HHsearch alignment for GI: 254780142 and conserved domain: pfam04998
>pfam04998 RNA_pol_Rpb1_5 RNA polymerase Rpb1, domain 5. RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound.
Probab=98.98 E-value=2.6e-10 Score=95.50 Aligned_cols=120 Identities=29% Similarity=0.286 Sum_probs=110.6
Q ss_pred CEEEEEECCCCEEEEECCCEEECCCEEECCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCE
Q ss_conf 02689813896589841987740864643899999998752799999999999999999809700612560124762861
Q gi|254780142|r 1179 EPAEYFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQK 1258 (1398)
Q Consensus 1179 ~~~e~~ip~~~~l~v~dgd~V~~gd~lt~Gsid~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~k 1258 (1398)
T Consensus 307 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~t~G~nl~~v~~~~gvid~~k~~sn~I~em~~~ 386 (447)
T pfam04998 307 LEEEELLLLNKILLVIPGIKVKYGVILTDGRVDPHTILEKLGKEWLLKTEGNNLQAVMRLQGVIDNDKTYSNDIREMLKK 386 (447)
T ss_pred CHHHHCCCCCCHHEECCCCEEEECCCCCCCCCCCHHHHCCCCCEEEEEEEHHHHHHHHHCCCCCCCCCEEEEEHHHHHHH
T ss_conf 11121252121020013868972232565777621320136837666440589999997289354781689829966522
Q ss_pred EEEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEE
Q ss_conf 4894188645456641069999999999997289875201
Q gi|254780142|r 1259 VEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFS 1298 (1398)
Q Consensus 1259 g~I~~~Gdt~~i~g~~Inr~~~~~~Nr~~~~~g~~pa~~~ 1298 (1398)
T Consensus 387 lGIEAAr~~i~~E~~~V~~~~g~~vn~RHl~llaD~MT~~ 426 (447)
T pfam04998 387 LGIEAARDSILLEIRNVFKFDGIYVNRRHLALLADLMTFK 426 (447)
T ss_pred EEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEC
T ss_conf 5999885121353899998877887699998589746235