HHsearch alignment for GI: 254780913 and conserved domain: cd04459
>cd04459 Rho_CSD Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA are released from DNA template by an mRNA stem loop structure, which resembles the transcription termination mechanism used by eukaryotic pol III. The second mechanism is mediated by Rho factor. Rho factor terminates transcription by using energy from ATP hydrolysis to forcibly dissociate the transcripts from RNA polymerase. Rho protein contains an N-terminal S1-like domain, which binds single-stranded RNA. Rho has a C-terminal ATPase domain which hydrolyzes ATP to provide energy to strip RNA polymerase and mRNA from the DNA template. Rho functions as a homohexamer.
Probab=95.71 E-value=0.013 Score=35.44 Aligned_cols=52 Identities=23% Similarity=0.433 Sum_probs=36.5
Q ss_pred CCCEEEEEECCC--CCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCC
Q ss_conf 887465885488--7788379999500023588446899889999998699971110
Q gi|254780913|r 13 DKGYGFITPEGS--TESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSA 67 (78)
Q Consensus 13 ~kGfGFI~~d~~--~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A 67 (78)
T Consensus 9 ~dGyGFLR~~~~ny~~~~~DvyVs~~~Irrf~---LR~GD~V~G~vR~p~~~Eky~a 62 (68)
T cd04459 9 PDGFGFLRSSGYNYLPGPDDIYVSPSQIRRFN---LRTGDTVVGQIRPPKEGERYFA 62 (68)
T ss_pred CCCCEEEECCCCCCCCCCCCEEECHHHHHHCC---CCCCCEEEEEEECCCCCCCCCC
T ss_conf 89828967898778899888789999997739---9889999997779998886410