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: GPA1_YEAST
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence SCGPA1_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 1148.24 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.
GPA1_YEAST 1 GCTVSTQTIGDESDPFLQNKRANDVIEQSLQLEKQRDKNEIKLLLLGAG
GCTVSTQTIGDESDPFLQNKRANDVIEQSLQLEKQRDKNEIKLLLLGAG
GCTVSTQTIGDESDPFLQNKRANDVIEQSLQLEKQRDKNEIKLLLLGAG
SCGPA1_2 4 gtagaacaagggagctccaaagaggagcttccgaccgaagaactctggg
ggctgcactgaagacttaaagcaattaactataaagaaaatattttgcg
gtagtgaaaacattttagcaacttccgagggggaatcgtaaagaaatct
GPA1_YEAST 50 ESGKSTVLKQLKLLHQGGFSHQERLQYAQVIWADAIQSMKILIIQARKL
ESGKSTVLKQLKLLHQGGFSHQERLQYAQVIWADAIQSMKILIIQARKL
ESGKSTVLKQLKLLHQGGFSHQERLQYAQVIWADAIQSMKILIIQARKL
SCGPA1_2 151 gtgatagtactattccggttccgatctgcgatgggactaaataacgaac
acgaccttaatattaaggtcaaagtaacattgcactactattttacgat
gataagtaaaaaaatactcctaagagttagagatcaaagatgttgcaaa
GPA1_YEAST 99 GIQLDCDDPINNKDLFACKRILLKAKALDYINASVAGGSDFLNDYVLKY
GIQLDCDDPINNKDLFACKRILLKAKALDYINASVAGGSDFLNDYVLKY
GIQLDCDDPINNKDLFACKRILLKAKALDYINASVAGGSDFLNDYVLKY
SCGPA1_2 298 gaccgtggcaaaagttgtaaaccagagtgtaagaggggtgtcagtgcat
gtatagaactaaaattcgagtttacactaatacgtcggcattaaattaa
ttatctttgcctatgtacgaagagtatattcccttctttttatttaggc
GPA1_YEAST 148 SERYETRRRVQSTGRAKAAFDEDGNISNVKSDTDRDAETVTQNEDADRN
SERYETRRRVQSTGRAKAAFDEDGNISNVKSDTDRDAETVTQNEDADRN
SERYETRRRVQSTGRAKAAFDEDGNISNVKSDTDRDAETVTQNEDADRN
SCGPA1_2 445 tgatgaaacgcaagcgaggtggggaatagaagagagggagacaggggaa
cagaacgggtagcggcacctaaagatcatagacagacactcaaaacaga
aagtatggttgtcaaaattctacattttcatctcattagggatgtttac
GPA1_YEAST 197 NSSRINLQDICKDLNQEGDDQMFVRKTSREIQGQNRRNLIHEDIAKAIK
NSSRINLQDICKDLNQEGDDQMFVRKTSREIQGQNRRNLIHEDIAKAIK
NSSRINLQDICKDLNQEGDDQMFVRKTSREIQGQNRRNLIHEDIAKAIK
SCGPA1_2 592 aaaaaaccgatagtacggggcatgaaatagacgcaacacacggagagaa
agggtataatgaataaagaaatttgaccgatagaaggattaaatcacta
cttatcagttcgcgcaactcggttaaaagataaataatttcacttgaag
GPA1_YEAST 246 QLWNNDKGIKQCFARSNEFQLEGSAAYYFDNIEKFASPNYVCTDEDILK
QLWNNDKGIKQCFARSNEFQLEGSAAYYFDNIEKFASPNYVCTDEDILK
QLWNNDKGIKQCFARSNEFQLEGSAAYYFDNIEKFASPNYVCTDEDILK
SCGPA1_2 739 cctaagagaacttgctagtctggtggtttgaagatgacatgtagggata
atgaaaagtaagtcgcaatatagcccaataataatcgcaatgcaaatta
atgtccataggttatttgtaggcataccttctgatttgttctgtactgg
GPA1_YEAST 295 GRIKTTGITETEFNIGSSKFKVLDAGGQRSERKKWIHCFEGITAVLFVL
GRIKTTGITETEFNIGSSKFKVLDAGGQRSERKKWIHCFEGITAVLFVL
GRIKTTGITETEFNIGSSKFKVLDAGGQRSERKKWIHCFEGITAVLFVL
SCGPA1_2 886 gcaaaagaagagtaagttatagcggggcctgcaatacttggaaggttgt
ggtaccgtcacatatgccatattacggagcagaagtagtagtccttttt
ctagtactaacatcccgcacgtccttggttatgggtttcaataatatta
GPA1_YEAST 344 AMSEYDQMLFEDERVNRMHESIMLFDTLLNSKWFKDTPFILFLNKIDLF
AMSEYDQMLFEDERVNRMHESIMLFDTLLNSKWFKDTPFILFLNKIDLF
AMSEYDQMLFEDERVNRMHESIMLFDTLLNSKWFKDTPFILFLNKIDLF
SCGPA1_2 1033 gaagtgcattgggagaaacgtaactgattatattagactatttaaagtt
ctgaaaatttaaagtagtaacttttacttacagtaacctttttaatatt
agtaccgggtgtaagcagtaaagatcgagctggcatagttgtatattgc
GPA1_YEAST 393 EEKVKSMPIRKYFPDYQGRVGDAEAGLKYFEKIFLSLNKTNKPIYVKRT
EEKVKSMPIRKYFPDYQGRVGDAEAGLKYFEKIFLSLNKTNKPIYVKRT
EEKVKSMPIRKYFPDYQGRVGDAEAGLKYFEKIFLSLNKTNKPIYVKRT
SCGPA1_2 1180 ggagaaacaaattcgtcgcgggggggcattgaattataaaaacatgaca
aaatagtctgaatcaaaggtgacacgtaataatttgtaacaactatagc
gagaacgcaagctttcgatcctaagtaattggatgcgtgacaaccgaac
GPA1_YEAST 442 CATDTQTMKFVLSAVTDLIIQQNLKKIGII
CATDTQTMKFVLSAVTDLIIQQNLKKIGII
CATDTQTMKFVLSAVTDLIIQQNLKKIGII
SCGPA1_2 1327 tgagacaaatgtaggagcaaccacaaagaa
gccacactatttgctcatttaaataatgtt
ctctcatggcagtacctaccgactaattta
//
cmbi.kun.nl), 24-May-2005