HHsearch alignment for GI: 254780694 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=96.06  E-value=0.014  Score=35.45  Aligned_cols=40  Identities=33%  Similarity=0.487  Sum_probs=33.8

Q ss_pred             CCCCCCHHH-HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             888889779-9999999859997999999499988999999
Q gi|254780694|r  182 KDFELTGRE-VECLTWISEGKTSDEIAVILGISRNTVNNYI  221 (246)
Q Consensus       182 ~~~~LT~RE-~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl  221 (246)
T Consensus         2 R~~~lt~~q~~~ar~l~~~G~~~~~iA~~~GVsr~Tiyr~l   42 (42)
T cd00569           2 RPPKLTPEQIEEARRLLAAGESVAEIARRLGVSRSTLYRYL   42 (42)
T ss_pred             CCCCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHC
T ss_conf             89869999999999999978989999999797999998659