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= psy5290
         (536 letters)

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

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



>pdb|3H0G|E Chain E, Rna Polymerase Ii From Schizosaccharomyces Pombe
 pdb|3H0G|Q Chain Q, Rna Polymerase Ii From Schizosaccharomyces Pombe
          Length = 210

 Score =  112 bits (280), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 59/146 (40%), Positives = 87/146 (59%), Gaps = 3/146 (2%)

Query: 2   QLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVA-HNDDPTDQMFVFFP 60
           QL HDRGY V+Q ELD TLDQFK         +   R+ L       ND     +++ F 
Sbjct: 20  QLVHDRGYGVSQAELDLTLDQFKAMHCGMG--RNLDRTTLSFYAKPSNDSNKGTIYIEFA 77

Query: 61  DEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLI 120
            EP +GIK ++T+   + +      I++    MTPSA + +  +  ++ +E F ES+L++
Sbjct: 78  KEPSVGIKEMRTFVHTLGDHNHKTGILIYANSMTPSAAKIIATVTGQFTIETFQESDLIV 137

Query: 121 NITEHELVPEHIVLTPEEKQELLTRY 146
           NIT HELVP+HI+L+P+EK+ELL RY
Sbjct: 138 NITHHELVPKHILLSPDEKKELLDRY 163


>pdb|1DZF|A Chain A, Rpb5 From S.Cerevisiae
 pdb|1I3Q|E Chain E, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
 pdb|1I50|E Chain E, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
 pdb|1I6H|E Chain E, Rna Polymerase Ii Elongation Complex
 pdb|1K83|E Chain E, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
           With The Inhibitor Alpha Amanitin
 pdb|1NIK|E Chain E, Wild Type Rna Polymerase Ii
 pdb|1NT9|E Chain E, Complete 12-Subunit Rna Polymerase Ii
 pdb|1PQV|E Chain E, Rna Polymerase Ii-Tfiis Complex
 pdb|1R5U|E Chain E, Rna Polymerase Ii Tfiib Complex
 pdb|1SFO|E Chain E, Rna Polymerase Ii Strand Separated Elongation Complex
 pdb|1R9S|E Chain E, Rna Polymerase Ii Strand Separated Elongation Complex,
           Matched Nucleotide
 pdb|1R9T|E Chain E, Rna Polymerase Ii Strand Separated Elongation Complex,
           Mismatched Nucleotide
 pdb|1TWA|E Chain E, Rna Polymerase Ii Complexed With Atp
 pdb|1TWC|E Chain E, Rna Polymerase Ii Complexed With Gtp
 pdb|1TWF|E Chain E, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
 pdb|1TWG|E Chain E, Rna Polymerase Ii Complexed With Ctp
 pdb|1TWH|E Chain E, Rna Polymerase Ii Complexed With 2'datp
 pdb|1WCM|E Chain E, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
 pdb|1Y1W|E Chain E, Complete Rna Polymerase Ii Elongation Complex
 pdb|1Y77|E Chain E, Complete Rna Polymerase Ii Elongation Complex With
           Substrate Analogue Gmpcpp
 pdb|1Y1V|E Chain E, Refined Rna Polymerase Ii-tfiis Complex
 pdb|1Y1Y|E Chain E, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
 pdb|2B63|E Chain E, Complete Rna Polymerase Ii-Rna Inhibitor Complex
 pdb|2B8K|E Chain E, 12-Subunit Rna Polymerase Ii
 pdb|2E2H|E Chain E, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With Gtp
 pdb|2E2I|E Chain E, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
           Dgtp
 pdb|2E2J|E Chain E, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
           Gmpcpp
 pdb|2NVQ|E Chain E, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
           2'dutp
 pdb|2NVT|E Chain E, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
           Gmpcpp
 pdb|2NVX|E Chain E, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
           Dutp
 pdb|2NVY|E Chain E, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
 pdb|2NVZ|E Chain E, Rna Polymerase Ii Elongation Complex With Utp, Updated
           112006
 pdb|2JA5|E Chain E, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           A
 pdb|2JA6|E Chain E, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           B
 pdb|2JA7|E Chain E, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           C
 pdb|2JA7|Q Chain Q, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           C
 pdb|2JA8|E Chain E, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           D
 pdb|2YU9|E Chain E, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
           Utp
 pdb|2R7Z|E Chain E, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
           Complex
 pdb|2R92|E Chain E, Elongation Complex Of Rna Polymerase Ii With Artificial
           Rdrp Scaffold
 pdb|2R93|E Chain E, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
           Delta Virus-Derived Rna Stem Loop
 pdb|2VUM|E Chain E, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
           Elongation Complex
 pdb|3CQZ|E Chain E, Crystal Structure Of 10 Subunit Rna Polymerase Ii In
           Complex With The Inhibitor Alpha-Amanitin
 pdb|3FKI|E Chain E, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
 pdb|3GTG|E Chain E, Backtracked Rna Polymerase Ii Complex With 12mer Rna
 pdb|3GTJ|E Chain E, Backtracked Rna Polymerase Ii Complex With 13mer Rna
 pdb|3GTK|E Chain E, Backtracked Rna Polymerase Ii Complex With 18mer Rna
 pdb|3GTL|E Chain E, Backtracked Rna Polymerase Ii Complex With 13mer With G<>u
           Mismatch
 pdb|3GTM|E Chain E, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
 pdb|3GTO|E Chain E, Backtracked Rna Polymerase Ii Complex With 15mer Rna
 pdb|3GTP|E Chain E, Backtracked Rna Polymerase Ii Complex With 24mer Rna
 pdb|3GTQ|E Chain E, Backtracked Rna Polymerase Ii Complex Induced By Damage
 pdb|3H3V|F Chain F, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
           Active Site
 pdb|3HOU|E Chain E, Complete Rna Polymerase Ii Elongation Complex I With A T-U
           Mismatch
 pdb|3HOU|Q Chain Q, Complete Rna Polymerase Ii Elongation Complex I With A T-U
           Mismatch
 pdb|3HOV|E Chain E, Complete Rna Polymerase Ii Elongation Complex Ii
 pdb|3HOW|E Chain E, Complete Rna Polymerase Ii Elongation Complex Iii With A
           T-U Mismatch And A Frayed Rna 3'-Uridine
 pdb|3HOX|E Chain E, Complete Rna Polymerase Ii Elongation Complex V
 pdb|3HOY|E Chain E, Complete Rna Polymerase Ii Elongation Complex Vi
 pdb|3HOZ|E Chain E, Complete Rna Polymerase Ii Elongation Complex Iv With A
           T-U Mismatch And A Frayed Rna 3'-Guanine
 pdb|3I4M|E Chain E, 8-oxoguanine Containing Rna Polymerase Ii Elongation
           Complex D
 pdb|3I4N|E Chain E, 8-oxoguanine Containing Rna Polymerase Ii Elongation
           Complex E
 pdb|3K1F|E Chain E, Crystal Structure Of Rna Polymerase Ii In Complex With
           Tfiib
 pdb|3K7A|E Chain E, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
 pdb|3M3Y|E Chain E, Rna Polymerase Ii Elongation Complex C
 pdb|3M4O|E Chain E, Rna Polymerase Ii Elongation Complex B
 pdb|3PO2|E Chain E, Arrested Rna Polymerase Ii Elongation Complex
 pdb|3PO3|E Chain E, Arrested Rna Polymerase Ii Reactivation Intermediate
 pdb|3QT1|E Chain E, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
           Subunit
 pdb|3RZD|E Chain E, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
 pdb|3RZO|E Chain E, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
 pdb|3S14|E Chain E, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
 pdb|3S15|E Chain E, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
 pdb|3S16|E Chain E, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
 pdb|3S17|E Chain E, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
 pdb|3S1M|E Chain E, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
           (Variant 1)
 pdb|3S1N|E Chain E, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
           (Variant 2)
 pdb|3S1Q|E Chain E, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
           Rna Soaked With Atp
 pdb|3S1R|E Chain E, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
           Rna Soaked With Gtp
 pdb|3S2D|E Chain E, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
           Containing A 5br- U
 pdb|3S2H|E Chain E, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
           Containing A 2[prime]-Iodo Atp
 pdb|3J0K|E Chain E, Orientation Of Rna Polymerase Ii Within The Human
           Vp16-Mediator-Pol Ii-Tfiif Assembly
 pdb|4A3C|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
           Dna-Rna Hybrid
 pdb|4A3B|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
           Dna-Rna Hybrid
 pdb|4A3D|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
           Dna-Rna Hybrid
 pdb|4A3E|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
           Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3F|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
           Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3J|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
           Dna-Rna Hybrid And Soaked With Gmpcpp
 pdb|4A3K|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
           Dna-Rna Hybrid
 pdb|4A3L|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
           Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3M|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
           Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3G|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
           Dna-Rna Hybrid
 pdb|4A3I|E Chain E, Rna Polymerase Ii Binary Complex With Dna
 pdb|4A93|E Chain E, Rna Polymerase Ii Elongation Complex Containing A Cpd
           Lesion
 pdb|4BBR|E Chain E, Structure Of Rna Polymerase Ii-tfiib Complex
 pdb|4BBS|E Chain E, Structure Of An Initially Transcribing Rna Polymerase Ii-
           Tfiib Complex
          Length = 215

