HHsearch alignment for GI: 254780431 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=95.77  E-value=0.015  Score=38.42  Aligned_cols=33  Identities=33%  Similarity=0.585  Sum_probs=30.7

Q ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHH
Q ss_conf             7789999999999818658899999678543466
Q gi|254780431|r    3 WTVERIDKLKKFWSEGLSASQIAVQLGGVTRNAV   36 (178)
Q Consensus         3 WTderve~LkkLW~eG~SasqIA~~lGgvtRNAV   36 (178)
T Consensus         6 lt~~q~~~ar~l~~~G~~~~~iA~~~G-Vsr~Ti   38 (42)
T cd00569           6 LTPEQIEEARRLLAAGESVAEIARRLG-VSRSTL   38 (42)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHC-CCHHHH
T ss_conf             999999999999997898999999979-799999