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= psy4067
(1384 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 = 215 bits (548), Expect = 1e-55, Method: Compositional matrix adjust.
Identities = 104/263 (39%), Positives = 161/263 (61%), Gaps = 3/263 (1%)
Query: 914 LVPYPHHNQAPRNTYQCAMGKQAMGCIGYNQQNRIDTLMYNLVYAQRPMVESKTIRITNF 973
++P+P HNQ+PRNTYQ AMGKQAMG N Q R+DT+ L Y Q+P+ ++++ F
Sbjct: 744 IIPFPDHNQSPRNTYQSAMGKQAMGVYLTNYQVRMDTMANILYYPQKPLATTRSMEYLKF 803
Query: 974 HKLPAGQNATIAVMSYSGYDIEDALIMNKASLDRGFGRCLVYRNSKCVLKQYPNQTHDRI 1033
+LPAGQNA +A++ YSGY+ ED++IMN+AS+DRG R + YR K+ +
Sbjct: 804 RELPAGQNAIVAILCYSGYNQEDSIIMNQASIDRGLFRSIFYRTYTDQEKKIGMTVMEEF 863
Query: 1034 LGPLLEADTRKPVYRHRALDQDGIVAPGEQICERQVLVNKSMPT-ISVSAISMATPEY-- 1090
P+ R + L+ DG++APG ++ +++ K+ P + + T +
Sbjct: 864 ERPVRSTTLRMKHGTYDKLEDDGLIAPGTRVSGEDIIIGKTAPIPLDHEELGQRTQLHAK 923
Query: 1091 KEVPVSYKGSVPSYLEKVLVSSNSEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVIGLIV 1150
++V + + +++V+V++N E +K+ +R TR P+IGDKF+SRHGQKG IG+
Sbjct: 924 RDVSTPLRSTESGIVDQVMVTTNQEGLKFVKVRMRSTRIPQIGDKFASRHGQKGTIGMTY 983
Query: 1151 EQEDMPFNESGICPDIIMNPHGL 1173
EDMPF+ GI PDII+NPH +
Sbjct: 984 RHEDMPFSAQGIVPDIIINPHAI 1006
Score = 180 bits (456), Expect = 5e-45, Method: Compositional matrix adjust.
Identities = 85/190 (44%), Positives = 119/190 (62%)
Query: 1183 KEVPVSYKGSVPSYLEKVLVSSNSEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVIGLIV 1242
++V + + +++V+V++N E +K+ +R TR P+IGDKF+SRHGQKG IG+
Sbjct: 924 RDVSTPLRSTESGIVDQVMVTTNQEGLKFVKVRMRSTRIPQIGDKFASRHGQKGTIGMTY 983
Query: 1243 EQEDMPFNESGICPDIIMNPHGYPSRMTVGKLIELLAGKAGLMEGNYKEGTAFGGTKLVD 1302
EDMPF+ GI PDII+NPH PSRMTV L+E K + G + T F +
Sbjct: 984 RHEDMPFSAQGIVPDIIINPHAIPSRMTVAHLVECQLSKVSALSGFEGDATPFTDVTVEA 1043
Query: 1303 VQEELIRHGYNYQGKDIFYSGITGEALEAYIYSGPVYYQKLKHMVQDKIHARSRGPRVVL 1362
V + L HG+ +G ++ Y G TG L A ++ GP YYQ+LKH+V DKIHAR+RGP +L
Sbjct: 1044 VSKLLRSHGFQSRGFEVMYHGHTGRKLVAQVFLGPTYYQRLKHLVDDKIHARARGPVQIL 1103
Query: 1363 TRQPTGRRWK 1372
TRQP R +
Sbjct: 1104 TRQPVEGRSR 1113
Score = 117 bits (292), Expect = 5e-26, Method: Compositional matrix adjust.
Identities = 55/151 (36%), Positives = 95/151 (62%), Gaps = 3/151 (1%)
Query: 185 QFDIVNHMRQDTITNALTAAIQTGNW-TIRRFKMERQGVTQVLSRLSYISGLGMMTRINS 243
+F++ ++ + ITN L ++ TGNW +R + R GV+QVL+R ++ S L + R N+
Sbjct: 427 EFNLTLAVKSNIITNGLRYSLATGNWGDQKRSMVNRVGVSQVLNRYTFASTLSHLRRTNT 486
Query: 244 QFEKTRKVSGPRSLQGSQWGMLCPSDTPEGEACGLVKNLALMTHITTENDEKNMLKIMYN 303
+ K++ PR L + WGM+CP++TPEG+ACGLVKNL+LM++++ + +++ +
Sbjct: 487 PIGRDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSVGSPSAPIIEFLEE 546
Query: 304 IGIEHIAMFNGEELSSPGVYLVFVNGILAGI 334
G+E + +N +SP VFVNG+ G+
Sbjct: 547 WGLETLEDYNPS--ASPNATKVFVNGVWLGV 575
Score = 86.7 bits (213), Expect = 8e-17, Method: Compositional matrix adjust.
Identities = 55/156 (35%), Positives = 75/156 (48%), Gaps = 42/156 (26%)
Query: 699 GKIEYLDVNEGNDSHIAVS----------ESG------------IRPG------VTTHLE 730
G IEYLD E IA+S ++G ++P TH E
Sbjct: 672 GLIEYLDAEEEETVMIAMSPEDLEASRQMQAGYEVKEELDPAQRVKPAPNPHVHAWTHCE 731
Query: 731 IAPFTLLGVCAGIELLQYNKRFHSPGLVPYPHHNQAPRNTYQCAMGKQAMGCIGYNQQNR 790
I P +LG+ A I +P+P HNQ+PRNTYQ AMGKQAMG N Q R
Sbjct: 732 IHPAMILGILASI--------------IPFPDHNQSPRNTYQSAMGKQAMGVYLTNYQVR 777
Query: 791 IDTLMYNLVYAQRPMVESKTIRITNFHKLPAGKCQI 826
+DT+ L Y Q+P+ ++++ F +LPAG+ I
Sbjct: 778 MDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAI 813
Score = 57.4 bits (137), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 36/114 (31%), Positives = 56/114 (49%), Gaps = 14/114 (12%)
Query: 456 ARDFLSSTCIAHIPVINMRFKMKAMYLAVMIRRMVLALSDPDMLDDRDYYGNKRLELAGS 515
A D L + HI + KA +L MI RM+L + DDRD++G KRL+LAG
Sbjct: 338 AHDILQKELLPHITTMEGFETRKAFFLGYMIHRMLLCALERREPDDRDHFGKKRLDLAGP 397
Query: 516 LLSLMFEDVFKRFNSEL-----------KETNLSGVVN---LVSGWWFELKYGN 555
LL+ +F +F++ ++ +E NL+ V + +G + L GN
Sbjct: 398 LLASLFRMLFRKMTRDVYKYMQKCVETNREFNLTLAVKSNIITNGLRYSLATGN 451
Score = 41.6 bits (96), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 41/83 (49%), Gaps = 17/83 (20%)
Query: 341 VCKPEIEESFNYTRQTTPHECRLRDLTYSAPITVDIE-----------------YTRGSQ 383
+ +P + E+ T P E RLR+LTYS+P+ VD+ + +
Sbjct: 84 LSRPTMTEADGSTTTMFPQEARLRNLTYSSPLYVDMRKKVMVAADSNVPIGEEEWLVEEE 143
Query: 384 RVVRSDLVIGRMPIMLQSSKCVL 406
S + IG++PIML+S+ C+L
Sbjct: 144 DEEPSKVFIGKIPIMLRSTFCIL 166
>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 = 209 bits (533), Expect = 6e-54, Method: Compositional matrix adjust.
