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_HUMAN
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence HSPPARGB_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 1175.46 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=505 (x3=1515) and cDNA length=1434
PPAT_HUMAN 29 MTMVDTEMPFWPTNFGISSVDLSVMEDHSHSFDIKPFTTVDFSSISTPH
MTMVDTEMPFWPTNFGISSVDLSVMEDHSHSFDIKPFTTVDFSSISTPH
MTMVDTEMPFWPTNFGISSVDLSVMEDHSHSFDIKPFTTVDFSSISTPH
HSPPARGB_2 1 aaaggagacttcaatgaatggctgaggctcttgaactaaggttaatacc
tcttacatctgccatgtgctatcttaaacactatactcctatcgtccca
gcgtcaggacgccctgcccgtccagacccccttcgcctttcccctttat
PPAT_HUMAN 78 YEDIPFTRTDPVVADYKYDLKLQEYQSAIKVEPASPPYYSEKTQLYNKP
YEDIPFTRTDPVVADYKYDLKLQEYQSAIKVEPASPPYYSEKTQLYNKP
YEDIPFTRTDPVVADYKYDLKLQEYQSAIKVEPASPPYYSEKTQLYNKP
HSPPARGB_2 148 tggactaaagcggggtatgcaccgtcagaaggcgtcctttgaacctaac
aaatctcgcacttcaaaaatataaaagctatacccccaacaacataaac
cactacaaatagtatcgtcgatagcatacaggtatattttggtgcctgt
PPAT_HUMAN 127 HEEPSNSLMAIECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLIYDR
HEEPSNSLMAIECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLIYDR
HEEPSNSLMAIECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLIYDR
HSPPARGB_2 295 cggctatcagagtcgtggagtgtctggcgtggtagttcaaaatacatga
aaaccacttctaggtggaaccgtaagtacgaggagttggctgtattaag
tagtccccgatattctatattatctattttaacgtccgaacaggtctca
PPAT_HUMAN 176 CDLNCRIHKKSRNKCQYCRFQKCLAVGMSHNAIRFGRMPQAEKEKLLAE
CDLNCRIHKKSRNKCQYCRFQKCLAVGMSHNAIRFGRMPQAEKEKLLAE
CDLNCRIHKKSRNKCQYCRFQKCLAVGMSHNAIRFGRMPQAEKEKLLAE
HSPPARGB_2 442 tgcatcacaaaaaatcttctcatcgggatcagaatgcaccggagactgg
gataggtaaaggaagaaggtaagtctgtcaactgtggtcacaaaattca
tttctgccaatatatgctgtgactagggtttccgtgggagcgggggggg
PPAT_HUMAN 225 ISSDIDQLNPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKS
ISSDIDQLNPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKS
ISSDIDQLNPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKS
HSPPARGB_2 589 atagagccacgtggccgcgacttgttaattccaagagagatagaaagat
tcgataatacaccatgctcaataacatactctcacacgcttcgaccaac
ccttccggtagctccgcgaatgtcacagccggcaaggggcgaagaacaa
PPAT_HUMAN 274 PFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQ
PFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQ
PFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQ
HSPPARGB_2 736 ctgatgaattaagggaaatacaacccgcaagggacatcgtctctggggc
ctttaatactttgaaatataatcctaaagaatctgttaggatgctacta
actctcgtcaggaatacgcaccccggggcaggcccctgccgtccggtgg
PPAT_HUMAN 323 EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISE
EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISE
EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISE
HSPPARGB_2 883 gaagtgaaacgtgacgtagcgaccatggcgaataacgttaaagggcatg
atcaacagtcgttatataaatcttaagtaattacttccttaaagtttca
gcagtcacttttattcgccaatccataccgctcaggccggtatgtcacg
PPAT_HUMAN 372 GQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVII
GQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVII
GQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVII
HSPPARGB_2 1030 gcgtaaagtcaaccactggtagcatgtggatagcgtggagtgataggaa
gagttcgattagtgactgattacatatctatactataagatctttcttt
caccgaggtagcgagtttctggcgtgttggctagaatcccgaatttctt
PPAT_HUMAN 421 LSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTD
LSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTD
LSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTD
HSPPARGB_2 1177 caggccgtcagacaggacgacccgcgcccacaccgttcctgacccaaag
tggagcgttatactaataaattactatatataacaccattcattaatca
ctaccatggtggctactaccgaacggcggggcctgcaggtcggcgagac
PPAT_HUMAN 470 LRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY
LRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY
LRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY
HSPPARGB_2 1324 cacagagcgccccgaaaagagaaccccccgatagtt
tgattcaatattattaacacatgtacttaataaata
cagtcgacggagggcggggacgttcgcgggccgcgc
//
cmbi.kun.nl), 18-Feb-2005