HHsearch alignment for GI: 254781217 and conserved domain: cd00569

>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=96.76  E-value=0.0014  Score=44.53  Aligned_cols=40  Identities=20%  Similarity=0.355  Sum_probs=37.8

Q ss_pred             CHHCCHHHHHHHHHHHHCCHHHHHHHHCCCCCHHHHHHHH
Q ss_conf             1242999999999997489579999721799978999999
Q gi|254781217|r    3 AHKYTKERIDNILASFSGGLSLSQSCKKHGVTVVSFHGWV   42 (162)
Q Consensus         3 ~~Kyt~el~d~Ic~~Ia~G~SLr~Ick~~gmp~~Tv~~Wl   42 (162)
T Consensus         3 ~~~lt~~q~~~ar~l~~~G~~~~~iA~~~GVsr~Tiyr~l   42 (42)
T cd00569           3 PPKLTPEQIEEARRLLAAGESVAEIARRLGVSRSTLYRYL   42 (42)
T ss_pred             CCCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHC
T ss_conf             9869999999999999978989999999797999998659