Identities = 104/265 (39%), Positives = 160/265 (60%), Gaps = 2/265 (0%)
Query: 911 SPGLVPYPHHNQAPRNTYQCAMGKQAMGCIGYNQQNRIDTLMYNLVYAQRPMVESKTIRI 970
+ ++PYP HNQ+PRNTYQ AM KQA+G N Q R DT + L Y QRP+V+++ + I
Sbjct: 651 TASIIPYPEHNQSPRNTYQSAMAKQALGLYAANYQLRTDTRAHLLHYPQRPLVQTRALDI 710
Query: 971 TNFHKLPAGQNATIAVMSYSGYDIEDALIMNKASLDRGFGRCLVYRNSKCVLKQYPNQTH 1030
+ PAG NA +AVMS++GY++ED++IMN++S++RG R +R +YP
Sbjct: 711 IGYTNRPAGNNAILAVMSFTGYNMEDSIIMNRSSVERGMYRSTFFRLYSTEEVKYPGGQE 770
Query: 1031 DRILGPLLEADTRKPVYRHRALDQDGIVAPGEQICERQVLVNKSMPTISVSAISMATPEY 1090
D+I+ P K +R L+ +G+V+P ++ VL+ K P + +PE
Sbjct: 771 DKIVMPEAGVRGYKGKEYYRLLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQEFKELSPEQ 830
Query: 1091 --KEVPVSYKGSVPSYLEKVLVSSNSEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVIGL 1148
++ + + ++ VL++ +E L+K+ +R R P IGDKF+SRHGQKGVIG+
Sbjct: 831 AKRDTSIVTRHGEMGIVDLVLITETAEGNKLVKVRVRDLRIPTIGDKFASRHGQKGVIGM 890
Query: 1149 IVEQEDMPFNESGICPDIIMNPHGL 1173
++ Q DMP+ G+ PDII+NPH L
Sbjct: 891 LIPQVDMPYTVKGVVPDIILNPHAL 915
Score = 184 bits (468), Expect = 2e-46, Method: Compositional matrix adjust.
Identities = 86/173 (49%), Positives = 121/173 (69%)
Query: 1200 VLVSSNSEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDII 1259
VL++ +E L+K+ +R R P IGDKF+SRHGQKGVIG+++ Q DMP+ G+ PDII
Sbjct: 850 VLITETAEGNKLVKVRVRDLRIPTIGDKFASRHGQKGVIGMLIPQVDMPYTVKGVVPDII 909
Query: 1260 MNPHGYPSRMTVGKLIELLAGKAGLMEGNYKEGTAFGGTKLVDVQEELIRHGYNYQGKDI 1319
+NPH PSRMT+G+++E +AGK + GN + T F T + +Q E++R+GY ++
Sbjct: 910 LNPHALPSRMTLGQIMEGIAGKYAALSGNIVDATPFYKTPIEQLQNEILRYGYLPDATEV 969
Query: 1320 FYSGITGEALEAYIYSGPVYYQKLKHMVQDKIHARSRGPRVVLTRQPTGRRWK 1372
Y G TG+ +++ IY G VYYQKL HMV DK+HAR+RGP +LTRQPT R +
Sbjct: 970 VYDGRTGQKIKSRIYFGVVYYQKLHHMVADKLHARARGPVQILTRQPTEGRAR 1022
Score = 108 bits (269), Expect = 3e-23, Method: Compositional matrix adjust.
Identities = 57/139 (41%), Positives = 78/139 (56%), Gaps = 15/139 (10%)
Query: 688 GFKRFDDFLYEGKIEYLDVNEGNDSHIAVSESGIRPGVTTHLEIAPFTLLGVCAGIELLQ 747
G FDD + +GKIEYLD E ++++A+ + + P THLEI +LG+ A I
Sbjct: 600 GAITFDDLVRQGKIEYLDAEEEENAYVALEPNDLTPD-HTHLEIWSPAILGITASI---- 654
Query: 748 YNKRFHSPGLVPYPHHNQAPRNTYQCAMGKQAMGCIGYNQQNRIDTLMYNLVYAQRPMVE 807
+PYP HNQ+PRNTYQ AM KQA+G N Q R DT + L Y QRP+V+
Sbjct: 655 ----------IPYPEHNQSPRNTYQSAMAKQALGLYAANYQLRTDTRAHLLHYPQRPLVQ 704
Query: 808 SKTIRITNFHKLPAGKCQI 826
++ + I + PAG I
Sbjct: 705 TRALDIIGYTNRPAGNNAI 723
Score = 87.8 bits (216), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 44/115 (38%), Positives = 66/115 (57%), Gaps = 5/115 (4%)
Query: 192 MRQDTITNALTAAIQTGNWTIRRFKMERQGVTQVLSRLSYISGLGMMTRINSQFEKTRKV 251
+R D +T + A+ TGNW R GV+Q+L R +++S L + R+ S + +
Sbjct: 385 VRPDIVTERIRHALATGNWV-----GGRTGVSQLLDRTNWLSMLSHLRRVISSLARGQPN 439
Query: 252 SGPRSLQGSQWGMLCPSDTPEGEACGLVKNLALMTHITTENDEKNMLKIMYNIGI 306
R L G+QWG +CP +TPEG GLVKNLALM I +E+ + K +Y +G+
Sbjct: 440 FEARDLHGTQWGRMCPFETPEGPNSGLVKNLALMAQIAVGINERIVEKTLYEMGV 494
Score = 47.8 bits (112), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 28/87 (32%), Positives = 45/87 (51%), Gaps = 6/87 (6%)
Query: 449 KKTPVDDARDFLSSTCIAHIPVINMRFKMKAMYLAVMIRRMV---LALSDPDMLDDRDYY 505
++ ++ A+ + + H+ K KA YLA I +++ L +PD D+D+Y
Sbjct: 282 RENRIEKAQQIIDKYFLPHLGTSAEDRKKKAYYLAYAISKVIELYLGRREPD---DKDHY 338
Query: 506 GNKRLELAGSLLSLMFEDVFKRFNSEL 532
NKRL LAG L + +F FK F +L
Sbjct: 339 ANKRLRLAGDLFASLFRVAFKAFVKDL 365
Score = 46.2 bits (108), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 37/62 (59%)
Query: 341 VCKPEIEESFNYTRQTTPHECRLRDLTYSAPITVDIEYTRGSQRVVRSDLVIGRMPIMLQ 400
+ KP + ES R+ +P E RLR+LTY+AP+ + + + ++ IG +PIML+
Sbjct: 65 IGKPRVRESDRGEREISPMEARLRNLTYAAPLWLTMIPVENNIEAEPEEVYIGDLPIMLK 124
Query: 401 SS 402
S+
Sbjct: 125 SA 126
Score = 40.0 bits (92), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 39/61 (63%), Gaps = 1/61 (1%)
Query: 112 IRDKWKLVLSFLKEKGLVKPHIDSFDYFINVEIKKLMQANANIYSDVDPLFYLKYLDIHV 171
I ++W+++ ++ K KGLV+ H+DS++ F+ ++++++ I +++ P ++ I +
Sbjct: 7 IDERWRVIEAYFKSKGLVRQHLDSYNDFVRNKLQEIIDEQGEIPTEI-PGLKVRLGKIRI 65
Query: 172 G 172
G
Sbjct: 66 G 66
>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 = 208 bits (529), Expect = 2e-53, Method: Compositional matrix adjust.
