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= 042741
         (166 letters)

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

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



>pdb|1GO3|E Chain E, Structure Of An Archeal Homolog Of The Eukaryotic Rna
          Polymerase Ii Rpb4RPB7 COMPLEX
 pdb|1GO3|M Chain M, Structure Of An Archeal Homolog Of The Eukaryotic Rna
          Polymerase Ii Rpb4RPB7 COMPLEX
          Length = 187

 Score = 36.6 bits (83), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 1/66 (1%)

Query: 28 RYTVPRLLEGWINQKACKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPVIFMCRTFLPVK 87
          + TV ++L      +  KD G+ LS+   K I  EG  V+G G    PV+F    ++P  
Sbjct: 23 KETVKKILMEKYEGRLDKDVGFVLSIVDVKDIG-EGKVVHGDGSAYHPVVFETLVYIPEM 81

Query: 88 GEILHG 93
           E++ G
Sbjct: 82 YELIEG 87


>pdb|2C35|B Chain B, Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii
 pdb|2C35|D Chain D, Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii
 pdb|2C35|F Chain F, Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii
 pdb|2C35|H Chain H, Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii
          Length = 172

 Score = 30.4 bits (67), Expect = 0.45,   Method: Compositional matrix adjust.
 Identities = 27/96 (28%), Positives = 43/96 (44%), Gaps = 10/96 (10%)

Query: 1  MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSID 60
          MF+ + L  +I +  +    N L      TV + L   +       +G+ ++VT   +ID
Sbjct: 1  MFYHISLEHEILLHPRYFGPNLLN-----TVKQKLFTEVEGTCTGKYGFVIAVT---TID 52

Query: 61 KEGPTVNGPG--VVSFPVIFMCRTFLPVKGEILHGV 94
            G  V  PG   V +PV +    F P KGE++  V
Sbjct: 53 NIGAGVIQPGRGFVLYPVKYKAIVFRPFKGEVVDAV 88


>pdb|3H0G|G Chain G, Rna Polymerase Ii From Schizosaccharomyces Pombe
 pdb|3H0G|S Chain S, Rna Polymerase Ii From Schizosaccharomyces Pombe
          Length = 172

 Score = 29.3 bits (64), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 19/69 (27%), Positives = 31/69 (44%), Gaps = 2/69 (2%)

Query: 27 QRYTVPRLLEGWINQKACKDHGYFLSVTKSKSID-KEGPTVNGPGVVSFPVIFMCRTFLP 85
          Q Y   +LL   +       +GY + V  S +ID  +G  V G G   F V +    + P
Sbjct: 24 QDYLKAKLLAD-VEGTCSGQYGYIICVLDSNTIDIDKGRVVPGQGFAEFEVKYRAVLWRP 82

Query: 86 VKGEILHGV 94
           +GE++  +
Sbjct: 83 FRGEVVDAI 91


>pdb|2B8K|G Chain G, 12-Subunit Rna Polymerase Ii
          Length = 215

 Score = 27.3 bits (59), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 26/96 (27%), Positives = 38/96 (39%), Gaps = 15/96 (15%)

Query: 27  QRYTVPRLLEGWINQKACKDHGYFLSVTKSKSID-KEGPTVNGPGVVSFPVIFMCRTFLP 85
           ++Y   +LLE  +        GY L V    +ID + G  +   G   F V +    F P
Sbjct: 23  KQYLKTKLLE-EVEGSCTGKFGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFKP 81

Query: 86  VKGEILHGV------------CGPMKYALMSPRRMP 109
            KGE++ G              GPMK   ++   MP
Sbjct: 82  FKGEVVDGTVVSCSQHGFEVQVGPMK-VFVTKHLMP 116


