>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=99.01 E-value=9e-10 Score=98.15 Aligned_cols=68 Identities=40% Similarity=0.671 Sum_probs=60.3 Q ss_pred CEEEEEEEEEEECCEEEECCCCCCEEEEEEECCCCCC-----------CCHHHHCCCCCEEEEEEEEECC------CCCE Q ss_conf 6789999999415369982879710488663144454-----------7855603259889999997868------9986 Q gi|254780784|r 621 KIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERV-----------AKTSDVVKEGDTVWVKLLDFDD------RGKI 683 (699) Q Consensus 621 ~~y~~~v~~i~~fGafve~~~g~~gl~HiS~l~~~~v-----------~~~~d~~~~Gd~i~vk~~~~d~------~g~i 683 (699) T Consensus 1 Ev~eG~Vs~Vt~fG~FV~L~-~ieGLvHiS~l~dD~~~fd~~~~~liG~r~~~~~~~GD~V~vrV~~V~~~~r~i~~~~I 79 (99) T cd04460 1 EVVEGEVVEVVDFGAFVRIG-PVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKI 79 (99) T ss_pred CEEEEEEEEEEECCEEEEEC-CCEEEEEHHHCCCCEEEECHHHCEEEECCCCCEECCCCEEEEEEEEEECCCCCCCCCEE T ss_conf 97999999588256699932-81068993675784399812446898512786984799999999998062067676466 Q ss_pred EEEEEE Q ss_conf 668730 Q gi|254780784|r 684 KLSMKV 689 (699) Q Consensus 684 ~lSrk~ 689 (699) T Consensus 80 gLtmrq 85 (99) T cd04460 80 GLTMRQ 85 (99) T ss_pred EECCCC T ss_conf 502247

HHsearch alignment for GI: 254780784 and conserved domain: cd04460