Identities = 104/267 (38%), Positives = 159/267 (59%), Gaps = 5/267 (1%)
Query: 911 SPGLVPYPHHNQAPRNTYQCAMGKQAMGCIGYNQQNRIDTLMYNLVYAQRPMVESKTIRI 970
+ ++P+P HNQ+PRNTYQ AMGKQAMG N R+DT+ L Y Q+P+ ++ +
Sbjct: 752 AASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEY 811
Query: 971 TNFHKLPAGQNATIAVMSYSGYDIEDALIMNKASLDRGFGRCLVYRNSKCVLKQYPNQTH 1030
F +LPAGQNA +A+ YSGY+ ED++IMN++S+DRG R L +R+ K+Y
Sbjct: 812 LKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSIT 871
Query: 1031 DRILGPLLEADTRKPVYRHRALDQDGIVAPGEQICERQVLVNKSMPTISVSAISM----A 1086
+ P R + LD DG++APG ++ V++ K+ P IS + A
Sbjct: 872 ETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTP-ISPDEEELGQRTA 930
Query: 1087 TPEYKEVPVSYKGSVPSYLEKVLVSSNSEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVI 1146
++ + + +++VLV++N + +K+ +R T+ P+IGDKF+SRHGQKG I
Sbjct: 931 YHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTI 990
Query: 1147 GLIVEQEDMPFNESGICPDIIMNPHGL 1173
G+ +EDMPF GI PD+I+NPH +
Sbjct: 991 GITYRREDMPFTAEGIVPDLIINPHAI 1017
Score = 184 bits (467), Expect = 3e-46, Method: Compositional matrix adjust.
Identities = 86/174 (49%), Positives = 117/174 (67%)
Query: 1197 LEKVLVSSNSEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGICP 1256
+++VLV++N + +K+ +R T+ P+IGDKF+SRHGQKG IG+ +EDMPF GI P
Sbjct: 949 VDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVP 1008
Query: 1257 DIIMNPHGYPSRMTVGKLIELLAGKAGLMEGNYKEGTAFGGTKLVDVQEELIRHGYNYQG 1316
D+I+NPH PSRMTV LIE L K + GN + + F + + + L HGY +G
Sbjct: 1009 DLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRG 1068
Query: 1317 KDIFYSGITGEALEAYIYSGPVYYQKLKHMVQDKIHARSRGPRVVLTRQPTGRR 1370
++ Y+G TG+ L A I+ GP YYQ+L+HMV DKIHAR+RGP VLTRQP R
Sbjct: 1069 FEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGR 1122
Score = 110 bits (275), Expect = 5e-24, Method: Compositional matrix adjust.
Identities = 57/150 (38%), Positives = 90/150 (60%), Gaps = 3/150 (2%)
Query: 186 FDIVNHMRQDTITNALTAAIQTGNWTIRRFKME-RQGVTQVLSRLSYISGLGMMTRINSQ 244
F++ + TIT+ L A+ TGNW ++ M R GV+QVL+R +Y S L + R N+
Sbjct: 442 FNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTP 501
Query: 245 FEKTRKVSGPRSLQGSQWGMLCPSDTPEGEACGLVKNLALMTHITTENDEKNMLKIMYNI 304
+ K++ PR L + WG++CP++TPEG+ACGLVKNL+LM+ I+ D ++ +
Sbjct: 502 IGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEW 561
Query: 305 GIEHIAMFNGEELSSPGVYLVFVNGILAGI 334
G+E + + + SP VFVNG+ G+
Sbjct: 562 GMEPLEDYVPHQ--SPDATRVFVNGVWHGV 589
Score = 88.6 bits (218), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 55/167 (32%), Positives = 76/167 (45%), Gaps = 42/167 (25%)
Query: 688 GFKRFDDF-----LYEGKIEYLDVNEGNDSHIAVSESGIRPG------------------ 724
GF+ +++ L EG +EY+D E IA+ + P
Sbjct: 672 GFEDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAEANEENDLDVDPAKRIRV 731
Query: 725 -----VTTHLEIAPFTLLGVCAGIELLQYNKRFHSPGLVPYPHHNQAPRNTYQCAMGKQA 779
TH EI P +LGV A I +P+P HNQ+PRNTYQ AMGKQA
Sbjct: 732 SHHATTFTHCEIHPSMILGVAASI--------------IPFPDHNQSPRNTYQSAMGKQA 777
Query: 780 MGCIGYNQQNRIDTLMYNLVYAQRPMVESKTIRITNFHKLPAGKCQI 826
MG N R+DT+ L Y Q+P+ ++ + F +LPAG+ I
Sbjct: 778 MGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAI 824
Score = 60.5 bits (145), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 38/121 (31%), Positives = 59/121 (48%), Gaps = 14/121 (11%)
Query: 449 KKTPVDDARDFLSSTCIAHIPVINMRFKMKAMYLAVMIRRMVLALSDPDMLDDRDYYGNK 508
K+ + A+D L + HI + KA +L MI R++L D DDRD++G K
Sbjct: 345 KEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKK 404
Query: 509 RLELAGSLLSLMFEDVFKRFN-----------SELKETNLSGVVN---LVSGWWFELKYG 554
RL+LAG LL+ +F+ +FK+ E + N+ +N + SG + L G
Sbjct: 405 RLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDFNMKLAINAKTITSGLKYALATG 464
Query: 555 N 555
N
Sbjct: 465 N 465
Score = 48.1 bits (113), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 32/90 (35%), Positives = 43/90 (47%), Gaps = 19/90 (21%)
Query: 341 VCKPEIEESFNYTRQTTPHECRLRDLTYSAPITVDI-----EYTRGSQRVVRSDLV---- 391
V KP + ES T P E RLR+LTYS+ + VD+ E R ++ +L+
Sbjct: 97 VTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEES 156
Query: 392 ----------IGRMPIMLQSSKCVLRNKTE 411
IGR+PIML+S C L TE
Sbjct: 157 EDDSESGKVFIGRLPIMLRSKNCYLSEATE 186
Score = 37.7 bits (86), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 27/41 (65%)
Query: 114 DKWKLVLSFLKEKGLVKPHIDSFDYFINVEIKKLMQANANI 154
D W ++ +F +EKGLV +DSF+ F++ ++ ++ ++ +
Sbjct: 29 DSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTL 69
>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 = 207 bits (526), Expect = 4e-53, Method: Compositional matrix adjust.
