PSIBLAST alignment of GI: 254780142 and protein with PDB id: 1iw7

gi|21730340|pdb|1IW7|D Chain D, Crystal Structure Of The Rna Polymerase Holoenzyme From Thermus Thermophilus At 2.6a Resolution Length = 1524
>gi|21730346|pdb|1IW7|N Chain N, Crystal Structure Of The Rna Polymerase Holoenzyme From Thermus Thermophilus At 2.6a Resolution Length = 1524
 Score =  708 bits (1828), Expect = 0.0,   Method: Composition-based stats.
 Identities = 387/985 (39%), Positives = 542/985 (55%), Gaps = 78/985 (7%)

Query: 177  QFIAMMGADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNP 236
               A MGA+AI +LL  LDL+ L   L +++ K  S  RR K  KRL++V +F+ SGN P
Sbjct: 451  DIDARMGAEAIQQLLKELDLEALEKELLEEM-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+VDAL DNGR    VT     RPL+SL+D+L GKQGRFR NLLGKRVDYSGRS
Sbjct: 570  EKRMLQEAVDALLDNGRRGAPVTNPGSDRPLRSLTDILSGKQGRFRQNLLGKRVDYSGRS 629

Query: 356  VIVAGPELQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQAKKFVEKER---PEVWD 412
            VIV GP+L+LHQCGLPK MALELFKPFL  ++E+KG    VK A++ +E++R    EVWD
Sbjct: 630  VIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKGIAPNVKAARRMLERQRDIKDEVWD 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 G+ FA  
Sbjct: 750  PLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGLEFATP 809

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

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

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

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

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

Query: 800  VAQNCVVNQVDCNTKKGLTITHIVDSGQVVYSLGSR--------VLGRTALDDIINPLTN 851
            V    VV + DC T        +    +V  SL  R        + GR    ++      
Sbjct: 1101 VTHEIVVREADCGTTN-YISVPLFQPDEVTRSLRLRKRADIEAGLYGRVLAREV---EVL 1156

Query: 852  ECIVKAGQLILESHVNEIEKCGI----RSVRIRSALTCESSRGVCVLCYGRDLARGSLVN 907
               ++ G+ +    V+ + K       + V +RS LTC++  GVC  CYG DL+    V+
Sbjct: 1157 GVRLEEGRYLSMDDVHLLIKAAEAGEIQEVPVRSPLTCQTRYGVCQKCYGYDLSMARPVS 1216

Query: 908  VGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNRNVCRNSTN 967
            +GEAVG++AAQSIGEPGTQLTMRTFH GG     D         G+ ++      R    
Sbjct: 1217 IGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAGAAD------ITQGLPRVIELFEARRPKA 1270

Query: 968  DLISMGRNTTLQILDMSGQ---------EQYSHRIMYGAKLFVDDGGVIECGQRISEWDP 1018
              +    +  ++I +   +             +++   A+L V DG  +E GQ ++    
Sbjct: 1271 KAVISEIDGVVRIEETEEKLSVFVESEGFSKEYKLPKEARLLVKDGDYVEAGQPLTRGAI 1330

Query: 1019 HTFPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDE 1078
                ++           LV+ I  +          K   I  R   +   +         
Sbjct: 1331 DPHQLLEAKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDSRLL 1390

Query: 1079 NGVVLKSARGTDARWFLPVDALLSV 1103
             G VL+          L  +    V
Sbjct: 1391 EGQVLEKWDVEALNERLIAEGKTPV 1415