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= psy8410
(951 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 247 bits (630), Expect = 2e-65, Method: Compositional matrix adjust.
Identities = 253/966 (26%), Positives = 412/966 (42%), Gaps = 158/966 (16%)
Query: 72 HIASFDFMLDEGLDLAVEDIAPIEFEIYGKTLKLNIVKAAISEPKVPAGPVGIHFNKYYP 131
H+ S++ + L +++ I EI G LK+ + K I +P+V G + P
Sbjct: 30 HLDSYNDFVRNKLQEIIDEQGEIPTEIPG--LKVRLGKIRIGKPRVRESDRG--EREISP 85
Query: 132 TEARQTRSVYSGPFNVTVAWSWDGKAGGTFTKEVGRVPIMLKSKRCHLRNLTPAQLIERG 191
EAR Y+ P +T+ + +G +PIMLKS + T +LIE G
Sbjct: 86 MEARLRNLTYAAPLWLTMIPVENNIEAEPEEVYIGDLPIMLKSAIDPISQYTLDKLIEIG 145
Query: 192 EHPDEWGGYFIVGGHEKLV---------RLLINNRRNHPIAIKRNAWKNRGLLFSDLGVY 242
E P + GGYFIV G E+++ R+L++ + N ++ S G
Sbjct: 146 EDPKDPGGYFIVNGSERVIVTQEDLAPNRVLVDTGKTGS-----NITHTAKIISSTAGYR 200
Query: 243 IR-SVKRDESATNNV--------LHFVTNGSARFMFSHRKSMCLLGMMQSLHEE------ 287
+ +++R + T +V + FV A + + R + + + + E
Sbjct: 201 VPVTIERLKDGTFHVSFPAVPGKIPFVILMRALGILTDRDIVYAVSLDPEIQNELFPSLE 260
Query: 288 ---GIHTQHDSKVFFGQIFKEKLQYDLRHLNEVEICDYMLTNCILPHL----DDYWDKFL 340
I D+ F G ++ + N +E ++ LPHL DD K
Sbjct: 261 QASSIANVDDALDFIGS----RVAIGQKRENRIEKAQQIIDKYFLPHLGTSADDRRKKAY 316
Query: 341 CLSHMTCKLFHVVQGMVQLDSEDSIMLQEIMTGGSLYL----------------QLLKKE 384
L++ K+ + G + D +D + + G L+ QL K +
Sbjct: 317 YLAYAISKVIELYLGRREPDDKDHYANKRLRLAGDLFASLFRVAFKAFVKDLTYQLEKSK 376
Query: 385 KSGTSAVLKESDIYAAFRASSIESAMTNFLATGNVSAGKNSTLQLMQASGFVIMAENINR 444
G LK A R + + + LATGN G+ QL+ + ++ M
Sbjct: 377 VRGRKLALK-----ALVRPDIVTERIRHALATGNWVGGRTGVSQLLDRTNWLSM------ 425
Query: 445 MRYMSHFRAVHRGSYFQEMRSSEPRQLRTDAWGFICPVHTPDGTPCGLLNHLTTNCQISE 504
+SH R V S + + E R L WG +CP TP+G GL+ +L QI+
Sbjct: 426 ---LSHLRRVI-SSLARGQPNFEARDLHGTQWGRMCPFETPEGPNSGLVKNLALMAQIAV 481
Query: 505 YIPSKVLAQIPSVLVSLGMLPLTPVIQSIPE---------QALMVMLDGRIVGYILDQIA 555
I K++ + L +G++P+ VI+ + E + V+L+GR+VGY D
Sbjct: 482 GINEKIVEK---TLYEMGVVPVEEVIRRVTEGGEDQNEYLKWSKVILNGRLVGYYRD--G 536
Query: 556 TSLVPKLRMLKIVGEKIPKSLEIVYLKRPEKGMGLYPGLYLFTGPGRMLRPVMNLAAGN- 614
L K+R + GE I + + ++ +++ GR+ RP++ ++ GN
Sbjct: 537 EELAKKIRERRRKGE-ISDEVNVGHIV-----TDFINEVHVNCDSGRVRRPLIIVSNGNP 590
Query: 615 ------IEWIGTFEQVFMDICITMK----------EAYPGIT--------THRELSKTDF 650
IE + + F D+ K AY + TH E+
Sbjct: 591 LVTREDIEKLDSGSITFDDLVRQGKIEYLDAEEEENAYVALEPSDLTPEHTHLEIWSPAI 650
Query: 651 LSNLANLIPMPDCNQSPRNMYQCQMGKQTMGTPCLNWRYQGVGKLYRLQTPASPFFRPVH 710
L A++IP P+ NQSPRN YQ M KQ +G N++ + + + L P P +
Sbjct: 651 LGITASIIPYPEHNQSPRNTYQSAMAKQALGLYAANYQLRTDTRAHLLHYPQRPLVQTRA 710
Query: 711 YDTLDMDNFPMGTNAIVAVISYTGYDMEDAMILNKSSYERGFAHGCIFKSMFIELESGYN 770
D + N P G NAI+AVIS+TGY+MED++I+N+SS ERG +++S F L
Sbjct: 711 LDIIGYTNRPAGNNAILAVISFTGYNMEDSIIMNRSSVERG-----MYRSTFFRL----- 760
Query: 771 YYGTETMYSG--VDGSMMQ---AQIFFGVVHYQRLRH--MVSDKWQTKDYFGRDPANKAL 823
Y E Y G D +M + + G +Y+ L +VS + + K L
Sbjct: 761 YSTEEVKYPGGQEDKIVMPEPGVRGYKGKEYYRLLEDNGVVSPEVEVK-------GGDVL 813
Query: 824 EDKLGPDGLVYVGAKLNERDPMYSYWKESENRYVTCRYSGKEEMCVEVVRMSSGFTEGGS 883
K+ P + + E P + S + R+ EM + + + + EG
Sbjct: 814 IGKVSPPRFL---QEFKELSPEQAKRDTS----IVTRHG---EMGIVDLVLITETAEGNK 863
Query: 884 VTPNCAYIGYRIQRNPTVGDKFASRAGQKGICSVKWPAEDLPFTDSGLVPDIVFNPHGFP 943
+ + R R P++GDKFASR GQKG+ + P D+P+T G+VPD++ NPH P
Sbjct: 864 LVK----VRVRDLRIPSIGDKFASRHGQKGVIGMLIPQVDMPYTVKGVVPDVILNPHALP 919
Query: 944 SRMTIG 949
SRMT+G
Sbjct: 920 SRMTLG 925
Score = 48.1 bits (113), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/47 (44%), Positives = 31/47 (65%)
Query: 765 LESGYNYYGTETMYSGVDGSMMQAQIFFGVVHYQRLRHMVSDKWQTK 811
L+ GY TE Y G G ++++I+FGVV+YQ+L HMV+DK +
Sbjct: 961 LKYGYLPDATEVTYDGRTGQKIKSRIYFGVVYYQKLHHMVADKIHAR 1007
>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 = 243 bits (620), Expect = 4e-64, Method: Compositional matrix adjust.
