CLUSTAL W multiple sequence alignment

KPYK1_ECOLI_        ATGAAAAAGACCAAAATTGTTTGCACCATCGGACCGAAAACCGAATCTGAAGAGATGTTA
Pyr_kin_Y.pestis    ATGAAAAAGACTAAAATTGTTTGTACTATCGGTCCAAAAACCGAATCCGAAGAAATGCTG

KPYK1_ECOLI_        GCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTAT
Pyr_kin_Y.pestis    ACAAACCTGCTGAATGCTGGCATGAACGTTATGCGTTTAAACTTCTCTCACGGTGACTAT

KPYK1_ECOLI_        GCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGTAAAACC
Pyr_kin_Y.pestis    GCAGAGCACGGTCAACGTATCAAAAACCTCCGGGCTGTAATGGCAAAAACAGGCAAAAAA

KPYK1_ECOLI_        GCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGT
Pyr_kin_Y.pestis    GCCGCGATTTTGCTGGATACTAAAGGCCCTGAAATCCGGACCATGAAACTGGAAGGCGGC

KPYK1_ECOLI_        AACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATC
Pyr_kin_Y.pestis    AAAGATGCTGCGCTGGTTGCAGGTCAGACCTTCACGTTCACGACTGATCAAAGCGTTGTC

KPYK1_ECOLI_        GGCAACAGCGAAATGGTTGCGGTAACGTATGAAGGTTTCACTACTGACCTGTCTGTTGGC
Pyr_kin_Y.pestis    GGTAACGACAAAATTGTTGCAGTCACCTACCCAGGCTTCGCCGCTGACCTGAAAATTGGT

KPYK1_ECOLI_        AACACCGTACTGGTTGACGATGGTCTGATCGGTATGGAAGTTACCGCCATTGAAGGTAAC
Pyr_kin_Y.pestis    AACACTGTTCTGGTTGACGATGGCTTGATCGGTATGGAAGTCATTGAAGTCACTGAACAC

KPYK1_ECOLI_        AAAGTTATCTGTAAAGTGCTGAACAACGGTGACCTGGGCGAAAACAAAGGTGTGAACCTG
Pyr_kin_Y.pestis    ACCGTTGTCTGTAAAGTCTTGAACAGTGGTGATTTGGGTGAAAACAAAGGCGTTAACCTG

KPYK1_ECOLI_        CCTGGCGTTTCCATTGCTCTGCCAGCACTGGCTGAAAAAGACAAACAGGACCTGATCTTT
Pyr_kin_Y.pestis    CCAGGCGTGTCGATCCAACTGCCCGCATTAGCAGAAAAAGATAAAGGCGACCTGATCTTC

KPYK1_ECOLI_        GGTTGCGAACAAGGCGTAGACTTTGTTGCTGCTTCCTTTATTCGTAAGCGTTCTGACGTT
Pyr_kin_Y.pestis    GGTTGCGAACAAGGCGTTGATTTCGTTGCCGCCTCCTTTATCCGTAAACGTTCTGATGTA

KPYK1_ECOLI_        ATCGAAATCCGTGAGCACCTGAAAGCGCACGGCGGCGAAAACATCCACATCATCTCCAAA
Pyr_kin_Y.pestis    CTGGAAATTCGTGAACACCTGAAAGCACACGGTGGCGAACATATCCAGATCATCTCTAAA

KPYK1_ECOLI_        ATCGAAAACCAGGAAGGCCTCAACAACTTCGACGAAATCCTCGAAGCCTCTGACGGCATC
Pyr_kin_Y.pestis    ATCGAAAATCAGGAAGGTCTGAATAACTTCGACGAAATCCTGGAAGCCTCTGACGGTATC

KPYK1_ECOLI_        ATGGTTGCGCGTGGCGACCTGGGTGTAGAAATCCCGGTAGAAGAAGTTATCTTCGCCCAG
Pyr_kin_Y.pestis    ATGGTTGCCCGTGGTGACTTAGGTGTTGAGATCCCTGTCGAAGAAGTCATCTTCGCGCAG

