version: 3.0
Alfin-like HMM
Sequence AAA20093 was used as a seed for a PSI BLAST search. The sequences aligning over the full length after the 4th iteration were kept, and aligned using ClustalX. The DNA-binding domain, similar to PHD, was extracted and an HMM was built.
CLUSTAL W(1.4) multiple sequence alignment gi|50924564|ref CGACGEAYANGEFWICCDICETWFHGKCVRITPAKAEHIKHYKCPGC gi|50909575|ref CGACGETYANGEFWICCDVCEKWFHGKCVRITPAKAEHIKQYKCPGC gi|34907474|ref CGTCGTNDGKDEFWICCDNCEKWYHGKCVKITPARAEHIKQYKCPDC gi|4091080|gb|A CGTCGTNDGKDEFWICCDNCEKWYHGKCVKITPARAEHIKQYKCPDC gi|4884860|gb|A CGTCGTNDGKDEFWICCDNCEKWYHGKCVKITPARAEHIKQYKCPDC gi|53982665|gb| CGSCGTNDGKDEFWICCDSCERWYHGKCVKITPARAEHIKHYKCPDC gi|14192880|gb| CGACGESYGADEFWICCDICEKWFHGKCVKITPAKAEHIKQYKCPSC gi|50939155|ref CGACGESYGADEFWICCDICEKWFHGKCVKITPAKAEHIKQYKCPSC gi|15239624|ref CGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSC gi|3319341|gb|A CGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSC gi|15229157|ref CGACGDSDGADEFWICCDLCEKWFHGKCVKITPARAEHIKQYKCPSC gi|75214624|gb| CGACGDSDGADEFWICCDLCEKWFHGKCVKITPARAEHIKQYKCPSC gi|57222198|gb| CGACGDNYASDEFWICCDMCEKWFHGECVKITPARAEHIKHYKCPTC gi|92892978|gb| CGACGDSNGADEFWICCDICEKWFHGKCVKITPARAEHIKQYKCPSC gi|21593407|gb| CGACGDNYGTDEFWICCDACEKWFHGKCVKITPAKAEHIKHYKCPTC gi|15226967|ref CGACGDNYGTDEFWICCDACEKWFHGKCVKITPAKAEHIKHYKCPTC gi|15223786|ref CGACGDNYGGDEFWICCDACEKWFHGKCVKITPAKAEHIKHYKCPSC gi|7262694|gb|A CGACGDNYGGDEFWICCDACEKWFHGKCVKITPAKAEHIKHYKCPSC gi|12651665|gb| CGACGDNYGTDEFWICCDMCEKWFHGKCVKITPAKAEHIKQYKCPGC gi|63028790|gb| CGACGDNYATDEFWICCDICERWFHGKCVKITPAKAEHIKQYKCPSC gi|29124114|gb| CGTCGGLYNANEFWIGCDICERWFHGKCVRITPAKAEHIKHYKCPDC gi|50919441|ref CGTCGGLYNANEFWIGCDICERWFHGKCVRITPAKAEHIKHYKCPDC gi|34900462|ref CGTCGGRYNANEFWIGCDICERWFHGKCVRITPAKAEHIKHYKCPDC gi|50932231|ref CGTCGGIYSADEFWIGCDVCERWYHGKCVKITPAKAESIKQYKCPSC gi|15239180|ref CGSCGGNYTNDEFWICCDVCERWYHGKCVKITPAKAESIKQYKCPSC gi|15229696|ref CGSCGGHYTNEEFWICCDVCERWYHGKCVKITPAKAESIKQYKCPPC gi|45387429|gb| CGSCGTNGNEDEFWIGCDMCEKWYHGKCVKITPAKAQSIKEYRCPSC