Identities = 253/966 (26%), Positives = 412/966 (42%), Gaps = 158/966 (16%)
Query: 72 HIASFDFMLDEGLDLAVEDIAPIEFEIYGKTLKLNIVKAAISEPKVPAGPVGIHFNKYYP 131
H+ S++ + L +++ I EI G LK+ + K I +P+V G + P
Sbjct: 27 HLDSYNDFVRNKLQEIIDEQGEIPTEIPG--LKVRLGKIRIGKPRVRESDRG--EREISP 82
Query: 132 TEARQTRSVYSGPFNVTVAWSWDGKAGGTFTKEVGRVPIMLKSKRCHLRNLTPAQLIERG 191
EAR Y+ P +T+ + +G +PIMLKS + T +LIE G
Sbjct: 83 MEARLRNLTYAAPLWLTMIPVENNIEAEPEEVYIGDLPIMLKSAIDPISQYTLDKLIEIG 142
Query: 192 EHPDEWGGYFIVGGHEKLV---------RLLINNRRNHPIAIKRNAWKNRGLLFSDLGVY 242
E P + GGYFIV G E+++ R+L++ + N ++ S G
Sbjct: 143 EDPKDPGGYFIVNGSERVIVTQEDLAPNRVLVDTGKTGS-----NITHTAKIISSTAGYR 197
Query: 243 IR-SVKRDESATNNV--------LHFVTNGSARFMFSHRKSMCLLGMMQSLHEE------ 287
+ +++R + T +V + FV A + + R + + + + E
Sbjct: 198 VPVTIERLKDGTFHVSFPAVPGKIPFVILMRALGILTDRDIVYAVSLDPEVQNELFPSLE 257
Query: 288 ---GIHTQHDSKVFFGQIFKEKLQYDLRHLNEVEICDYMLTNCILPHL----DDYWDKFL 340
I D+ F G ++ + N +E ++ LPHL +D K
Sbjct: 258 QASSIANVDDALDFIGS----RVAIGQKRENRIEKAQQIIDKYFLPHLGTSAEDRKKKAY 313
Query: 341 CLSHMTCKLFHVVQGMVQLDSEDSIMLQEIMTGGSLYL----------------QLLKKE 384
L++ K+ + G + D +D + + G L+ QL K +
Sbjct: 314 YLAYAISKVIELYLGRREPDDKDHYANKRLRLAGDLFASLFRVAFKAFVKDLTYQLEKSK 373
Query: 385 KSGTSAVLKESDIYAAFRASSIESAMTNFLATGNVSAGKNSTLQLMQASGFVIMAENINR 444
G LK A R + + + LATGN G+ QL+ + ++ M
Sbjct: 374 VRGRKLALK-----ALVRPDIVTERIRHALATGNWVGGRTGVSQLLDRTNWLSM------ 422
Query: 445 MRYMSHFRAVHRGSYFQEMRSSEPRQLRTDAWGFICPVHTPDGTPCGLLNHLTTNCQISE 504
+SH R V S + + E R L WG +CP TP+G GL+ +L QI+
Sbjct: 423 ---LSHLRRVI-SSLARGQPNFEARDLHGTQWGRMCPFETPEGPNSGLVKNLALMAQIAV 478
Query: 505 YIPSKVLAQIPSVLVSLGMLPLTPVIQSIPE---------QALMVMLDGRIVGYILDQIA 555
I +++ + L +G++P+ VI+ + E + V+L+GR++GY D
Sbjct: 479 GINERIVEK---TLYEMGVVPVEEVIRRVTEGGEDQNEYLKWSKVILNGRLIGYYQD--G 533
Query: 556 TSLVPKLRMLKIVGEKIPKSLEIVYLKRPEKGMGLYPGLYLFTGPGRMLRPVMNLAAGN- 614
L K+R + GE I + + ++ +++ GR+ RP++ ++ GN
Sbjct: 534 GELANKIRERRRKGE-ISDEVNVGHIV-----TDFINEVHVNCDSGRVRRPLIIVSNGNP 587
Query: 615 ---IEWIGTFEQ---VFMDICITMK----------EAYPGIT--------THRELSKTDF 650
IE I E F D+ K AY + TH E+
Sbjct: 588 LVTIEDIEKLESGAITFDDLVRQGKIEYLDAEEEENAYVALEPNDLTPDHTHLEIWSPAI 647
Query: 651 LSNLANLIPMPDCNQSPRNMYQCQMGKQTMGTPCLNWRYQGVGKLYRLQTPASPFFRPVH 710
L A++IP P+ NQSPRN YQ M KQ +G N++ + + + L P P +
Sbjct: 648 LGITASIIPYPEHNQSPRNTYQSAMAKQALGLYAANYQLRTDTRAHLLHYPQRPLVQTRA 707
Query: 711 YDTLDMDNFPMGTNAIVAVISYTGYDMEDAMILNKSSYERGFAHGCIFKSMFIELESGYN 770
D + N P G NAI+AV+S+TGY+MED++I+N+SS ERG +++S F L
Sbjct: 708 LDIIGYTNRPAGNNAILAVMSFTGYNMEDSIIMNRSSVERG-----MYRSTFFRL----- 757
Query: 771 YYGTETMYSGVDGS---MMQAQI--FFGVVHYQRLRH--MVSDKWQTKDYFGRDPANKAL 823
Y E Y G M +A + + G +Y+ L +VS + + K L
Sbjct: 758 YSTEEVKYPGGQEDKIVMPEAGVRGYKGKEYYRLLEDNGVVSPEVEVK-------GGDVL 810
Query: 824 EDKLGPDGLVYVGAKLNERDPMYSYWKESENRYVTCRYSGKEEMCVEVVRMSSGFTEGGS 883
K+ P + + E P + S + R+ EM + + + + EG
Sbjct: 811 IGKVSPPRFL---QEFKELSPEQAKRDTS----IVTRHG---EMGIVDLVLITETAEGNK 860
Query: 884 VTPNCAYIGYRIQRNPTVGDKFASRAGQKGICSVKWPAEDLPFTDSGLVPDIVFNPHGFP 943
+ + R R PT+GDKFASR GQKG+ + P D+P+T G+VPDI+ NPH P
Sbjct: 861 LVK----VRVRDLRIPTIGDKFASRHGQKGVIGMLIPQVDMPYTVKGVVPDIILNPHALP 916
Query: 944 SRMTIG 949
SRMT+G
Sbjct: 917 SRMTLG 922
Score = 48.5 bits (114), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/47 (44%), Positives = 31/47 (65%)
Query: 765 LESGYNYYGTETMYSGVDGSMMQAQIFFGVVHYQRLRHMVSDKWQTK 811
L GY TE +Y G G ++++I+FGVV+YQ+L HMV+DK +
Sbjct: 958 LRYGYLPDATEVVYDGRTGQKIKSRIYFGVVYYQKLHHMVADKLHAR 1004
