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= 033869
         (110 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>pdb|3QT1|I Chain I, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
           Subunit
          Length = 133

 Score = 58.2 bits (139), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 39/117 (33%), Positives = 55/117 (47%), Gaps = 15/117 (12%)

Query: 1   MEFCPTCGTMLQYELPHMDRPSR---FSCPACPYVCNMESRVKIKRKQPLSKKE----IQ 53
             FC  C  ML    P  D+ +    F C  C YV    S +  + +   +  E    +Q
Sbjct: 24  FRFCRDCNNML---YPREDKENNRLLFECRTCSYVEEAGSPLVYRHELITNIGETAGVVQ 80

Query: 54  PIFTQDAMMEGPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
            I +   +   P+++  CP C   + V+ +LQ RSADEPM+ FY C   NC HRW E
Sbjct: 81  DIGSDPTL---PRSDRECPKCHSRENVFFQLQIRSADEPMTTFYKCV--NCGHRWKE 132


>pdb|1QYP|A Chain A, Thermococcus Celer Rpb9, Nmr, 25 Structures
          Length = 57

 Score = 50.1 bits (118), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 21/44 (47%), Positives = 28/44 (63%), Gaps = 2/44 (4%)

Query: 65  PQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRW 108
           P T++TCP C +  A + E+QTR+ DEP +IFY C    C H W
Sbjct: 12  PTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCT--KCGHTW 53


>pdb|3H0G|I Chain I, Rna Polymerase Ii From Schizosaccharomyces Pombe
 pdb|3H0G|U Chain U, Rna Polymerase Ii From Schizosaccharomyces Pombe
          Length = 113

 Score = 47.0 bits (110), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 26/103 (25%), Positives = 48/103 (46%), Gaps = 3/103 (2%)

Query: 1   MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDA 60
            ++C  C  ML      +DR  R +C  C Y   + +  K+ R +  S        + DA
Sbjct: 4   FQYCIECNNMLYPREDKVDRVLRLACRNCDYS-EIAATSKVYRHELQSSNVENTTVSHDA 62

Query: 61  MME--GPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCAN 101
             +   P+++  CP C   +AV+++  +R  D  M++ Y+C +
Sbjct: 63  STDPTLPRSDKECPRCHQHEAVFYQTHSRRGDTMMTLIYVCVH 105


>pdb|1Y1V|S Chain S, Refined Rna Polymerase Ii-tfiis Complex
 pdb|1Y1Y|S Chain S, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
          Length = 179

 Score = 45.8 bits (107), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 27/67 (40%), Positives = 39/67 (58%), Gaps = 4/67 (5%)

Query: 44  KQPLSKKEIQPIFT-QDAMMEGPQTE-VTCPACKHGKAVYHELQTRSADEPMSIFYMCAN 101
           KQ + +   Q ++  Q A +E   T+  TC  CK  K  Y++LQTRSADEP++ F  C  
Sbjct: 112 KQKIEEIAKQNLYNAQGATIERSVTDRFTCGKCKEKKVSYYQLQTRSADEPLTTFCTC-- 169

Query: 102 KNCKHRW 108
           + C +RW
Sbjct: 170 EACGNRW 176


>pdb|1TFI|A Chain A, A Novel Zn Finger Motif In The Basal Transcriptional
           Machinery: Three-Dimensional Nmr Studies Of The Nucleic-
           Acid Binding Domain Of Transcriptional Elongation Factor
           Tfiis
          Length = 50

 Score = 45.4 bits (106), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 22/46 (47%), Positives = 29/46 (63%), Gaps = 3/46 (6%)

Query: 64  GPQTEV-TCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRW 108
           G QT++ TC  CK     Y ++QTRSADEPM+ F +C    C +RW
Sbjct: 4   GTQTDLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVC--NECGNRW 47


>pdb|1PQV|S Chain S, Rna Polymerase Ii-Tfiis Complex
          Length = 309

 Score = 45.4 bits (106), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 27/67 (40%), Positives = 39/67 (58%), Gaps = 4/67 (5%)

