BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= psy7582
(661 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3H0G|B Chain B, Rna Polymerase Ii From Schizosaccharomyces Pombe
pdb|3H0G|N Chain N, Rna Polymerase Ii From Schizosaccharomyces Pombe
Length = 1210
Score = 736 bits (1901), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 375/685 (54%), Positives = 471/685 (68%), Gaps = 61/685 (8%)
Query: 1 LWQEACWIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSTEVET 60
L QE CW VI+++F+E L RQQL SFDEF+Q ++Q IV+D + L AQHT + +
Sbjct: 12 LTQEDCWTVISSFFEETSLARQQLFSFDEFVQNTMQEIVDDDSTLTLDQYAQHTGAQGDV 71
Query: 61 PPRYLLKFEQIYLSKPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGEEPV 120
RY + F QIYLS+PT E DGS + M P EARLRNLTYS+PLYVD+ K V+ + V
Sbjct: 72 TRRYEINFGQIYLSRPTMTEADGSTTTMFPQEARLRNLTYSSPLYVDMRKKVMVAADSNV 131
Query: 121 ------------TTQHQKSFIGKIPIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIIN 168
+ K FIGKIPIMLRST+C+LNG++D +L +LNECP D GGYFIIN
Sbjct: 132 PIGEEEWLVEEEDEEPSKVFIGKIPIMLRSTFCILNGVSDSELYDLNECPYDQGGYFIIN 191
Query: 169 GSEKVLIAQEKMATNTVYVFS-MKDSKYAYKTEIRSCLEHSSRPTSTLWVNMMARGGQSL 227
GSEKV+IAQE+ A N V VF S AY EIRS LE SR S++ + +MAR ++
Sbjct: 192 GSEKVIIAQERSAANIVQVFKKAAPSPIAYVAEIRSALERGSRLISSMQIKLMARNTEN- 250
Query: 228 KKSAIGQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDE 287
GQ I A LPYI+ +IPI+IVFRALG V DRDILEHI YD +D +M+EM+KP ++E
Sbjct: 251 ----SGQTIRATLPYIRSDIPIVIVFRALGVVPDRDILEHICYDPNDFQMLEMMKPCIEE 306
Query: 288 AFVIQEQNVALNFIGARGARPGVTKERRIKYAREILQKEMLPHVGVSDFCETKKAYFLGY 347
AFVIQ++++AL++IG RG+ GVT+E+R++YA +ILQKE+LPH+ + ET+KA+FLGY
Sbjct: 307 AFVIQDKDIALDYIGKRGSTTGVTREKRLRYAHDILQKELLPHITTMEGFETRKAFFLGY 366
Query: 348 MVHRLLLASLGRRELDDRDHY--------------------------VRMYAQKFIDRGK 381
M+HR+LL +L RRE DDRDH+ V Y QK ++ +
Sbjct: 367 MIHRMLLCALERREPDDRDHFGKKRLDLAGPLLASLFRMLFRKMTRDVYKYMQKCVETNR 426
Query: 382 DFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASSLSHLRRVNS 441
+FNL LA+K+ IIT+GLRYSLATGNWGDQK++ R GVSQVLNR TFAS+LSHLRR N+
Sbjct: 427 EFNLTLAVKSNIITNGLRYSLATGNWGDQKRSMVNRVGVSQVLNRYTFASTLSHLRRTNT 486
Query: 442 PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEE 501
PIGRDGKLAKPRQLHNT WGM+CPAETPEG A GLVKNL+LM+Y+SVGS +PI+EFLEE
Sbjct: 487 PIGRDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSVGSPSAPIIEFLEE 546
Query: 502 WSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVSXXXXX 561
W +E LE+ PSA +ATK+FVNG W+G+HRDP L TLR LRR++D I +EVS
Sbjct: 547 WGLETLEDYNPSASPNATKVFVNGVWLGVHRDPAHLTETLRSLRRRLD-ISAEVSIVRDI 605
Query: 562 XXXXXXXHTDAGRICRPLLIAEN-------GSLLLKKRHIDNLKERDYNNY--------G 606
TDAGRICRPL I +N G L ++K HI L E D + Y G
Sbjct: 606 REKELRLFTDAGRICRPLFIVDNNPNSERRGELCIRKEHIQQLIE-DKDRYDIDPEQRFG 664
Query: 607 WQVLVQSGVVEYIDTLEEETTMIAM 631
W LV SG++EY+D EEET MIAM
Sbjct: 665 WTALVSSGLIEYLDAEEEETVMIAM 689
>pdb|1I3Q|B Chain B, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
pdb|1I50|B Chain B, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
pdb|1I6H|B Chain B, Rna Polymerase Ii Elongation Complex
pdb|1K83|B Chain B, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
With The Inhibitor Alpha Amanitin
pdb|1NIK|B Chain B, Wild Type Rna Polymerase Ii
pdb|1NT9|B Chain B, Complete 12-Subunit Rna Polymerase Ii
pdb|1PQV|B Chain B, Rna Polymerase Ii-Tfiis Complex
pdb|1R5U|B Chain B, Rna Polymerase Ii Tfiib Complex
pdb|1SFO|B Chain B, Rna Polymerase Ii Strand Separated Elongation Complex
pdb|1R9S|B Chain B, Rna Polymerase Ii Strand Separated Elongation Complex,
Matched Nucleotide
pdb|1R9T|B Chain B, Rna Polymerase Ii Strand Separated Elongation Complex,
Mismatched Nucleotide
pdb|1TWA|B Chain B, Rna Polymerase Ii Complexed With Atp
pdb|1TWC|B Chain B, Rna Polymerase Ii Complexed With Gtp
pdb|1TWF|B Chain B, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
pdb|1TWG|B Chain B, Rna Polymerase Ii Complexed With Ctp
pdb|1TWH|B Chain B, Rna Polymerase Ii Complexed With 2'datp
pdb|1WCM|B Chain B, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
pdb|1Y1W|B Chain B, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|B Chain B, Complete Rna Polymerase Ii Elongation Complex With
Substrate Analogue Gmpcpp
pdb|1Y1V|B Chain B, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|B Chain B, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|2B63|B Chain B, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2B8K|B Chain B, 12-Subunit Rna Polymerase Ii
pdb|2E2H|B Chain B, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With Gtp
pdb|2E2I|B Chain B, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dgtp
pdb|2E2J|B Chain B, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
Gmpcpp
pdb|2NVQ|B Chain B, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
2'dutp
pdb|2NVT|B Chain B, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Gmpcpp
pdb|2NVX|B Chain B, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dutp
pdb|2NVY|B Chain B, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
pdb|2NVZ|B Chain B, Rna Polymerase Ii Elongation Complex With Utp, Updated
112006
pdb|2JA5|B Chain B, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
A
pdb|2JA6|B Chain B, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
B