>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 = 156 bits (394), Expect = 5e-38, Method: Compositional matrix adjust.
Identities = 104/323 (32%), Positives = 149/323 (46%), Gaps = 47/323 (14%)
Query: 641 THRELSKTDFLSNLANLIPMPDCNQSPRNMYQCQMGKQTMGTPCLNWRYQGVGKLYRLQT 700
TH E+ + L A++IP PD NQSPRN YQ MGKQ MG N+ + L
Sbjct: 739 THCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYY 798
Query: 701 PASPFFRPVHYDTLDMDNFPMGTNAIVAVISYTGYDMEDAMILNKSSYERGFAHGCIFKS 760
P P + L P G NAIVA+ Y+GY+ ED+MI+N+SS +RG F+S
Sbjct: 799 PQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRS 858
Query: 761 MFIELESGYNYYGTETMYSGVDGSMMQAQIFFGVVHYQRLRHMVSDKWQTKDYFGRDPAN 820
+++ E Y TET + + R++H
Sbjct: 859 -YMDQEKKYGMSITETFEKPQRTNTL------------RMKH------------------ 887
Query: 821 KALEDKLGPDGLVYVGAKLNERD-------PMYSYWKESENRYVTCRYSGKEEMCVEVVR 873
DKL DGL+ G +++ D P+ +E R Y K + +
Sbjct: 888 -GTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDEEELGQRTA---YHSKRDASTPLRS 943
Query: 874 MSSGFTEGGSVTPN---CAYIGYRIQ--RNPTVGDKFASRAGQKGICSVKWPAEDLPFTD 928
+G + VT N ++ R++ + P +GDKFASR GQKG + + ED+PFT
Sbjct: 944 TENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTA 1003
Query: 929 SGLVPDIVFNPHGFPSRMTIGFL 951
G+VPD++ NPH PSRMT+ L
Sbjct: 1004 EGIVPDLIINPHAIPSRMTVAHL 1026
Score = 92.4 bits (228), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 125/516 (24%), Positives = 205/516 (39%), Gaps = 99/516 (19%)
Query: 154 DGKAGGTFTKEVGRVPIMLKSKRCHLRNLTPAQLIERGEHPDEWGGYFIVGGHEKLVRLL 213
D ++G F +GR+PIML+SK C+L T + L + E P + GGYFI+ G EK+ L
Sbjct: 159 DSESGKVF---IGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKV---L 212
Query: 214 INNRRN-------------HPI---AIKRNAWKNRGLLFSDLGVYIRSVKRDESATNNV- 256
I R+ PI A R+A + S L V + R+ S+ +
Sbjct: 213 IAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYG--REGSSARTIK 270
Query: 257 ------------------LHFVTNGSARFMFSHRKSMC-------LLGMMQSLHEEGIHT 291
L + +G + H +C +L M++ E+G
Sbjct: 271 ATLPYIKQDIPIVIIFRALGIIPDGE---ILEH---ICYDVNDWQMLEMLKPCVEDGFVI 324
Query: 292 QHDSKVFFGQIFKEKLQYDLRHLNEVEICDYMLTNCILPHLDDYWD----KFLCLSHMTC 347
Q D + I + ++ ++ +L LPH+ K L +M
Sbjct: 325 Q-DRETALDFIGRRGTALGIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMIN 383
Query: 348 KLFHVVQGMVQLDSEDSIMLQEIMTGGSLYLQLLKKE-KSGTSAVLK----------ESD 396
+L D D + + G L QL K K T + + + +
Sbjct: 384 RLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDFN 443
Query: 397 IYAAFRASSIESAMTNFLATGNVSAGKNSTLQLMQASGFVIMAENINRMRYMSHFRAVHR 456
+ A A +I S + LATGN K + S +++ +NR Y S + R
Sbjct: 444 MKLAINAKTITSGLKYALATGNWGEQKKAM------SSRAGVSQVLNRYTYSSTLSHLRR 497
Query: 457 GS--YFQEMRSSEPRQLRTDAWGFICPVHTPDGTPCGLLNHLTTNCQIS---EYIPSKVL 511
+ ++ + ++PRQL WG +CP TP+G CGL+ +L+ IS + +P
Sbjct: 498 TNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMP---- 553
Query: 512 AQIPSVLVSLGMLPLTPVIQSIPEQALMVMLDGRIVGYILDQIATSLVPKLRMLKIVGEK 571
I + L GM PL + A V ++G V + + + L+ LR L+ G+
Sbjct: 554 --IITFLSEWGMEPLEDYVPHQSPDATRVFVNG--VWHGVHRNPARLMETLRTLRRKGDI 609
Query: 572 IPKSLEIVYLKRPEKGMGLYPGLYLFTGPGRMLRPV 607
P+ I ++ E L +FT GR+ RP+
Sbjct: 610 NPEVSMIRDIREKE--------LKIFTDAGRVYRPL 637
Score = 55.1 bits (131), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 25/46 (54%), Positives = 29/46 (63%)
Query: 766 ESGYNYYGTETMYSGVDGSMMQAQIFFGVVHYQRLRHMVSDKWQTK 811
E GY G E MY+G G + AQIFFG +YQRLRHMV DK +
Sbjct: 1061 EHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHAR 1106
>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 = 152 bits (383), Expect = 1e-36, Method: Compositional matrix adjust.