Identities = 102/265 (38%), Positives = 160/265 (60%), Gaps = 2/265 (0%)
Query: 911 SPGLVPYPHHNQAPRNTYQCAMGKQAMGCIGYNQQNRIDTLMYNLVYAQRPMVESKTIRI 970
+ ++PYP HNQ+PRNTYQ AM KQA+G N Q R DT + L Y QRP+V+++ + I
Sbjct: 654 TASIIPYPEHNQSPRNTYQSAMAKQALGLYAANYQLRTDTRAHLLHYPQRPLVQTRALDI 713
Query: 971 TNFHKLPAGQNATIAVMSYSGYDIEDALIMNKASLDRGFGRCLVYRNSKCVLKQYPNQTH 1030
+ PAG NA +AV+S++GY++ED++IMN++S++RG R +R +YP
Sbjct: 714 IGYTNRPAGNNAILAVISFTGYNMEDSIIMNRSSVERGMYRSTFFRLYSTEEVKYPGGQE 773
Query: 1031 DRILGPLLEADTRKPVYRHRALDQDGIVAPGEQICERQVLVNKSMPTISVSAISMATPEY 1090
D+I+ P K +R L+ +G+V+P ++ VL+ K P + +PE
Sbjct: 774 DKIVMPEPGVRGYKGKEYYRLLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQEFKELSPEQ 833
Query: 1091 --KEVPVSYKGSVPSYLEKVLVSSNSEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVIGL 1148
++ + + ++ VL++ +E L+K+ +R R P IGDKF+SRHGQKGVIG+
Sbjct: 834 AKRDTSIVTRHGEMGIVDLVLITETAEGNKLVKVRVRDLRIPSIGDKFASRHGQKGVIGM 893
Query: 1149 IVEQEDMPFNESGICPDIIMNPHGL 1173
++ Q DMP+ G+ PD+I+NPH L
Sbjct: 894 LIPQVDMPYTVKGVVPDVILNPHAL 918
Score = 183 bits (465), Expect = 5e-46, Method: Compositional matrix adjust.
Identities = 85/173 (49%), Positives = 121/173 (69%)
Query: 1200 VLVSSNSEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDII 1259
VL++ +E L+K+ +R R P IGDKF+SRHGQKGVIG+++ Q DMP+ G+ PD+I
Sbjct: 853 VLITETAEGNKLVKVRVRDLRIPSIGDKFASRHGQKGVIGMLIPQVDMPYTVKGVVPDVI 912
Query: 1260 MNPHGYPSRMTVGKLIELLAGKAGLMEGNYKEGTAFGGTKLVDVQEELIRHGYNYQGKDI 1319
+NPH PSRMT+G+++E +AGK + GN + T F T + +Q E++++GY ++
Sbjct: 913 LNPHALPSRMTLGQIMEGIAGKYAALSGNIVDATPFYKTPIEQLQNEILKYGYLPDATEV 972
Query: 1320 FYSGITGEALEAYIYSGPVYYQKLKHMVQDKIHARSRGPRVVLTRQPTGRRWK 1372
Y G TG+ +++ IY G VYYQKL HMV DKIHAR+RGP +LTRQPT R +
Sbjct: 973 TYDGRTGQKIKSRIYFGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAR 1025
Score = 108 bits (271), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 57/135 (42%), Positives = 77/135 (57%), Gaps = 15/135 (11%)
Query: 692 FDDFLYEGKIEYLDVNEGNDSHIAVSESGIRPGVTTHLEIAPFTLLGVCAGIELLQYNKR 751
FDD + +GKIEYLD E ++++A+ S + P THLEI +LG+ A I
Sbjct: 607 FDDLVRQGKIEYLDAEEEENAYVALEPSDLTPE-HTHLEIWSPAILGITASI-------- 657
Query: 752 FHSPGLVPYPHHNQAPRNTYQCAMGKQAMGCIGYNQQNRIDTLMYNLVYAQRPMVESKTI 811
+PYP HNQ+PRNTYQ AM KQA+G N Q R DT + L Y QRP+V+++ +
Sbjct: 658 ------IPYPEHNQSPRNTYQSAMAKQALGLYAANYQLRTDTRAHLLHYPQRPLVQTRAL 711
Query: 812 RITNFHKLPAGKCQI 826
I + PAG I
Sbjct: 712 DIIGYTNRPAGNNAI 726
Score = 90.1 bits (222), Expect = 9e-18, Method: Compositional matrix adjust.
Identities = 56/159 (35%), Positives = 81/159 (50%), Gaps = 12/159 (7%)
Query: 192 MRQDTITNALTAAIQTGNWTIRRFKMERQGVTQVLSRLSYISGLGMMTRINSQFEKTRKV 251
+R D +T + A+ TGNW R GV+Q+L R +++S L + R+ S + +
Sbjct: 388 VRPDIVTERIRHALATGNWV-----GGRTGVSQLLDRTNWLSMLSHLRRVISSLARGQPN 442
Query: 252 SGPRSLQGSQWGMLCPSDTPEGEACGLVKNLALMTHITTENDEKNMLKIMYNIG---IEH 308
R L G+QWG +CP +TPEG GLVKNLALM I +EK + K +Y +G +E
Sbjct: 443 FEARDLHGTQWGRMCPFETPEGPNSGLVKNLALMAQIAVGINEKIVEKTLYEMGVVPVEE 502
Query: 309 IAMFNGEELSSPGVYL----VFVNGILAGITCHHKEVCK 343
+ E YL V +NG L G +E+ K
Sbjct: 503 VIRRVTEGGEDQNEYLKWSKVILNGRLVGYYRDGEELAK 541
Score = 46.6 bits (109), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 27/87 (31%), Positives = 45/87 (51%), Gaps = 6/87 (6%)
Query: 449 KKTPVDDARDFLSSTCIAHIPVINMRFKMKAMYLAVMIRRMV---LALSDPDMLDDRDYY 505
++ ++ A+ + + H+ + KA YLA I +++ L +PD D+D+Y
Sbjct: 285 RENRIEKAQQIIDKYFLPHLGTSADDRRKKAYYLAYAISKVIELYLGRREPD---DKDHY 341
Query: 506 GNKRLELAGSLLSLMFEDVFKRFNSEL 532
NKRL LAG L + +F FK F +L
Sbjct: 342 ANKRLRLAGDLFASLFRVAFKAFVKDL 368
Score = 45.8 bits (107), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 37/62 (59%)
Query: 341 VCKPEIEESFNYTRQTTPHECRLRDLTYSAPITVDIEYTRGSQRVVRSDLVIGRMPIMLQ 400
+ KP + ES R+ +P E RLR+LTY+AP+ + + + ++ IG +PIML+
Sbjct: 68 IGKPRVRESDRGEREISPMEARLRNLTYAAPLWLTMIPVENNIEAEPEEVYIGDLPIMLK 127
Query: 401 SS 402
S+
Sbjct: 128 SA 129
Score = 42.0 bits (97), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/69 (24%), Positives = 43/69 (62%), Gaps = 1/69 (1%)
Query: 104 SKLKDSPEIRDKWKLVLSFLKEKGLVKPHIDSFDYFINVEIKKLMQANANIYSDVDPLFY 163
++L + I ++WK++ ++ K KGLV+ H+DS++ F+ ++++++ I +++ P
Sbjct: 2 NELSSNLSIDERWKVIEAYFKSKGLVRQHLDSYNDFVRNKLQEIIDEQGEIPTEI-PGLK 60
Query: 164 LKYLDIHVG 172
++ I +G
Sbjct: 61 VRLGKIRIG 69
>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 = 109 bits (272), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 67/201 (33%), Positives = 98/201 (48%), Gaps = 43/201 (21%)
Query: 1211 LIKMLLRQTRRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDIIMNPHGYPSRMT 1270
++++ + Q R+ ++GDK ++RHG KGV+ I+ EDMP G D+I+NP G PSRM
Sbjct: 822 VVRVYVAQKRKLQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMN 881
Query: 1271 VGKLIELLAGKAGLMEGNYKEGTAFGGTKLVDVQEELI---------RHGYNY------- 1314
+G+++E G AG G F G K +++E L R G +
Sbjct: 882 LGQILETHLGLAGYFLGQRYISPIFDGAKEPEIKELLAQAFEVYFGKRKGEGFGVDKREV 941
Query: 1315 ---------------------------QGKDIFYSGITGEALEAYIYSGPVYYQKLKHMV 1347
QGK + Y G TGE +E I G ++ KL HMV
Sbjct: 942 EVLRRAEKLGLVTPGKTPEEQLKELFLQGKVVLYDGRTGEPIEGPIVVGQMFIMKLYHMV 1001
Query: 1348 QDKIHARSRGPRVVLTRQPTG 1368