pdb|2JA7|B Chain B, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA7|N Chain N, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA8|B Chain B, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
D
pdb|2YU9|B Chain B, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Utp
pdb|2R7Z|B Chain B, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|B Chain B, Elongation Complex Of Rna Polymerase Ii With Artificial
Rdrp Scaffold
pdb|2R93|B Chain B, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|B Chain B, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3CQZ|B Chain B, Crystal Structure Of 10 Subunit Rna Polymerase Ii In
Complex With The Inhibitor Alpha-Amanitin
pdb|3FKI|B Chain B, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3GTG|B Chain B, Backtracked Rna Polymerase Ii Complex With 12mer Rna
pdb|3GTJ|B Chain B, Backtracked Rna Polymerase Ii Complex With 13mer Rna
pdb|3GTK|B Chain B, Backtracked Rna Polymerase Ii Complex With 18mer Rna
pdb|3GTL|B Chain B, Backtracked Rna Polymerase Ii Complex With 13mer With G<>u
Mismatch
pdb|3GTM|B Chain B, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
pdb|3GTO|B Chain B, Backtracked Rna Polymerase Ii Complex With 15mer Rna
pdb|3GTP|B Chain B, Backtracked Rna Polymerase Ii Complex With 24mer Rna
pdb|3GTQ|B Chain B, Backtracked Rna Polymerase Ii Complex Induced By Damage
pdb|3H3V|C Chain C, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|B Chain B, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOU|N Chain N, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOV|B Chain B, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3HOW|B Chain B, Complete Rna Polymerase Ii Elongation Complex Iii With A
T-U Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|B Chain B, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|B Chain B, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|B Chain B, Complete Rna Polymerase Ii Elongation Complex Iv With A
T-U Mismatch And A Frayed Rna 3'-Guanine
pdb|3I4M|B Chain B, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex D
pdb|3I4N|B Chain B, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex E
pdb|3K1F|B Chain B, Crystal Structure Of Rna Polymerase Ii In Complex With
Tfiib
pdb|3K7A|B Chain B, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
pdb|3M3Y|B Chain B, Rna Polymerase Ii Elongation Complex C
pdb|3M4O|B Chain B, Rna Polymerase Ii Elongation Complex B
pdb|3PO2|B Chain B, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|B Chain B, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3QT1|B Chain B, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
pdb|3RZD|B Chain B, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
pdb|3RZO|B Chain B, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
pdb|3S14|B Chain B, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
pdb|3S15|B Chain B, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
pdb|3S16|B Chain B, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
pdb|3S17|B Chain B, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
pdb|3S1M|B Chain B, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 1)
pdb|3S1N|B Chain B, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 2)
pdb|3S1Q|B Chain B, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Atp
pdb|3S1R|B Chain B, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Gtp
pdb|3S2D|B Chain B, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
Containing A 5br- U
pdb|3S2H|B Chain B, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
Containing A 2[prime]-Iodo Atp
pdb|3J0K|B Chain B, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
pdb|4A3C|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid
pdb|4A3B|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid
pdb|4A3D|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid
pdb|4A3E|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3F|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3J|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid And Soaked With Gmpcpp
pdb|4A3K|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid
pdb|4A3L|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3M|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3G|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid
pdb|4A3I|B Chain B, Rna Polymerase Ii Binary Complex With Dna
pdb|4A93|B Chain B, Rna Polymerase Ii Elongation Complex Containing A Cpd
Lesion
pdb|4BBR|B Chain B, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|B Chain B, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 1224
Score = 640 bits (1650), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 340/702 (48%), Positives = 446/702 (63%), Gaps = 69/702 (9%)
Query: 4 EACWIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSTEVETPPR 63
E W VI+A+F EKGLV QQLDSF++F+ ++Q I+ + + L+ AQHT+ +
Sbjct: 28 EDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHTTESDNISRK 87
Query: 64 YLLKFEQIYLSKPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGEEPV--- 120
Y + F +IY++KP E DG + P EARLRNLTYS+ L+VD+ K + P
Sbjct: 88 YEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEAIDVPGREL 147
Query: 121 -----------TTQHQKSFIGKIPIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIING 169
++ K FIG++PIMLRS C L+ T+ DL +L ECP D GGYFIING
