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: PXR_RAT
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence AF151377_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 1078.20 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.
PXR_RAT 1 MRPEERWNHVGLVQREEADSVLEEPINVDEEDGGLQICRVCGDKANGYH
MRPEERWNHVGLVQREEADSVLEEPINVDEEDGGLQICRVCGDKANGYH
MRPEERWNHVGLVQREEADSVLEEPINVDEEDGGLQICRVCGDKANGYH
AF151377_2 1 aacggatacggcgccggggtgtggcaagggggggccatcgtggagagtc
tgcaaggaatgttagaacacttaactataaaaggtatggtggaacagaa
gatggggcttctaataaattcgagtccatgatattacctatgcgctctc
PXR_RAT 50 FNVMTCEGCKGFFRRAMKRNVRLRCPFRKGTCEITRKTRRQCQACRLRK
FNVMTCEGCKGFFRRAMKRNVRLRCPFRKGTCEITRKTRRQCQACRLRK
FNVMTCEGCKGFFRRAMKRNVRLRCPFRKGTCEITRKTRRQCQACRLRK
AF151377_2 148 tagaatggtagttaagaacagccatctcagatgaacaaccctcgtctca
tattcgaggagttggctagatgtggctgagcgatcgacggagacggtga
ctcgctaatgatcagcgactcgggccccggccgccggcaggcgcctgcg
PXR_RAT 99 CLESGMKKEMIMSDAAVEQRRALIKRKKREKIEAPPPGGQGLTEEQQAL
CLESGMKKEMIMSDAAVEQRRALIKRKKREKIEAPPPGGQGLTEEQQAL
CLESGMKKEMIMSDAAVEQRRALIKRKKREKIEAPPPGGQGLTEEQQAL
AF151377_2 295 tcgagaaagaaatgggggcacgtaaaaaagaaggcccggcgcaggccgc
gtaggtaaatttcacctaaggcttagaagaataccccggagtcaaaact
cggtcggaggcgttctgagggcgcgggggagtgtagtaggggaaagggg
PXR_RAT 148 IQELMDAQMQTFDTTFSHFKDFRLPAVFHSDCELPEVLQASLLEDPATW
IQELMDAQMQTFDTTFSHFKDFRLPAVFHSDCELPEVLQASLLEDPATW
IQELMDAQMQTFDTTFSHFKDFRLPAVFHSDCELPEVLQASLLEDPATW
AF151377_2 442 acgcaggcacatgaattctagtcccggtcagtgccggccgtctggcgat
taattacatactacctcataatgtccttagagatcattaccttaacccg
cggggctggactcatccccgtcgatggtctccgtggtggcaggactcag
PXR_RAT 197 SQIMKDSVPMKISVQLRGEDGSIWNYQPPSKSDGKEIIPLLPHLADVST
SQIMKDSVPMKISVQLRGEDGSIWNYQPPSKSDGKEIIPLLPHLADVST
SQIMKDSVPMKISVQLRGEDGSIWNYQPPSKSDGKEIIPLLPHLADVST
AF151377_2 589 acaaagagcaaatgcccggggaatatccctaaggagaaccccccgggta
gattaagtctatctatggaaggtgaaacccagagaattcttcatcatcc
tacgacttaggctgggcaaccccgccatccgccgagccccggcgctgac
PXR_RAT 246 YMFKGVINFAKVISHFRELPIEDQISLLKGATFEMCILRFNTMFDTETG
YMFKGVINFAKVISHFRELPIEDQISLLKGATFEMCILRFNTMFDTETG
YMFKGVINFAKVISHFRELPIEDQISLLKGATFEMCILRFNTMFDTETG
AF151377_2 736 tataggaatgagatctagccaggcatccaggatgatacataaatgagag
attagttatcattcatgatctaaatcttagcctatgttgtacttacacg
cgcgccccccacacccgggtcgcgccggggctcggccggccggccgaaa
PXR_RAT 295 TWECGRLAYCFEDPNGGFQKLLLDPLMKFHCMLKKLQLREEEYVLMQAI
TWECGRLAYCFEDPNGGFQKLLLDPLMKFHCMLKKLQLREEEYVLMQAI
TWECGRLAYCFEDPNGGFQKLLLDPLMKFHCMLKKLQLREEEYVLMQAI
AF151377_2 883 atgtgccgtttggcaggtcacccgctaatctacaaccccgggtgcacga
cgagggtcagtaacaggtaatttacttatagttaatatgaaaatttact
cggctggtcccacttcccggcggcgggacccggggaggtgggcggggcc
PXR_RAT 344 SLFSPDRPGVVQRSVVDQLQERFALTLKAYIECSRPYPAHRFLFLKIMA
SLFSPDRPGVVQRSVVDQLQERFALTLKAYIECSRPYPAHRFLFLKIMA
SLFSPDRPGVVQRSVVDQLQERFALTLKAYIECSRPYPAHRFLFLKIMA
AF151377_2 1030 tcttcgccgggccagggcccgctgcacagtagtacctcgcatctcaaag
cttccagcgttaggttaataagtctctacatagggcaccagttttattc
ccccatctcgtatcgacggggatcccggcccgttgcttacgcgcggcgt
PXR_RAT 393 VLTELRSINAQQTQQLLRIQDTHPFATPLMQELFSSTDG
VLTELRSINAQQTQQLLRIQDTHPFATPLMQELFSSTDG
VLTELRSINAQQTQQLLRIQDTHPFATPLMQELFSSTDG
AF151377_2 1177 gcagccaaagccacccccacgacctgaccacgttaaagg
ttcatggtacaacaattgtaacactcccttaattggcag
cccggctctcggcggagccgcgcctcatcgggacccgcc
//
cmbi.kun.nl), 18-Feb-2005