+DK+HARS GP ++T+QP G
Sbjct: 1002 EDKMHARSTGPYSLITQQPLG 1022
Score = 75.9 bits (185), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 59/224 (26%), Positives = 101/224 (45%), Gaps = 39/224 (17%)
Query: 976 LPAGQNATIAVMSYSGYDIEDALIMNKASLDRGFGRCLVYRNSKCVLKQYPNQTHDRILG 1035
L GQN +A+M + GY+ EDA+++++ L R F + +++Y + D LG
Sbjct: 666 LALGQNVLVAIMPFDGYNFEDAIVISEELLKRDF-------YTSIHIERYEIEARDTKLG 718
Query: 1036 PLLEADTRKPVYRHRA----LDQDGIVAPGEQICERQVLVNKSMPTISVSAISMATPEYK 1091
P E TR + A LD++G+V G ++ +LV ++ S S TPE +
Sbjct: 719 P--ERITRDIPHLSEAALRDLDEEGVVRIGAEVKPGDILVGRT----SFKGESEPTPEER 772
Query: 1092 EVPVSYKGSVPSYLEKVLVSSNSEDAFLIKML----------------------LRQTRR 1129
+ + + L E +++ + + Q R+
Sbjct: 773 LLRSIFGEKARDVKDTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVREVVRVYVAQKRK 832
Query: 1130 PEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDIIMNPHGL 1173
++GDK ++RHG KGV+ I+ EDMP G D+I+NP G+
Sbjct: 833 LQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGV 876
Score = 36.2 bits (82), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 28/113 (24%), Positives = 49/113 (43%), Gaps = 9/113 (7%)
Query: 194 QDTITNALTAAIQTGNWTIRRFKMERQGVTQVLSRLSYISGLGMMTRINS----QFEKTR 249
+D++T A + IR F R ++Q + +S L RI++ + R
Sbjct: 364 EDSLTPAKLVNSRPLEAAIREF-FSRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRER 422
Query: 250 KVSGPRSLQGSQWGMLCPSDTPEGEACGLVKNLALMTHITTENDEKNMLKIMY 302
R + + +G +CP +TPEG GL+ +LA + DE ++ Y
Sbjct: 423 AGFDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARV----DELGFIRTPY 471
Score = 32.7 bits (73), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 360 ECRLRDLTYSAPITVDIEYTRGSQRVVRSDLV-IGRMPIMLQSSKCVL 406
ECR +DLTY AP+ ++ +++ D V +G +P+M + ++
Sbjct: 82 ECREKDLTYQAPLYARLQLIHKDTGLIKEDEVFLGHIPLMTEDGSFII 129
>pdb|1I6V|C Chain C, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1118
Score = 105 bits (263), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 65/201 (32%), Positives = 95/201 (47%), Gaps = 43/201 (21%)
Query: 1211 LIKMLLRQTRRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDIIMNPHGYPSRMT 1270
++++ + Q R+ ++GDK ++RHG KGV+ I+ EDMP G D+I+NP G PSRM
Sbjct: 821 VVRVFVAQKRKLQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMN 880
Query: 1271 VGKLIELLAGKAGLMEGNYKEGTAFGGTKLVDVQEELI---------RHGYNYQ------ 1315
+G+++E G AG G F G +++E L R G +
Sbjct: 881 LGQILETHLGLAGYFLGQRYISPVFDGATEPEIKELLAEAFNLYFGKRQGEGFGVDKREK 940
Query: 1316 ----------------------------GKDIFYSGITGEALEAYIYSGPVYYQKLKHMV 1347
GK + Y G TGE E I G ++ KL HMV
Sbjct: 941 EVLARAEKLGLVSPGKSPEEQLKELFDLGKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMV 1000
Query: 1348 QDKIHARSRGPRVVLTRQPTG 1368
+DK+HARS GP ++T+QP G
Sbjct: 1001 EDKMHARSTGPYSLITQQPLG 1021
Score = 74.7 bits (182), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 62/226 (27%), Positives = 103/226 (45%), Gaps = 43/226 (19%)
Query: 976 LPAGQNATIAVMSYSGYDIEDALIMNKASLDRGFGRCLVYRNSKCVLKQYPNQTHDRILG 1035
L GQN +A+M + GY+ EDA+++++ L R F + +++Y + D LG
Sbjct: 665 LALGQNVLVAIMPFDGYNFEDAIVISEELLKRDF-------YTSIHIERYEIEARDTKLG 717
Query: 1036 PLLEADTRKPVYRHRA----LDQDGIVAPGEQICERQVLVNKSMPTISVSAISMATPEYK 1091
P E TR + A LD++GIV G ++ +LV ++ S +PE +
Sbjct: 718 P--ERITRDIPHLSEAALRDLDEEGIVRIGAEVKPGDILVGRT----SFKGEQEPSPEER 771
Query: 1092 ------------------EVPVSYKGSVPSYLE------KVLVSSNSEDAFLIKMLLRQT 1127
VP G V L V + + ++++ + Q
Sbjct: 772 LLRSIFGEKARDVKDTSLRVPPGEGGIVVGRLRLRRGDPGVELKPGVRE--VVRVFVAQK 829
Query: 1128 RRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDIIMNPHGL 1173
R+ ++GDK ++RHG KGV+ I+ EDMP G D+I+NP G+
Sbjct: 830 RKLQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGV 875
Score = 35.0 bits (79), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 25/98 (25%), Positives = 43/98 (43%), Gaps = 5/98 (5%)
Query: 195 DTITNALTAAIQTGNWTIRRFKMERQGVTQVLSRLSYISGLGMMTRINS----QFEKTRK 250
DT+T A + +R F R ++Q + +S L RI++ + R
Sbjct: 365 DTLTPAKLVNSRPLEAALREF-FSRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERA 423
Query: 251 VSGPRSLQGSQWGMLCPSDTPEGEACGLVKNLALMTHI 288
R + + +G +CP +TPEG GL+ +LA +
Sbjct: 424 GFDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARV 461
Score = 33.1 bits (74), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 360 ECRLRDLTYSAPITVDIEYTRGSQRVVRSDLV-IGRMPIMLQSSKCVL 406
ECR +DLTY AP+ ++ +++ D V +G +P+M + ++
Sbjct: 82 ECREKDLTYQAPLYARLQLIHKDTGLIKEDEVFLGHLPLMTEDGSFII 129
>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 = 105 bits (263), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 65/201 (32%), Positives = 95/201 (47%), Gaps = 43/201 (21%)
Query: 1211 LIKMLLRQTRRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDIIMNPHGYPSRMT 1270
++++ + Q R+ ++GDK ++RHG KGV+ I+ EDMP G D+I+NP G PSRM
Sbjct: 822 VVRVFVAQKRKLQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMN 881
Query: 1271 VGKLIELLAGKAGLMEGNYKEGTAFGGTKLVDVQEELI---------RHGYNYQ------ 1315
+G+++E G AG G F G +++E L R G +
Sbjct: 882 LGQILETHLGLAGYFLGQRYISPVFDGATEPEIKELLAEAFNLYFGKRQGEGFGVDKREK 941
Query: 1316 ----------------------------GKDIFYSGITGEALEAYIYSGPVYYQKLKHMV 1347
GK + Y G TGE E I G ++ KL HMV