Sbjct: 148 KYELIAEESEDDSESGKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIING 207
Query: 170 SEKVLIAQEKMATNTVYVFS-MKDSKYAYKTEIRSCLEHSSRPTSTLWVNMMARGGQSLK 228
SEKVLIAQE+ A N V VF S ++ EIRS LE SR STL V + R G S +
Sbjct: 208 SEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSAR 267
Query: 229 KSAIGQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEA 288
I A LPYIKQ+IPI+I+FRALG + D +ILEHI YD +D +M+EM+KP +++
Sbjct: 268 T------IKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDG 321
Query: 289 FVIQEQNVALNFIGARGARPGVTKERRIKYAREILQKEMLPHVGVSDFCETKKAYFLGYM 348
FVIQ++ AL+FIG RG G+ KE+RI+YA++ILQKE LPH+ + E++KA+FLGYM
Sbjct: 322 FVIQDRETALDFIGRRGTALGIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYM 381
Query: 349 VHRLLLASLGRRELDDRDHY--------------------------VRMYAQKFIDRGKD 382
++RLLL +L R++ DDRDH+ + Y Q+ ++ D
Sbjct: 382 INRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHD 441
Query: 383 FNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASSLSHLRRVNSP 442
FN++LAI K IT GL+Y+LATGNWG+QKKA +RAGVSQVLNR T++S+LSHLRR N+P
Sbjct: 442 FNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTP 501
Query: 443 IGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEW 502
IGRDGKLAKPRQLHNT WG++CPAETPEG A GLVKNL+LM+ ISVG+ P PI+ FL EW
Sbjct: 502 IGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEW 561
Query: 503 SMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVSXXXXXX 562
ME LE+ P DAT++FVNG W G+HR+P +LM TLR LRR+ DI EVS
Sbjct: 562 GMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDI-NPEVSMIRDIR 620
Query: 563 XXXXXXHTDAGRICRPLLIAENGSLL------LKKRHIDNLKERDYNNYGWQVLVQSGVV 616
TDAGR+ RPL I E+ L ++K HI L +Y + ++ G
Sbjct: 621 EKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQD------IEGG-- 672
Query: 617 EYIDTLEEETTMIAMWQVLVQSGVVEYIDTLEEETTMIAMSP 658
+ +EE T W L+ G+VEYID EEE+ +IAM P
Sbjct: 673 --FEDVEEYT-----WSSLLNEGLVEYIDAEEEESILIAMQP 707
>pdb|2WAQ|B Chain B, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|B Chain B, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|R Chain R, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2Y0S|B Chain B, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|R Chain R, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|B Chain B, Rnap At 3.2ang
pdb|4B1O|B Chain B, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|R Chain R, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 1131
Score = 351 bits (900), Expect = 7e-97, Method: Compositional matrix adjust.
Identities = 232/662 (35%), Positives = 349/662 (52%), Gaps = 81/662 (12%)
Query: 7 WIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSTEVETPPRYLL 66
W VI AYF KGLVRQ LDS+++F++ +Q I+++ +I TE+ P +
Sbjct: 14 WKVIEAYFKSKGLVRQHLDSYNDFVRNKLQEIIDEQGEI---------PTEI---PGLKV 61
Query: 67 KFEQIYLSKPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGEEPVTTQHQK 126
+ +I + KP E D + P EARLRNLTY+APL++ + E + + ++
Sbjct: 62 RLGKIRIGKPRVRESDRGEREISPMEARLRNLTYAAPLWLTMIPV-----ENNIEAEPEE 116
Query: 127 SFIGKIPIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVY 186
+IG +PIML+S ++ T L E+ E P DPGGYFI+NGSE+V++ QE +A N V
Sbjct: 117 VYIGDLPIMLKSAIDPISQYTLDKLIEIGEDPKDPGGYFIVNGSERVIVTQEDLAPNRVL 176
Query: 187 VFSMKDSKYAYKTEIRSCLEHSSRPTSTLWVNMMARGGQSLKKSAIGQRIIAILPYIKQE 246
V + K S + H+++ S+ + + LK P + +
Sbjct: 177 VDTGKTG---------SNITHTAKIISSTAGYRVPVTIERLKDGTFH----VSFPAVPGK 223
Query: 247 IPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGARGA 306
IP +I+ RALG + DRDI+ + D PE+ + PSL++A I + AL+FIG+R A
Sbjct: 224 IPFVILMRALGILTDRDIVYAVSLD---PEIQNELFPSLEQASSIANVDDALDFIGSRVA 280
Query: 307 RPGVTKERRIKYAREILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLASLGRRELDDRD 366
G +E RI+ A++I+ K LPH+G S KKAY+L Y + +++ LGRRE DD+D
Sbjct: 281 -IGQKRENRIEKAQQIIDKYFLPHLGTSADDRRKKAYYLAYAISKVIELYLGRREPDDKD 339
Query: 367 HYV---------------RMYAQKFID-----------RGKDFNLELAIKTKIITDGLRY 400
HY R+ + F+ RG+ L+ ++ I+T+ +R+
Sbjct: 340 HYANKRLRLAGDLFASLFRVAFKAFVKDLTYQLEKSKVRGRKLALKALVRPDIVTERIRH 399
Query: 401 SLATGNWGDQKKAHQARAGVSQVLNRLTFASSLSHLRRVNSPIGRDGKLAKPRQLHNTLW 460
+LATGNW R GVSQ+L+R + S LSHLRRV S + R + R LH T W
Sbjct: 400 ALATGNW------VGGRTGVSQLLDRTNWLSMLSHLRRVISSLARGQPNFEARDLHGTQW 453
Query: 461 GMICPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSAIADA-- 518
G +CP ETPEG GLVKNLALMA I+VG + + L E + +EE+
Sbjct: 454 GRMCPFETPEGPNSGLVKNLALMAQIAVGINEKIVEKTLYEMGVVPVEEVIRRVTEGGED 513
Query: 519 -------TKIFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVSXXXXXXXXXXXXHT- 570
+K+ +NG VG +RD E+L +R+ RR+ + I EV+ H
Sbjct: 514 QNEYLKWSKVILNGRLVGYYRDGEELAKKIRERRRKGE-ISDEVNVGHIVTDFINEVHVN 572
Query: 571 -DAGRICRPLLIAENGSLLLKKRHIDNLKERDYNNYGWQVLVQSGVVEYIDTLEEETTMI 629
D+GR+ RPL+I NG+ L+ + I+ L D + + LV+ G +EY+D EEE +
Sbjct: 573 CDSGRVRRPLIIVSNGNPLVTREDIEKL---DSGSITFDDLVRQGKIEYLDAEEEENAYV 629
Query: 630 AM 631
A+
Sbjct: 630 AL 631
>pdb|2PMZ|B Chain B, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|R Chain R, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|3HKZ|B Chain B, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
pdb|3HKZ|J Chain J, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Length = 1124
Score = 342 bits (876), Expect = 6e-94, Method: Compositional matrix adjust.
