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