Table 3 of Nickerson, Mol Vis 2006; 12:1565-1585.


Table 3. Percent identities and scores comparing Repeat 1 protein orthologs and paralogs

A: Data suggest that the zebrafish and fugu IRBP loci as a pair of orthologs (Z1-F1 and Z2-F2) diverged more recently than Gene 1 and Gene 2 paralogs (Z1-Z2 and F1-F2). The paralogs Z1-F2 and Z2-F1 are consistent with the paralogs Z1-Z2 and F1-F2, in percent identity and score, suggesting that there has been no recent gene conversion. The greater conservation of the orthologs than the paralogs suggests that the divergence of Gene 1 from Gene 2 was an early event in teleost evolution, as the divergence of fugu and zebrafish was in the moderate to distant past in the history of the teleosts. B: Pairwise comparisons between the indicated two versions of Repeat 1 were conducted using BL2SEQ at the Biology Workbench (San Diego Supercomputer Center). The percent identity is indicated in the lower left half of each table. The raw bit score is indicated in the upper left right of the table.

A. Orthologs and paralogs compared in zebrafish and fugu

                                          Repeat 1 gene and species
                               ------------------------------------------
 Repeat 1 gene and species      Z1       Z2       F1     F2    HR1
----------------------------   ----   --------   ----   ----   ----

zfish Gene 1 Repeat 1 (Z1)     ---    337        392    343    326


zfish Gene 2 Repeat 1 (Z2)     52%    ---        302    416    289

                                                                   score
fugu Gene 1 Repeat 1 (F1)      59%    48%        ---    306    312 (bits)


fugu Gene 2 Repeat 1 (F2)      52%    63%        49%    ---    297


human Repeat 1 (HR1)           53%    42%        51%    47%    ---
                                      percent
                                      identity



B. Repeat 1 orthologs compared among teleost fish


                                          Repeat 1 gene and species
                                --------------------------------------------------------
 Repeat 1 gene and species     Z2R1     F2R1      MR1   TR1     GR1    SR1    HR1
----------------------------   ----   --------   ----   ----   -----   ----   ----

zfish Gene 2 Repeat 1 (Z2R1)   --     416        384    406    543     402    289


fugu Gene 2 Repeat 1 (Z2R1)    63%    --         488    565    408     515    179

                                                                                  score
Medaka Repeat 1 (MR1)          59%    74%        --     488    379     491    295 (bits)


Tetraodon Repeat 1 (TR1)       63%    89%        75%    --     379     508    298


Goldfish Repeat 1   (GR1)      86%    62%        59%    61%    --      400    281


Stickleback Repeat 1 (SR1)     61%    79%        76%    78%    61%     --     295


Human Repeat 1 (HR1)           42%    47%        45%    47%    42%     46%    --
                                      percent
                                      identity

Nickerson, Mol Vis 2006; 12:1565-1585 <http://www.molvis.org/molvis/v12/a180/>
©2006 Molecular Vision <http://www.molvis.org/molvis/>
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