sequence alignment of constans-like proteins to understand the similarity of epcol and arabidopsis...
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Sequence Alignment of CONSTANS-Like Proteins
To understand the similarity of EpCOL and Arabidopsis CO and COL amino acid sequences, these protein sequences are performed the alignment. In Group I, two B-box domains (B-box I and B-box II) and CCT domain are focus. The EpCOL1 in Group V and the EpCOL11 in Group I both have truncated B-box I domain. The similarity between the EpCOL5 and AtCO in B-box I domain is 55.81%. In B-box II domain, the similarity between the EpCOL and AtCO is 53.49% (EpCOL1), 69.77% (EpCOL5), and 58.14% (EpCOL11). In CCT domain, the identity between AtCO and EpCOL5 is 88.37% (EpCOL5) and 86.05% (EpCOL11), however only 20.93% identity in EpCOL1(Supplemental file 6A). In AtCOL proteins, there are four domains (M1 to M4) also identified in Group I. However, M1 and M2 is not found in EpCOL5 and EpCOL11. The identity between EpCOL5 and AtCO in M3 domain is 50%. The M4 domain can be identified in EpCOL5 and EpCOL11. The identify is 72.73% (EpCOL5 vs. AtCOL4) and 45.45% (EpCOL11 vs. AtCO; Supplemental file 6A).
In Group II, we are focus on the B-box I domain and Group B-box II domain which has one more diverged zinc finger domain. Base on the result of the phylogenetic analysis, this group can be divided to two: AtCOL9 to AtCOL11 and AtCOL13 to AtCOL15 (Supplemental file 6B). EpCOL6 and EpCOL8 is first subgroup. EpCOL3, 4, 10 is the second subgroup. The sequence alignment result is correlated to the phylogenetic analysis, the proteins which belong to same subgroup have higher identity.In B-box I, the identity of EpCOL3 between the Group II AtCOL is 58.14% (AtCOL13) to 65.12% (AtCOL14). The identity of EpCOL4 between Group II AtCOL is 53.49% (AtCOL13) to 62.79% (AtCOL14). EpCOL10 is 55.81% (AtCOL14) to 62.79% (AtCOL13). EpCOL6 is 81.40% (AtCOL9) and EpCOL8 is 86.05% (AtCOL10).In Group II B-box II domain, identifies of EpCOL3, EpCOL4, and EpCOL5 are lower (25.81% to 41.86%).
There is only one B-box I domain in Group III,, the identity of EpCOL7 and EpCOL12 to AtCOL6/ AtCOL16 are between 79.07% to 72.09% (Supplemental file 6C). However, the identity of EpCOL7 and EpCOL12 to AtCOL6/ AtCOL16 are between 97.67% to 95.35% in CCT domain (Supplemental file 6C).
B-box I
B-box II
M1 M2
M3
M4 CCT
aGroup I and V – B-box domain
B-box I
B-box II
CCT
Group II– B-box domain
Group II–CCT domain
b
B-box I
CCT
Group III and unclassification – B-box domain
Group III –CCT domain
c