Sbjct: 942 EVLARAEKLGLVSPGKSPEEQLKELFDLGKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMV 1001
Query: 1348 QDKIHARSRGPRVVLTRQPTG 1368
+DK+HARS GP ++T+QP G
Sbjct: 1002 EDKMHARSTGPYSLITQQPLG 1022
Score = 74.3 bits (181), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 62/226 (27%), Positives = 103/226 (45%), Gaps = 43/226 (19%)
Query: 976 LPAGQNATIAVMSYSGYDIEDALIMNKASLDRGFGRCLVYRNSKCVLKQYPNQTHDRILG 1035
L GQN +A+M + GY+ EDA+++++ L R F + +++Y + D LG
Sbjct: 666 LALGQNVLVAIMPFDGYNFEDAIVISEELLKRDF-------YTSIHIERYEIEARDTKLG 718
Query: 1036 PLLEADTRKPVYRHRA----LDQDGIVAPGEQICERQVLVNKSMPTISVSAISMATPEYK 1091
P E TR + A LD++GIV G ++ +LV ++ S +PE +
Sbjct: 719 P--ERITRDIPHLSEAALRDLDEEGIVRIGAEVKPGDILVGRT----SFKGEQEPSPEER 772
Query: 1092 ------------------EVPVSYKGSVPSYLE------KVLVSSNSEDAFLIKMLLRQT 1127
VP G V L V + + ++++ + Q
Sbjct: 773 LLRSIFGEKARDVKDTSLRVPPGEGGIVVGRLRLRRGDPGVELKPGVRE--VVRVFVAQK 830
Query: 1128 RRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDIIMNPHGL 1173
R+ ++GDK ++RHG KGV+ I+ EDMP G D+I+NP G+
Sbjct: 831 RKLQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGV 876
Score = 35.0 bits (79), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 25/98 (25%), Positives = 43/98 (43%), Gaps = 5/98 (5%)
Query: 195 DTITNALTAAIQTGNWTIRRFKMERQGVTQVLSRLSYISGLGMMTRINS----QFEKTRK 250
DT+T A + +R F R ++Q + +S L RI++ + R
Sbjct: 365 DTLTPAKLVNSRPLEAALREF-FSRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERA 423
Query: 251 VSGPRSLQGSQWGMLCPSDTPEGEACGLVKNLALMTHI 288
R + + +G +CP +TPEG GL+ +LA +
Sbjct: 424 GFDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARV 461
Score = 33.1 bits (74), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 360 ECRLRDLTYSAPITVDIEYTRGSQRVVRSDLV-IGRMPIMLQSSKCVL 406
ECR +DLTY AP+ ++ +++ D V +G +P+M + ++
Sbjct: 82 ECREKDLTYQAPLYARLQLIHKDTGLIKEDEVFLGHLPLMTEDGSFII 129
>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 = 105 bits (263), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 65/201 (32%), Positives = 95/201 (47%), Gaps = 43/201 (21%)
Query: 1211 LIKMLLRQTRRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDIIMNPHGYPSRMT 1270
++++ + Q R+ ++GDK ++RHG KGV+ I+ EDMP G D+I+NP G PSRM
Sbjct: 821 VVRVFVAQKRKLQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMN 880
Query: 1271 VGKLIELLAGKAGLMEGNYKEGTAFGGTKLVDVQEELI---------RHGYNYQ------ 1315
+G+++E G AG G F G +++E L R G +
Sbjct: 881 LGQILETHLGLAGYFLGQRYISPVFDGATEPEIKELLAEAFNLYFGKRQGEGFGVDKREK 940
Query: 1316 ----------------------------GKDIFYSGITGEALEAYIYSGPVYYQKLKHMV 1347
GK + Y G TGE E I G ++ KL HMV
Sbjct: 941 EVLARAEKLGLVSPGKSPEEQLKELFDLGKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMV 1000
Query: 1348 QDKIHARSRGPRVVLTRQPTG 1368
+DK+HARS GP ++T+QP G
Sbjct: 1001 EDKMHARSTGPYSLITQQPLG 1021
Score = 74.7 bits (182), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 62/226 (27%), Positives = 103/226 (45%), Gaps = 43/226 (19%)
Query: 976 LPAGQNATIAVMSYSGYDIEDALIMNKASLDRGFGRCLVYRNSKCVLKQYPNQTHDRILG 1035
L GQN +A+M + GY+ EDA+++++ L R F + +++Y + D LG
Sbjct: 665 LALGQNVLVAIMPFDGYNFEDAIVISEELLKRDF-------YTSIHIERYEIEARDTKLG 717
Query: 1036 PLLEADTRKPVYRHRA----LDQDGIVAPGEQICERQVLVNKSMPTISVSAISMATPEYK 1091
P E TR + A LD++GIV G ++ +LV ++ S +PE +
Sbjct: 718 P--ERITRDIPHLSEAALRDLDEEGIVRIGAEVKPGDILVGRT----SFKGEQEPSPEER 771
Query: 1092 ------------------EVPVSYKGSVPSYLE------KVLVSSNSEDAFLIKMLLRQT 1127
VP G V L V + + ++++ + Q
Sbjct: 772 LLRSIFGEKARDVKDTSLRVPPGEGGIVVGRLRLRRGDPGVELKPGVRE--VVRVFVAQK 829
Query: 1128 RRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDIIMNPHGL 1173
R+ ++GDK ++RHG KGV+ I+ EDMP G D+I+NP G+
Sbjct: 830 RKLQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGV 875
Score = 35.0 bits (79), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 25/98 (25%), Positives = 43/98 (43%), Gaps = 5/98 (5%)
Query: 195 DTITNALTAAIQTGNWTIRRFKMERQGVTQVLSRLSYISGLGMMTRINS----QFEKTRK 250
DT+T A + +R F R ++Q + +S L RI++ + R
Sbjct: 365 DTLTPAKLVNSRPLEAALREF-FSRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERA 423
Query: 251 VSGPRSLQGSQWGMLCPSDTPEGEACGLVKNLALMTHI 288
R + + +G +CP +TPEG GL+ +LA +
Sbjct: 424 GFDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARV 461
Score = 33.1 bits (74), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 360 ECRLRDLTYSAPITVDIEYTRGSQRVVRSDLV-IGRMPIMLQSSKCVL 406
ECR +DLTY AP+ ++ +++ D V +G +P+M + ++
Sbjct: 82 ECREKDLTYQAPLYARLQLIHKDTGLIKEDEVFLGHLPLMTEDGSFII 129
>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 = 105 bits (263), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 65/201 (32%), Positives = 95/201 (47%), Gaps = 43/201 (21%)
Query: 1211 LIKMLLRQTRRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDIIMNPHGYPSRMT 1270
++++ + Q R+ ++GDK ++RHG KGV+ I+ EDMP G D+I+NP G PSRM
Sbjct: 822 VVRVFVAQKRKLQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMN 881
Query: 1271 VGKLIELLAGKAGLMEGNYKEGTAFGGTKLVDVQEELI---------RHGYNYQ------ 1315
+G+++E G AG G F G +++E L R G +
Sbjct: 882 LGQILETHLGLAGYFLGQRYISPVFDGATEPEIKELLAEAFNLYFGKRQGEGFGVDKREK 941
Query: 1316 ----------------------------GKDIFYSGITGEALEAYIYSGPVYYQKLKHMV 1347
