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=100.00 E-value=0 Score=690.53 Aligned_cols=434 Identities=28% Similarity=0.386 Sum_probs=269.1
Q ss_pred CCCHHHHHHCCCCCCHHHHCCCCCCCCCCEEEEHHHHHHCCCEEEEECCCCCCCCEEEEEEECCEEEEEECCCCCCCCCH
Q ss_conf 88898976405761032210121015674011015423014327751388766651211100884886500010122114
Q gi|254780142|r 763 GLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVYSLGSRVLGRTAL 842 (1398)
Q Consensus 763 GL~p~EfFfhamgGReGLiDTAvKTA~SGYlqRrLvk~~eDl~V~~~D~~t~~g~~~~~~~~~~~~~~~l~~~~~~r~~~ 842 (1398)
T Consensus 1 GL~p~EfFfh~m~gReGLiDTAvKTa~SGYlqRrLvk~ledl~V~yD~tvr~~~g~ivqf~yG~Dg~d~~~~~~~~~~~~ 80 (447)
T pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAETGYLQRRLVKALEDLVVQYDDTVRNSGGEIVQFLYGEDGLDPLKIEGQGRFTI 80 (447)
T ss_pred CCCHHHHHHCCCHHCCHHHHCCHHHHHHHHHHHHHHHHHCEEEEEECCCCCCCCEEEEEEEECCCCEECCEEEEECCEEE
T ss_conf 96878998768401233876731565554689998887174799945982389906999898885665126896264356
Q ss_pred HHCCCCC--------CCCEEEECCCCCCHHHHHHHHHCCCCEEECCCCCCHHHHHCCCHHHHHHHCCCCCEECHHHCCCC
Q ss_conf 4201778--------97188517865789999999975984020233100035518657887542017852000101460
Q gi|254780142|r 843 DDIINPL--------TNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDLARGSLVNVGEAVGV 914 (1398)
Q Consensus 843 ~di~~~~--------~~~~i~~~~~~i~~~~~~~i~~~~i~~v~irs~lt~~~~~~v~~~cy~~~l~~~~lv~pGe~VG~ 914 (1398)
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~slv~pGEaVGi 160 (447)
T pfam04998 81 EDSDLKLEKKFKIDLNDVLLLLSEFSLSTLLFEILLRSGIESKRVRSELTCNSKAGVCFLCYGRDKYRRSLVEPGEAVGI 160 (447)
T ss_pred EECCCCCCCCEEECCCCCEEECCCHHHHHHHHHHHHHHCCCEEEEEEEEECCCHHHHHHHHHHHHHHHHCCCCCCCCHHH
T ss_conf 76257223747745998554002214558899999972767378865530261889999999987542132478741102
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCEEEEEEEEE-EECCCCCEEEEECCCCEEEEECCCCEEEEEEC
Q ss_conf 21111007889877642024543222112202401487689721134-65178877897427604664067760000001
Q gi|254780142|r 915 IAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNRNV-CRNSTNDLISMGRNTTLQILDMSGQEQYSHRI 993 (1398)
Q Consensus 915 iAAQSIGEP~TQmTLnTFHfAGVAS~~~~~~iknvTlGVPRlkEi~~-~~n~~~~~i~vs~~~~~~i~d~~~~~~~~~ki 993 (1398)
T Consensus 161 IAAQSIGEP~TQmTLnTFH~AGvas~-------nvT~GvPRl~Eil~~~~~~~tp~~~~~~~~~~------~~~~~~~~~ 227 (447)
T pfam04998 161 IAAQSIGEPGTQMTLNTFHFAGVASK-------NVTLGVPRLKEIINVAKNNKKPVITVLLIKNI------VSDKARVKK 227 (447)
T ss_pred HHHCCCCCCHHHHHHHHHHHCCCCCC-------CCCCCCEEEEEEEEEEEECCEEEEECCCCEEE------ECCCCEEEE
T ss_conf 33202467035564776543331012-------33226349985249996154357853785444------323450687
Q ss_pred CCHHCCCCCCCCEEECCEEEEECCCCCCEEEECCCCEEEEEEECCCCEEHHHHHCCCCCEEEEEEEHHHCCCCCCCCCCE
Q ss_conf 10000135678553225078621354311320246368975312783200123023686026775101101221238534
Q gi|254780142|r 994 MYGAKLFVDDGGVIECGQRISEWDPHTFPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAI 1073 (1398)
Q Consensus 994 ~~~~~~~v~~~~~v~~~~ii~~~Dp~~~~i~~e~~~~v~~~~~~~~~~~~~~~~~~t~~~~~~~i~~~~~~~~~~~~~~~ 1073 (1398)
T Consensus 228 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~------------~~~~~~~~ 290 (447)
