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= 035461
         (51 letters)

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

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



>pdb|3H0G|L Chain L, Rna Polymerase Ii From Schizosaccharomyces Pombe
 pdb|3H0G|X Chain X, Rna Polymerase Ii From Schizosaccharomyces Pombe
          Length = 63

 Score = 68.9 bits (167), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 27/49 (55%), Positives = 40/49 (81%)

Query: 3  PQPEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51
          P+P  + Y+C DCG  NT++  +VI+CRECG+R++YK RT+R+VQ+EAR
Sbjct: 15 PRPATMIYLCADCGARNTIQAKEVIRCRECGHRVMYKMRTKRMVQFEAR 63


>pdb|1I3Q|L Chain L, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
 pdb|1I50|L Chain L, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
 pdb|1I6H|L Chain L, Rna Polymerase Ii Elongation Complex
 pdb|1K83|L Chain L, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
          With The Inhibitor Alpha Amanitin
 pdb|1NIK|L Chain L, Wild Type Rna Polymerase Ii
 pdb|1NT9|L Chain L, Complete 12-Subunit Rna Polymerase Ii
 pdb|1PQV|L Chain L, Rna Polymerase Ii-Tfiis Complex
 pdb|1R5U|L Chain L, Rna Polymerase Ii Tfiib Complex
 pdb|1SFO|L Chain L, Rna Polymerase Ii Strand Separated Elongation Complex
 pdb|1R9S|L Chain L, Rna Polymerase Ii Strand Separated Elongation Complex,
          Matched Nucleotide
 pdb|1R9T|L Chain L, Rna Polymerase Ii Strand Separated Elongation Complex,
          Mismatched Nucleotide
 pdb|1TWA|L Chain L, Rna Polymerase Ii Complexed With Atp
 pdb|1TWC|L Chain L, Rna Polymerase Ii Complexed With Gtp
 pdb|1TWF|L Chain L, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
 pdb|1TWG|L Chain L, Rna Polymerase Ii Complexed With Ctp
 pdb|1TWH|L Chain L, Rna Polymerase Ii Complexed With 2'datp
 pdb|1WCM|L Chain L, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
 pdb|1Y1W|L Chain L, Complete Rna Polymerase Ii Elongation Complex
 pdb|1Y77|L Chain L, Complete Rna Polymerase Ii Elongation Complex With
          Substrate Analogue Gmpcpp
 pdb|1Y1V|L Chain L, Refined Rna Polymerase Ii-tfiis Complex
 pdb|1Y1Y|L Chain L, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
 pdb|2B63|L Chain L, Complete Rna Polymerase Ii-Rna Inhibitor Complex
 pdb|2B8K|L Chain L, 12-Subunit Rna Polymerase Ii
 pdb|2E2H|L Chain L, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With
          Gtp
 pdb|2E2I|L Chain L, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
          2'- Dgtp
 pdb|2E2J|L Chain L, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
          Gmpcpp
 pdb|2NVQ|L Chain L, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
          2'dutp
 pdb|2NVT|L Chain L, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
          Gmpcpp
 pdb|2NVX|L Chain L, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
          2'- Dutp
 pdb|2NVY|L Chain L, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
 pdb|2NVZ|L Chain L, Rna Polymerase Ii Elongation Complex With Utp, Updated
          112006
 pdb|2JA5|L Chain L, Cpd Lesion Containing Rna Polymerase Ii Elongation
          Complex A
 pdb|2JA6|L Chain L, Cpd Lesion Containing Rna Polymerase Ii Elongation
          Complex B
 pdb|2JA7|L Chain L, Cpd Lesion Containing Rna Polymerase Ii Elongation
          Complex C
 pdb|2JA7|X Chain X, Cpd Lesion Containing Rna Polymerase Ii Elongation
          Complex C
 pdb|2JA8|L Chain L, Cpd Lesion Containing Rna Polymerase Ii Elongation
          Complex D
 pdb|2YU9|L Chain L, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
          Utp
 pdb|2R7Z|L Chain L, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
          Complex
 pdb|2R92|L Chain L, Elongation Complex Of Rna Polymerase Ii With Artificial
          Rdrp Scaffold
 pdb|2R93|L Chain L, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
          Delta Virus-Derived Rna Stem Loop
 pdb|3CQZ|L Chain L, Crystal Structure Of 10 Subunit Rna Polymerase Ii In
          Complex With The Inhibitor Alpha-Amanitin
 pdb|2VUM|L Chain L, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
          Elongation Complex
 pdb|3FKI|L Chain L, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
 pdb|3GTG|L Chain L, Backtracked Rna Polymerase Ii Complex With 12mer Rna
 pdb|3GTJ|L Chain L, Backtracked Rna Polymerase Ii Complex With 13mer Rna
 pdb|3GTK|L Chain L, Backtracked Rna Polymerase Ii Complex With 18mer Rna
