HHsearch alignment for GI: 254780810 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=99.75 E-value=1.5e-18 Score=141.10 Aligned_cols=68 Identities=75% Similarity=1.269 Sum_probs=65.9
Q ss_pred EEEEEEEECCCCEEEEECCCCCCCCCCCCEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCCEEECC
Q ss_conf 99998540477026750454866665560460100001221259879998862468887630002222
Q gi|254780810|r 54 GEGVIEVLQDGFGFLRSPDANYLAGPDDIYVSPSQIKSFSLKTGDTVEGSIRAPREGERYFALLKVNA 121 (423)
Q Consensus 54 ~eGvLEIl~dGyGFLR~~~~~yl~~~~DiyVs~slir~f~Lr~GD~V~g~~r~~~~~~~~~~L~rV~~ 121 (423)
T Consensus 1 ~~GiLei~~dGyGFLR~~~~ny~~~~~DvyVs~~~Irrf~LR~GD~V~G~vR~p~~~Eky~al~~ves 68 (68)
T cd04459 1 GSGVLEILPDGFGFLRSSGYNYLPGPDDIYVSPSQIRRFNLRTGDTVVGQIRPPKEGERYFALLKVEA 68 (68)
T ss_pred CCEEEEECCCCCEEEECCCCCCCCCCCCEEECHHHHHHCCCCCCCEEEEEEECCCCCCCCCCEEEEEC
T ss_conf 96689974898289678987788998887899999977399889999997779998886410088619