HHsearch alignment for GI: 254780444 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=94.28  E-value=0.11  Score=30.96  Aligned_cols=38  Identities=18%  Similarity=0.326  Sum_probs=30.3

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             7755899999999999964999889999828998798899
Q gi|254780444|r    2 TSFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKS   41 (223)
Q Consensus         2 ~~~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~   41 (223)
T Consensus         4 ~~lt~~q~~~a-r~l~-~~G~~~~~iA~~~GVsr~Tiyr~   41 (42)
T cd00569           4 PKLTPEQIEEA-RRLL-AAGESVAEIARRLGVSRSTLYRY   41 (42)
T ss_pred             CCCCHHHHHHH-HHHH-HCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             86999999999-9999-97898999999979799999865