 pdb|3GTL|L Chain L, Backtracked Rna Polymerase Ii Complex With 13mer With
          G<>u Mismatch
 pdb|3GTM|L Chain L, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
 pdb|3GTO|L Chain L, Backtracked Rna Polymerase Ii Complex With 15mer Rna
 pdb|3GTP|L Chain L, Backtracked Rna Polymerase Ii Complex With 24mer Rna
 pdb|3GTQ|L Chain L, Backtracked Rna Polymerase Ii Complex Induced By Damage
 pdb|3H3V|M Chain M, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
          Active Site
 pdb|3HOU|L Chain L, Complete Rna Polymerase Ii Elongation Complex I With A
          T-U Mismatch
 pdb|3HOU|X Chain X, Complete Rna Polymerase Ii Elongation Complex I With A
          T-U Mismatch
 pdb|3HOV|L Chain L, Complete Rna Polymerase Ii Elongation Complex Ii
 pdb|3HOW|L Chain L, Complete Rna Polymerase Ii Elongation Complex Iii With A
          T-U Mismatch And A Frayed Rna 3'-Uridine
 pdb|3HOX|L Chain L, Complete Rna Polymerase Ii Elongation Complex V
 pdb|3HOY|L Chain L, Complete Rna Polymerase Ii Elongation Complex Vi
 pdb|3HOZ|L Chain L, Complete Rna Polymerase Ii Elongation Complex Iv With A
          T-U Mismatch And A Frayed Rna 3'-Guanine
 pdb|3I4M|L Chain L, 8-oxoguanine Containing Rna Polymerase Ii Elongation
          Complex D
 pdb|3I4N|L Chain L, 8-oxoguanine Containing Rna Polymerase Ii Elongation
          Complex E
 pdb|3K1F|L Chain L, Crystal Structure Of Rna Polymerase Ii In Complex With
          Tfiib
 pdb|3K7A|L Chain L, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
 pdb|3M3Y|L Chain L, Rna Polymerase Ii Elongation Complex C
 pdb|3M4O|L Chain L, Rna Polymerase Ii Elongation Complex B
 pdb|3PO2|L Chain L, Arrested Rna Polymerase Ii Elongation Complex
 pdb|3PO3|L Chain L, Arrested Rna Polymerase Ii Reactivation Intermediate
 pdb|3QT1|L Chain L, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
          Subunit
 pdb|3RZD|L Chain L, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
 pdb|3RZO|L Chain L, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
 pdb|3S14|L Chain L, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
 pdb|3S15|L Chain L, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
 pdb|3S16|L Chain L, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
 pdb|3S17|L Chain L, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
 pdb|3S1M|L Chain L, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
          (Variant 1)
 pdb|3S1N|L Chain L, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
          (Variant 2)
 pdb|3S1Q|L Chain L, Rna Polymerase Ii Initiation Complex With A 5-Nt
          3'-Deoxy Rna Soaked With Atp
 pdb|3S1R|L Chain L, Rna Polymerase Ii Initiation Complex With A 5-Nt
          3'-Deoxy Rna Soaked With Gtp
 pdb|3S2D|L Chain L, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
          Containing A 5br- U
 pdb|3S2H|L Chain L, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
          Containing A 2[prime]-Iodo Atp
 pdb|4A3C|L Chain L, Rna Polymerase Ii Initial Transcribing Complex With A
          5nt Dna-Rna Hybrid
 pdb|4A3B|L Chain L, Rna Polymerase Ii Initial Transcribing Complex With A
          4nt Dna-Rna Hybrid
 pdb|4A3D|L Chain L, Rna Polymerase Ii Initial Transcribing Complex With A
          6nt Dna-Rna Hybrid
 pdb|4A3E|L Chain L, Rna Polymerase Ii Initial Transcribing Complex With A
          5nt Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3F|L Chain L, Rna Polymerase Ii Initial Transcribing Complex With A
          6nt Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3J|L Chain L, Rna Polymerase Ii Initial Transcribing Complex With A
          2nt Dna-Rna Hybrid And Soaked With Gmpcpp
 pdb|4A3K|L Chain L, Rna Polymerase Ii Initial Transcribing Complex With A
          7nt Dna-Rna Hybrid
 pdb|4A3L|L Chain L, Rna Polymerase Ii Initial Transcribing Complex With A
          7nt Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3M|L Chain L, Rna Polymerase Ii Initial Transcribing Complex With A
          4nt Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3G|L Chain L, Rna Polymerase Ii Initial Transcribing Complex With A
          2nt Dna-Rna Hybrid
 pdb|4A3I|L Chain L, Rna Polymerase Ii Binary Complex With Dna
 pdb|4A93|L Chain L, Rna Polymerase Ii Elongation Complex Containing A Cpd
          Lesion
 pdb|4BBR|L Chain L, Structure Of Rna Polymerase Ii-tfiib Complex
 pdb|4BBS|L Chain L, Structure Of An Initially Transcribing Rna Polymerase
          Ii- Tfiib Complex
          Length = 70

