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= 046830
(518 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 = 596 bits (1536), Expect = e-170, Method: Compositional matrix adjust.
Identities = 295/539 (54%), Positives = 378/539 (70%), Gaps = 45/539 (8%)
Query: 22 WAVISAYFEEKGLVRQQLDSFDEFNQNTMQEIVDESADIEIRPESQHNPGQ-------QS 74
W VIS++FEE L RQQL SFDEF QNTMQEIVD+ + + + +QH Q +
Sbjct: 18 WTVISSFFEETSLARQQLFSFDEFVQNTMQEIVDDDSTLTLDQYAQHTGAQGDVTRRYEI 77
Query: 75 DFAEIYLSKPMMTESDGETATLFLKAARLRNLTYSAPLYVDVTKRVIKKGHDGE------ 128
+F +IYLS+P MTE+DG T T+F + ARLRNLTYS+PLYVD+ K+V+
Sbjct: 78 NFGQIYLSRPTMTEADGSTTTMFPQEARLRNLTYSSPLYVDMRKKVMVAADSNVPIGEEE 137
Query: 129 ----------------EVPIMLRSSYCTLYQNSQKALTELGECPYDEGGYFIINGSEKVL 172
++PIMLRS++C L S L +L ECPYD+GGYFIINGSEKV+
Sbjct: 138 WLVEEEDEEPSKVFIGKIPIMLRSTFCILNGVSDSELYDLNECPYDQGGYFIINGSEKVI 197
Query: 173 IAQEKMSTNHVYVFKKRQPNKYAYVAEVCSMAESQNRPPSTIFVPMLSRTSAKGGSSGQY 232
IAQE+ + N V VFKK P+ AYVAE+ S E +R S++ + +++R + +SGQ
Sbjct: 198 IAQERSAANIVQVFKKAAPSPIAYVAEIRSALERGSRLISSMQIKLMARNTE---NSGQT 254
Query: 233 IHATLPYIRTEIPIIILFRALGFTADEDILEHICYDFQDTQMMELLRPSLEEAFFIQNQQ 292
I ATLPYIR++IPI+I+FRALG D DILEHICYD D QM+E+++P +EEAF IQ++
Sbjct: 255 IRATLPYIRSDIPIVIVFRALGVVPDRDILEHICYDPNDFQMLEMMKPCIEEAFVIQDKD 314
Query: 293 ----YIGKRGATVGVTREKMIKYAKEILQKEMLPHVGTGDFCETKKAYYFGHIIHRLLLC 348
YIGKRG+T GVTREK ++YA +ILQKE+LPH+ T + ET+KA++ G++IHR+LLC
Sbjct: 315 IALDYIGKRGSTTGVTREKRLRYAHDILQKELLPHITTMEGFETRKAFFLGYMIHRMLLC 374
Query: 349 ALGRRAEDDRDHYGNKRLDLAGPLLGGLFRTLFRKLTGDVRSYVQKCVDNGKDVNLQFAI 408
AL RR DDRDH+G KRLDLAGPLL LFR LFRK+T DV Y+QKCV+ ++ NL A+
Sbjct: 375 ALERREPDDRDHFGKKRLDLAGPLLASLFRMLFRKMTRDVYKYMQKCVETNREFNLTLAV 434
Query: 409 KAKTITGGLKYSLATGNWG-QGNAAGTRAGVSQVLNCLTYASTFTYY--------LSWKL 459
K+ IT GL+YSLATGNWG Q + R GVSQVLN T+AST ++ KL
Sbjct: 435 KSNIITNGLRYSLATGNWGDQKRSMVNRVGVSQVLNRYTFASTLSHLRRTNTPIGRDGKL 494
Query: 460 AKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITIGSAAYPILEFLEEWGTENFE 518
AKPRQLHN+ WGM+CPAETPEGQACGLVKNL+LM Y+++GS + PI+EFLEEWG E E
Sbjct: 495 AKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSVGSPSAPIIEFLEEWGLETLE 553
>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 = 541 bits (1395), Expect = e-154, Method: Compositional matrix adjust.
