>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.

Probab=99.24 E-value=3.6e-11 Score=84.96 Aligned_cols=68 Identities=26% Similarity=0.407 Sum_probs=30.3 Q ss_pred EEEEEEEEEECCEEEEEECCCCCEEEEEEHHHCCHHHH-----------CCCHHHCCCCCEEEEEEEEECCCCC-----E Q ss_conf 79999999708908999617798499999747182121-----------0420110689879999999705768-----6 Q gi|254780456|r 461 VVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRV-----------DQDPGRFSKGQIVDACVVNVSKKDG-----K 524 (576) Q Consensus 461 iv~g~V~~v~~~G~~V~l~~~~gv~G~i~~s~is~~~~-----------~~~~~~~~vG~~v~~~Vi~id~~~~-----r 524 (576) T Consensus 2 v~eG~Vs~Vt~fG~FV~L~---~ieGLvHiS~l~dD~~~fd~~~~~liG~r~~~~~~~GD~V~vrV~~V~~~~r~i~~~~ 78 (99) T cd04460 2 VVEGEVVEVVDFGAFVRIG---PVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESK 78 (99) T ss_pred EEEEEEEEEEECCEEEEEC---CCEEEEEHHHCCCCEEEECHHHCEEEECCCCCEECCCCEEEEEEEEEECCCCCCCCCE T ss_conf 7999999588256699932---8106899367578439981244689851278698479999999999806206767646 Q ss_pred EEEEEHH Q ss_conf 9987036 Q gi|254780456|r 525 VSLSIKA 531 (576) Q Consensus 525 i~LS~k~ 531 (576) T Consensus 79 IgLtmrq 85 (99) T cd04460 79 IGLTMRQ 85 (99) T ss_pred EEECCCC T ss_conf 6502247

HHsearch alignment for GI: 254780456 and conserved domain: cd04460