 Score = 55.8 bits (133), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 21/49 (42%), Positives = 34/49 (69%)

Query: 3  PQPEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51
           +   + YIC +C  + +L   D ++C++CG+RIL K RT+R+VQ+EAR
Sbjct: 22 ARTATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQFEAR 70


>pdb|3J0K|L Chain L, Orientation Of Rna Polymerase Ii Within The Human
          Vp16-Mediator-Pol Ii-Tfiif Assembly
          Length = 46

 Score = 55.1 bits (131), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 21/45 (46%), Positives = 33/45 (73%)

Query: 7  PVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51
           + YIC +C  + +L   D ++C++CG+RIL K RT+R+VQ+EAR
Sbjct: 2  TLKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQFEAR 46


>pdb|3J21|GG Chain g, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
          Revealed By Cryo-em: Implications For Evolution Of
          Eukaryotic Ribosomes (50s Ribosomal Proteins)
          Length = 51

 Score = 26.6 bits (57), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 12/29 (41%), Positives = 16/29 (55%), Gaps = 3/29 (10%)

Query: 9  SYICGDCGMENTLKPGDVIQCRECGYRIL 37
           Y+C  CG  N   P    +CR+CGY+ L
Sbjct: 14 KYVCLRCGATN---PWGAKKCRKCGYKRL 39


  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
   0.324    0.143    0.465 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,696,523
Number of Sequences: 62578
Number of extensions: 47114
Number of successful extensions: 93
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 87
Number of HSP's gapped (non-prelim): 9
length of query: 51
length of database: 14,973,337
effective HSP length: 23
effective length of query: 28
effective length of database: 13,534,043
effective search space: 378953204
effective search space used: 378953204
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 45 (21.9 bits)