 Score =  106 bits (264), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 61/155 (39%), Positives = 94/155 (60%), Gaps = 17/155 (10%)

Query: 2   QLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQ------- 54
           ++  DRGY +TQ+E++  L+ FK ++ D  S  RP R     +++   +PT++       
Sbjct: 21  EMVKDRGYFITQEEVELPLEDFKAKYCD--SMGRPQRK----MMSFQANPTEESISKFPD 74

Query: 55  ---MFVFFPDEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILE 111
              ++V F DEP +G+KT+KT+   +QE+     I V Q  +TPSA + LV   P   +E
Sbjct: 75  MGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMK-LVPSIPPATIE 133

Query: 112 YFLESELLINITEHELVPEHIVLTPEEKQELLTRY 146
            F E+ L++NIT HELVP+HI L+ +EK+ELL RY
Sbjct: 134 TFNEAALVVNITHHELVPKHIRLSSDEKRELLKRY 168


>pdb|1HMJ|A Chain A, Solution Structure Of Rna Polymerase Subunit H
          Length = 78

 Score = 30.8 bits (68), Expect = 2.2,   Method: Composition-based stats.
 Identities = 12/27 (44%), Positives = 20/27 (74%)

Query: 120 INITEHELVPEHIVLTPEEKQELLTRY 146
           + +T+H LVP+H ++  EE +E+L RY
Sbjct: 1   MKVTDHILVPKHEIVPKEEVEEILKRY 27


  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
   0.314    0.134    0.400 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,764,342
Number of Sequences: 62578
Number of extensions: 820352
Number of successful extensions: 1315
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1309
Number of HSP's gapped (non-prelim): 5
length of query: 536
length of database: 14,973,337
effective HSP length: 103
effective length of query: 433
effective length of database: 8,527,803
effective search space: 3692538699
effective search space used: 3692538699
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 54 (25.4 bits)