HHsearch alignment for GI: 254780916 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=91.88  E-value=0.26  Score=28.85  Aligned_cols=28  Identities=43%  Similarity=0.662  Sum_probs=23.1

Q ss_conf             9999828727899978489988999999
Q gi|254780916|r  445 LAMKLYRAQMSEVARRLGIGRSTLYRKI  472 (482)
Q Consensus       445 ~aL~~~~Gn~~~aA~~LGIsR~tL~rKl  472 (482)
T Consensus        15 r~l~~~G~~~~~iA~~~GVsr~Tiyr~l   42 (42)
T cd00569          15 RRLLAAGESVAEIARRLGVSRSTLYRYL   42 (42)
T ss_conf             9999978989999999797999998659