KPYK1_ECOLI_        AAGATGATGATCGAAAAATGTATCCGTGCACGTAAAGTCGTTATCACTGCGACCCAGATG
Pyr_kin_Y.pestis    AAGATGATGATCGAGAAATGTAACCGCGCACGTAAAGTTGTTATTACTGCAACTCAAATG

KPYK1_ECOLI_        CTGGATTCCATGATCAAAAACCCACGCCCGACTCGCGCAGAAGCCGGTGACGTTGCAAAC
Pyr_kin_Y.pestis    CTCGATTCCATGATCAAAAACCCACGTCCTACCCGCGCAGAAGCCGGTGACGTTGCAAAC

KPYK1_ECOLI_        GCCATCCTCGACGGTACTGACGCAGTGATGCTGTCTGGTGAATCCGCAAAAGGTAAATAC
Pyr_kin_Y.pestis    GCCATCCTTGACGGTACCGACGCGGTCATGCTGTCCGGCGAAAGTGCTAAGGGTAAGTAC

KPYK1_ECOLI_        CCGCTGGAAGCGGTTTCTATCATGGCGACCATCTGCGAACGTACCGACCGCGTGATGAAC
Pyr_kin_Y.pestis    CCATTAGAGTCTGTCACCATCATGGCGACCATCTGTGAGCGTACAGACCGTGTTATGCCT

KPYK1_ECOLI_        AGCCGTCTCGAGTTCAACAATGACAACCGTAAACTGCGCATTACCGAAGCGGTATGCCGT
Pyr_kin_Y.pestis    AGCCGCATTGAGTCACTGAACGACAACCGTAAAATGCGAATCACTGAAGCCGTTTGCCGT

KPYK1_ECOLI_        GGTGCCGTTGAAACTGCTGAAAAACTGGATGCTCCGCTGATCGTGGTTGCTACTCAGGGC
Pyr_kin_Y.pestis    GGTGCTGTTGAAACCGCAGAAAAACTGGAAGCCAAAGTGATTGTGGTCGCAACCGGGGGG

KPYK1_ECOLI_        GGTAAATCTGCTCGCGCAGTACGTAAATACTTCCCGGATGCCACCATCCTGGCACTGACC
Pyr_kin_Y.pestis    GGTAAATCTGCAAAATCTGTCCGTAAATACTTCCCTACTGCGACCATTCTGGCACTGACG

KPYK1_ECOLI_        ACCAACGAAAAAACGGCTCATCAGTTGGTACTGAGCAAAGGCGTTGTGCCGCAGCTTGTT
Pyr_kin_Y.pestis    ACCAATGAAATGACAGCCCATCAGTTAATTCTGACTAAAGGCGTAATCACTCAGTTGGTA

KPYK1_ECOLI_        AAAGAGATCACTTCTACTGATGATTTCTACCGTCTGGGTAAAGAACTGGCTCTGCAGAGC
Pyr_kin_Y.pestis    GACGAAATCGCCTCAACCGATGATTTCTACCGTCTCGGTAAAGAAGCGGCTCTGGCGAGC

KPYK1_ECOLI_        GGTCTGGCACACAAAGGTGACGTTGTAGTTATGGTTTCTGGTGCACTGGTACCGAGCGGC
Pyr_kin_Y.pestis    GGCCTGGCACAGAAAGGCGACGTGGTCATCATGGTTTCAGGTGCCTTGGTACCAAGCGGT

KPYK1_ECOLI_        ACTACTAACACCGCATCTGTTCACGTCCTG
Pyr_kin_Y.pestis    ACGACCAATACCTCTTCAGTACACGTGTTA






Synonymous (KS) and non-synonymous (KA) substitution rates calcualted by codeml in the PAML package:
	KS = 1.4145
	KA = 0.0890
	KA/KS = 0.0629
You can see the parameters used in codeml to calculate these values.
If you use these values, please cite the following peper:
	

    * Goldman, N. and Yang, Z. 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Molecular Biology and Evolution 11:725-736.