Identities = 279/544 (51%), Positives = 371/544 (68%), Gaps = 52/544 (9%)
Query: 21 AWAVISAYFEEKGLVRQQLDSFDEFNQNTMQEIVDESADIEIRPESQHNPGQQSD----- 75
+WAVISA+F EKGLV QQLDSF++F T+Q+I+ E + + + +QH +SD
Sbjct: 30 SWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHT--TESDNISRK 87
Query: 76 ----FAEIYLSKPMMTESDGETATLFLKAARLRNLTYSAPLYVDVTKR------------ 119
F +IY++KPM+ ESDG T L+ + ARLRNLTYS+ L+VDV KR
Sbjct: 88 YEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEAIDVPGREL 147
Query: 120 ----VIKKGHDGEE--------VPIMLRSSYCTLYQNSQKALTELGECPYDEGGYFIING 167
+ ++ D E +PIMLRS C L + ++ L +L ECP+D GGYFIING
Sbjct: 148 KYELIAEESEDDSESGKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIING 207
Query: 168 SEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVCSMAESQNRPPSTIFVPMLSRTSAKGG 227
SEKVLIAQE+ + N V VFKK P+ ++VAE+ S E +R ST+ V + R G
Sbjct: 208 SEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGRE----G 263
Query: 228 SSGQYIHATLPYIRTEIPIIILFRALGFTADEDILEHICYDFQDTQMMELLRPSLEEAFF 287
SS + I ATLPYI+ +IPI+I+FRALG D +ILEHICYD D QM+E+L+P +E+ F
Sbjct: 264 SSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDGFV 323
Query: 288 IQNQQ----YIGKRGATVGVTREKMIKYAKEILQKEMLPHVGTGDFCETKKAYYFGHIIH 343
IQ+++ +IG+RG +G+ +EK I+YAK+ILQKE LPH+ + E++KA++ G++I+
Sbjct: 324 IQDRETALDFIGRRGTALGIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMIN 383
Query: 344 RLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRTLFRKLTGDVRSYVQKCVDNGKDVN 403
RLLLCAL R+ +DDRDH+G KRLDLAGPLL LF+TLF+KLT D+ Y+Q+ V+ D N
Sbjct: 384 RLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDFN 443
Query: 404 LQFAIKAKTITGGLKYSLATGNWG-QGNAAGTRAGVSQVLNCLTYASTFTYY-------- 454
++ AI AKTIT GLKY+LATGNWG Q A +RAGVSQVLN TY+ST ++
Sbjct: 444 MKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIG 503
Query: 455 LSWKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITIGSAAYPILEFLEEWGT 514
KLAKPRQLHN+ WG++CPAETPEGQACGLVKNL+LM I++G+ PI+ FL EWG
Sbjct: 504 RDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGM 563
Query: 515 ENFE 518
E E
Sbjct: 564 EPLE 567
>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 = 317 bits (812), Expect = 1e-86, Method: Compositional matrix adjust.
Identities = 195/514 (37%), Positives = 277/514 (53%), Gaps = 43/514 (8%)
Query: 22 WAVISAYFEEKGLVRQQLDSFDEFNQNTMQEIVDESADIEIRPESQHNPGQQSDFAEIYL 81
W VI AYF+ KGLVRQ LDS+++F +N +QEI+DE +I PG + +I +
Sbjct: 11 WRVIEAYFKSKGLVRQHLDSYNDFVRNKLQEIIDEQGEI-----PTEIPGLKVRLGKIRI 65
Query: 82 SKPMMTESDGETATLFLKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEV-----PIMLRS 136
KP + ESD + ARLRNLTY+APL++ + + EEV PIML+S
Sbjct: 66 GKPRVRESDRGEREISPMEARLRNLTYAAPLWLTMIPVENNIEAEPEEVYIGDLPIMLKS 125
Query: 137 SYCTLYQNSQKALTELGECPYDEGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAY 196
+ + Q + L E+GE P D GGYFI+NGSE+V++ QE ++ N V V + + +
Sbjct: 126 AIDPISQYTLDKLIEIGEDPKDPGGYFIVNGSERVIVTQEDLAPNRVLVDTGKTGSNITH 185
Query: 197 VAEVCSMAESQNRPPSTIFVPMLSRTSAKGGSSGQYIHATLPYIRTEIPIIILFRALGFT 256
A++ S + + R P TI K G+ H + P + +IP +IL RALG
Sbjct: 186 TAKIIS-STAGYRVPVTI-------ERLKDGT----FHVSFPAVPGKIPFVILMRALGIL 233
Query: 257 ADEDILEHICYDFQDTQMMELLRPSLEEAFFIQNQQ----YIGKRGATVGVTREKMIKYA 312
D DI+ + D ++ L PSLE+A I N +IG R A +G RE I+ A
Sbjct: 234 TDRDIVYAVSLD---PEVQNELFPSLEQASSIANVDDALDFIGSRVA-IGQKRENRIEKA 289
Query: 313 KEILQKEMLPHVGTGDFCETKKAYYFGHIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPL 372
++I+ K LPH+GT KKAYY + I +++ LGRR DD+DHY NKRL LAG L
Sbjct: 290 QQIIDKYFLPHLGTSAEDRKKKAYYLAYAISKVIELYLGRREPDDKDHYANKRLRLAGDL 349
Query: 373 LGGLFRTLFRKLTGDVRSYVQKCVDNGKDVNLQFAIKAKTITGGLKYSLATGNWGQGNAA 432
LFR F+ D+ ++K G+ + L+ ++ +T ++++LATGNW
Sbjct: 350 FASLFRVAFKAFVKDLTYQLEKSKVRGRKLALKALVRPDIVTERIRHALATGNW-----V 404
Query: 433 GTRAGVSQVLNCLTYASTFTYYL----SWKLAKP----RQLHNSQWGMMCPAETPEGQAC 484
G R GVSQ+L+ + S ++ S +P R LH +QWG MCP ETPEG
Sbjct: 405 GGRTGVSQLLDRTNWLSMLSHLRRVISSLARGQPNFEARDLHGTQWGRMCPFETPEGPNS 464
Query: 485 GLVKNLALMVYITIGSAAYPILEFLEEWGTENFE 518
GLVKNLALM I +G + + L E G E
Sbjct: 465 GLVKNLALMAQIAVGINERIVEKTLYEMGVVPVE 498
>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 = 317 bits (811), Expect = 1e-86, Method: Compositional matrix adjust.