Identities = 227/662 (34%), Positives = 349/662 (52%), Gaps = 81/662 (12%)
Query: 7 WIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSTEVETPPRYLL 66
W VI AYF KGLVRQ LDS+++F++ +Q I+++ +I TE+ P +
Sbjct: 11 WRVIEAYFKSKGLVRQHLDSYNDFVRNKLQEIIDEQGEI---------PTEI---PGLKV 58
Query: 67 KFEQIYLSKPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGEEPVTTQHQK 126
+ +I + KP E D + P EARLRNLTY+APL++ + E + + ++
Sbjct: 59 RLGKIRIGKPRVRESDRGEREISPMEARLRNLTYAAPLWLTMIPV-----ENNIEAEPEE 113
Query: 127 SFIGKIPIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVY 186
+IG +PIML+S ++ T L E+ E P DPGGYFI+NGSE+V++ QE +A N V
Sbjct: 114 VYIGDLPIMLKSAIDPISQYTLDKLIEIGEDPKDPGGYFIVNGSERVIVTQEDLAPNRVL 173
Query: 187 VFSMKDSKYAYKTEIRSCLEHSSRPTSTLWVNMMARGGQSLKKSAIGQRIIAILPYIKQE 246
V + K S + H+++ S+ + + LK P + +
Sbjct: 174 VDTGKTG---------SNITHTAKIISSTAGYRVPVTIERLKDGTFH----VSFPAVPGK 220
Query: 247 IPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGARGA 306
IP +I+ RALG + DRDI+ + D PE+ + PSL++A I + AL+FIG+R A
Sbjct: 221 IPFVILMRALGILTDRDIVYAVSLD---PEVQNELFPSLEQASSIANVDDALDFIGSRVA 277
Query: 307 RPGVTKERRIKYAREILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLASLGRRELDDRD 366
G +E RI+ A++I+ K LPH+G S KKAY+L Y + +++ LGRRE DD+D
Sbjct: 278 -IGQKRENRIEKAQQIIDKYFLPHLGTSAEDRKKKAYYLAYAISKVIELYLGRREPDDKD 336
Query: 367 HYV---------------RMYAQKFID-----------RGKDFNLELAIKTKIITDGLRY 400
HY R+ + F+ RG+ L+ ++ I+T+ +R+
Sbjct: 337 HYANKRLRLAGDLFASLFRVAFKAFVKDLTYQLEKSKVRGRKLALKALVRPDIVTERIRH 396
Query: 401 SLATGNWGDQKKAHQARAGVSQVLNRLTFASSLSHLRRVNSPIGRDGKLAKPRQLHNTLW 460
+LATGNW R GVSQ+L+R + S LSHLRRV S + R + R LH T W
Sbjct: 397 ALATGNW------VGGRTGVSQLLDRTNWLSMLSHLRRVISSLARGQPNFEARDLHGTQW 450
Query: 461 GMICPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSAIADA-- 518
G +CP ETPEG GLVKNLALMA I+VG + + L E + +EE+
Sbjct: 451 GRMCPFETPEGPNSGLVKNLALMAQIAVGINERIVEKTLYEMGVVPVEEVIRRVTEGGED 510
Query: 519 -------TKIFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVSXXXXXXXXXXXXHT- 570
+K+ +NG +G ++D +L +R+ RR+ + I EV+ H
Sbjct: 511 QNEYLKWSKVILNGRLIGYYQDGGELANKIRERRRKGE-ISDEVNVGHIVTDFINEVHVN 569
Query: 571 -DAGRICRPLLIAENGSLLLKKRHIDNLKERDYNNYGWQVLVQSGVVEYIDTLEEETTMI 629
D+GR+ RPL+I NG+ L+ I+++++ + + LV+ G +EY+D EEE +
Sbjct: 570 CDSGRVRRPLIIVSNGNPLVT---IEDIEKLESGAITFDDLVRQGKIEYLDAEEEENAYV 626
Query: 630 AM 631
A+
Sbjct: 627 AL 628
>pdb|1I6V|C Chain C, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1118
Score = 62.8 bits (151), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 107/451 (23%), Positives = 181/451 (40%), Gaps = 110/451 (24%)
Query: 83 GSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGEEPVTTQHQKSFIGKIPIMLRSTYCL 142
G P P +E R ++LTY APLY + G + + F+G +P+M
Sbjct: 74 GDP-PFSQDECREKDLTYQAPLYARLQLIHKDTG----LIKEDEVFLGHLPLMTED---- 124
Query: 143 LNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFS-MKDSKYAYKTEI 201
G FIING+++V+++Q + + + +Y I
Sbjct: 125 --------------------GSFIINGADRVIVSQIHRSPGVYFTPDPARPGRY-----I 159
Query: 202 RSCLEHSSRPTSTLWVNMMARGGQSLKKSAIGQRIIAILPYIKQEIPIMIVFRALGFVAD 261
S + P W++ L+ A G + + K++ P++++ R LG+ D
Sbjct: 160 ASII---PLPKRGPWID--------LEVEASG---VVTMKVNKRKFPLVLLLRVLGY--D 203
Query: 262 RDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ--EQNVALNFIGARGARPGVTKERRIKYA 319
++ L + + D +V+ LDEA + E+ + F R P K++ + Y
Sbjct: 204 QETLVRELSAYGD-----LVQGLLDEAVLAMRPEEAMVRLFTLLRPGDP-PKKDKALAYL 257
Query: 320 REIL--------------QKEMLPHVGVS-------DFCETKKAYFLGYMVHRL-LLASL 357
+L + E VG+S + E K FL + + L A +
Sbjct: 258 FGLLADPKRYDLGEAGRYKAEEKLGVGLSGRTLVRFEDGEFKDEVFLPTLRYLFALTAGV 317
Query: 358 GRRELDDRDHY----VRMYAQKFIDRGKDFNLELAIKTKIITDGLRYSLATGNWGDQKKA 413
E+DD DH +R + D+ F + LA + G+R + G+ A
Sbjct: 318 PGHEVDDIDHLGNRRIRTVGELMADQ---FRVGLAR----LARGVRERMVMGSPDTLTPA 370
Query: 414 HQ--------------ARAGVSQVLNRLTFASSLSHLRRVNS--PIG--RDGKLAKPRQL 455
+R+ +SQ + SSL H RR+++ P G R+ R +
Sbjct: 371 KLVNSRPLEAALREFFSRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVRDV 430
Query: 456 HNTLWGMICPAETPEGAAVGLVKNLALMAYI 486
H T +G ICP ETPEGA +GL+ +LA A +
Sbjct: 431 HRTHYGRICPVETPEGANIGLITSLAAYARV 461
>pdb|1YNJ|C Chain C, Taq Rna Polymerase-Sorangicin Complex
pdb|1YNN|C Chain C, Taq Rna Polymerase-rifampicin Complex
pdb|2GHO|C Chain C, Recombinant Thermus Aquaticus Rna Polymerase For
Structural Studies
Length = 1119
