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= psy12711
(639 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1I3Q|K Chain K, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
pdb|1I50|K Chain K, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
pdb|1I6H|K Chain K, Rna Polymerase Ii Elongation Complex
pdb|1K83|K Chain K, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
With The Inhibitor Alpha Amanitin
pdb|1NIK|K Chain K, Wild Type Rna Polymerase Ii
pdb|1NT9|K Chain K, Complete 12-Subunit Rna Polymerase Ii
pdb|1PQV|K Chain K, Rna Polymerase Ii-Tfiis Complex
pdb|1R5U|K Chain K, Rna Polymerase Ii Tfiib Complex
pdb|1SFO|K Chain K, Rna Polymerase Ii Strand Separated Elongation Complex
pdb|1R9S|K Chain K, Rna Polymerase Ii Strand Separated Elongation Complex,
Matched Nucleotide
pdb|1R9T|K Chain K, Rna Polymerase Ii Strand Separated Elongation Complex,
Mismatched Nucleotide
pdb|1TWA|K Chain K, Rna Polymerase Ii Complexed With Atp
pdb|1TWC|K Chain K, Rna Polymerase Ii Complexed With Gtp
pdb|1TWF|K Chain K, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
pdb|1TWG|K Chain K, Rna Polymerase Ii Complexed With Ctp
pdb|1TWH|K Chain K, Rna Polymerase Ii Complexed With 2'datp
pdb|1WCM|K Chain K, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
pdb|1Y1W|K Chain K, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|K Chain K, Complete Rna Polymerase Ii Elongation Complex With
Substrate Analogue Gmpcpp
pdb|1Y1V|K Chain K, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|K Chain K, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|2B63|K Chain K, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2B8K|K Chain K, 12-Subunit Rna Polymerase Ii
pdb|2E2H|K Chain K, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With Gtp
pdb|2E2I|K Chain K, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dgtp
pdb|2E2J|K Chain K, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
Gmpcpp
pdb|2NVQ|K Chain K, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
2'dutp
pdb|2NVT|K Chain K, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Gmpcpp
pdb|2NVX|K Chain K, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dutp
pdb|2NVY|K Chain K, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
pdb|2NVZ|K Chain K, Rna Polymerase Ii Elongation Complex With Utp, Updated
112006
pdb|2JA5|K Chain K, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
A
pdb|2JA6|K Chain K, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
B
pdb|2JA7|K Chain K, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA7|W Chain W, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA8|K Chain K, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
D
pdb|2YU9|K Chain K, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Utp
pdb|2R7Z|K Chain K, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|K Chain K, Elongation Complex Of Rna Polymerase Ii With Artificial
Rdrp Scaffold
pdb|2R93|K Chain K, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|K Chain K, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3CQZ|K Chain K, Crystal Structure Of 10 Subunit Rna Polymerase Ii In
Complex With The Inhibitor Alpha-Amanitin
pdb|3FKI|K Chain K, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3GTG|K Chain K, Backtracked Rna Polymerase Ii Complex With 12mer Rna
pdb|3GTJ|K Chain K, Backtracked Rna Polymerase Ii Complex With 13mer Rna
pdb|3GTK|K Chain K, Backtracked Rna Polymerase Ii Complex With 18mer Rna
pdb|3GTL|K Chain K, Backtracked Rna Polymerase Ii Complex With 13mer With G<>u
Mismatch
pdb|3GTM|K Chain K, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
pdb|3GTO|K Chain K, Backtracked Rna Polymerase Ii Complex With 15mer Rna
pdb|3GTP|K Chain K, Backtracked Rna Polymerase Ii Complex With 24mer Rna
pdb|3GTQ|K Chain K, Backtracked Rna Polymerase Ii Complex Induced By Damage
pdb|3H3V|L Chain L, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|K Chain K, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOU|W Chain W, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOV|K Chain K, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3HOW|K Chain K, Complete Rna Polymerase Ii Elongation Complex Iii With A
T-U Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|K Chain K, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|K Chain K, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|K Chain K, Complete Rna Polymerase Ii Elongation Complex Iv With A
T-U Mismatch And A Frayed Rna 3'-Guanine
pdb|3I4M|K Chain K, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex D
pdb|3I4N|K Chain K, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex E
pdb|3K1F|K Chain K, Crystal Structure Of Rna Polymerase Ii In Complex With
Tfiib
pdb|3K7A|K Chain K, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
pdb|3M3Y|K Chain K, Rna Polymerase Ii Elongation Complex C
pdb|3M4O|K Chain K, Rna Polymerase Ii Elongation Complex B
pdb|3PO2|K Chain K, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|K Chain K, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3QT1|K Chain K, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
pdb|3RZD|K Chain K, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
pdb|3RZO|K Chain K, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
pdb|3S14|K Chain K, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
pdb|3S15|K Chain K, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
pdb|3S16|K Chain K, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
pdb|3S17|K Chain K, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
pdb|3S1M|K Chain K, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 1)
pdb|3S1N|K Chain K, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 2)
pdb|3S1Q|K Chain K, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Atp
pdb|3S1R|K Chain K, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Gtp
pdb|3S2D|K Chain K, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
Containing A 5br- U
pdb|3S2H|K Chain K, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
Containing A 2[prime]-Iodo Atp
pdb|3J0K|K Chain K, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
pdb|4A3C|K Chain K, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid
pdb|4A3B|K Chain K, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid
pdb|4A3D|K Chain K, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid
pdb|4A3E|K Chain K, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3F|K Chain K, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3J|K Chain K, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid And Soaked With Gmpcpp
pdb|4A3K|K Chain K, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid
pdb|4A3L|K Chain K, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3M|K Chain K, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3G|K Chain K, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid
pdb|4A3I|K Chain K, Rna Polymerase Ii Binary Complex With Dna
pdb|4A93|K Chain K, Rna Polymerase Ii Elongation Complex Containing A Cpd
Lesion
pdb|4BBR|K Chain K, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|K Chain K, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 120
Score = 51.2 bits (121), Expect = 2e-06, Method: Composition-based stats.