Identities = 102/320 (31%), Positives = 153/320 (47%), Gaps = 41/320 (12%)
Query: 641 THRELSKTDFLSNLANLIPMPDCNQSPRNMYQCQMGKQTMGTPCLNWRYQGVGKLYRLQT 700
TH E+ L LA++IP PD NQSPRN YQ MGKQ MG N++ + L
Sbjct: 728 THCEIHPAMILGILASIIPFPDHNQSPRNTYQSAMGKQAMGVYLTNYQVRMDTMANILYY 787
Query: 701 PASPFFRPVHYDTLDMDNFPMGTNAIVAVISYTGYDMEDAMILNKSSYERGFAHGCIFKS 760
P P + L P G NAIVA++ Y+GY+ ED++I+N++S +RG +F+S
Sbjct: 788 PQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSIIMNQASIDRG-----LFRS 842
Query: 761 MFIELESGYNYYGTETMYSGVDGSMMQAQIFFGVVHYQRLRHMVSDKWQTKDYFGRDPAN 820
+F Y Y + G+ ++M+ ++R + + + Y
Sbjct: 843 IF------YRTYTDQEKKIGM--TVME--------EFERPVRSTTLRMKHGTY------- 879
Query: 821 KALEDKLGPDGLVYVGAKLNERDPMYSYWK----ESENRYVTCRYSGKEEMCVEVVRMSS 876
DKL DGL+ G +++ D + + E + K ++ + S
Sbjct: 880 ----DKLEDDGLIAPGTRVSGEDIIIGKTAPIPLDHEELGQRTQLHAKRDVSTPLRSTES 935
Query: 877 GFTEGGSVTPNCAYIGY-----RIQRNPTVGDKFASRAGQKGICSVKWPAEDLPFTDSGL 931
G + VT N + + R R P +GDKFASR GQKG + + ED+PF+ G+
Sbjct: 936 GIVDQVMVTTNQEGLKFVKVRMRSTRIPQIGDKFASRHGQKGTIGMTYRHEDMPFSAQGI 995
Query: 932 VPDIVFNPHGFPSRMTIGFL 951
VPDI+ NPH PSRMT+ L
Sbjct: 996 VPDIIINPHAIPSRMTVAHL 1015
Score = 83.2 bits (204), Expect = 7e-16, Method: Compositional matrix adjust.
Identities = 134/620 (21%), Positives = 232/620 (37%), Gaps = 104/620 (16%)
Query: 67 TLGAPHIASFDFMLDEGLDLAVEDIAPIEFEIYG----------KTLKLNIVKAAISEPK 116
+L + SFD + + V+D + + + Y + ++N + +S P
Sbjct: 29 SLARQQLFSFDEFVQNTMQEIVDDDSTLTLDQYAQHTGAQGDVTRRYEINFGQIYLSRPT 88
Query: 117 VPAGPVGIHFNKYYPTEARQTRSVYSGPF------NVTVAWSWDGKAGGTFTKE------ 164
+ +P EAR YS P V VA + G
Sbjct: 89 MTEADGST--TTMFPQEARLRNLTYSSPLYVDMRKKVMVAADSNVPIGEEEWLVEEEDEE 146
Query: 165 -----VGRVPIMLKSKRCHLRNLTPAQLIERGEHPDEWGGYFIVGGHEKLVRLLINNRRN 219
+G++PIML+S C L ++ ++L + E P + GGYFI+ G EK++ + N
Sbjct: 147 PSKVFIGKIPIMLRSTFCILNGVSDSELYDLNECPYDQGGYFIINGSEKVIIAQERSAAN 206
Query: 220 ----------HPIAIK---RNAWKNRGLLFSDLGVYI--RSVKRDESATNNVLHFVTNG- 263
PIA R+A + L S + + + R+ + L ++ +
Sbjct: 207 IVQVFKKAAPSPIAYVAEIRSALERGSRLISSMQIKLMARNTENSGQTIRATLPYIRSDI 266
Query: 264 ------------SARFMFSHRKSMC-------LLGMMQSLHEEGIHTQHDSKVFFGQIFK 304
R + H +C +L MM+ EE Q D + I K
Sbjct: 267 PIVIVFRALGVVPDRDILEH---ICYDPNDFQMLEMMKPCIEEAFVIQ-DKDIALDYIGK 322
Query: 305 EKLQYDLRHLNEVEICDYMLTNCILPHLDDY----WDKFLCLSHMTCKLFHVVQGMVQLD 360
+ + +L +LPH+ K L +M ++ + D
Sbjct: 323 RGSTTGVTREKRLRYAHDILQKELLPHITTMEGFETRKAFFLGYMIHRMLLCALERREPD 382
Query: 361 SEDSIMLQEIMTGG----SLYLQLLKKEKSGTSAVL-------KESDIYAAFRASSIESA 409
D + + G SL+ L +K + +E ++ A +++ I +
Sbjct: 383 DRDHFGKKRLDLAGPLLASLFRMLFRKMTRDVYKYMQKCVETNREFNLTLAVKSNIITNG 442
Query: 410 MTNFLATGNVSAGKNSTLQLMQASGFVIMAENINRMRYMSHFRAVHRGS--YFQEMRSSE 467
+ LATGN K S + + S + +NR + S + R + ++ + ++
Sbjct: 443 LRYSLATGNWGDQKRSMVNRVGVS------QVLNRYTFASTLSHLRRTNTPIGRDGKLAK 496
Query: 468 PRQLRTDAWGFICPVHTPDGTPCGLLNHLTTNCQISEYIPSKVLAQIPSVLVSLGMLPLT 527
PRQL WG +CP TP+G CGL+ +L+ +S PS A I L G+ L
Sbjct: 497 PRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSVGSPS---APIIEFLEEWGLETLE 553
Query: 528 PVIQSIPEQALMVMLDGRIVGYILDQIATSLVPKLRMLKIVGEKIPKSLEIVYLKRPEKG 587
S A V ++G +G D L LR L+ ++ S E+ ++ +
Sbjct: 554 DYNPSASPNATKVFVNGVWLGVHRD--PAHLTETLRSLR---RRLDISAEVSIVRDIRE- 607
Query: 588 MGLYPGLYLFTGPGRMLRPV 607
L LFT GR+ RP+
Sbjct: 608 ----KELRLFTDAGRICRPL 623
Score = 45.1 bits (105), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/44 (43%), Positives = 26/44 (59%)
Query: 768 GYNYYGTETMYSGVDGSMMQAQIFFGVVHYQRLRHMVSDKWQTK 811
G+ G E MY G G + AQ+F G +YQRL+H+V DK +
Sbjct: 1052 GFQSRGFEVMYHGHTGRKLVAQVFLGPTYYQRLKHLVDDKIHAR 1095
>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 = 64.3 bits (155), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 65/255 (25%), Positives = 106/255 (41%), Gaps = 65/255 (25%)
Query: 721 MGTNAIVAVISYTGYDMEDAMILNKSSYERGFAHGCIFKSMFIELESGYNYYGTETMYSG 780