Query: 44  KQPLSKKEIQPIFT-QDAMMEGPQTE-VTCPACKHGKAVYHELQTRSADEPMSIFYMCAN 101
           KQ + +   Q ++  Q A +E   T+  TC  CK  K  Y++LQTRSADEP++ F  C  
Sbjct: 242 KQKIEEIAKQNLYNAQGATIERSVTDRFTCGKCKEKKVSYYQLQTRSADEPLTTFCTC-- 299

Query: 102 KNCKHRW 108
           + C +RW
Sbjct: 300 EACGNRW 306


>pdb|3GTM|S Chain S, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
          Length = 173

 Score = 43.9 bits (102), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/67 (38%), Positives = 38/67 (56%), Gaps = 4/67 (5%)

Query: 44  KQPLSKKEIQPIFT-QDAMMEGPQTE-VTCPACKHGKAVYHELQTRSADEPMSIFYMCAN 101
           KQ + +   Q ++  Q A +E   T+  TC  CK  K  Y++LQTRSAD P++ F  C  
Sbjct: 106 KQKIEEIAKQNLYNAQGATIERSVTDRFTCGKCKEKKVSYYQLQTRSADHPLTTFCTC-- 163

Query: 102 KNCKHRW 108
           + C +RW
Sbjct: 164 EACGNRW 170


>pdb|3PO3|S Chain S, Arrested Rna Polymerase Ii Reactivation Intermediate
          Length = 178

 Score = 40.4 bits (93), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/67 (37%), Positives = 37/67 (55%), Gaps = 4/67 (5%)

Query: 44  KQPLSKKEIQPIFT-QDAMMEGPQTE-VTCPACKHGKAVYHELQTRSADEPMSIFYMCAN 101
           KQ + +   Q ++  Q A +E   T+  TC  CK  K  Y++LQTRSA  P++ F  C  
Sbjct: 111 KQKIEEIAKQNLYNAQGATIERSVTDRFTCGKCKEKKVSYYQLQTRSAAAPLTTFCTC-- 168