Score = 62.8 bits (151), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 107/451 (23%), Positives = 181/451 (40%), Gaps = 110/451 (24%)
Query: 83 GSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGEEPVTTQHQKSFIGKIPIMLRSTYCL 142
G P P +E R ++LTY APLY + G + + F+G +P+M
Sbjct: 74 GDP-PFSQDECREKDLTYQAPLYARLQLIHKDTG----LIKEDEVFLGHLPLMTED---- 124
Query: 143 LNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFS-MKDSKYAYKTEI 201
G FIING+++V+++Q + + + +Y I
Sbjct: 125 --------------------GSFIINGADRVIVSQIHRSPGVYFTPDPARPGRY-----I 159
Query: 202 RSCLEHSSRPTSTLWVNMMARGGQSLKKSAIGQRIIAILPYIKQEIPIMIVFRALGFVAD 261
S + P W++ L+ A G + + K++ P++++ R LG+ D
Sbjct: 160 ASII---PLPKRGPWID--------LEVEASG---VVTMKVNKRKFPLVLLLRVLGY--D 203
Query: 262 RDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ--EQNVALNFIGARGARPGVTKERRIKYA 319
++ L + + D +V+ LDEA + E+ + F R P K++ + Y
Sbjct: 204 QETLVRELSAYGD-----LVQGLLDEAVLAMRPEEAMVRLFTLLRPGDP-PKKDKALAYL 257
Query: 320 REIL--------------QKEMLPHVGVS-------DFCETKKAYFLGYMVHRL-LLASL 357
+L + E VG+S + E K FL + + L A +
Sbjct: 258 FGLLADPKRYDLGEAGRYKAEEKLGVGLSGRTLVRFEDGEFKDEVFLPTLRYLFALTAGV 317
Query: 358 GRRELDDRDHY----VRMYAQKFIDRGKDFNLELAIKTKIITDGLRYSLATGNWGDQKKA 413
E+DD DH +R + D+ F + LA + G+R + G+ A
Sbjct: 318 PGHEVDDIDHLGNRRIRTVGELMADQ---FRVGLAR----LARGVRERMVMGSPDTLTPA 370
Query: 414 HQ--------------ARAGVSQVLNRLTFASSLSHLRRVNS--PIG--RDGKLAKPRQL 455
+R+ +SQ + SSL H RR+++ P G R+ R +
Sbjct: 371 KLVNSRPLEAALREFFSRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVRDV 430
Query: 456 HNTLWGMICPAETPEGAAVGLVKNLALMAYI 486
H T +G ICP ETPEGA +GL+ +LA A +
Sbjct: 431 HRTHYGRICPVETPEGANIGLITSLAAYARV 461
>pdb|1HQM|C Chain C, Crystal Structure Of Thermus Aquaticus Core Rna
Polymerase- Includes Complete Structure With Side-Chains
(Except For Disordered Regions)-Further Refined From
Original Deposition-Contains Additional Sequence
Information
Length = 1119
Score = 62.8 bits (151), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 107/451 (23%), Positives = 181/451 (40%), Gaps = 110/451 (24%)
Query: 83 GSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGEEPVTTQHQKSFIGKIPIMLRSTYCL 142
G P P +E R ++LTY APLY + G + + F+G +P+M
Sbjct: 74 GDP-PFSQDECREKDLTYQAPLYARLQLIHKDTG----LIKEDEVFLGHLPLMTED---- 124
Query: 143 LNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFS-MKDSKYAYKTEI 201
G FIING+++V+++Q + + + +Y I
Sbjct: 125 --------------------GSFIINGADRVIVSQIHRSPGVYFTPDPARPGRY-----I 159
Query: 202 RSCLEHSSRPTSTLWVNMMARGGQSLKKSAIGQRIIAILPYIKQEIPIMIVFRALGFVAD 261
S + P W++ L+ A G + + K++ P++++ R LG+ D
Sbjct: 160 ASII---PLPKRGPWID--------LEVEASG---VVTMKVNKRKFPLVLLLRVLGY--D 203
Query: 262 RDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ--EQNVALNFIGARGARPGVTKERRIKYA 319
++ L + + D +V+ LDEA + E+ + F R P K++ + Y
Sbjct: 204 QETLVRELSAYGD-----LVQGLLDEAVLAMRPEEAMVRLFTLLRPGDP-PKKDKALAYL 257
Query: 320 REIL--------------QKEMLPHVGVS-------DFCETKKAYFLGYMVHRL-LLASL 357
+L + E VG+S + E K FL + + L A +
Sbjct: 258 FGLLADPKRYDLGEAGRYKAEEKLGVGLSGRTLVRFEDGEFKDEVFLPTLRYLFALTAGV 317
Query: 358 GRRELDDRDHY----VRMYAQKFIDRGKDFNLELAIKTKIITDGLRYSLATGNWGDQKKA 413
E+DD DH +R + D+ F + LA + G+R + G+ A
Sbjct: 318 PGHEVDDIDHLGNRRIRTVGELMADQ---FRVGLAR----LARGVRERMVMGSPDTLTPA 370
Query: 414 HQ--------------ARAGVSQVLNRLTFASSLSHLRRVNS--PIG--RDGKLAKPRQL 455
+R+ +SQ + SSL H RR+++ P G R+ R +
Sbjct: 371 KLVNSRPLEAALREFFSRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVRDV 430
Query: 456 HNTLWGMICPAETPEGAAVGLVKNLALMAYI 486
H T +G ICP ETPEGA +GL+ +LA A +
Sbjct: 431 HRTHYGRICPVETPEGANIGLITSLAAYARV 461
>pdb|1L9U|C Chain C, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9U|L Chain L, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9Z|C Chain C, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
Length = 1118
Score = 62.8 bits (151), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 107/451 (23%), Positives = 181/451 (40%), Gaps = 110/451 (24%)
Query: 83 GSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGEEPVTTQHQKSFIGKIPIMLRSTYCL 142
G P P +E R ++LTY APLY + G + + F+G +P+M
Sbjct: 74 GDP-PFSQDECREKDLTYQAPLYARLQLIHKDTG----LIKEDEVFLGHLPLMTED---- 124
Query: 143 LNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFS-MKDSKYAYKTEI 201
G FIING+++V+++Q + + + +Y I
Sbjct: 125 --------------------GSFIINGADRVIVSQIHRSPGVYFTPDPARPGRY-----I 159