Identities = 30/74 (40%), Positives = 39/74 (52%), Gaps = 7/74 (9%)
Query: 104 PNCRTFVFEKEGHTFGSVITHILQSYPEVDFAGYSVPHPADFQIFIRIQVKDGYDSIDIL 163
PN FEKE HT G++I L + +V FA Y V HP + +RIQ +GYD D L
Sbjct: 28 PNAVVITFEKEDHTLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEGYDPKDAL 87
Query: 164 KKGIKELESACDRI 177
K +AC+ I
Sbjct: 88 K-------NACNSI 94
>pdb|3H0G|K Chain K, Rna Polymerase Ii From Schizosaccharomyces Pombe
pdb|3H0G|W Chain W, Rna Polymerase Ii From Schizosaccharomyces Pombe
Length = 123
Score = 47.8 bits (112), Expect = 2e-05, Method: Composition-based stats.
Identities = 26/87 (29%), Positives = 40/87 (45%)
Query: 104 PNCRTFVFEKEGHTFGSVITHILQSYPEVDFAGYSVPHPADFQIFIRIQVKDGYDSIDIL 163
PN EKE HT +++ + L S V FAGY VPHP + +R+Q + ++
Sbjct: 27 PNAAVVTLEKEDHTLANMLANQLLSDERVLFAGYKVPHPLNHNFILRVQTVEDCSPKQVI 86
Query: 164 KKGIKELESACDRITETFNDAMQCKVI 190
K L + + I F + K+I
Sbjct: 87 VDAAKSLITHLEEIKVNFMREWELKMI 113
>pdb|2PA8|L Chain L, X-Ray Crystal Structure Of The DL SUBCOMPLEX OF THE
SULFOLOBUS Solfataricus Rna Polymerase
pdb|2PMZ|L Chain L, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|X Chain X, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|3HKZ|L Chain L, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
pdb|3HKZ|V Chain V, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Length = 92
Score = 38.1 bits (87), Expect = 0.016, Method: Composition-based stats.
Identities = 20/59 (33%), Positives = 28/59 (47%)
Query: 112 EKEGHTFGSVITHILQSYPEVDFAGYSVPHPADFQIFIRIQVKDGYDSIDILKKGIKEL 170
E E HT G++I L+ V FA Y PHP +I ++I D L K I+ +
Sbjct: 18 EGEDHTLGNLIAGTLRRISGVSFASYYQPHPLSDKIIVKILTDGSITPKDALLKAIENI 76
>pdb|2WAQ|L Chain L, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|L Chain L, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|M Chain M, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2Y0S|L Chain L, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|M Chain M, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|L Chain L, Rnap At 3.2ang
pdb|4B1O|L Chain L, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|M Chain M, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 92
Score = 37.0 bits (84), Expect = 0.030, Method: Composition-based stats.
Identities = 22/69 (31%), Positives = 30/69 (43%)
Query: 100 LNVKPNCRTFVFEKEGHTFGSVITHILQSYPEVDFAGYSVPHPADFQIFIRIQVKDGYDS 159
L + N E E HT G++I L+ V FA Y PHP +I ++I
Sbjct: 6 LKSESNYLELEIEGEDHTLGNLIAGTLRKISGVSFASYYQPHPLTDKIIVKILTDGSIAP 65
Query: 160 IDILKKGIK 168
D L K I+
Sbjct: 66 KDALLKAIE 74
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.320 0.134 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,822,837
Number of Sequences: 62578
Number of extensions: 776157
Number of successful extensions: 1650
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1644
Number of HSP's gapped (non-prelim): 10
length of query: 639
length of database: 14,973,337
effective HSP length: 105
effective length of query: 534
effective length of database: 8,402,647
effective search space: 4487013498
effective search space used: 4487013498
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)