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= 035172
         (71 letters)

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

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



>pdb|3H0G|J Chain J, Rna Polymerase Ii From Schizosaccharomyces Pombe
 pdb|3H0G|V Chain V, Rna Polymerase Ii From Schizosaccharomyces Pombe
          Length = 71

 Score =  112 bits (279), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 52/68 (76%), Positives = 58/68 (85%)

Query: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
          MIIP+RCF+CGKVIG+KWDTYL LLQ D  EG+ALD LGL RYCCRRM++THVDLIEKLL
Sbjct: 1  MIIPIRCFSCGKVIGDKWDTYLTLLQEDNTEGEALDKLGLQRYCCRRMILTHVDLIEKLL 60

Query: 61 NYNTLDKS 68
           YN L K 
Sbjct: 61 CYNPLSKQ 68


>pdb|1I3Q|J Chain J, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
 pdb|1I50|J Chain J, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
 pdb|1I6H|J Chain J, Rna Polymerase Ii Elongation Complex
 pdb|1K83|J Chain J, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
          With The Inhibitor Alpha Amanitin
 pdb|1NIK|J Chain J, Wild Type Rna Polymerase Ii
 pdb|1NT9|J Chain J, Complete 12-Subunit Rna Polymerase Ii
 pdb|1PQV|J Chain J, Rna Polymerase Ii-Tfiis Complex
 pdb|1R5U|J Chain J, Rna Polymerase Ii Tfiib Complex
 pdb|1SFO|J Chain J, Rna Polymerase Ii Strand Separated Elongation Complex
 pdb|1R9S|J Chain J, Rna Polymerase Ii Strand Separated Elongation Complex,
          Matched Nucleotide
 pdb|1R9T|J Chain J, Rna Polymerase Ii Strand Separated Elongation Complex,
          Mismatched Nucleotide
 pdb|1TWA|J Chain J, Rna Polymerase Ii Complexed With Atp
 pdb|1TWC|J Chain J, Rna Polymerase Ii Complexed With Gtp
 pdb|1TWF|J Chain J, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
 pdb|1TWG|J Chain J, Rna Polymerase Ii Complexed With Ctp
 pdb|1TWH|J Chain J, Rna Polymerase Ii Complexed With 2'datp
 pdb|1WCM|J Chain J, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
 pdb|1Y1W|J Chain J, Complete Rna Polymerase Ii Elongation Complex
 pdb|1Y77|J Chain J, Complete Rna Polymerase Ii Elongation Complex With
          Substrate Analogue Gmpcpp
 pdb|1Y1V|J Chain J, Refined Rna Polymerase Ii-tfiis Complex
 pdb|1Y1Y|J Chain J, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
 pdb|2B63|J Chain J, Complete Rna Polymerase Ii-Rna Inhibitor Complex
 pdb|2B8K|J Chain J, 12-Subunit Rna Polymerase Ii
 pdb|2E2H|J Chain J, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With
          Gtp
 pdb|2E2I|J Chain J, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
          2'- Dgtp
 pdb|2E2J|J Chain J, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
          Gmpcpp
 pdb|2NVQ|J Chain J, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
          2'dutp
 pdb|2NVT|J Chain J, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
          Gmpcpp
 pdb|2NVX|J Chain J, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
          2'- Dutp
 pdb|2NVY|J Chain J, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
 pdb|2NVZ|J Chain J, Rna Polymerase Ii Elongation Complex With Utp, Updated
          112006
 pdb|2JA5|J Chain J, Cpd Lesion Containing Rna Polymerase Ii Elongation
          Complex A
 pdb|2JA6|J Chain J, Cpd Lesion Containing Rna Polymerase Ii Elongation
          Complex B
 pdb|2JA7|J Chain J, Cpd Lesion Containing Rna Polymerase Ii Elongation
          Complex C
 pdb|2JA7|V Chain V, Cpd Lesion Containing Rna Polymerase Ii Elongation
          Complex C
 pdb|2JA8|J Chain J, Cpd Lesion Containing Rna Polymerase Ii Elongation
          Complex D
 pdb|2YU9|J Chain J, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
          Utp
 pdb|2R7Z|J Chain J, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
          Complex
 pdb|2R92|J Chain J, Elongation Complex Of Rna Polymerase Ii With Artificial
          Rdrp Scaffold
 pdb|2R93|J Chain J, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
          Delta Virus-Derived Rna Stem Loop
 pdb|2VUM|J Chain J, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
          Elongation Complex
 pdb|3CQZ|J Chain J, Crystal Structure Of 10 Subunit Rna Polymerase Ii In
          Complex With The Inhibitor Alpha-Amanitin
 pdb|3FKI|J Chain J, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
 pdb|3GTG|J Chain J, Backtracked Rna Polymerase Ii Complex With 12mer Rna
 pdb|3GTJ|J Chain J, Backtracked Rna Polymerase Ii Complex With 13mer Rna
 pdb|3GTK|J Chain J, Backtracked Rna Polymerase Ii Complex With 18mer Rna
 pdb|3GTL|J Chain J, Backtracked Rna Polymerase Ii Complex With 13mer With