Query: 202 RSCLEHSSRPTSTLWVNMMARGGQSLKKSAIGQRIIAILPYIKQEIPIMIVFRALGFVAD 261
S + P W++ L+ A G + + K++ P++++ R LG+ D
Sbjct: 160 ASII---PLPKRGPWID--------LEVEASG---VVTMKVNKRKFPLVLLLRVLGY--D 203
Query: 262 RDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ--EQNVALNFIGARGARPGVTKERRIKYA 319
++ L + + D +V+ LDEA + E+ + F R P K++ + Y
Sbjct: 204 QETLVRELSAYGD-----LVQGLLDEAVLAMRPEEAMVRLFTLLRPGDP-PKKDKALAYL 257
Query: 320 REIL--------------QKEMLPHVGVS-------DFCETKKAYFLGYMVHRL-LLASL 357
+L + E VG+S + E K FL + + L A +
Sbjct: 258 FGLLADPKRYDLGEAGRYKAEEKLGVGLSGRTLVRFEDGEFKDEVFLPTLRYLFALTAGV 317
Query: 358 GRRELDDRDHY----VRMYAQKFIDRGKDFNLELAIKTKIITDGLRYSLATGNWGDQKKA 413
E+DD DH +R + D+ F + LA + G+R + G+ A
Sbjct: 318 PGHEVDDIDHLGNRRIRTVGELMADQ---FRVGLAR----LARGVRERMVMGSPDTLTPA 370
Query: 414 HQ--------------ARAGVSQVLNRLTFASSLSHLRRVNS--PIG--RDGKLAKPRQL 455
+R+ +SQ + SSL H RR+++ P G R+ R +
Sbjct: 371 KLVNSRPLEAALREFFSRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVRDV 430
Query: 456 HNTLWGMICPAETPEGAAVGLVKNLALMAYI 486
H T +G ICP ETPEGA +GL+ +LA A +
Sbjct: 431 HRTHYGRICPVETPEGANIGLITSLAAYARV 461
>pdb|1IW7|C Chain C, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1IW7|M Chain M, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1SMY|C Chain C, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1SMY|M Chain M, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1ZYR|C Chain C, Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Streptolydigin
pdb|1ZYR|M Chain M, Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Streptolydigin
pdb|2A68|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A68|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A69|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A69|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A6E|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6E|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6H|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2A6H|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2CW0|C Chain C, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2CW0|M Chain M, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2BE5|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2BE5|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2O5I|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Elongation Complex
pdb|2O5I|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Elongation Complex
pdb|2O5J|C Chain C, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog
pdb|2O5J|M Chain M, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog
pdb|2PPB|C Chain C, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog And
Antibiotic Streptolydigin
pdb|2PPB|M Chain M, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog And
Antibiotic Streptolydigin
pdb|3DXJ|C Chain C, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3DXJ|M Chain M, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3EQL|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3EQL|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3AOH|C Chain C, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOH|H Chain H, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOH|M Chain M, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOI|C Chain C, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|3AOI|H Chain H, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|3AOI|M Chain M, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|4G7H|C Chain C, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7H|M Chain M, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7O|C Chain C, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7O|M Chain M, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7Z|C Chain C, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
pdb|4G7Z|M Chain M, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
pdb|4GZY|C Chain C, Crystal Structures Of Bacterial Rna Polymerase Paused
Elongation Complexes
pdb|4GZZ|C Chain C, Crystal Structures Of Bacterial Rna Polymerase Paused
Elongation Complexes
Length = 1119
Score = 60.1 bits (144), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 101/450 (22%), Positives = 179/450 (39%), Gaps = 108/450 (24%)
Query: 83 GSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGEEPVTTQHQKSFIGKIPIMLRSTYCL 142
G P P +E R ++LTY APLY + G + + F+G IP+M