Identities = 195/514 (37%), Positives = 277/514 (53%), Gaps = 43/514 (8%)
Query: 22 WAVISAYFEEKGLVRQQLDSFDEFNQNTMQEIVDESADIEIRPESQHNPGQQSDFAEIYL 81
W VI AYF+ KGLVRQ LDS+++F +N +QEI+DE +I PG + +I +
Sbjct: 14 WKVIEAYFKSKGLVRQHLDSYNDFVRNKLQEIIDEQGEI-----PTEIPGLKVRLGKIRI 68
Query: 82 SKPMMTESDGETATLFLKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEV-----PIMLRS 136
KP + ESD + ARLRNLTY+APL++ + + EEV PIML+S
Sbjct: 69 GKPRVRESDRGEREISPMEARLRNLTYAAPLWLTMIPVENNIEAEPEEVYIGDLPIMLKS 128
Query: 137 SYCTLYQNSQKALTELGECPYDEGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAY 196
+ + Q + L E+GE P D GGYFI+NGSE+V++ QE ++ N V V + + +
Sbjct: 129 AIDPISQYTLDKLIEIGEDPKDPGGYFIVNGSERVIVTQEDLAPNRVLVDTGKTGSNITH 188
Query: 197 VAEVCSMAESQNRPPSTIFVPMLSRTSAKGGSSGQYIHATLPYIRTEIPIIILFRALGFT 256
A++ S + + R P TI K G+ H + P + +IP +IL RALG
Sbjct: 189 TAKIIS-STAGYRVPVTI-------ERLKDGT----FHVSFPAVPGKIPFVILMRALGIL 236
Query: 257 ADEDILEHICYDFQDTQMMELLRPSLEEAFFIQNQQ----YIGKRGATVGVTREKMIKYA 312
D DI+ + D ++ L PSLE+A I N +IG R A +G RE I+ A
Sbjct: 237 TDRDIVYAVSLD---PEIQNELFPSLEQASSIANVDDALDFIGSRVA-IGQKRENRIEKA 292
Query: 313 KEILQKEMLPHVGTGDFCETKKAYYFGHIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPL 372
++I+ K LPH+GT KKAYY + I +++ LGRR DD+DHY NKRL LAG L
Sbjct: 293 QQIIDKYFLPHLGTSADDRRKKAYYLAYAISKVIELYLGRREPDDKDHYANKRLRLAGDL 352
Query: 373 LGGLFRTLFRKLTGDVRSYVQKCVDNGKDVNLQFAIKAKTITGGLKYSLATGNWGQGNAA 432
LFR F+ D+ ++K G+ + L+ ++ +T ++++LATGNW
Sbjct: 353 FASLFRVAFKAFVKDLTYQLEKSKVRGRKLALKALVRPDIVTERIRHALATGNW-----V 407
Query: 433 GTRAGVSQVLNCLTYASTFTYYL----SWKLAKP----RQLHNSQWGMMCPAETPEGQAC 484
G R GVSQ+L+ + S ++ S +P R LH +QWG MCP ETPEG
Sbjct: 408 GGRTGVSQLLDRTNWLSMLSHLRRVISSLARGQPNFEARDLHGTQWGRMCPFETPEGPNS 467
Query: 485 GLVKNLALMVYITIGSAAYPILEFLEEWGTENFE 518
GLVKNLALM I +G + + L E G E
Sbjct: 468 GLVKNLALMAQIAVGINEKIVEKTLYEMGVVPVE 501
>pdb|1I6V|C Chain C, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1118
Score = 57.4 bits (137), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 99/488 (20%), Positives = 172/488 (35%), Gaps = 121/488 (24%)
Query: 61 EIRPESQHNPGQQSDFAEIYLSKPMMTESDGETATLFLK--------------AARLRNL 106
++ PE + N G Q+ F E + + E D L L R ++L
Sbjct: 33 DVPPEKRENVGIQAAFKETF----PIEEGDKGKGGLVLDFLEYRIGDPPFSQDECREKDL 88
Query: 107 TYSAPLYVDVTKRVIKKGHDGEEVPIMLRSSYCTLYQNSQKALTELGECPY-DEGGYFII 165
TY APLY + L L + + LG P E G FII
Sbjct: 89 TYQAPLYAR----------------LQLIHKDTGLIKEDE---VFLGHLPLMTEDGSFII 129
Query: 166 NGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVCSMAESQNRPPSTIFVPMLSRTSAK 225
NG+++V+++Q S + +P +Y + S+ R P ++ + S
Sbjct: 130 NGADRVIVSQIHRSPGVYFTPDPARPGRY-----IASIIPLPKRGP---WIDLEVEASGV 181
Query: 226 GGSSGQYIHATLPYIRTEIPIIILFRALGFTADEDILEHICY-----------------D 268
T+ + + P+++L R LG+ + + E Y +
Sbjct: 182 ---------VTMKVNKRKFPLVLLLRVLGYDQETLVRELSAYGDLVQGLLDEAVLAMRPE 232