          G<>u Mismatch
 pdb|3GTM|J Chain J, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
 pdb|3GTO|J Chain J, Backtracked Rna Polymerase Ii Complex With 15mer Rna
 pdb|3GTP|J Chain J, Backtracked Rna Polymerase Ii Complex With 24mer Rna
 pdb|3GTQ|J Chain J, Backtracked Rna Polymerase Ii Complex Induced By Damage
 pdb|3H3V|K Chain K, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
          Active Site
 pdb|3HOU|J Chain J, Complete Rna Polymerase Ii Elongation Complex I With A
          T-U Mismatch
 pdb|3HOU|V Chain V, Complete Rna Polymerase Ii Elongation Complex I With A
          T-U Mismatch
 pdb|3HOV|J Chain J, Complete Rna Polymerase Ii Elongation Complex Ii
 pdb|3HOW|J Chain J, Complete Rna Polymerase Ii Elongation Complex Iii With A
          T-U Mismatch And A Frayed Rna 3'-Uridine
 pdb|3HOX|J Chain J, Complete Rna Polymerase Ii Elongation Complex V
 pdb|3HOY|J Chain J, Complete Rna Polymerase Ii Elongation Complex Vi
 pdb|3HOZ|J Chain J, Complete Rna Polymerase Ii Elongation Complex Iv With A
          T-U Mismatch And A Frayed Rna 3'-Guanine
 pdb|3I4M|J Chain J, 8-oxoguanine Containing Rna Polymerase Ii Elongation
          Complex D
 pdb|3I4N|J Chain J, 8-oxoguanine Containing Rna Polymerase Ii Elongation
          Complex E
 pdb|3K1F|J Chain J, Crystal Structure Of Rna Polymerase Ii In Complex With
          Tfiib
 pdb|3K7A|J Chain J, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
 pdb|3M3Y|J Chain J, Rna Polymerase Ii Elongation Complex C
 pdb|3M4O|J Chain J, Rna Polymerase Ii Elongation Complex B
 pdb|3PO2|J Chain J, Arrested Rna Polymerase Ii Elongation Complex
 pdb|3PO3|J Chain J, Arrested Rna Polymerase Ii Reactivation Intermediate
 pdb|3QT1|J Chain J, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
          Subunit
 pdb|3RZD|J Chain J, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
 pdb|3RZO|J Chain J, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
 pdb|3S14|J Chain J, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
 pdb|3S15|J Chain J, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
 pdb|3S16|J Chain J, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
 pdb|3S17|J Chain J, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
 pdb|3S1M|J Chain J, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
          (Variant 1)
 pdb|3S1N|J Chain J, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
          (Variant 2)
 pdb|3S1Q|J Chain J, Rna Polymerase Ii Initiation Complex With A 5-Nt
          3'-Deoxy Rna Soaked With Atp
 pdb|3S1R|J Chain J, Rna Polymerase Ii Initiation Complex With A 5-Nt
          3'-Deoxy Rna Soaked With Gtp
 pdb|3S2D|J Chain J, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
          Containing A 5br- U
 pdb|3S2H|J Chain J, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
          Containing A 2[prime]-Iodo Atp
 pdb|3J0K|J Chain J, Orientation Of Rna Polymerase Ii Within The Human
          Vp16-Mediator-Pol Ii-Tfiif Assembly
 pdb|4A3C|J Chain J, Rna Polymerase Ii Initial Transcribing Complex With A
          5nt Dna-Rna Hybrid
 pdb|4A3B|J Chain J, Rna Polymerase Ii Initial Transcribing Complex With A
          4nt Dna-Rna Hybrid
 pdb|4A3D|J Chain J, Rna Polymerase Ii Initial Transcribing Complex With A
          6nt Dna-Rna Hybrid
 pdb|4A3E|J Chain J, Rna Polymerase Ii Initial Transcribing Complex With A
          5nt Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3F|J Chain J, Rna Polymerase Ii Initial Transcribing Complex With A
          6nt Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3J|J Chain J, Rna Polymerase Ii Initial Transcribing Complex With A
          2nt Dna-Rna Hybrid And Soaked With Gmpcpp
 pdb|4A3K|J Chain J, Rna Polymerase Ii Initial Transcribing Complex With A
          7nt Dna-Rna Hybrid
 pdb|4A3L|J Chain J, Rna Polymerase Ii Initial Transcribing Complex With A
          7nt Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3M|J Chain J, Rna Polymerase Ii Initial Transcribing Complex With A
          4nt Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3G|J Chain J, Rna Polymerase Ii Initial Transcribing Complex With A
          2nt Dna-Rna Hybrid
 pdb|4A3I|J Chain J, Rna Polymerase Ii Binary Complex With Dna
 pdb|4A93|J Chain J, Rna Polymerase Ii Elongation Complex Containing A Cpd
          Lesion
 pdb|4BBR|J Chain J, Structure Of Rna Polymerase Ii-tfiib Complex
 pdb|4BBS|J Chain J, Structure Of An Initially Transcribing Rna Polymerase
          Ii- Tfiib Complex
          Length = 70