Query: 102 KNCKHRW 108
           + C +RW
Sbjct: 169 EACGNRW 175


>pdb|1I3Q|I Chain I, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
 pdb|1I50|I Chain I, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
 pdb|1I6H|I Chain I, Rna Polymerase Ii Elongation Complex
 pdb|1K83|I Chain I, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
           With The Inhibitor Alpha Amanitin
 pdb|1NIK|I Chain I, Wild Type Rna Polymerase Ii
 pdb|1NT9|I Chain I, Complete 12-Subunit Rna Polymerase Ii
 pdb|1PQV|I Chain I, Rna Polymerase Ii-Tfiis Complex
 pdb|1R5U|I Chain I, Rna Polymerase Ii Tfiib Complex
 pdb|1SFO|I Chain I, Rna Polymerase Ii Strand Separated Elongation Complex
 pdb|1R9S|I Chain I, Rna Polymerase Ii Strand Separated Elongation Complex,
           Matched Nucleotide
 pdb|1R9T|I Chain I, Rna Polymerase Ii Strand Separated Elongation Complex,
           Mismatched Nucleotide
 pdb|1TWA|I Chain I, Rna Polymerase Ii Complexed With Atp
 pdb|1TWC|I Chain I, Rna Polymerase Ii Complexed With Gtp
 pdb|1TWF|I Chain I, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
 pdb|1TWG|I Chain I, Rna Polymerase Ii Complexed With Ctp
 pdb|1TWH|I Chain I, Rna Polymerase Ii Complexed With 2'datp
 pdb|1WCM|I Chain I, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
 pdb|1Y1W|I Chain I, Complete Rna Polymerase Ii Elongation Complex
 pdb|1Y77|I Chain I, Complete Rna Polymerase Ii Elongation Complex With
           Substrate Analogue Gmpcpp
 pdb|1Y1V|I Chain I, Refined Rna Polymerase Ii-tfiis Complex
 pdb|1Y1Y|I Chain I, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
 pdb|2B63|I Chain I, Complete Rna Polymerase Ii-Rna Inhibitor Complex
 pdb|2B8K|I Chain I, 12-Subunit Rna Polymerase Ii
 pdb|2E2H|I Chain I, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With Gtp
 pdb|2E2I|I Chain I, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
           Dgtp
 pdb|2E2J|I Chain I, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
           Gmpcpp
 pdb|2NVQ|I Chain I, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
           2'dutp
 pdb|2NVT|I Chain I, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
           Gmpcpp
 pdb|2NVX|I Chain I, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
           Dutp
 pdb|2NVY|I Chain I, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
 pdb|2NVZ|I Chain I, Rna Polymerase Ii Elongation Complex With Utp, Updated
           112006
 pdb|2JA5|I Chain I, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           A
 pdb|2JA6|I Chain I, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           B
 pdb|2JA7|I Chain I, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           C
 pdb|2JA7|U Chain U, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           C
 pdb|2JA8|I Chain I, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           D
 pdb|2YU9|I Chain I, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
           Utp
 pdb|2R7Z|I Chain I, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
           Complex
 pdb|2R92|I Chain I, Elongation Complex Of Rna Polymerase Ii With Artificial
           Rdrp Scaffold
 pdb|2R93|I Chain I, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
           Delta Virus-Derived Rna Stem Loop
 pdb|2VUM|I Chain I, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
           Elongation Complex
 pdb|3CQZ|I Chain I, Crystal Structure Of 10 Subunit Rna Polymerase Ii In
           Complex With The Inhibitor Alpha-Amanitin
 pdb|3FKI|I Chain I, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
 pdb|3GTG|I Chain I, Backtracked Rna Polymerase Ii Complex With 12mer Rna
 pdb|3GTJ|I Chain I, Backtracked Rna Polymerase Ii Complex With 13mer Rna
 pdb|3GTK|I Chain I, Backtracked Rna Polymerase Ii Complex With 18mer Rna
 pdb|3GTL|I Chain I, Backtracked Rna Polymerase Ii Complex With 13mer With G<>u
           Mismatch
 pdb|3GTM|I Chain I, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
 pdb|3GTO|I Chain I, Backtracked Rna Polymerase Ii Complex With 15mer Rna
 pdb|3GTP|I Chain I, Backtracked Rna Polymerase Ii Complex With 24mer Rna
 pdb|3GTQ|I Chain I, Backtracked Rna Polymerase Ii Complex Induced By Damage
 pdb|3H3V|J Chain J, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
           Active Site
 pdb|3HOU|I Chain I, Complete Rna Polymerase Ii Elongation Complex I With A T-U
           Mismatch
 pdb|3HOU|U Chain U, Complete Rna Polymerase Ii Elongation Complex I With A T-U
           Mismatch
 pdb|3HOV|I Chain I, Complete Rna Polymerase Ii Elongation Complex Ii
 pdb|3HOW|I Chain I, Complete Rna Polymerase Ii Elongation Complex Iii With A
           T-U Mismatch And A Frayed Rna 3'-Uridine
 pdb|3HOX|I Chain I, Complete Rna Polymerase Ii Elongation Complex V
 pdb|3HOY|I Chain I, Complete Rna Polymerase Ii Elongation Complex Vi
 pdb|3HOZ|I Chain I, Complete Rna Polymerase Ii Elongation Complex Iv With A
           T-U Mismatch And A Frayed Rna 3'-Guanine
 pdb|3I4M|I Chain I, 8-oxoguanine Containing Rna Polymerase Ii Elongation
           Complex D
 pdb|3I4N|I Chain I, 8-oxoguanine Containing Rna Polymerase Ii Elongation
           Complex E
 pdb|3K1F|I Chain I, Crystal Structure Of Rna Polymerase Ii In Complex With
           Tfiib
 pdb|3K7A|I Chain I, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
 pdb|3M3Y|I Chain I, Rna Polymerase Ii Elongation Complex C
 pdb|3M4O|I Chain I, Rna Polymerase Ii Elongation Complex B
 pdb|3PO2|I Chain I, Arrested Rna Polymerase Ii Elongation Complex
 pdb|3PO3|I Chain I, Arrested Rna Polymerase Ii Reactivation Intermediate
 pdb|3RZD|I Chain I, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
 pdb|3RZO|I Chain I, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
 pdb|3S14|I Chain I, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
 pdb|3S15|I Chain I, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
 pdb|3S16|I Chain I, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
 pdb|3S17|I Chain I, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
 pdb|3S1M|I Chain I, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
           (Variant 1)
 pdb|3S1N|I Chain I, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
           (Variant 2)
 pdb|3S1Q|I Chain I, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
           Rna Soaked With Atp
 pdb|3S1R|I Chain I, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
           Rna Soaked With Gtp
 pdb|3S2D|I Chain I, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
           Containing A 5br- U
 pdb|3S2H|I Chain I, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
           Containing A 2[prime]-Iodo Atp
 pdb|3J0K|I Chain I, Orientation Of Rna Polymerase Ii Within The Human
           Vp16-Mediator-Pol Ii-Tfiif Assembly
 pdb|4A3C|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
           Dna-Rna Hybrid
 pdb|4A3B|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
           Dna-Rna Hybrid
 pdb|4A3D|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
           Dna-Rna Hybrid
 pdb|4A3E|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
           Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3F|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
           Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3J|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
           Dna-Rna Hybrid And Soaked With Gmpcpp
 pdb|4A3K|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
           Dna-Rna Hybrid
 pdb|4A3L|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
           Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3M|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
           Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3G|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
           Dna-Rna Hybrid
 pdb|4A3I|I Chain I, Rna Polymerase Ii Binary Complex With Dna
 pdb|4A93|I Chain I, Rna Polymerase Ii Elongation Complex Containing A Cpd
           Lesion
 pdb|4BBR|I Chain I, Structure Of Rna Polymerase Ii-tfiib Complex
 pdb|4BBS|I Chain I, Structure Of An Initially Transcribing Rna Polymerase Ii-
           Tfiib Complex
          Length = 122