Query: 269 FQDTQMMELLRP--------SLEEAFFI----------QNQQYIGKRGATVGVTREKMIK 310
++ LLRP +L F + + +Y + VG++ +++
Sbjct: 233 EAMVRLFTLLRPGDPPKKDKALAYLFGLLADPKRYDLGEAGRYKAEEKLGVGLSGRTLVR 292
Query: 311 YAKEILQKEMLPHVGTGDFCETKKAYYFGHIIHRLLLCALGRRAEDDRDHYGNKRLDLAG 370
+ + E+ F T + Y F L + DD DH GN+R+ G
Sbjct: 293 FEDGEFKDEV--------FLPTLR-YLFA------LTAGVPGHEVDDIDHLGNRRIRTVG 337
Query: 371 PLLGGLFRTLFRKLTGDVRS-YVQKCVDNGKDVNLQFAIKAKTITGGLKYSLATGNWGQG 429
L+ FR +L VR V D L + ++ + L+ + Q
Sbjct: 338 ELMADQFRVGLARLARGVRERMVMGSPDTLTPAKL---VNSRPLEAALREFFSRSQLSQF 394
Query: 430 NAAGTRAGVSQVLNCLTYASTFTYYLSWKLAKPR------QLHNSQWGMMCPAETPEGQA 483
+ L+ L + + L + R +H + +G +CP ETPEG
Sbjct: 395 KDE------TNPLSSLRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGAN 448
Query: 484 CGLVKNLA 491
GL+ +LA
Sbjct: 449 IGLITSLA 456
>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 = 57.4 bits (137), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 98/493 (19%), Positives = 173/493 (35%), Gaps = 131/493 (26%)
Query: 61 EIRPESQHNPGQQSDFAEIYLSKPMMTESDGETATLFLK--------------AARLRNL 106
++ PE + N G Q+ F E + + E D L L R ++L
Sbjct: 33 DVPPEKRENVGIQAAFKETF----PIEEGDKGKGGLVLDFLEYRIGDPPFSQDECREKDL 88
Query: 107 TYSAPLYVDVTKRVIKKGHDGEEVPIMLRSSYCTLYQNSQKALTELGECPY-DEGGYFII 165
TY APLY + ++ + ++ LG P E G FII
Sbjct: 89 TYQAPLYARLQ---------------LIHKDTGLIKEDE----VFLGHLPLMTEDGSFII 129
Query: 166 NGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVCSMAESQNRPPSTIFVPMLSRTSAK 225
NG+++V+++Q S + +P +Y + S+ R P ++ + S
Sbjct: 130 NGADRVIVSQIHRSPGVYFTPDPARPGRY-----IASIIPLPKRGP---WIDLEVEASGV 181
Query: 226 GGSSGQYIHATLPYIRTEIPIIILFRALGFTADEDILEHICY-----------------D 268
T+ + + P+++L R LG+ + + E Y +
Sbjct: 182 ---------VTMKVNKRKFPLVLLLRVLGYDQETLVRELSAYGDLVQGLLDEAVLAMRPE 232
Query: 269 FQDTQMMELLRP-----------------------SLEEAFFIQNQQYIGKRGATVGVTR 305
++ LLRP L EA + ++ +G VG++
Sbjct: 233 EAMVRLFTLLRPGDPPKKDKALAYLFGLLADPKRYDLGEAGRYKAEEKLG-----VGLSG 287
Query: 306 EKMIKYAKEILQKEMLPHVGTGDFCETKKAYYFGHIIHRLLLCALGRRAEDDRDHYGNKR 365
++++ + E+ F T + Y F L + DD DH GN+R
Sbjct: 288 RTLVRFEDGEFKDEV--------FLPTLR-YLFA------LTAGVPGHEVDDIDHLGNRR 332
Query: 366 LDLAGPLLGGLFRTLFRKLTGDVRS-YVQKCVDNGKDVNLQFAIKAKTITGGLKYSLATG 424
+ G L+ FR +L VR V D L + ++ + L+ +
Sbjct: 333 IRTVGELMADQFRVGLARLARGVRERMVMGSPDTLTPAKL---VNSRPLEAALREFFSRS 389
Query: 425 NWGQGNAAGTRAGVSQVLNCLTYASTFTYYLSWKLAKPR------QLHNSQWGMMCPAET 478
Q + L+ L + + L + R +H + +G +CP ET
Sbjct: 390 QLSQFKDE------TNPLSSLRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICPVET 443
Query: 479 PEGQACGLVKNLA 491
PEG GL+ +LA
Sbjct: 444 PEGANIGLITSLA 456
>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 = 57.0 bits (136), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 98/493 (19%), Positives = 173/493 (35%), Gaps = 131/493 (26%)
Query: 61 EIRPESQHNPGQQSDFAEIYLSKPMMTESDGETATLFLK--------------AARLRNL 106