GK + Y G TGE E I G ++ KL HMV
Sbjct: 942 EVLARAEKLGLVSPGKSPEEQLKELFDLGKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMV 1001
Query: 1348 QDKIHARSRGPRVVLTRQPTG 1368
+DK+HARS GP ++T+QP G
Sbjct: 1002 EDKMHARSTGPYSLITQQPLG 1022
Score = 74.3 bits (181), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 62/226 (27%), Positives = 103/226 (45%), Gaps = 43/226 (19%)
Query: 976 LPAGQNATIAVMSYSGYDIEDALIMNKASLDRGFGRCLVYRNSKCVLKQYPNQTHDRILG 1035
L GQN +A+M + GY+ EDA+++++ L R F + +++Y + D LG
Sbjct: 666 LALGQNVLVAIMPFDGYNFEDAIVISEELLKRDF-------YTSIHIERYEIEARDTKLG 718
Query: 1036 PLLEADTRKPVYRHRA----LDQDGIVAPGEQICERQVLVNKSMPTISVSAISMATPEYK 1091
P E TR + A LD++GIV G ++ +LV ++ S +PE +
Sbjct: 719 P--ERITRDIPHLSEAALRDLDEEGIVRIGAEVKPGDILVGRT----SFKGEQEPSPEER 772
Query: 1092 ------------------EVPVSYKGSVPSYLE------KVLVSSNSEDAFLIKMLLRQT 1127
VP G V L V + + ++++ + Q
Sbjct: 773 LLRSIFGEKARDVKDTSLRVPPGEGGIVVGRLRLRRGDPGVELKPGVRE--VVRVFVAQK 830
Query: 1128 RRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDIIMNPHGL 1173
R+ ++GDK ++RHG KGV+ I+ EDMP G D+I+NP G+
Sbjct: 831 RKLQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGV 876
Score = 35.0 bits (79), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 25/98 (25%), Positives = 43/98 (43%), Gaps = 5/98 (5%)
Query: 195 DTITNALTAAIQTGNWTIRRFKMERQGVTQVLSRLSYISGLGMMTRINS----QFEKTRK 250
DT+T A + +R F R ++Q + +S L RI++ + R
Sbjct: 365 DTLTPAKLVNSRPLEAALREF-FSRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERA 423
Query: 251 VSGPRSLQGSQWGMLCPSDTPEGEACGLVKNLALMTHI 288
R + + +G +CP +TPEG GL+ +LA +
Sbjct: 424 GFDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARV 461
Score = 33.1 bits (74), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 360 ECRLRDLTYSAPITVDIEYTRGSQRVVRSDLV-IGRMPIMLQSSKCVL 406
ECR +DLTY AP+ ++ +++ D V +G +P+M + ++
Sbjct: 82 ECREKDLTYQAPLYARLQLIHKDTGLIKEDEVFLGHLPLMTEDGSFII 129
>pdb|3LU0|C Chain C, Molecular Model Of Escherichia Coli Core Rna Polymerase
Length = 1342
Score = 88.2 bits (217), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 66/217 (30%), Positives = 93/217 (42%), Gaps = 54/217 (24%)
Query: 1211 LIKMLLRQTRRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDIIMNPHGYPSRMT 1270
++K+ L RR + GDK + RHG KGVI I EDMP++E+G DI++NP G PSRM
Sbjct: 1049 IVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMN 1108
Query: 1271 -----------------------------VGKLIELLAGKAGL----------------- 1284
V KL E + L
Sbjct: 1109 IGQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEE 1168
Query: 1285 ---MEGNYKEGT-----AFGGTKLVDVQEELIRHGYNYQGKDIFYSGITGEALEAYIYSG 1336
+ N ++G F G K +++E L G+ Y G TGE E + G
Sbjct: 1169 VMRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVG 1228
Query: 1337 PVYYQKLKHMVQDKIHARSRGPRVVLTRQPTGRRWKL 1373
+Y KL H+V DK+HARS G ++T+QP G + +
Sbjct: 1229 YMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQF 1265
Score = 56.2 bits (134), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 26/55 (47%), Positives = 37/55 (67%)
Query: 1119 LIKMLLRQTRRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDIIMNPHGL 1173
++K+ L RR + GDK + RHG KGVI I EDMP++E+G DI++NP G+
Sbjct: 1049 IVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGV 1103
Score = 39.7 bits (91), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 34/124 (27%), Positives = 55/124 (44%), Gaps = 15/124 (12%)
Query: 971 TNFHKLPAGQNATIAVMSYSGYDIEDALIMNKASLDRGFGRCLVYRNSKCVLKQYPNQTH 1030
T+ +L GQN +A M ++GY+ ED++++++ + + + CV +
Sbjct: 789 TDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACV-------SR 841
Query: 1031 DRILGPLLEADTRKPVYRHRA---LDQDGIVAPGEQICERQVLVNKSMPTISVSAISMAT 1087
D LGP E P A LD+ GIV G ++ +LV K P + T
Sbjct: 842 DTKLGP-EEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTP----KGETQLT 896
Query: 1088 PEYK 1091
PE K
Sbjct: 897 PEEK 900
Score = 37.4 bits (85), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 28/103 (27%), Positives = 55/103 (53%), Gaps = 13/103 (12%)
Query: 187 DIVNHMRQDTI-TNALTAAIQT--GNWTIRRFKMERQGVTQVL--SRLSYISGLGMMTRI 241
D+ M QD I ++AA++ G+ + +F ++ ++++ R+S + G G +TR
Sbjct: 483 DLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMVQNNPLSEITHKRRISAL-GPGGLTRE 541
Query: 242 NSQFEKTRKVSGPRSLQGSQWGMLCPSDTPEGEACGLVKNLAL 284
+ FE R + + +G +CP +TPEG GL+ +L++
Sbjct: 542 RAGFE-------VRDVHPTHYGRVCPIETPEGPNIGLINSLSV 577
Score = 31.6 bits (70), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 29/113 (25%), Positives = 50/113 (44%), Gaps = 12/113 (10%)
Query: 359 HECRLRDLTYSAPITVDI-------EYTRGSQRVVRS-DLVIGRMPIMLQSSKCVLRNKT 410
EC++R +TYSAP+ V + E G+ + ++ ++ +G +P+M + V+ N T
Sbjct: 83 QECQIRGVTYSAPLRVKLRLVIYEREAPEGTVKDIKEQEVYMGEIPLMTDNGTFVI-NGT 141
Query: 411 EYXXXXXXXXXXXVTMHSQRTSPLLSCKKLRQKRFQTYKKTPVD---DARDFL 460
E V S + S K L R Y+ + +D D +D L
Sbjct: 142 ERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNL 194
>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 = 88.2 bits (217), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 66/217 (30%), Positives = 93/217 (42%), Gaps = 54/217 (24%)
Query: 1211 LIKMLLRQTRRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDIIMNPHGYPSRMT 1270
