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: NR2E1_XENLA
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence XLU67886_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 946.47 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.
NR2E1_XENLA 1 MSNPTGSTSRILDIPCKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNRS
MSNPTGSTSRILDIPCKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNRS
MSNPTGSTSRILDIPCKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNRS
XLU67886_2 1 aaacagtaacacgactagtggcatgactggtgtggttgttaaaaacaaa
tgaccgccggttatcgatggaggcgaaagtacgaggcgttaggtggagg
gccgcaaatgcgcaacaacatccatactagccttatagtcaaccagcac
NR2E1_XENLA 50 YVCKSGNQGGCPVDKTHRNQCRACRLKKCLEVNMNKDAVQHERGPRTST
YVCKSGNQGGCPVDKTHRNQCRACRLKKCLEVNMNKDAVQHERGPRTST
YVCKSGNQGGCPVDKTHRNQCRACRLKKCLEVNMNKDAVQHERGPRTST
XLU67886_2 148 tgtatgacggtcggaacaactcgtccaatcggaaaagggccgagcaata
atgacgaagggctaacagaaggcggtaagtatataaactaaaggcgccc
tccatatggttatcgtcgtgcagttggatgaccgtatttataaaaaacc
NR2E1_XENLA 99 IRKQVALYFRGHKEVNGSTQHFSSTALPTPTFFTTVRQLEAHNLELAAI
IRKQVALYFRGHKEVNGSTQHFSSTALPTPTFFTTVRQLEAHNLELAAI
IRKQVALYFRGHKEVNGSTQHFSSTALPTPTFFTTVRQLEAHNLELAAI
XLU67886_2 295 aaacggcttagcaggagaacctttagccacattaagactggcacgcgga
tgaatctatggaaataggcaatcccctccccttcctgatacaatatcct
agaagaactaacaagtacaactaaaaggcaccccttgagaactgggatc
NR2E1_XENLA 148 STVPERQTLVGLAQPTPKYPHEVNGAPLYLYEFATESVCESAARLLFMS
STVPERQTLVGLAQPTPKYPHEVNGAPLYLYEFATESVCESAARLLFMS
STVPERQTLVGLAQPTPKYPHEVNGAPLYLYEFATESVCESAARLLFMS
XLU67886_2 442 tagcgacatggcgccacatccggaggcctctgtgagtgtgtggccctaa
cctcagacttgtcacccaacaatagcctataatccactgacccgttttg
cacaaaacaaagagacagcttagtactgtgtgcctgactaataatatgc
NR2E1_XENLA 197 IKWAKSVPAFSTLSLQDQLMLLEDAWRELFVLGIAQWAIPVDASTLLAV
IKWAKSVPAFSTLSLQDQLMLLEDAWRELFVLGIAQWAIPVDASTLLAV
IKWAKSVPAFSTLSLQDQLMLLEDAWRELFVLGIAQWAIPVDASTLLAV
XLU67886_2 589 aatgaagcgttactccgccaccgggtagctgcgagctgacgggaaccgg
tagcagtcctcctctaaattttaacggattttgtcagctctacgcttct
tggagtatactagaaacgggtagcggaggttcaaaaggcatttcaagta
NR2E1_XENLA 246 SGMNNENTESPKLNKIISEIQALQDVVSRFRQLRLDATEFACLKCIVTF
SGMNNENTESPKLNKIISEIQALQDVVSRFRQLRLDATEFACLKCIVTF
SGMNNENTESPKLNKIISEIQALQDVVSRFRQLRLDATEFACLKCIVTF
XLU67886_2 736 tgaaagaagtcacaaaatgacgtcgggtatcccccggagtgtcatagat
cgtaaaacaccataattcatactaattcgtgatgtaccatcgtagttct
tagctgcaataggtgccggcgtaatgttatagtgacatatttcactctt
NR2E1_XENLA 295 KAGVSTHSGSELRNFRNAAAISALQDEAQLTLNSYIHTRYPTQPCRFGK
KAGVSTHSGSELRNFRNAAAISALQDEAQLTLNSYIHTRYPTQPCRFGK
KAGVSTHSGSELRNFRNAAAISALQDEAQLTLNSYIHTRYPTQPCRFGK
XLU67886_2 883 agggtacagtgtaatcagggatgtcgggccacaatacaatcacctctga
acgtccaggcatgatgaccctcctaaacatctagatacgaccacggtga
gttgtatttaaagtcattttcacaacaagcaccccaccactaaatctaa
NR2E1_XENLA 344 LLLLLPALRSINPSTIEEVFFKKTIGNVPITRVLSDMYKSSDI
LLLLLPALRSINPSTIEEVFFKKTIGNVPITRVLSDMYKSSDI
LLLLLPALRSINPSTIEEVFFKKTIGNVPITRVLSDMYKSSDI
XLU67886_2 1030 cctcccgtctaactaagggttaaaagagcaacgctgatataga
tttttcctgctaccctaatttaactgatctcgttcataacgat
cagcgaaaccactagaagttcgaatgttaaagatatgcagtcc
//
cmbi.kun.nl), 18-Feb-2005