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: PPAT_PIG
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence SSC6756_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 1168.38 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: protein length=504 (x3=1512) and cDNA length=1428
PPAT_PIG 30 MVDTEMPFWPTNFGISSVDLSVMDDHSHSFDIKPFTTVDFSSISTPHYE
MVDTEMPFWPTNFGISSVDLSVMDDHSHSFDIKPFTTVDFSSISTPHYE
MVDTEMPFWPTNFGISSVDLSVMDDHSHSFDIKPFTTVDFSSISTPHYE
SSC6756_2 1 aggagacttcaatgaatggctgaggctcttgaactaaggttaatacctg
ttacatctgccatgtgctatcttaaacactatactcctatcgtcccaaa
gtccgggtgccctgcctgcggggcccccctccgccctttccctctacta
PPAT_PIG 79 DIPFPRADPMVADYKYDLKLQDYQSAIKVEPVSPPYYSEKTQLYNKPHE
DIPFPRADPMVADYKYDLKLQDYQSAIKVEPVSPPYYSEKTQLYNKPHE
DIPFPRADPMVADYKYDLKLQDYQSAIKVEPVSPPYYSEKTQLYNKPHE
SSC6756_2 148 gactcaggcagggtatgcaccgtcagaaggcgtcctttgaacctaaccg
atctcgcacttcaaaaatataaaagctatactcccaacaacataaacaa
ccacgattagtattgccggcgccatccaggtgcgttttagtggccatca
PPAT_PIG 128 EPSNSLMAIECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLIYDRCD
EPSNSLMAIECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLIYDRCD
EPSNSLMAIECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLIYDRCD
SSC6756_2 295 gctatcagagtcgtggagtgtctggcgtggtagttcaaaatacatgatg
accacttctaggtggaaccgtaagtacgaggagttggctgtattaagga
gtccccgatactctgtacggcctattttaacgtccggtcaggttttgct
PPAT_PIG 177 LNCRIHKKSRNKCQYCRFQKCLAVGMSHNAIRFGRMPQAEKEKLLAEIS
LNCRIHKKSRNKCQYCRFQKCLAVGMSHNAIRFGRMPQAEKEKLLAEIS
LNCRIHKKSRNKCQYCRFQKCLAVGMSHNAIRFGRMPQAEKEKLLAEIS
SSC6756_2 442 catcacaaaaaatcttctcatcgggatcagaatgcaccggagactggat
taggtaaaggaagaaggtaagtctgtcaactgtggtcacaaaattcatc
tctgccaatatatgctgtgacttgggttcccgtgggagtggggggagcc
PPAT_PIG 226 SDIDQLNPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPF
SDIDQLNPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPF
SDIDQLNPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPF
SSC6756_2 589 agagccacgtggccgcgacttgttaattccaagagagatagaaagatct
gataatacaccatgctcaataacatactctcacacgcttcgaccaacct
ttccggcagttccccgagcgtcacagccggcaaggggcgaagcacaact
PPAT_PIG 275 VIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEI
VIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEI
VIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEI
SSC6756_2 736 gatgaattaagggaaatacaacccgcaagggacatcgtctctggggcga
ttaatactttgaaatataatcctaaagaatctgttaggatgctactaat
cctcgtcaggaatacgcaccccggggcaggctcctggtgtccggcgggc
PPAT_PIG 324 TEYAKNIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQ
TEYAKNIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQ
TEYAKNIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQ
SSC6756_2 883 agtgaaacgtgacgcagcgaccatggcgaataacgttaaagggcatggc
caacaatcgttatataaatcttaagtaattacttccttaaagtttcaga
agtcgcctgtactcgtcaatcagtcccgctccggccggtacgccccgca
PPAT_PIG 373 GFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILS
GFMTREFL+SLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILS
GFMTREFLRSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILS
SSC6756_2 1030 gtaaagtcaacaactggtagcatgtggatagcgtggagcgataggaaca
gttcgattggtgactgattacatatctatactataagatctttcttttg
acgaggtagcgaacttctggcgcgttggccagaatcccggatatcttct
PPAT_PIG 422 GDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLR
GDRP LLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLR
GDRPRLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLR
SSC6756_2 1177 ggccctcagacaggacgatccgtgcccataccgttcctgacccaaagca
gagcgttatactaataaattactatatataacaccattcattaatcatg
accatggtggccgctactggacggggcggccagccgcttggcgagacca
PPAT_PIG 471 QIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY
QIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY
QIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY
SSC6756_2 1324 cagagcgccccgaaaagagaaccccccgatagtt
attcaatattattaacacatgtacttaataaata
gtgagcggggaaaggaggcgctcacagaacgcgc
//
cmbi.kun.nl), 18-Feb-2005