>pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
           Promoter Dna Complex At 6.5 A Resolution
          Length = 438

 Score =  258 bits (658), Expect = 2e-69
 Identities = 139/311 (44%), Positives = 214/311 (68%), Gaps = 8/311 (2%)

Query: 365 KILANITNMTKEDIIAQVPEATMVSVYMDLKKLFLTKEASEEGFDLAPNKLKEILEQIKR 424
           K L+  T + +E +I +V  A ++      K   L ++   +  +    KLK + +++KR
Sbjct: 129 KKLSEATGLDQE-LIREVVRAKILGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKR 187

Query: 425 GKLIS---DRAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKG 481
              I+   + A+  + ++NLRLVVSIAK++T RGL FLDLIQEGN GL++AV+KFE+++ 
Sbjct: 188 YLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRR 247

Query: 482 FKFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINRINKVMRKHIQENGKEPDLEVVA 541
           FKFSTYATWWI+QAI+RAIADQARTIRIP+HM++TIN++++  R+  QE G+EP  E +A
Sbjct: 248 FKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIA 307

Query: 542 EEVGLSLD--KVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIMREDLKA 599
           E +G   D  +V+  +K+ +EP+SLETP+G++ D  +GDF+ D+N+ S ++   +  L  
Sbjct: 308 EAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDENLPSPVEAAAQSLLSE 367

Query: 600 QIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR-S 658
           ++E  L +L+ERE  V+++R GL+D   + TLEE+G    VTRER+RQIE+ A++KL+  
Sbjct: 368 ELEKALSKLSEREAMVLKLRKGLIDGR-EHTLEEVGAYFGVTRERIRQIENKALRKLKYH 426

Query: 659 PQYGRILRNYL 669
               R LR++L
Sbjct: 427 ESRTRKLRDFL 437