+G N +VA++ + GY+ EDA+++++ +R F + S+ IE Y E
Sbjct: 668 LGQNVLVAIMPFDGYNFEDAIVISEELLKRDF-----YTSIHIE------RYEIEAR--- 713
Query: 781 VDGSMMQAQIFFGVVHYQRLRHMVSDKWQTKDYFGRDPANKALEDKLGPDGLVYVGAKLN 840
D + +I + H + AL D L +G+V +GA++
Sbjct: 714 -DTKLGPERITRDIPHL---------------------SEAALRD-LDEEGVVRIGAEVK 750
Query: 841 ERDPMY---SYWKESE----NRYVTCRYS---------------GKEEMCVEVVRMSSGF 878
D + S+ ESE R + + G+ + V VR+ G
Sbjct: 751 PGDILVGRTSFKGESEPTPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVRTVRLRRG- 809
Query: 879 TEGGSVTPNCAYIGYRI----QRNPTVGDKFASRAGQKGICSVKWPAEDLPFTDSGLVPD 934
G + P + R+ +R VGDK A+R G KG+ + P ED+P G D
Sbjct: 810 DPGVELKPGVREV-VRVYVAQKRKLQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVD 868
Query: 935 IVFNPHGFPSRMTIG 949
++ NP G PSRM +G
Sbjct: 869 VILNPLGVPSRMNLG 883
Score = 40.0 bits (92), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 24/102 (23%), Positives = 43/102 (42%), Gaps = 13/102 (12%)
Query: 403 ASSIESAMTNFLATGNVSAGKNSTLQLMQASGFVIMAENINRMRYMSHFRAVHRGSYFQE 462
+ +E+A+ F + +S K+ T L + +R+ A+ G +E
Sbjct: 375 SRPLEAAIREFFSRSQLSQFKDETNPL-------------SSLRHKRRISALGPGGLTRE 421
Query: 463 MRSSEPRQLRTDAWGFICPVHTPDGTPCGLLNHLTTNCQISE 504
+ R + +G ICPV TP+G GL+ L ++ E
Sbjct: 422 RAGFDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARVDE 463
>pdb|1I6V|C Chain C, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1118
Score = 60.5 bits (145), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 57/254 (22%), Positives = 96/254 (37%), Gaps = 63/254 (24%)
Query: 721 MGTNAIVAVISYTGYDMEDAMILNKSSYERGFAHGCIFKSMFIE---LESGYNYYGTETM 777
+G N +VA++ + GY+ EDA+++++ +R F + S+ IE +E+ G E +
Sbjct: 667 LGQNVLVAIMPFDGYNFEDAIVISEELLKRDF-----YTSIHIERYEIEARDTKLGPERI 721
Query: 778 YSGV-------------------DGSMMQAQIFFGVVHYQRLRHMVSDKWQTKDYFG--- 815
+ + I G ++ + ++ + FG
Sbjct: 722 TRDIPHLSEAALRDLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRSIFGEKA 781
Query: 816 RDPANKALEDKLGPDGLVYVGAKLNERDPMYSYWKESENRYVTCRYSGKEEMCVEVVRMS 875
RD + +L G G+V +L DP V +
Sbjct: 782 RDVKDTSLRVPPGEGGIVVGRLRLRRGDPG--------------------------VELK 815
Query: 876 SGFTEGGSVTPNCAYIGYRIQRNPTVGDKFASRAGQKGICSVKWPAEDLPFTDSGLVPDI 935
G E + +R VGDK A+R G KG+ + P ED+P G D+
Sbjct: 816 PGVRE-------VVRVFVAQKRKLQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDV 868
Query: 936 VFNPHGFPSRMTIG 949
+ NP G PSRM +G
Sbjct: 869 ILNPLGVPSRMNLG 882
Score = 38.5 bits (88), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 22/98 (22%), Positives = 41/98 (41%), Gaps = 13/98 (13%)
Query: 406 IESAMTNFLATGNVSAGKNSTLQLMQASGFVIMAENINRMRYMSHFRAVHRGSYFQEMRS 465
+E+A+ F + +S K+ T ++ +R+ A+ G +E
Sbjct: 378 LEAALREFFSRSQLSQFKDET-------------NPLSSLRHKRRISALGPGGLTRERAG 424
Query: 466 SEPRQLRTDAWGFICPVHTPDGTPCGLLNHLTTNCQIS 503
+ R + +G ICPV TP+G GL+ L ++
Sbjct: 425 FDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARVD 462
>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 = 60.5 bits (145), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 57/254 (22%), Positives = 96/254 (37%), Gaps = 63/254 (24%)
Query: 721 MGTNAIVAVISYTGYDMEDAMILNKSSYERGFAHGCIFKSMFIE---LESGYNYYGTETM 777
+G N +VA++ + GY+ EDA+++++ +R F + S+ IE +E+ G E +
Sbjct: 668 LGQNVLVAIMPFDGYNFEDAIVISEELLKRDF-----YTSIHIERYEIEARDTKLGPERI 722
Query: 778 YSGV-------------------DGSMMQAQIFFGVVHYQRLRHMVSDKWQTKDYFG--- 815
+ + I G ++ + ++ + FG
Sbjct: 723 TRDIPHLSEAALRDLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRSIFGEKA 782
Query: 816 RDPANKALEDKLGPDGLVYVGAKLNERDPMYSYWKESENRYVTCRYSGKEEMCVEVVRMS 875
RD + +L G G+V +L DP V +
Sbjct: 783 RDVKDTSLRVPPGEGGIVVGRLRLRRGDPG--------------------------VELK 816
Query: 876 SGFTEGGSVTPNCAYIGYRIQRNPTVGDKFASRAGQKGICSVKWPAEDLPFTDSGLVPDI 935
G E + +R VGDK A+R G KG+ + P ED+P G D+
Sbjct: 817 PGVRE-------VVRVFVAQKRKLQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDV 869
Query: 936 VFNPHGFPSRMTIG 949
+ NP G PSRM +G
