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