>pdb|1I6V|D Chain D, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
          Length = 1264

 Score =  862 bits (2227), Expect = 0.0
 Identities = 476/993 (47%), Positives = 643/993 (63%), Gaps = 88/993 (8%)

Query: 1394 KDFSSFQLTLASPEKIHSWSYGEVKKPETINYRTLKPERDGLFCMKIFGPTKDYECLCGK 1453
            K+    ++ LASPEKI SWSYGEV+KPETINYRTLKPERDGLF  +IFGP KDYEC CGK
Sbjct: 3    KEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGK 62

Query: 1454 YKKPRFKDIGTCEKCGVAITHSKVRRFRMGHIELATPVAHIWYVNSLPSRIGTLLGVKMK 1513
            YK+ RF +   CE+C V +T S VRR+RM HIELATP AHIW+V  +PS+I TLL +   
Sbjct: 63   YKRQRF-EAKVCERCAVEVTRSIVRRYRMAHIELATPAAHIWFVKDVPSKIATLLDLSAT 121

Query: 1514 DLERVLYYEAYIVKEPGEAAYDNEGTKLVMKYDILNEEQYQNISRRYEDRGFV------- 1566
            +LE+VLY+  YIV +P  A  D      V K  +L +                       
Sbjct: 122  ELEQVLYFNKYIVLDPKAAVLD---AVPVEKRQLLTDXXXXXXXXXXXXXXXXXXXXXXX 178

Query: 1567 ---------------AQMGGEAIKDLLEEIDLITLLQSLKEEVKDTNSDAKKKKLIKRLK 1611
                           A+MG EAI++LL+E+DL  L + L EE+K   S A++ K  KRL+
Sbjct: 179  XXXXXXXXXXXXXIDARMGAEAIQELLKELDLEKLERELLEEMKHP-SRARRAKARKRLE 237

Query: 1612 VVESFLNSGNRPEWMMLTVLPVLPPDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRL 1671
            VV +FL+SGNRPEWM+L  +PVLPPDLRP+V +DGG+FA SD+N+LYRR+INRN RLK+L
Sbjct: 238  VVRAFLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKL 297

Query: 1672 MELGAPEIIVRNEKRMLQEAVDVLFDNGRSTNAVKG-ANKRPLKSLSEIIKGKQGRFRQN 1730
            +  GAPEII+RNEKRMLQEAVD + DNGR  + V    ++RPL+SL++I+ GKQGRFRQN
Sbjct: 298  LAQGAPEIIIRNEKRMLQEAVDAVIDNGRRGSPVTNPGSERPLRSLTDILSGKQGRFRQN 357

Query: 1731 LLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPHLLSKLEERGYATTLKQAKRMI 1790
            LLGKRVD+SGRSVIVVGP LK+ +CGLPK MALELFKP LL K+EE+ +A  +K A+RM+
Sbjct: 358  LLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKAFAPNVKAARRML 417

Query: 1791 EQK---SNEVWECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFN 1847
            E++    +EVW+ L+E+  G  VLLNRAPTLH+  IQAF P L++G++IQLHPLVC AFN
Sbjct: 418  ERQRDIKDEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFN 477

Query: 1848 ADFDGDQMAVHVPLSQEAIAECKVLMLSSMNILLPASGKAVAIPSQDMVLGLYYLSLEKS 1907
            ADFDGDQMAVHVPLS  A AE ++ MLS+ N+L PASG+ +A PS+D++LGLYY++  + 
Sbjct: 478  ADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRK 537

Query: 1908 GVKGEHKLFSSVNEIITAIDTKELDIHAKIRVLDQ------------------------- 1942
              KG    F++  E + A +  E+ ++A I V  +                         
Sbjct: 538  EKKGAGMAFATPEEALAAYERGEVALNAPIVVAGRETSVGRLKFVFANPDEALLAVAHGL 597

Query: 1943 ------------GNIIATSAGRMIIKSILPDFIPTDLWNRPMKKKDI----GVLVDYVHK 1986
                        G  + TS GR++   I+ + +  +   + + + D+      L D V++
Sbjct: 598  LDLQDTVTTRYLGRRLETSPGRILFARIVGEAVGDEKVAQELIQMDVPQEKNSLKDLVYQ 657

Query: 1987 VG---GIGITATFLDNLKTLGFRYATKAGISISMEDIITPKDKQKMVEKAKVEVKKIQQQ 2043
                 G+  TA  LD LK  GF  +T +GI+I ++D + P++KQ+ +E+A  ++++I+Q 
Sbjct: 658  AFLRLGMEKTARLLDALKYYGFTLSTTSGITIGIDDAVIPEEKQRYLEEADRKLRQIEQA 717

Query: 2044 YDQGLLTDQERYNKIIDTWTEVNDKMSKEMMTAIAQDKEGFNSIYMMADSGARGSAAQIR 2103
            Y+ G LTD+ERY+++I  WTE  +K+++ +     ++   FN +Y+MA SGARG+  QIR
Sbjct: 718  YEMGFLTDRERYDQVIQLWTETTEKVTQAVFNNF-EENYPFNPLYVMAQSGARGNPQQIR 776

Query: 2104 QLSAMRGLMTKPDGSIIETPIISNFKEGLNVLEYFNSTHGARKGLADTALKTANAGYLTR 2163
            QL  MRGLM KP G   E P+ S+F+EGL VLEYF S+HGARKG ADTAL+TA++GYLTR
Sbjct: 777  QLCGMRGLMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTR 836

Query: 2164 KLIDVSQNVKVVSDDCGTHEGIEITDIAVGS-------ELIEPLEERIFGRVLLEDVIDP 2216
            KL+DV+  + V   DCGT   I +    +              +E  ++GRVL  +V + 
Sbjct: 837  KLVDVAHEIVVREADCGTTNYISVPLFQMDEVTRTLRLRKRSDIESGLYGRVLAREV-EA 895

Query: 2217 ITNEIL--LYADTLIDEEGAKKVVEAG-IKSITIRTPVTCKAPKGVCAKCYGLNLGEGKM 2273
            +   +    Y  +L D     K  EAG ++ + +R+P+TC+   GVC KCYG +L   + 
Sbjct: 896  LGRRLEEGRYL-SLEDVHFLIKAAEAGEVREVPVRSPLTCQTRYGVCQKCYGYDLSMARP 954

Query: 2274 SYPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTA 2306
               GEAVGVVAA+SIGEPGTQLT+RTFH GG A
Sbjct: 955  VSIGEAVGVVAAESIGEPGTQLTMRTFHTGGVA 987