PSIBLAST alignment of GI: 254780142 and protein with PDB id: 1l9u

gi|21466006|pdb|1L9U|D Chain D, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 1524
>gi|21466012|pdb|1L9U|M Chain M, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 1524
 Score =  700 bits (1806), Expect = 0.0,   Method: Composition-based stats.
 Identities = 391/984 (39%), Positives = 541/984 (54%), Gaps = 76/984 (7%)

Query: 177  QFIAMMGADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNP 236
               A MGA+AI ELL  LDL+ L   L +++ K  S  RR K  KRL++V +F+ SGN P
Sbjct: 451  DIDARMGAEAIQELLKELDLEKLERELLEEM-KHPSRARRAKARKRLEVVRAFLDSGNRP 509

Query: 237  GWMIIRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRN 296
             WMI+  +PVLPPDLRP+V +D GRFA SDLNDLYRR+I RNNRL +L +  APEIIIRN
Sbjct: 510  EWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRN 569

Query: 297  EKRMLQESVDALFDNGRHKRVVTGAN-RRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRS 355
            EKRMLQE+VDA+ DNGR    VT     RPL+SL+D+L GKQGRFR NLLGKRVDYSGRS
Sbjct: 570  EKRMLQEAVDAVIDNGRRGSPVTNPGSERPLRSLTDILSGKQGRFRQNLLGKRVDYSGRS 629

Query: 356  VIVAGPELQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQAKKFVEKER---PEVWD 412
            VIV GP+L+LHQCGLPK MALELFKPFL  ++E+K +   VK A++ +E++R    EVWD
Sbjct: 630  VIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKAFAPNVKAARRMLERQRDIKDEVWD 689

Query: 413  VLAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYA 472
             L EV+H  VVLLNRAP+LHRL +QAF+P ++ G++IQLHPLVC  +NADFDGDQMAV+ 
Sbjct: 690  ALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHV 749

Query: 473  VISPEAQLEARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADM 532
             +S  AQ EAR+ MLS +NLL PASG P+  PS+D++LGL Y++ V +   G GM FA  
Sbjct: 750  PLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGMAFATP 809

Query: 533  GEVYHALENKIVTLHSKIRGRYKSV----------------------------DKDGNSI 564
             E   A E   V L++ I    +                                    +
Sbjct: 810  EEALAAYERGEVALNAPIVVAGRETSVGRLKFVFANPDEALLAVAHGLLDLQDVVTVRYL 869

Query: 565  SKIYDTTPGRMIIGEIL---PRHHEISFDIC--NQEMIKKNISAMVDTIYRHCGQKSTVA 619
             +  +T+PGR++   I+       +++ ++   +    K ++  +V   +   G + T  
Sbjct: 870  GRRLETSPGRILFARIVGEAVGDEKVAQELIQMDVPQEKNSLKDLVYQAFLRLGMEKTAR 929

Query: 620  FCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKMVKEYENQYNDGLITRGEKY 679
              D L   GF  + +SGI+ G DD ++PE K++ + EAD+ +++ E  Y  G +T  E+Y
Sbjct: 930  LLDALKYYGFTLSTTSGITIGIDDAVIPEEKQRYLEEADRKLRQIEQAYEMGFLTDRERY 989

Query: 680  NKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIFMMSHSGARGSIHQMRQLGG 739
            ++V+ LW +TT+KVT+ +                   N +++M+ SGARG+  Q+RQL G
Sbjct: 990  DQVIQLWTETTEKVTQAVFKNF---------EENYPFNPLYVMAQSGARGNPQQIRQLCG 1040

Query: 740  MRGLIAKPSGEIIESPIRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVD 799
            MRGL+ KPSGE  E P+RS F+ GL   E+F S  G RKG  D  +RTA SGYL+R+LVD
Sbjct: 1041 MRGLMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVD 1100

Query: 800  VAQNCVVNQVDCNTKKGLTITHIVDSGQVVYSLGSR--------VLGRTALDDIINPLTN 851
            VA   VV + DC T        +    +V  +L  R        + GR    ++      
Sbjct: 1101 VAHEIVVREADCGTTN-YISVPLFQMDEVTRTLRLRKRSDIESGLYGRVLAREV--EALG 1157

Query: 852  ECIVKAGQLILESHVNEIEKC---GIRSVRIRSALTCESSRGVCVLCYGRDLARGSLVNV 908
              + +   L LE     I+      +R V +RS LTC++  GVC  CYG DL+    V++
Sbjct: 1158 RRLEEGRYLSLEDVHFLIKAAEAGEVREVPVRSPLTCQTRYGVCQKCYGYDLSMARPVSI 1217

Query: 909  GEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNRNVCRNSTND 968
            GEAVGV+AA+SIGEPGTQLTMRTFH GG     D         G+ ++      R     
Sbjct: 1218 GEAVGVVAAESIGEPGTQLTMRTFHTGGVAVGTD------ITQGLPRVIELFEARRPKAK 1271

Query: 969  LISMGRNTTLQILDMSGQ---------EQYSHRIMYGAKLFVDDGGVIECGQRISEWDPH 1019
             +    +  ++I +   +             +++   A+L V DG  +E GQ ++     
Sbjct: 1272 AVISEIDGVVRIEEGEDRLSVFVESEGFSKEYKLPKDARLLVKDGDYVEAGQPLTRGAID 1331

Query: 1020 TFPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDEN 1079
               ++           LVD I  +          K   I  R   +   +          
Sbjct: 1332 PHQLLEAKGPEAVERYLVDEIQKVYRAQGVKLHDKHIEIVVRQMLKYVEVTDPGDSRLLE 1391

Query: 1080 GVVLKSARGTDARWFLPVDALLSV 1103
            G VL+          L  +  + V
Sbjct: 1392 GQVLEKWDVEALNERLIAEGKVPV 1415