 Score = 36.2 bits (82), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 29/111 (26%), Positives = 47/111 (42%), Gaps = 11/111 (9%)

Query: 1   MEFCPTCGTMLQYELPHMDRPSR---FSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFT 57
             FC  C  ML    P  D+ +    F C  C YV    S +  + +   +  E   +  
Sbjct: 4   FRFCRDCNNML---YPREDKENNRLLFECRTCSYVEEAGSPLVYRHELITNIGETAGV-V 59

Query: 58  QDAMME--GPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKH 106
           QD   +   P+++  CP C   + V+ + Q R  D  M +F++C   +C H
Sbjct: 60  QDIGSDPTLPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCL--SCSH 108


>pdb|3D79|A Chain A, Crystal Structure Of Hypothetical Protein Ph0734.1 From
          Hyperthermophilic Archaea Pyrococcus Horikoshii Ot3
          Length = 179

 Score = 27.3 bits (59), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 13/35 (37%), Positives = 22/35 (62%)

Query: 33 CNMESRVKIKRKQPLSKKEIQPIFTQDAMMEGPQT 67
           +M  R+++K K PLSKK+++ I  Q + M G + 
Sbjct: 2  SHMVFRMELKIKHPLSKKDVKEIIAQLSQMFGEEI 36


>pdb|3CNG|A Chain A, Crystal Structure Of Nudix Hydrolase From Nitrosomonas
          Europaea
 pdb|3CNG|B Chain B, Crystal Structure Of Nudix Hydrolase From Nitrosomonas
          Europaea
 pdb|3CNG|C Chain C, Crystal Structure Of Nudix Hydrolase From Nitrosomonas
          Europaea
 pdb|3CNG|D Chain D, Crystal Structure Of Nudix Hydrolase From Nitrosomonas
          Europaea
          Length = 189

 Score = 26.2 bits (56), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 10/28 (35%), Positives = 14/28 (50%)

Query: 2  EFCPTCGTMLQYELPHMDRPSRFSCPAC 29
          +FC  CG  +   +P  D   R+ CP C
Sbjct: 4  KFCSQCGGEVILRIPEGDTLPRYICPKC 31


  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    0.133    0.444 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,090,346
Number of Sequences: 62578
Number of extensions: 95021
Number of successful extensions: 240
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 227
Number of HSP's gapped (non-prelim): 11
length of query: 110
length of database: 14,973,337
effective HSP length: 74
effective length of query: 36
effective length of database: 10,342,565
effective search space: 372332340
effective search space used: 372332340
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 45 (21.9 bits)