T pfam04998 228 QREEKTLLLLKKVTIIIVIYYDDDSESTVIKKDRIWVLAYFVIPEEVA-----EEVALAI------------IIIGKRKS 290 (447)
T ss_pred EECCCEEEEEEEECEEEEEEECCCCEEEECCEEEEECCCCCCCCHHHH-----CHHHHHH------------HCCCEEEE
T ss_conf 722674999998330589997589656623300133331266531221-----2123344------------15616530
Q ss_pred EEECCCC-CEEECCCCCCCEEECCCCCEEEECCCCCCCCCCEEEECHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCEECC
Q ss_conf 7742778-253224788420213778445413676135484222101320245543367732889887525111101113
Q gi|254780142|r 1074 VVTDENG-VVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFEARRPKNHAILAE 1152 (1398)
Q Consensus 1074 ~i~d~~~-~~~~~~~~~~~~~~~~~~~~~~v~~~~~v~~~d~l~~~~~~~~k~~DIt~GLPrV~eLFEar~pk~~aiise 1152 (1398)
T Consensus 291 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------------------------------ 334 (447)
T pfam04998 291 RKRKKNNLGVAKDEKGLEEEELLLLNKILLVIPGIKVKYGVILT------------------------------------ 334 (447)
T ss_pred EEECCCEEEEEECCCCCHHHHCCCCCCHHEECCCCEEEECCCCC------------------------------------
T ss_conf 68336407998537751112125212102001386897223256------------------------------------
Q ss_pred CCCEEEE-EEECCCCEEEEEEECCCCCCEEEEEECCCCEEEEECCCEEECCCEEECCCCCHHHHHHHHCHHHHHHHHHHH
Q ss_conf 4786786-331279449999836898402689813896589841987740864643899999998752799999999999
Q gi|254780142|r 1153 ISGTIRI-KRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDILRIKGVEALASYLINE 1231 (1398)
Q Consensus 1153 i~Giv~i-~~~~~~k~~~vi~~~~~g~~~~e~~ip~~~~l~v~dgd~V~~gd~lt~Gsid~~eIl~vlGIEAAR~~Ii~E 1231 (1398)
T Consensus 335 -~~~~~~~~~~~~~~~~~~l~--t~G~nl~~v~~~~----gvid~~k~~--------sn~I~em~~~lGIEAAr~~i~~E 399 (447)
T pfam04998 335 -DGRVDPHTILEKLGKEWLLK--TEGNNLQAVMRLQ----GVIDNDKTY--------SNDIREMLKKLGIEAARDSILLE 399 (447)
T ss_pred -CCCCCCHHHHCCCCCEEEEE--EEHHHHHHHHHCC----CCCCCCCEE--------EEEHHHHHHHEEEEECCCCHHHH
T ss_conf -57776213201368376664--4058999999728----935478168--------98299665225999885121353
Q ss_pred HHHHHHHHCCEECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEECHHHHHHCC
Q ss_conf 99999980970061256012476286148941886454566410699999999999972898752012100001453023
Q gi|254780142|r 1232 VQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQT 1311 (1398)
Q Consensus 1232 Iq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~~~~~Nr~~~~~g~~pa~~~p~llGITKasl~t 1311 (1398)
T Consensus 400 ~~~V~~~~g~~vn~RHl~llaD~MT~~G~l~----------------------------------------gitR~Gl~~ 439 (447)
T pfam04998 400 IRNVFKFDGIYVNRRHLALLADLMTFKGELL----------------------------------------GITRAGLNR 439 (447)
T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCEECCEEE----------------------------------------EECHHHHCC
T ss_conf 8999988778876999985897462356176----------------------------------------330645166
Q ss_pred --CCHHHH
Q ss_conf --107765
Q gi|254780142|r 1312 --KSFISA 1317 (1398)
Q Consensus 1312 --~S~Ls~ 1317 (1398)
T Consensus 440 ~~~s~l~~ 447 (447)
T pfam04998 440 EKSSFILM 447 (447)
T ss_pred CCCCCCCC
T ss_conf 99886157