Sbjct: 870 ILNPLGVPSRMNLG 883
Score = 38.5 bits (88), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 22/98 (22%), Positives = 41/98 (41%), Gaps = 13/98 (13%)
Query: 406 IESAMTNFLATGNVSAGKNSTLQLMQASGFVIMAENINRMRYMSHFRAVHRGSYFQEMRS 465
+E+A+ F + +S K+ T ++ +R+ A+ G +E
Sbjct: 378 LEAALREFFSRSQLSQFKDET-------------NPLSSLRHKRRISALGPGGLTRERAG 424
Query: 466 SEPRQLRTDAWGFICPVHTPDGTPCGLLNHLTTNCQIS 503
+ R + +G ICPV TP+G GL+ L ++
Sbjct: 425 FDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARVD 462
>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 = 60.5 bits (145), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 57/254 (22%), Positives = 96/254 (37%), Gaps = 63/254 (24%)
Query: 721 MGTNAIVAVISYTGYDMEDAMILNKSSYERGFAHGCIFKSMFIE---LESGYNYYGTETM 777
+G N +VA++ + GY+ EDA+++++ +R F + S+ IE +E+ G E +
Sbjct: 668 LGQNVLVAIMPFDGYNFEDAIVISEELLKRDF-----YTSIHIERYEIEARDTKLGPERI 722
Query: 778 YSGV-------------------DGSMMQAQIFFGVVHYQRLRHMVSDKWQTKDYFG--- 815
+ + I G ++ + ++ + FG
Sbjct: 723 TRDIPHLSEAALRDLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRSIFGEKA 782
Query: 816 RDPANKALEDKLGPDGLVYVGAKLNERDPMYSYWKESENRYVTCRYSGKEEMCVEVVRMS 875
RD + +L G G+V +L DP V +
Sbjct: 783 RDVKDTSLRVPPGEGGIVVGRLRLRRGDPG--------------------------VELK 816
Query: 876 SGFTEGGSVTPNCAYIGYRIQRNPTVGDKFASRAGQKGICSVKWPAEDLPFTDSGLVPDI 935
G E + +R VGDK A+R G KG+ + P ED+P G D+
Sbjct: 817 PGVRE-------VVRVFVAQKRKLQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDV 869
Query: 936 VFNPHGFPSRMTIG 949
+ NP G PSRM +G
Sbjct: 870 ILNPLGVPSRMNLG 883
Score = 38.5 bits (88), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 22/98 (22%), Positives = 41/98 (41%), Gaps = 13/98 (13%)
Query: 406 IESAMTNFLATGNVSAGKNSTLQLMQASGFVIMAENINRMRYMSHFRAVHRGSYFQEMRS 465
+E+A+ F + +S K+ T ++ +R+ A+ G +E
Sbjct: 378 LEAALREFFSRSQLSQFKDET-------------NPLSSLRHKRRISALGPGGLTRERAG 424
Query: 466 SEPRQLRTDAWGFICPVHTPDGTPCGLLNHLTTNCQIS 503
+ R + +G ICPV TP+G GL+ L ++
Sbjct: 425 FDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARVD 462
>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 = 60.5 bits (145), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 57/254 (22%), Positives = 96/254 (37%), Gaps = 63/254 (24%)
Query: 721 MGTNAIVAVISYTGYDMEDAMILNKSSYERGFAHGCIFKSMFIE---LESGYNYYGTETM 777
+G N +VA++ + GY+ EDA+++++ +R F + S+ IE +E+ G E +
Sbjct: 667 LGQNVLVAIMPFDGYNFEDAIVISEELLKRDF-----YTSIHIERYEIEARDTKLGPERI 721
Query: 778 YSGV-------------------DGSMMQAQIFFGVVHYQRLRHMVSDKWQTKDYFG--- 815
+ + I G ++ + ++ + FG
Sbjct: 722 TRDIPHLSEAALRDLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRSIFGEKA 781
Query: 816 RDPANKALEDKLGPDGLVYVGAKLNERDPMYSYWKESENRYVTCRYSGKEEMCVEVVRMS 875
RD + +L G G+V +L DP V +
Sbjct: 782 RDVKDTSLRVPPGEGGIVVGRLRLRRGDPG--------------------------VELK 815
Query: 876 SGFTEGGSVTPNCAYIGYRIQRNPTVGDKFASRAGQKGICSVKWPAEDLPFTDSGLVPDI 935
G E + +R VGDK A+R G KG+ + P ED+P G D+
Sbjct: 816 PGVRE-------VVRVFVAQKRKLQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDV 868
Query: 936 VFNPHGFPSRMTIG 949
+ NP G PSRM +G
Sbjct: 869 ILNPLGVPSRMNLG 882
Score = 38.5 bits (88), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 22/98 (22%), Positives = 41/98 (41%), Gaps = 13/98 (13%)
Query: 406 IESAMTNFLATGNVSAGKNSTLQLMQASGFVIMAENINRMRYMSHFRAVHRGSYFQEMRS 465
+E+A+ F + +S K+ T ++ +R+ A+ G +E
Sbjct: 378 LEAALREFFSRSQLSQFKDET-------------NPLSSLRHKRRISALGPGGLTRERAG 424
Query: 466 SEPRQLRTDAWGFICPVHTPDGTPCGLLNHLTTNCQIS 503
+ R + +G ICPV TP+G GL+ L ++
Sbjct: 425 FDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARVD 462
>pdb|3LU0|C Chain C, Molecular Model Of Escherichia Coli Core Rna Polymerase
Length = 1342
Score = 59.3 bits (142), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 31/75 (41%), Positives = 40/75 (53%), Gaps = 3/75 (4%)
Query: 878 FTEGGSVTPNCAYIG---YRIQRNPTVGDKFASRAGQKGICSVKWPAEDLPFTDSGLVPD 934
