttaataaagctactagactcaaatatttcttacgaccgccaa 
                     cgccgattctatctgctgtctccaaacatctgtggatcttttctaatca 


IRK16_HUMAN      295 SRSSYVPREILWGHRFNDVLEVKRKYYKVNCLQFEGSVEVYAPFCSAKQ 
                     SRSSYVPREILWGHRFNDVLEVKRKYYKVNCLQFEGSVEVYAPFCSAKQ 
                     SRSSYVPREILWGHRFNDVLEVKRKYYKVNCLQFEGSVEVYAPFCSAKQ 
AF153817_2       883 taattgccgactgcataggtggaaattagattctggagggtgcttagac 
                     cggcatcgattggagtaattatagaaaatagtataggtatacctggcaa 
                     taccttcaatcgctgtttcgatgggtcagccagtaatgaatcctctcga 


IRK16_HUMAN      344 LDWKDQQLHIEKAPPVRESCTSDTKARRRSFSAVAIVSSCENPEETTTS 
                     LDWKDQQLHIEKAPPVRESCTSDTKARRRSFSAVAIVSSCENPEETTTS 
                     LDWKDQQLHIEKAPPVRESCTSDTKARRRSFSAVAIVSSCENPEETTTS 
AF153817_2      1030 tgtagccccagagccgcgttatgaagacattagggagaatgacggaaat 
                     tagaaaatataaccctgacgccacacgggctgctcttgggaacaacccc 
                     gcgacggccaaaaaataaccggccggaagattatctccctactggcctc 


IRK16_HUMAN      393 ATHEYRETPYQKALLTLNRISVESQM                        
                     ATHEYRETPYQKALLTLNRISVESQM                        
                     ATHEYRETPYQKALLTLNRISVESQM                        
AF153817_2      1177 gacgtagactcagccataaatggtca                        
                     ccaaagaccaaacttctagtctacat                        
                     catatgaattgatcgtacactaacag                        


//

F.Horn (kchanneldbcmbi.kun.nl), 28-Jun-2005