Sbjct: 74 GEP-PFPQDECREKDLTYQAPLYARLQLIHKDTG----LIKEDEVFLGHIPLMTED---- 124
Query: 143 LNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFS-MKDSKYAYKTEI 201
G FIING+++V+++Q + + + +Y I
Sbjct: 125 --------------------GSFIINGADRVIVSQIHRSPGVYFTPDPARPGRY-----I 159
Query: 202 RSCLEHSSRPTSTLWVNMMAR--GGQSLKKSAIGQRIIAILPYIKQEIPIMIVFRALGFV 259
S + P W+++ G S+K + K++ P++++ R LG+
Sbjct: 160 ASII---PLPKRGPWIDLEVEPNGVVSMKVN-------------KRKFPLVLLLRVLGY- 202
Query: 260 ADRDILEHIIYDFDDPEMMEMVKPSLDEA-FVIQEQNVALNFIGARGARPG--VTKERRI 316
D++ L + + E+V+ +DE+ F ++ + + RPG +++ +
Sbjct: 203 -DQETLARELGAYG-----ELVQGLMDESVFAMRPEEALIRLFTL--LRPGDPPKRDKAV 254
Query: 317 KYAREILQKEMLPHVGVS---------------------DFCETKKAYFLGYMVHRL-LL 354
Y ++ +G + + E K FL + + L
Sbjct: 255 AYVYGLIADPRRYDLGEAGRYKAEEKLGIRLSGRTLARFEDGEFKDEVFLPTLRYLFALT 314
Query: 355 ASLGRRELDDRDHY----VRMYAQKFIDRGKDFNLELAIKTKIITD----GLRYSLATGN 406
A + E+DD DH +R + D+ F + LA + + + G SL
Sbjct: 315 AGVPGHEVDDIDHLGNRRIRTVGELMTDQ---FRVGLARLARGVRERMLMGSEDSLTPAK 371
Query: 407 WGDQKKAHQA------RAGVSQVLNRLTFASSLSHLRRVNS--PIG--RDGKLAKPRQLH 456
+ + A R+ +SQ + SSL H RR+++ P G R+ R +H
Sbjct: 372 LVNSRPLEAAIREFFSRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVRDVH 431
Query: 457 NTLWGMICPAETPEGAAVGLVKNLALMAYI 486
T +G ICP ETPEGA +GL+ +LA A +
Sbjct: 432 RTHYGRICPVETPEGANIGLITSLAAYARV 461
>pdb|3IYD|C Chain C, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
pdb|4IGC|C Chain C, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
pdb|4IGC|H Chain H, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
Length = 1342
Score = 47.0 bits (110), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 43/69 (62%), Gaps = 4/69 (5%)
Query: 420 VSQVLNRLTFASSLSHLRRVNS--PIG--RDGKLAKPRQLHNTLWGMICPAETPEGAAVG 475
+SQ +++ S ++H RR+++ P G R+ + R +H T +G +CP ETPEG +G
Sbjct: 511 LSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIG 570
Query: 476 LVKNLALMA 484
L+ +L++ A
Sbjct: 571 LINSLSVYA 579
Score = 42.4 bits (98), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 49/210 (23%), Positives = 88/210 (41%), Gaps = 63/210 (30%)
Query: 92 EARLRNLTYSAPLYVDITKTVVRQGEEPVTT----QHQKSFIGKIPIMLRSTYCLLNGLT 147
E ++R +TYSAPL V + + V+ + E P T + Q+ ++G+IP+M T
Sbjct: 84 ECQIRGVTYSAPLRVKL-RLVIYEREAPEGTVKDIKEQEVYMGEIPLM-----------T 131
Query: 148 DRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVF----SMKDSKYAYKTEI-- 201
D G F+ING+E+V+++Q + + + K Y I
Sbjct: 132 DN-------------GTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNARIIP 178
Query: 202 --RSCLEHSSRPTSTLWVNMMARGGQSLKKSAIGQRIIAILPYIKQEIPIMIVFRALGFV 259
S L+ P L+V + R +++P I+ RAL +
Sbjct: 179 YRGSWLDFEFDPKDNLFVRIDRR----------------------RKLPATIILRALNYT 216
Query: 260 ADRDI---LEHIIYDFDDPEM-MEMVKPSL 285
++ + E +I++ D ++ ME+V L
Sbjct: 217 TEQILDLFFEKVIFEIRDNKLQMELVPERL 246
>pdb|3LU0|C Chain C, Molecular Model Of Escherichia Coli Core Rna Polymerase
Length = 1342
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 42/69 (60%), Gaps = 4/69 (5%)
Query: 420 VSQVLNRLTFASSLSHLRRVNS--PIG--RDGKLAKPRQLHNTLWGMICPAETPEGAAVG 475
+SQ + + S ++H RR+++ P G R+ + R +H T +G +CP ETPEG +G
Sbjct: 511 LSQFMVQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIG 570
Query: 476 LVKNLALMA 484
L+ +L++ A
Sbjct: 571 LINSLSVYA 579
Score = 42.7 bits (99), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 49/210 (23%), Positives = 88/210 (41%), Gaps = 63/210 (30%)
Query: 92 EARLRNLTYSAPLYVDITKTVVRQGEEPVTT----QHQKSFIGKIPIMLRSTYCLLNGLT 147
E ++R +TYSAPL V + + V+ + E P T + Q+ ++G+IP+M T
Sbjct: 84 ECQIRGVTYSAPLRVKL-RLVIYEREAPEGTVKDIKEQEVYMGEIPLM-----------T 131
Query: 148 DRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVF----SMKDSKYAYKTEI-- 201
D G F+ING+E+V+++Q + + + K Y I
Sbjct: 132 DN-------------GTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNARIIP 178
Query: 202 --RSCLEHSSRPTSTLWVNMMARGGQSLKKSAIGQRIIAILPYIKQEIPIMIVFRALGFV 259
S L+ P L+V + R +++P I+ RAL +
Sbjct: 179 YRGSWLDFEFDPKDNLFVRIDRR----------------------RKLPATIILRALNYT 216
Query: 260 ADRDI---LEHIIYDFDDPEM-MEMVKPSL 285
++ + E +I++ D ++ ME+V L
Sbjct: 217 TEQILDLFFEKVIFEIRDNKLQMELVPERL 246
>pdb|3MLQ|A Chain A, Crystal Structure Of The Thermus Thermophilus
Transcription-Repair Coupling Factor Rna Polymerase
Interacting Domain With The Thermus Aquaticus Rna
Polymerase Beta1 Domain