T+G + P I ++R GDK A R G KG+ S P ED+P+ ++G D
Sbjct: 1036 ITQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVD 1095
Query: 935 IVFNPHGFPSRMTIG 949
IV NP G PSRM IG
Sbjct: 1096 IVLNPLGVPSRMNIG 1110
Score = 45.8 bits (107), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 44/220 (20%), Positives = 87/220 (39%), Gaps = 17/220 (7%)
Query: 291 TQHDSKVFFGQIFKEKLQYDLRHLNEVEICDYMLTNCI----LPHLDDYWDKFLCLSHMT 346
T+ ++ F +F + +YDL + ++ +L I + DD D +
Sbjct: 377 TREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLREEIEGSGILSKDDIID-------VM 429
Query: 347 CKLFHVVQGMVQLDSEDSIMLQEIMTGGSLYLQLLKKEKSGTSAVLKESDIYAAFRASSI 406
KL + G ++D D + + I + G + + V E + +
Sbjct: 430 KKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFR-----VGLVRVERAVKERLSLGDL 484
Query: 407 ESAM-TNFLATGNVSAGKNSTLQLMQASGFVIMAENINRMRYMSHFRAVHRGSYFQEMRS 465
++ M + + +SA Q S F++ ++ + + A+ G +E
Sbjct: 485 DTLMPQDMINAKPISAAVKEFFGSSQLSQFMVQNNPLSEITHKRRISALGPGGLTRERAG 544
Query: 466 SEPRQLRTDAWGFICPVHTPDGTPCGLLNHLTTNCQISEY 505
E R + +G +CP+ TP+G GL+N L+ Q +EY
Sbjct: 545 FEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEY 584
>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 = 59.3 bits (142), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 31/75 (41%), Positives = 40/75 (53%), Gaps = 3/75 (4%)
Query: 878 FTEGGSVTPNCAYIG---YRIQRNPTVGDKFASRAGQKGICSVKWPAEDLPFTDSGLVPD 934
T+G + P I ++R GDK A R G KG+ S P ED+P+ ++G D
Sbjct: 1036 ITQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVD 1095
Query: 935 IVFNPHGFPSRMTIG 949
IV NP G PSRM IG
Sbjct: 1096 IVLNPLGVPSRMNIG 1110
Score = 43.5 bits (101), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 44/220 (20%), Positives = 86/220 (39%), Gaps = 17/220 (7%)
Query: 291 TQHDSKVFFGQIFKEKLQYDLRHLNEVEICDYMLTNCI----LPHLDDYWDKFLCLSHMT 346
T+ ++ F +F + +YDL + ++ +L I + DD D +
Sbjct: 377 TREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLREEIEGSGILSKDDIID-------VM 429
Query: 347 CKLFHVVQGMVQLDSEDSIMLQEIMTGGSLYLQLLKKEKSGTSAVLKESDIYAAFRASSI 406
KL + G ++D D + + I + G + + V E + +
Sbjct: 430 KKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFR-----VGLVRVERAVKERLSLGDL 484
Query: 407 ESAM-TNFLATGNVSAGKNSTLQLMQASGFVIMAENINRMRYMSHFRAVHRGSYFQEMRS 465
++ M + + +SA Q S F+ ++ + + A+ G +E
Sbjct: 485 DTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAG 544
Query: 466 SEPRQLRTDAWGFICPVHTPDGTPCGLLNHLTTNCQISEY 505
E R + +G +CP+ TP+G GL+N L+ Q +EY
Sbjct: 545 FEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEY 584
>pdb|3MEK|A Chain A, Crystal Structure Of Human Histone-Lysine N-
Methyltransferase Smyd3 In Complex With S-Adenosyl-L-
Methionine
Length = 429
Score = 33.5 bits (75), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 31/74 (41%), Gaps = 12/74 (16%)
Query: 553 QIATSLVPKLRMLKIVGEKIPKSLEIVYLKRPEKGMGLYPGLYL------------FTGP 600
Q A+ L P + + + I S I + E G+GLYP + L F GP
Sbjct: 161 QDASQLPPAFDLFEAFAKVICNSFTICNAEXQEVGVGLYPSISLLNHSCDPNCSIVFNGP 220
Query: 601 GRMLRPVMNLAAGN 614
+LR V ++ G
Sbjct: 221 HLLLRAVRDIEVGE 234
>pdb|3PDN|A Chain A, Crystal Structure Of Smyd3 In Complex With
Methyltransferase Inhibitor Sinefungin
pdb|3OXL|A Chain A, Human Lysine Methyltransferase Smyd3 In Complex With
Adohcy (Form Ii)
Length = 428
Score = 32.7 bits (73), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 31/74 (41%), Gaps = 12/74 (16%)
Query: 553 QIATSLVPKLRMLKIVGEKIPKSLEIVYLKRPEKGMGLYPGLYL------------FTGP 600
Q A+ L P + + + I S I + E G+GLYP + L F GP
Sbjct: 160 QDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYPSISLLNHSCDPNCSIVFNGP 219
Query: 601 GRMLRPVMNLAAGN 614
+LR V ++ G
Sbjct: 220 HLLLRAVRDIEVGE 233
>pdb|3OXF|A Chain A, Human Lysine Methyltransferase Smyd3 In Complex With
Adohcy (Form I)
pdb|3OXF|B Chain B, Human Lysine Methyltransferase Smyd3 In Complex With
Adohcy (Form I)
Length = 436
