PSIBLAST alignment of GI: 254780142 and protein with PDB id: 1i6v

>gi|14278484|pdb|1I6V|D Chain D, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex Length = 1264
 Score =  965 bits (2494), Expect = 0.0,   Method: Composition-based stats.
 Identities = 484/1172 (41%), Positives = 659/1172 (56%), Gaps = 103/1172 (8%)

Query: 16   RGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGK 75
            +    VRI++ASP KI S SYGE++KPETINYRT KPERDGLF  RIFGPIKDYEC CGK
Sbjct: 3    KEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGK 62

Query: 76   YKRMKYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSLRD 135
            YKR +++  +CE+C VEVT S VRR RMAHI+LA+P AH WF+K +PS+I+TLL +S  +
Sbjct: 63   YKRQRFEAKVCERCAVEVTRSIVRRYRMAHIELATPAAHIWFVKDVPSKIATLLDLSATE 122

Query: 136  VERVLYFESYVVVDPGLSSL-----EKYQILTEEEYVEAVSQFGQDQ------------- 177
            +E+VLYF  Y+V+DP  + L     EK Q+LT+                           
Sbjct: 123  LEQVLYFNKYIVLDPKAAVLDAVPVEKRQLLTDXXXXXXXXXXXXXXXXXXXXXXXXXXX 182

Query: 178  ---------FIAMMGADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDS 228
                       A MGA+AI ELL  LDL+ L   L +++ K  S  RR K  KRL++V +
Sbjct: 183  XXXXXXXXXIDARMGAEAIQELLKELDLEKLERELLEEM-KHPSRARRAKARKRLEVVRA 241

Query: 229  FITSGNNPGWMIIRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLH 288
            F+ SGN P WMI+  +PVLPPDLRP+V +D GRFA SDLNDLYRR+I RNNRL +L +  
Sbjct: 242  FLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQG 301

Query: 289  APEIIIRNEKRMLQESVDALFDNGRHKRVVTGAN-RRPLKSLSDMLKGKQGRFRTNLLGK 347
            APEIIIRNEKRMLQE+VDA+ DNGR    VT     RPL+SL+D+L GKQGRFR NLLGK
Sbjct: 302  APEIIIRNEKRMLQEAVDAVIDNGRRGSPVTNPGSERPLRSLTDILSGKQGRFRQNLLGK 361

Query: 348  RVDYSGRSVIVAGPELQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQAKKFVEKER 407
            RVDYSGRSVIV GP+L+LHQCGLPK MALELFKPFL  ++E+K +   VK A++ +E++R
Sbjct: 362  RVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKAFAPNVKAARRMLERQR 421

Query: 408  ---PEVWDVLAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFD 464
                EVWD L EV+H  VVLLNRAP+LHRL +QAF+P ++ G++IQLHPLVC  +NADFD
Sbjct: 422  DIKDEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFD 481

Query: 465  GDQMAVYAVISPEAQLEARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCYLSTVHEGDPG 524
            GDQMAV+  +S  AQ EAR+ MLS +NLL PASG P+  PS+D++LGL Y++ V +   G
Sbjct: 482  GDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKG 541

Query: 525  EGMLFADMGEVYHALENKIVTLHSKIRGRYKSV--------------------------- 557
             GM FA   E   A E   V L++ I    +                             
Sbjct: 542  AGMAFATPEEALAAYERGEVALNAPIVVAGRETSVGRLKFVFANPDEALLAVAHGLLDLQ 601

Query: 558  -DKDGNSISKIYDTTPGRMIIGEIL---PRHHEISFDIC--NQEMIKKNISAMVDTIYRH 611
                   + +  +T+PGR++   I+       +++ ++   +    K ++  +V   +  
Sbjct: 602  DTVTTRYLGRRLETSPGRILFARIVGEAVGDEKVAQELIQMDVPQEKNSLKDLVYQAFLR 661

Query: 612  CGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKMVKEYENQYNDG 671
             G + T    D L   GF  + +SGI+ G DD ++PE K++ + EAD+ +++ E  Y  G
Sbjct: 662  LGMEKTARLLDALKYYGFTLSTTSGITIGIDDAVIPEEKQRYLEEADRKLRQIEQAYEMG 721

Query: 672  LITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIFMMSHSGARGSI 731
             +T  E+Y++V+ LW +TT+KVT+ +                   N +++M+ SGARG+ 
Sbjct: 722  FLTDRERYDQVIQLWTETTEKVTQAVFNNF---------EENYPFNPLYVMAQSGARGNP 772

Query: 732  HQMRQLGGMRGLIAKPSGEIIESPIRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSG 791
             Q+RQL GMRGL+ KPSGE  E P+RS F+ GL   E+F S  G RKG  D  +RTA SG
Sbjct: 773  QQIRQLCGMRGLMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSG 832

Query: 792  YLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVYSLGSR--------VLGRTALD 843
            YL+R+LVDVA   VV + DC T        +    +V  +L  R        + GR    
Sbjct: 833  YLTRKLVDVAHEIVVREADCGTTN-YISVPLFQMDEVTRTLRLRKRSDIESGLYGRVLAR 891

Query: 844  DIINPLTNECIVKAGQLILESHVNEIEKC---GIRSVRIRSALTCESSRGVCVLCYGRDL 900
            ++        + +   L LE     I+      +R V +RS LTC++  GVC  CYG DL
Sbjct: 892  EV--EALGRRLEEGRYLSLEDVHFLIKAAEAGEVREVPVRSPLTCQTRYGVCQKCYGYDL 949

Query: 901  ARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNRN 960
            +    V++GEAVGV+AA+SIGEPGTQLTMRTFH GG     D         G+ ++    
Sbjct: 950  SMARPVSIGEAVGVVAAESIGEPGTQLTMRTFHTGGVAVGTD------ITQGLPRVIELF 1003

Query: 961  VCRNSTNDLISMGRNTTLQILDMSGQ---------EQYSHRIMYGAKLFVDDGGVIECGQ 1011
              R      +    +  ++I +   +             +++   A+L V DG  +E GQ
Sbjct: 1004 EARRPKAKAVISEIDGVVRIEEGEDRLSVFVESEGFSKEYKLPKDARLLVKDGDYVEAGQ 1063

Query: 1012 RISEWDPHTFPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKP 1071
             ++        ++           LVD I  +          K   I  R   +   +  
Sbjct: 1064 PLTRGAIDPHQLLEAKGPEAVERYLVDEIQKVYRAQGVKLHDKHIEIVVRQMLKYVEVTD 1123

Query: 1072 AIVVTDENGVVLKSARGTDARWFLPVDALLSV 1103
                    G VL+          L  +  + V
Sbjct: 1124 PGDSRLLEGQVLEKWDVEALNERLIAEGKVPV 1155