++ PE + N G Q+ F E + + E D L L R ++L
Sbjct: 33 DVPPEKRENVGIQAAFKETF----PIEEGDKGKGGLVLDFLEYRIGDPPFSQDECREKDL 88
Query: 107 TYSAPLYVDVTKRVIKKGHDGEEVPIMLRSSYCTLYQNSQKALTELGECPY-DEGGYFII 165
TY APLY + ++ + ++ LG P E G FII
Sbjct: 89 TYQAPLYARLQ---------------LIHKDTGLIKEDE----VFLGHLPLMTEDGSFII 129
Query: 166 NGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVCSMAESQNRPPSTIFVPMLSRTSAK 225
NG+++V+++Q S + +P +Y + S+ R P ++ + S
Sbjct: 130 NGADRVIVSQIHRSPGVYFTPDPARPGRY-----IASIIPLPKRGP---WIDLEVEASGV 181
Query: 226 GGSSGQYIHATLPYIRTEIPIIILFRALGFTADEDILEHICY-----------------D 268
T+ + + P+++L R LG+ + + E Y +
Sbjct: 182 ---------VTMKVNKRKFPLVLLLRVLGYDQETLVRELSAYGDLVQGLLDEAVLAMRPE 232
Query: 269 FQDTQMMELLRP-----------------------SLEEAFFIQNQQYIGKRGATVGVTR 305
++ LLRP L EA + ++ +G VG++
Sbjct: 233 EAMVRLFTLLRPGDPPKKDKALAYLFGLLADPKRYDLGEAGRYKAEEKLG-----VGLSG 287
Query: 306 EKMIKYAKEILQKEMLPHVGTGDFCETKKAYYFGHIIHRLLLCALGRRAEDDRDHYGNKR 365
++++ + E+ F T + Y F L + DD DH GN+R
Sbjct: 288 RTLVRFEDGEFKDEV--------FLPTLR-YLFA------LTAGVPGHEVDDIDHLGNRR 332
Query: 366 LDLAGPLLGGLFRTLFRKLTGDVRS-YVQKCVDNGKDVNLQFAIKAKTITGGLKYSLATG 424
+ G L+ FR +L VR V D L + ++ + L+ +
Sbjct: 333 IRTVGELMADQFRVGLARLARGVRERMVMGSPDTLTPAKL---VNSRPLEAALREFFSRS 389
Query: 425 NWGQGNAAGTRAGVSQVLNCLTYASTFTYYLSWKLAKPR------QLHNSQWGMMCPAET 478
Q + L+ L + + L + R +H + +G +CP ET
Sbjct: 390 QLSQFKDE------TNPLSSLRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICPVET 443
Query: 479 PEGQACGLVKNLA 491
PEG GL+ +LA
Sbjct: 444 PEGANIGLITSLA 456
>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 = 57.0 bits (136), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 99/488 (20%), Positives = 172/488 (35%), Gaps = 121/488 (24%)
Query: 61 EIRPESQHNPGQQSDFAEIYLSKPMMTESDGETATLFLK--------------AARLRNL 106
++ PE + N G Q+ F E + + E D L L R ++L
Sbjct: 33 DVPPEKRENVGIQAAFKETF----PIEEGDKGKGGLVLDFLEYRIGDPPFSQDECREKDL 88
Query: 107 TYSAPLYVDVTKRVIKKGHDGEEVPIMLRSSYCTLYQNSQKALTELGECPY-DEGGYFII 165
TY APLY + L L + + LG P E G FII
Sbjct: 89 TYQAPLYAR----------------LQLIHKDTGLIKEDE---VFLGHLPLMTEDGSFII 129
Query: 166 NGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVCSMAESQNRPPSTIFVPMLSRTSAK 225
NG+++V+++Q S + +P +Y + S+ R P ++ + S
Sbjct: 130 NGADRVIVSQIHRSPGVYFTPDPARPGRY-----IASIIPLPKRGP---WIDLEVEASGV 181
Query: 226 GGSSGQYIHATLPYIRTEIPIIILFRALGFTADEDILEHICY-----------------D 268
T+ + + P+++L R LG+ + + E Y +
Sbjct: 182 ---------VTMKVNKRKFPLVLLLRVLGYDQETLVRELSAYGDLVQGLLDEAVLAMRPE 232
Query: 269 FQDTQMMELLRP--------SLEEAFFI----------QNQQYIGKRGATVGVTREKMIK 310
++ LLRP +L F + + +Y + VG++ +++
Sbjct: 233 EAMVRLFTLLRPGDPPKKDKALAYLFGLLADPKRYDLGEAGRYKAEEKLGVGLSGRTLVR 292
Query: 311 YAKEILQKEMLPHVGTGDFCETKKAYYFGHIIHRLLLCALGRRAEDDRDHYGNKRLDLAG 370
+ + E+ F T + Y F L + DD DH GN+R+ G
Sbjct: 293 FEDGEFKDEV--------FLPTLR-YLFA------LTAGVPGHEVDDIDHLGNRRIRTVG 337