Score = 32.3 bits (72), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 31/74 (41%), Gaps = 12/74 (16%)
Query: 553 QIATSLVPKLRMLKIVGEKIPKSLEIVYLKRPEKGMGLYPGLYL------------FTGP 600
Q A+ L P + + + I S I + E G+GLYP + L F GP
Sbjct: 160 QDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYPSISLLNHSCDPNCSIVFNGP 219
Query: 601 GRMLRPVMNLAAGN 614
+LR V ++ G
Sbjct: 220 HLLLRAVRDIEVGE 233
>pdb|3RU0|A Chain A, Cocrystal Structure Of Human Smyd3 With Inhibitor
Sinefungin Bound
pdb|3RU0|B Chain B, Cocrystal Structure Of Human Smyd3 With Inhibitor
Sinefungin Bound
Length = 438
Score = 32.3 bits (72), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 31/74 (41%), Gaps = 12/74 (16%)
Query: 553 QIATSLVPKLRMLKIVGEKIPKSLEIVYLKRPEKGMGLYPGLYL------------FTGP 600
Q A+ L P + + + I S I + E G+GLYP + L F GP
Sbjct: 162 QDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYPSISLLNHSCDPNCSIVFNGP 221
Query: 601 GRMLRPVMNLAAGN 614
+LR V ++ G
Sbjct: 222 HLLLRAVRDIEVGE 235
>pdb|3QWP|A Chain A, Crystal Structure Of Set And Mynd Domain Containing 3;
Zinc Finger Mynd Domain-Containing Protein 1
Length = 429
Score = 32.3 bits (72), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 31/74 (41%), Gaps = 12/74 (16%)
Query: 553 QIATSLVPKLRMLKIVGEKIPKSLEIVYLKRPEKGMGLYPGLYL------------FTGP 600
Q A+ L P + + + I S I + E G+GLYP + L F GP
Sbjct: 161 QDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYPSISLLNHSCDPNCSIVFNGP 220
Query: 601 GRMLRPVMNLAAGN 614
+LR V ++ G
Sbjct: 221 HLLLRAVRDIEVGE 234
>pdb|3OXG|A Chain A, Human Lysine Methyltransferase Smyd3 In Complex With
Adohcy (Form Iii)
Length = 464
Score = 32.3 bits (72), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 25/94 (26%), Positives = 40/94 (42%), Gaps = 17/94 (18%)
Query: 553 QIATSLVPKLRMLKIVGEKIPKSLEIVYLKRPEKGMGLYPGLYL------------FTGP 600
Q A+ L P + + + I S I + E G+GLYP + L F GP
Sbjct: 196 QDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYPSISLLNHSCDPNCSIVFNGP 255
Query: 601 GRMLRPVMNLAAGNIEWIGTFEQVFMDICITMKE 634
+LR V ++ G I ++D+ +T +E
Sbjct: 256 HLLLRAVRDIEVGEELTI-----CYLDMLMTSEE 284
>pdb|2RDO|7 Chain 7, 50s Subunit With Ef-G(Gdpnp) And Rrf Bound
Length = 704
Score = 32.0 bits (71), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 26/98 (26%), Positives = 45/98 (45%), Gaps = 6/98 (6%)
Query: 817 DPANKALEDKLGPDGLVYVGAKLNERDPMYSYWKESENRYVTCRYSGKEEMCVEVVRMSS 876
+P KA ++K+G + +G +L + DP + W + E+ G+ + + V RM
Sbjct: 421 EPKTKADQEKMG----LALG-RLAKEDPSFRVWTDEESNQTIIAGMGELHLDIIVDRMKR 475
Query: 877 GFTEGGSV-TPNCAYIGYRIQRNPTVGDKFASRAGQKG 913
F +V P AY Q+ V K A ++G +G
Sbjct: 476 EFNVEANVGKPQVAYRETIRQKVTDVEGKHAKQSGGRG 513
>pdb|3J0E|H Chain H, Models For The T. Thermophilus Ribosome Recycling Factor
And The E. Coli Elongation Factor G Bound To The E. Coli
Post-Termination Complex
Length = 702
Score = 32.0 bits (71), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 26/98 (26%), Positives = 45/98 (45%), Gaps = 6/98 (6%)
Query: 817 DPANKALEDKLGPDGLVYVGAKLNERDPMYSYWKESENRYVTCRYSGKEEMCVEVVRMSS 876
+P KA ++K+G + +G +L + DP + W + E+ G+ + + V RM
Sbjct: 420 EPKTKADQEKMG----LALG-RLAKEDPSFRVWTDEESNQTIIAGMGELHLDIIVDRMKR 474
Query: 877 GFTEGGSV-TPNCAYIGYRIQRNPTVGDKFASRAGQKG 913
F +V P AY Q+ V K A ++G +G
Sbjct: 475 EFNVEANVGKPQVAYRETIRQKVTDVEGKHAKQSGGRG 512
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
0.322 0.138 0.424
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 29,602,617
Number of Sequences: 62578
Number of extensions: 1316223
Number of successful extensions: 3661
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 3605
Number of HSP's gapped (non-prelim): 57
length of query: 951
length of database: 14,973,337
effective HSP length: 108
effective length of query: 843
effective length of database: 8,214,913
effective search space: 6925171659
effective search space used: 6925171659
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: 56 (26.2 bits)