++K+ L RR + GDK + RHG KGVI I EDMP++E+G DI++NP G PSRM
Sbjct: 1049 IVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMN 1108
Query: 1271 -----------------------------VGKLIELLAGKAGL----------------- 1284
V KL E + L
Sbjct: 1109 IGQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEE 1168
Query: 1285 ---MEGNYKEGT-----AFGGTKLVDVQEELIRHGYNYQGKDIFYSGITGEALEAYIYSG 1336
+ N ++G F G K +++E L G+ Y G TGE E + G
Sbjct: 1169 VMRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVG 1228
Query: 1337 PVYYQKLKHMVQDKIHARSRGPRVVLTRQPTGRRWKL 1373
+Y KL H+V DK+HARS G ++T+QP G + +
Sbjct: 1229 YMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQF 1265
Score = 56.2 bits (134), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 26/55 (47%), Positives = 37/55 (67%)
Query: 1119 LIKMLLRQTRRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDIIMNPHGL 1173
++K+ L RR + GDK + RHG KGVI I EDMP++E+G DI++NP G+
Sbjct: 1049 IVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGV 1103
Score = 39.7 bits (91), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 34/124 (27%), Positives = 55/124 (44%), Gaps = 15/124 (12%)
Query: 971 TNFHKLPAGQNATIAVMSYSGYDIEDALIMNKASLDRGFGRCLVYRNSKCVLKQYPNQTH 1030
T+ +L GQN +A M ++GY+ ED++++++ + + + CV +
Sbjct: 789 TDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACV-------SR 841
Query: 1031 DRILGPLLEADTRKPVYRHRA---LDQDGIVAPGEQICERQVLVNKSMPTISVSAISMAT 1087
D LGP E P A LD+ GIV G ++ +LV K P + T
Sbjct: 842 DTKLGP-EEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTP----KGETQLT 896
Query: 1088 PEYK 1091
PE K
Sbjct: 897 PEEK 900
Score = 36.2 bits (82), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 28/103 (27%), Positives = 54/103 (52%), Gaps = 13/103 (12%)
Query: 187 DIVNHMRQDTI-TNALTAAIQT--GNWTIRRFKMERQGVTQVL--SRLSYISGLGMMTRI 241
D+ M QD I ++AA++ G+ + +F + ++++ R+S + G G +TR
Sbjct: 483 DLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISAL-GPGGLTRE 541
Query: 242 NSQFEKTRKVSGPRSLQGSQWGMLCPSDTPEGEACGLVKNLAL 284
+ FE R + + +G +CP +TPEG GL+ +L++
Sbjct: 542 RAGFE-------VRDVHPTHYGRVCPIETPEGPNIGLINSLSV 577
Score = 31.6 bits (70), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 29/113 (25%), Positives = 50/113 (44%), Gaps = 12/113 (10%)
Query: 359 HECRLRDLTYSAPITVDI-------EYTRGSQRVVRS-DLVIGRMPIMLQSSKCVLRNKT 410
EC++R +TYSAP+ V + E G+ + ++ ++ +G +P+M + V+ N T
Sbjct: 83 QECQIRGVTYSAPLRVKLRLVIYEREAPEGTVKDIKEQEVYMGEIPLMTDNGTFVI-NGT 141
Query: 411 EYXXXXXXXXXXXVTMHSQRTSPLLSCKKLRQKRFQTYKKTPVD---DARDFL 460
E V S + S K L R Y+ + +D D +D L
Sbjct: 142 ERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNL 194
>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 = 33.5 bits (75), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 360 ECRLRDLTYSAPITVDIEYTRGSQRVVRSDLV-IGRMPIMLQSSKCVL 406
ECR +DLTY AP+ ++ +++ D V +G +P+M + ++
Sbjct: 67 ECREKDLTYQAPLYARLQLIHKDTGLIKEDEVFLGHLPLMTEDGSFII 114
>pdb|4ED9|A Chain A, Crystal Structure Of A CaibBAIF FAMILY PROTEIN FROM
BRUCELLA SUIS
Length = 385
Score = 33.5 bits (75), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 29/124 (23%), Positives = 50/124 (40%), Gaps = 3/124 (2%)
Query: 701 IEYLDVNEGNDSHIAVSESGI---RPGVTTHLEIAPFTLLGVCAGIELLQYNKRFHSPGL 757
+ + D+ G S IA+ + I R G H+++A F + + + Y SP
Sbjct: 173 VAFADIFTGLYSVIAIQSALIMRARTGKGQHIDMALFDCMSGVLANQAMNYLASGKSPKR 232
Query: 758 VPYPHHNQAPRNTYQCAMGKQAMGCIGYNQQNRIDTLMYNLVYAQRPMVESKTIRITNFH 817
+ H N AP T + G + C Q ++ TL+ A+ + + R+ N
Sbjct: 233 MGNAHPNIAPYQTLSVSDGYFIIACGNDGQFGKLSTLLGIGELAKDERFATNSARVANRA 292
Query: 818 KLPA 821
L A
Sbjct: 293 ALTA 296
>pdb|3LOT|A Chain A, Crystal Structure Of Protein Of Unknown Function
(Np_070038.1) From Archaeoglobus Fulgidus At 1.89 A
Resolution
pdb|3LOT|B Chain B, Crystal Structure Of Protein Of Unknown Function
(Np_070038.1) From Archaeoglobus Fulgidus At 1.89 A
Resolution
pdb|3LOT|C Chain C, Crystal Structure Of Protein Of Unknown Function
(Np_070038.1) From Archaeoglobus Fulgidus At 1.89 A
Resolution
pdb|3LOT|D Chain D, Crystal Structure Of Protein Of Unknown Function
(Np_070038.1) From Archaeoglobus Fulgidus At 1.89 A
Resolution
Length = 314
Score = 30.8 bits (68), Expect = 5.7, Method: Composition-based stats.
Identities = 22/56 (39%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 280 KNLALMTHITTENDEKNMLKIMYNIG-IEHIAMFNGEELSSPGVYLVFVNGILAGI 334
K+L ++ I END K L+ Y+IG I + A E P + L F++GIL GI
Sbjct: 155 KDLEALSRIFKENDTKPELEC-YDIGQIYNTAFXFHEGYLEPPLRLQFIHGILGGI 209
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
0.321 0.137 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 40,986,970
Number of Sequences: 62578
Number of extensions: 1737111
Number of successful extensions: 3323
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 3216
Number of HSP's gapped (non-prelim): 85
length of query: 1384
length of database: 14,973,337
effective HSP length: 111
effective length of query: 1273
effective length of database: 8,027,179
effective search space: 10218598867
effective search space used: 10218598867
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 58 (26.9 bits)