 Score =  104 bits (260), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 48/70 (68%), Positives = 58/70 (82%), Gaps = 1/70 (1%)

Query: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQAD-YPEGDALDALGLVRYCCRRMLMTHVDLIEKL 59
          MI+PVRCF+CGKV+G+KW++YL+LLQ D   EG AL  LGL RYCCRRM++THVDLIEK 
Sbjct: 1  MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRYCCRRMILTHVDLIEKF 60

Query: 60 LNYNTLDKSD 69
          L YN L+K D
Sbjct: 61 LRYNPLEKRD 70


>pdb|2PMZ|N Chain N, Archaeal Rna Polymerase From Sulfolobus Solfataricus
 pdb|2PMZ|Y Chain Y, Archaeal Rna Polymerase From Sulfolobus Solfataricus
 pdb|3HKZ|N Chain N, The X-Ray Crystal Structure Of Rna Polymerase From
          Archaea
 pdb|3HKZ|W Chain W, The X-Ray Crystal Structure Of Rna Polymerase From
          Archaea
          Length = 66

 Score = 78.6 bits (192), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 31/62 (50%), Positives = 47/62 (75%)

Query: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
          M+IP+RCFTCG +I +KW +++  + A    G  LD LG+ RYCCRRML++HVD+I +++
Sbjct: 1  MLIPIRCFTCGSLIADKWQSFITRVNAGENPGKVLDDLGVKRYCCRRMLLSHVDIINEVI 60

Query: 61 NY 62
          +Y
Sbjct: 61 HY 62


>pdb|2WAQ|N Chain N, The Complete Structure Of The Archaeal 13-Subunit Dna-
          Directed Rna Polymerase
 pdb|2WB1|N Chain N, The Complete Structure Of The Archaeal 13-Subunit Dna-
          Directed Rna Polymerase
 pdb|2WB1|O Chain O, The Complete Structure Of The Archaeal 13-Subunit Dna-
          Directed Rna Polymerase
 pdb|2Y0S|N Chain N, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase
          In P21 Space Group
 pdb|2Y0S|O Chain O, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase
          In P21 Space Group
 pdb|4AYB|N Chain N, Rnap At 3.2ang
 pdb|4B1O|N Chain N, Archaeal Rnap-Dna Binary Complex At 4.32ang
 pdb|4B1P|O Chain O, Archaeal Rnap-Dna Binary Complex At 4.32ang
          Length = 66

 Score = 77.4 bits (189), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 30/63 (47%), Positives = 46/63 (73%)

Query: 1  MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60
          M+IP+RCFTCG +I +KW  ++  + A    G  LD LG+ RYCCRRML++H+D+I +++
Sbjct: 1  MMIPIRCFTCGSLIADKWQPFITRVNAGENPGKVLDDLGVKRYCCRRMLLSHIDIISEVI 60

Query: 61 NYN 63
          +Y 
Sbjct: 61 HYT 63


>pdb|1EF4|A Chain A, Solution Structure Of The Essential Rna Polymerase
          Subunit Rpb10 From Methanobacterium Thermoautotrophicum
          Length = 55

 Score = 54.7 bits (130), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 25/52 (48%), Positives = 33/52 (63%)

Query: 3  IPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVD 54
          IPVRC +CGK +   ++ Y   +       D LD LGL RYCCRRML++HV+
Sbjct: 2  IPVRCLSCGKPVSAYFNEYQRRVADGEDPKDVLDDLGLKRYCCRRMLISHVE 53


  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
   0.326    0.143    0.457 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,294,674
Number of Sequences: 62578
Number of extensions: 78129
Number of successful extensions: 171
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 164
Number of HSP's gapped (non-prelim): 5
length of query: 71
length of database: 14,973,337
effective HSP length: 41
effective length of query: 30
effective length of database: 12,407,639
effective search space: 372229170
effective search space used: 372229170
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 45 (21.9 bits)