HHsearch alignment for GI: 254780611 and conserved domain: pfam04542
>pfam04542 Sigma70_r2 Sigma-70 region 2. Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation.
Probab=99.11 E-value=2.4e-10 Score=88.69 Aligned_cols=70 Identities=36% Similarity=0.576 Sum_probs=66.0
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 9994307787565555799998889999998889989862185345689997577899999985320246
Q gi|254780611|r 53 LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122 (302)
Q Consensus 53 Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~ 122 (302)
T Consensus 1 L~~~y~~~l~~~~~~~~~~~~~aeDl~Qe~f~~~~~~~~~~~~~~~~~f~~wl~~i~~n~~~d~~Rk~~r 70 (71)
T pfam04542 1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLLRAVERFDPERGVSFSTWLYTIIRNAIIDALRKQRR 70 (71)
T ss_pred CHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 9998999999999988398602999999999999999875796136609989999999999999997399