>pdb|1NT9|G Chain G, Complete 12-Subunit Rna Polymerase Ii
 pdb|1PQV|G Chain G, Rna Polymerase Ii-Tfiis Complex
 pdb|1WCM|G Chain G, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
 pdb|1Y1W|G Chain G, Complete Rna Polymerase Ii Elongation Complex
 pdb|1Y77|G Chain G, Complete Rna Polymerase Ii Elongation Complex With
           Substrate Analogue Gmpcpp
 pdb|1Y1V|G Chain G, Refined Rna Polymerase Ii-tfiis Complex
 pdb|1Y1Y|G Chain G, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
 pdb|1Y14|B Chain B, Crystal Structure Of Yeast Subcomplex Of Rpb4 And Rpb7
 pdb|1Y14|D Chain D, Crystal Structure Of Yeast Subcomplex Of Rpb4 And Rpb7
 pdb|2B63|G Chain G, Complete Rna Polymerase Ii-Rna Inhibitor Complex
 pdb|2JA5|G Chain G, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           A
 pdb|2JA6|G Chain G, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           B
 pdb|2JA7|G Chain G, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           C
 pdb|2JA7|S Chain S, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           C
 pdb|2JA8|G Chain G, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           D
 pdb|2R7Z|G Chain G, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
           Complex
 pdb|2R92|G Chain G, Elongation Complex Of Rna Polymerase Ii With Artificial
           Rdrp Scaffold
 pdb|2R93|G Chain G, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
           Delta Virus-Derived Rna Stem Loop
 pdb|2VUM|G Chain G, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
           Elongation Complex
 pdb|3FKI|G Chain G, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
 pdb|3H3V|H Chain H, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
           Active Site
 pdb|3HOU|G Chain G, Complete Rna Polymerase Ii Elongation Complex I With A T-U
           Mismatch
 pdb|3HOU|S Chain S, Complete Rna Polymerase Ii Elongation Complex I With A T-U
           Mismatch
 pdb|3HOV|G Chain G, Complete Rna Polymerase Ii Elongation Complex Ii
 pdb|3HOW|G Chain G, Complete Rna Polymerase Ii Elongation Complex Iii With A
           T-U Mismatch And A Frayed Rna 3'-Uridine
 pdb|3HOX|G Chain G, Complete Rna Polymerase Ii Elongation Complex V
 pdb|3HOY|G Chain G, Complete Rna Polymerase Ii Elongation Complex Vi
 pdb|3HOZ|G Chain G, Complete Rna Polymerase Ii Elongation Complex Iv With A
           T-U Mismatch And A Frayed Rna 3'-Guanine
 pdb|3I4M|G Chain G, 8-oxoguanine Containing Rna Polymerase Ii Elongation
           Complex D
 pdb|3I4N|G Chain G, 8-oxoguanine Containing Rna Polymerase Ii Elongation
           Complex E
 pdb|3K1F|G Chain G, Crystal Structure Of Rna Polymerase Ii In Complex With
           Tfiib
 pdb|3PO2|G Chain G, Arrested Rna Polymerase Ii Elongation Complex
 pdb|3PO3|G Chain G, Arrested Rna Polymerase Ii Reactivation Intermediate
 pdb|3QT1|G Chain G, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
           Subunit
 pdb|3J0K|G Chain G, Orientation Of Rna Polymerase Ii Within The Human
           Vp16-Mediator-Pol Ii-Tfiif Assembly
 pdb|4A3C|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
           Dna-Rna Hybrid
 pdb|4A3B|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
           Dna-Rna Hybrid
 pdb|4A3D|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
           Dna-Rna Hybrid
 pdb|4A3E|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
           Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3F|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
           Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3J|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
           Dna-Rna Hybrid And Soaked With Gmpcpp
 pdb|4A3K|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
           Dna-Rna Hybrid
 pdb|4A3L|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
           Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3M|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
           Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3G|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
           Dna-Rna Hybrid
 pdb|4A3I|G Chain G, Rna Polymerase Ii Binary Complex With Dna
 pdb|4A93|G Chain G, Rna Polymerase Ii Elongation Complex Containing A Cpd
           Lesion
 pdb|4BBR|G Chain G, Structure Of Rna Polymerase Ii-tfiib Complex
 pdb|4BBS|G Chain G, Structure Of An Initially Transcribing Rna Polymerase Ii-
           Tfiib Complex
          Length = 171

 Score = 26.9 bits (58), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 26/96 (27%), Positives = 38/96 (39%), Gaps = 15/96 (15%)

Query: 27  QRYTVPRLLEGWINQKACKDHGYFLSVTKSKSID-KEGPTVNGPGVVSFPVIFMCRTFLP 85
           ++Y   +LLE  +        GY L V    +ID + G  +   G   F V +    F P
Sbjct: 23  KQYLKTKLLE-EVEGSCTGKFGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFKP 81

Query: 86  VKGEILHGV------------CGPMKYALMSPRRMP 109
            KGE++ G              GPMK   ++   MP
Sbjct: 82  FKGEVVDGTVVSCSQHGFEVQVGPMK-VFVTKHLMP 116


  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
   0.323    0.140    0.430 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,096,832
Number of Sequences: 62578
Number of extensions: 197292
Number of successful extensions: 262
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 261
Number of HSP's gapped (non-prelim): 8
length of query: 166
length of database: 14,973,337
effective HSP length: 92
effective length of query: 74
effective length of database: 9,216,161
effective search space: 681995914
effective search space used: 681995914
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: 47 (22.7 bits)