pdb|3MLQ|B Chain B, Crystal Structure Of The Thermus Thermophilus
Transcription-Repair Coupling Factor Rna Polymerase
Interacting Domain With The Thermus Aquaticus Rna
Polymerase Beta1 Domain
pdb|3MLQ|C Chain C, Crystal Structure Of The Thermus Thermophilus
Transcription-Repair Coupling Factor Rna Polymerase
Interacting Domain With The Thermus Aquaticus Rna
Polymerase Beta1 Domain
pdb|3MLQ|D Chain D, Crystal Structure Of The Thermus Thermophilus
Transcription-Repair Coupling Factor Rna Polymerase
Interacting Domain With The Thermus Aquaticus Rna
Polymerase Beta1 Domain
Length = 188
Score = 35.4 bits (80), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 40/95 (42%), Gaps = 29/95 (30%)
Query: 83 GSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGEEPVTTQHQKSFIGKIPIMLRSTYCL 142
G P P +E R ++LTY APLY + G + + F+G +P+M
Sbjct: 59 GDP-PFSQDECREKDLTYQAPLYARLQLIHKDTG----LIKEDEVFLGHLPLMTED---- 109
Query: 143 LNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQ 177
G FIING+++V+++Q
Sbjct: 110 --------------------GSFIINGADRVIVSQ 124
>pdb|3MAW|A Chain A, Structure Of The Newcastle Disease Virus F Protein In The
Po Conformation
pdb|3MAW|B Chain B, Structure Of The Newcastle Disease Virus F Protein In The
Po Conformation
Length = 483
Score = 30.4 bits (67), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 32/120 (26%), Positives = 51/120 (42%), Gaps = 13/120 (10%)
Query: 89 MPNEARLRNL--TYSAPLYVDITKTVVRQGEEPVTTQHQKSFIGKIPIMLRSTYCLLNGL 146
+P+ L N+ TY L V TK V TQ +G + L ++YC+
Sbjct: 258 LPSVGNLNNMRATYLETLSVSTTKGFASALVPKVVTQ-----VGSVIEELDTSYCIE--- 309
Query: 147 TDRDL--TELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKDSKYAYKTEIRSC 204
TD DL T + P+ PG Y +NG+ + + T ++K S A ++ +C
Sbjct: 310 TDLDLYCTRIVTFPMSPGIYSCLNGNTSACMYSKTEGALTTPYMTLKGSVIA-NCKMTTC 368
>pdb|2BYV|E Chain E, Structure Of The Camp Responsive Exchange Factor Epac2 In
Its Auto-Inhibited State
Length = 999
Score = 28.9 bits (63), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 9/31 (29%), Positives = 19/31 (61%)
Query: 615 VVEYIDTLEEETTMIAMWQVLVQSGVVEYID 645
+++ + T + MWQVL++ GV+ ++D
Sbjct: 233 MIQQTSCVHSRTQAVGMWQVLLEDGVLNHVD 263
>pdb|3ICJ|A Chain A, Crystal Structure Of An Uncharacterized Metal-Dependent
Hydrolase From Pyrococcus Furiosus
Length = 534
Score = 28.9 bits (63), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 13/54 (24%), Positives = 30/54 (55%)
Query: 309 GVTKERRIKYAREILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLASLGRREL 362
G+ +ER ++ +R+I+ +++L + E+ + + L VH + S+G + L
Sbjct: 196 GIVRERALEESRKIINEKILTVKDYKHYIESAQEHLLSLGVHSVGFMSVGEKAL 249
>pdb|4F7Z|A Chain A, Conformational Dynamics Of Exchange Protein Directly
Activated By Camp
Length = 999
Score = 28.9 bits (63), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 9/31 (29%), Positives = 19/31 (61%)
Query: 615 VVEYIDTLEEETTMIAMWQVLVQSGVVEYID 645
+++ + T + MWQVL++ GV+ ++D
Sbjct: 233 MIQQTSCVHSRTQAVGMWQVLLEDGVLNHVD 263
>pdb|4B4Y|A Chain A, Crystal Structure Of The Neuroglobin From The
Photosymbiotic Marine Acoel Symsagittifera Roscoffensis
Length = 154
Score = 28.9 bits (63), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 29/44 (65%), Gaps = 3/44 (6%)
Query: 24 LDSFDEFIQMSVQRIVEDSP---QIDLQAEAQHTSTEVETPPRY 64
L ++D+F++ +Q+ +E++P QI A+A T+ E+ + PR+
Sbjct: 25 LPNYDDFVEDVLQQFMEENPETFQIFPWADASKTAKEMRSHPRF 68
>pdb|1O7F|A Chain A, Crystal Structure Of The Regulatory Domain Of Epac2
Length = 469
Score = 28.9 bits (63), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 14/54 (25%), Positives = 31/54 (57%), Gaps = 5/54 (9%)
Query: 597 LKERDYNNYGW-QVLVQSGVVEYI----DTLEEETTMIAMWQVLVQSGVVEYID 645
+++R Y+ + Q V + +V+++ + T + MWQVL++ GV+ ++D
Sbjct: 210 IRDRKYHLKTYRQCCVGTELVDWMIQQTSCVHSRTQAVGMWQVLLEDGVLNHVD 263
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.320 0.136 0.400
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,557,013
Number of Sequences: 62578
Number of extensions: 748436
Number of successful extensions: 1938
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1860
Number of HSP's gapped (non-prelim): 44
length of query: 661
length of database: 14,973,337
effective HSP length: 105
effective length of query: 556
effective length of database: 8,402,647
effective search space: 4671871732
effective search space used: 4671871732
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)