Query: 371 PLLGGLFRTLFRKLTGDVRS-YVQKCVDNGKDVNLQFAIKAKTITGGLKYSLATGNWGQG 429
L+ FR +L VR V D L + ++ + L+ + Q
Sbjct: 338 ELMADQFRVGLARLARGVRERMVMGSPDTLTPAKL---VNSRPLEAALREFFSRSQLSQF 394
Query: 430 NAAGTRAGVSQVLNCLTYASTFTYYLSWKLAKPR------QLHNSQWGMMCPAETPEGQA 483
+ L+ L + + L + R +H + +G +CP ETPEG
Sbjct: 395 KDE------TNPLSSLRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGAN 448
Query: 484 CGLVKNLA 491
GL+ +LA
Sbjct: 449 IGLITSLA 456
>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 = 54.7 bits (130), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 102/492 (20%), Positives = 171/492 (34%), Gaps = 129/492 (26%)
Query: 61 EIRPESQHNPGQQSDFAEIYLSKPMMTESDGETATL--FLK-----------AARLRNLT 107
++ PE + N G Q+ F E + P+ E G+ + FL+ R ++LT
Sbjct: 33 DVPPEKRENVGIQAAFRETF---PIEEEDKGKGGLVLDFLEYRLGEPPFPQDECREKDLT 89
Query: 108 YSAPLYVDVTKRVIKKGHDGEEVPIMLRSSYCTLYQNSQKALTELGECPY-DEGGYFIIN 166
Y APLY + L L + + LG P E G FIIN
Sbjct: 90 YQAPLYAR----------------LQLIHKDTGLIKEDE---VFLGHIPLMTEDGSFIIN 130
Query: 167 GSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVCSMAESQNRPPSTIFVPMLSRTSAKG 226
G+++V+++Q S + +P +Y +A + + + P +
Sbjct: 131 GADRVIVSQIHRSPGVYFTPDPARPGRY--IASIIPLPKRG---------PWIDLEVEPN 179
Query: 227 GSSGQYIHATLPYIRTEIPIIILFRALGFTADEDILEHICYDFQDTQMMELLRPSLEEAF 286
G ++ + + P+++L R LG+ + E Y EL++ ++E+
Sbjct: 180 GVVSMKVN------KRKFPLVLLLRVLGYDQETLARELGAYG-------ELVQGLMDESV 226
Query: 287 FIQNQQYIGKRGATV-----GVTREKMIKYAKEIL---QKEMLPHVGTGDFCETKKAYYF 338
F + R T+ R+K + Y ++ ++ L G E
Sbjct: 227 FAMRPEEALIRLFTLLRPGDPPKRDKAVAYVYGLIADPRRYDLGEAGRYKAEEKLGIRLS 286
Query: 339 GHIIHRL-------------------LLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRT 379
G + R L + DD DH GN+R+ G L+ FR
Sbjct: 287 GRTLARFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMTDQFRV 346
Query: 380 LFRKLTGDVRSYV----QKCVDNGKDVN---LQFAIKA-------------KTITGGLKY 419
+L VR + + + K VN L+ AI+ L++
Sbjct: 347 GLARLARGVRERMLMGSEDSLTPAKLVNSRPLEAAIREFFSRSQLSQFKDETNPLSSLRH 406
Query: 420 SLATGNWGQGNAAGTRAGVSQVLNCLTYASTFTYYLSWKLAKPRQLHNSQWGMMCPAETP 479
G G RAG R +H + +G +CP ETP
Sbjct: 407 KRRISALGPGGLTRERAGFDV----------------------RDVHRTHYGRICPVETP 444
Query: 480 EGQACGLVKNLA 491
EG GL+ +LA
Sbjct: 445 EGANIGLITSLA 456
>pdb|3LU0|C Chain C, Molecular Model Of Escherichia Coli Core Rna Polymerase
Length = 1342
Score = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 36/154 (23%), Positives = 71/154 (46%), Gaps = 6/154 (3%)
Query: 341 IIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRTLFRKLTGDVRSYVQKCVDNGK 400
++ +L+ G+ DD DH GN+R+ G + FR ++ V+ + + +
Sbjct: 428 VMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERL--SLGDLD 485
Query: 401 DVNLQFAIKAKTITGGLKYSLATGNWGQGNAAGTRAGVSQVLNCLTYASTFTYYLSWKLA 460
+ Q I AK I+ +K + Q +S++ + ++ L+ + A
Sbjct: 486 TLMPQDMINAKPISAAVKEFFGSSQLSQFMVQNN--PLSEITHKRRISALGPGGLTRERA 543
Query: 461 --KPRQLHNSQWGMMCPAETPEGQACGLVKNLAL 492
