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= psy11162
         (91 letters)

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

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



>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 =  100 bits (248), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 45/81 (55%), Positives = 57/81 (70%)

Query: 4  KIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQT 63
          K+  ELD+K PNAA+ T+ KEDHTL NM+ NQLL D  VLFAGYK PHPL H FILR+QT
Sbjct: 17 KVTYELDSKSPNAAVVTLEKEDHTLANMLANQLLSDERVLFAGYKVPHPLNHNFILRVQT 76

Query: 64 TAESTPHDALMNAITDLLAEL 84
            + +P   +++A   L+  L
Sbjct: 77 VEDCSPKQVIVDAAKSLITHL 97


>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 = 87.0 bits (214), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 43/82 (52%), Positives = 51/82 (62%)

Query: 10  DTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTP 69
           DTK PNA + T  KEDHTLGN+IR +LL D  VLFA YK  HP   +F LRIQTT    P
Sbjct: 24  DTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEGYDP 83

Query: 70  HDALMNAITDLLAELSLFEERF 91
            DAL NA   ++ +L   +  F
Sbjct: 84  KDALKNACNSIINKLGALKTNF 105


>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 = 61.6 bits (148), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 29/60 (48%), Positives = 37/60 (61%)

Query: 21 VNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDL 80
          +  EDHTLGN+I   L +   V FA Y QPHPL  K I++I T    TP DAL+ AI ++
Sbjct: 17 IEGEDHTLGNLIAGTLRRISGVSFASYYQPHPLSDKIIVKILTDGSITPKDALLKAIENI 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 = 60.5 bits (145), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 29/57 (50%), Positives = 34/57 (59%)

Query: 21 VNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAI 77
          +  EDHTLGN+I   L K   V FA Y QPHPL  K I++I T     P DAL+ AI
Sbjct: 17 IEGEDHTLGNLIAGTLRKISGVSFASYYQPHPLTDKIIVKILTDGSIAPKDALLKAI 73


>pdb|3QNA|A Chain A, Crystal Structure Of A 6-Pyruvoyltetrahydropterin
          Synthase Homologue From Esherichia Coli Complexed
          Sepiapterin
 pdb|3QNA|B Chain B, Crystal Structure Of A 6-Pyruvoyltetrahydropterin
          Synthase Homologue From Esherichia Coli Complexed
          Sepiapterin
 pdb|3QNA|C Chain C, Crystal Structure Of A 6-Pyruvoyltetrahydropterin
          Synthase Homologue From Esherichia Coli Complexed
          Sepiapterin
 pdb|3QNA|D Chain D, Crystal Structure Of A 6-Pyruvoyltetrahydropterin
          Synthase Homologue From Esherichia Coli Complexed
          Sepiapterin
 pdb|3QNA|E Chain E, Crystal Structure Of A 6-Pyruvoyltetrahydropterin
          Synthase Homologue From Esherichia Coli Complexed
          Sepiapterin
 pdb|3QNA|F Chain F, Crystal Structure Of A 6-Pyruvoyltetrahydropterin
          Synthase Homologue From Esherichia Coli Complexed
          Sepiapterin
          Length = 141

 Score = 26.6 bits (57), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 20/71 (28%), Positives = 29/71 (40%), Gaps = 10/71 (14%)

Query: 30 NMIRNQLLKD---------PHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDL 80
          +M+   L KD         PHV   G+K      H F++R++ T E  PH   +    +L
Sbjct: 20 HMMSTTLFKDFTFEAAHRLPHVP-EGHKAGRLHGHSFMVRLEITGEVDPHTGWIIDFAEL 78

Query: 81 LAELSLFEERF 91
           A      ER 
Sbjct: 79 KAAFKPTYERL 89


>pdb|3QN0|A Chain A, Structure Of 6-Pyruvoyltetrahydropterin Synthase
 pdb|3QN0|B Chain B, Structure Of 6-Pyruvoyltetrahydropterin Synthase
 pdb|3QN0|C Chain C, Structure Of 6-Pyruvoyltetrahydropterin Synthase
 pdb|3QN0|D Chain D, Structure Of 6-Pyruvoyltetrahydropterin Synthase
 pdb|3QN0|E Chain E, Structure Of 6-Pyruvoyltetrahydropterin Synthase
 pdb|3QN0|F Chain F, Structure Of 6-Pyruvoyltetrahydropterin Synthase
 pdb|3QN9|A Chain A, Crystal Structure Of A 6-Pyruvoyltetrahydropterin
          Synthase Homologue From Esherichia Coli
 pdb|3QN9|B Chain B, Crystal Structure Of A 6-Pyruvoyltetrahydropterin
          Synthase Homologue From Esherichia Coli
          Length = 141

 Score = 26.2 bits (56), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 20/71 (28%), Positives = 29/71 (40%), Gaps = 10/71 (14%)

Query: 30 NMIRNQLLKD---------PHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALMNAITDL 80
          +M+   L KD         PHV   G+K      H F++R++ T E  PH   +    +L
Sbjct: 20 HMMSTTLFKDFTFEAAHRLPHVP-EGHKCGRLHGHSFMVRLEITGEVDPHTGWIIDFAEL 78

Query: 81 LAELSLFEERF 91
           A      ER 
Sbjct: 79 KAAFKPTYERL 89


  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    0.137    0.390 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,407,602
Number of Sequences: 62578
Number of extensions: 77623
Number of successful extensions: 215
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 211
Number of HSP's gapped (non-prelim): 9
length of query: 91
length of database: 14,973,337
effective HSP length: 58
effective length of query: 33
effective length of database: 11,343,813
effective search space: 374345829
effective search space used: 374345829
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: 45 (21.9 bits)