+ R +H + +G +CP ETPEG GL+ +L++
Sbjct: 544 GFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSV 577
Score = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 60/264 (22%), Positives = 111/264 (42%), Gaps = 67/264 (25%)
Query: 34 LVRQQLDSFDEFNQNTMQEIVDESADIEIRPESQHNPGQQSDFAEIYLSKPMMTESDGET 93
L+ QLDSF +F IE PE Q+ G ++ F ++ + S+ +
Sbjct: 27 LLSIQLDSFQKF--------------IEQDPEGQY--GLEAAFRSVFPIQSYSGNSELQY 70
Query: 94 ATLFL-------KAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVPIMLRSSYCTLYQNSQ 146
+ L + ++R +TYSAPL V + R++ I R + ++ +
Sbjct: 71 VSYRLGEPVFDVQECQIRGVTYSAPLRVKL--RLV----------IYEREAPEGTVKDIK 118
Query: 147 KALTELGECPY-DEGGYFIINGSEKVLIAQEKMSTNHVYVFKK---RQPNKYAYVAEVC- 201
+ +GE P + G F+ING+E+V+++Q S + K K Y A +
Sbjct: 119 EQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNARIIP 178
Query: 202 ---SMAESQNRPPSTIFVPMLSRTSAKGGSSGQYIHATLPYIRTEIPIIILFRALGFTAD 258
S + + P +FV + R R ++P I+ RAL +T +
Sbjct: 179 YRGSWLDFEFDPKDNLFV-RIDR-------------------RRKLPATIILRALNYTTE 218
Query: 259 EDI---LEHICYDFQDTQM-MELL 278
+ + E + ++ +D ++ MEL+
Sbjct: 219 QILDLFFEKVIFEIRDNKLQMELV 242
>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 = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 36/154 (23%), Positives = 71/154 (46%), Gaps = 6/154 (3%)
Query: 341 IIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRTLFRKLTGDVRSYVQKCVDNGK 400
++ +L+ G+ DD DH GN+R+ G + FR ++ V+ + + +
Sbjct: 428 VMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERL--SLGDLD 485
Query: 401 DVNLQFAIKAKTITGGLKYSLATGNWGQGNAAGTRAGVSQVLNCLTYASTFTYYLSWKLA 460
+ Q I AK I+ +K + Q +S++ + ++ L+ + A
Sbjct: 486 TLMPQDMINAKPISAAVKEFFGSSQLSQ--FMDQNNPLSEITHKRRISALGPGGLTRERA 543
Query: 461 --KPRQLHNSQWGMMCPAETPEGQACGLVKNLAL 492
+ R +H + +G +CP ETPEG GL+ +L++
Sbjct: 544 GFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSV 577
Score = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 60/264 (22%), Positives = 111/264 (42%), Gaps = 67/264 (25%)
Query: 34 LVRQQLDSFDEFNQNTMQEIVDESADIEIRPESQHNPGQQSDFAEIYLSKPMMTESDGET 93
L+ QLDSF +F IE PE Q+ G ++ F ++ + S+ +
Sbjct: 27 LLSIQLDSFQKF--------------IEQDPEGQY--GLEAAFRSVFPIQSYSGNSELQY 70
Query: 94 ATLFL-------KAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVPIMLRSSYCTLYQNSQ 146
+ L + ++R +TYSAPL V + R++ I R + ++ +
Sbjct: 71 VSYRLGEPVFDVQECQIRGVTYSAPLRVKL--RLV----------IYEREAPEGTVKDIK 118
Query: 147 KALTELGECPY-DEGGYFIINGSEKVLIAQEKMSTNHVYVFKK---RQPNKYAYVAEVC- 201
+ +GE P + G F+ING+E+V+++Q S + K K Y A +
Sbjct: 119 EQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNARIIP 178
Query: 202 ---SMAESQNRPPSTIFVPMLSRTSAKGGSSGQYIHATLPYIRTEIPIIILFRALGFTAD 258
S + + P +FV + R R ++P I+ RAL +T +
Sbjct: 179 YRGSWLDFEFDPKDNLFV-RIDR-------------------RRKLPATIILRALNYTTE 218
Query: 259 EDI---LEHICYDFQDTQM-MELL 278
+ + E + ++ +D ++ MEL+
Sbjct: 219 QILDLFFEKVIFEIRDNKLQMELV 242
>pdb|2Q88|A Chain A, Crystal Structure Of Ehub In Complex With Ectoine
pdb|2Q89|A Chain A, Crystal Structure Of Ehub In Complex With Hydroxyectoine
Length = 257
Score = 30.8 bits (68), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 5/47 (10%)
Query: 90 DGETATLFLKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVPIMLRS 136
D TA LF+K R + YS P+ D +KKG+ P+ L+S
Sbjct: 74 DAITAGLFMKPERCAAVAYSQPILCDAEAFALKKGN-----PLGLKS 115
>pdb|1CCI|A Chain A, How Flexible Are Proteins? Trapping Of A Flexible Loop
pdb|1CCJ|A Chain A, Conformer Selection By Ligand Binding Observed With
Protein Crystallography
Length = 294
Score = 28.9 bits (63), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 30/100 (30%), Positives = 38/100 (38%), Gaps = 18/100 (18%)
Query: 383 KLTGDVRSYVQKCVDNGKDVNLQFAIKAKTITGGLKYSLATGNWGQGNAAGTRAGVSQVL 442
K G VR++ Q+ N ++V A T LK S G WG N T G +L
Sbjct: 149 KDAGYVRTFFQRLNMNDREVVALMGAHALGKTH-LKNSGYEGPWGAANNVFTNEGYLNLL 207
Query: 443 NCLTYASTFTYYLSWKLAKPRQLHNSQWG-----MMCPAE 477
N WKL K +N QW MM P +
Sbjct: 208 NE-----------DWKLEK-NDANNEQWDSKSGYMMLPTD 235
>pdb|2W41|A Chain A, Crystal Structure Of Plasmodium Falciparum Glycerol Kinase
With Adp
pdb|2W41|B Chain B, Crystal Structure Of Plasmodium Falciparum Glycerol Kinase
With Adp
Length = 507
Score = 28.5 bits (62), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 2/51 (3%)
Query: 147 KALTELGE--CPYDEGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYA 195
+A+ + GE C Y G + +IN EKV+ + + T Y F KYA
Sbjct: 260 QAIFDEGEAKCTYGTGVFLLINTGEKVVYSTCGLITTICYKFNDNDKPKYA 310
>pdb|2W40|A Chain A, Crystal Structure Of Plasmodium Falciparum Glycerol Kinase
With Bound Glycerol
pdb|2W40|B Chain B, Crystal Structure Of Plasmodium Falciparum Glycerol Kinase
With Bound Glycerol
pdb|2W40|C Chain C, Crystal Structure Of Plasmodium Falciparum Glycerol Kinase
With Bound Glycerol
pdb|2W40|D Chain D, Crystal Structure Of Plasmodium Falciparum Glycerol Kinase
With Bound Glycerol
Length = 503
Score = 28.5 bits (62), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 2/51 (3%)
Query: 147 KALTELGE--CPYDEGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYA 195
+A+ + GE C Y G + +IN EKV+ + + T Y F KYA
Sbjct: 256 QAIFDEGEAKCTYGTGVFLLINTGEKVVYSTCGLITTICYKFNDNDKPKYA 306
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 0.135 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,923,066
Number of Sequences: 62578
Number of extensions: 631943
Number of successful extensions: 1410
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1345
Number of HSP's gapped (non-prelim): 38
length of query: 518
length of database: 14,973,337
effective HSP length: 103
effective length of query: 415
effective length of database: 8,527,803
effective search space: 3539038245
effective search space used: 3539038245
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: 54 (25.4 bits)