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= 021314
         (314 letters)

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

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



>pdb|3J0K|A Chain A, Orientation Of Rna Polymerase Ii Within The Human
           Vp16-Mediator-Pol Ii-Tfiif Assembly
          Length = 1455

 Score = 29.3 bits (64), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 13/32 (40%), Positives = 19/32 (59%)

Query: 119 VSFASAGSGYDDLTANLSSVLSVSRQLEYLKH 150
           +SF  +  G DDLT  L+ +L  +  LE L+H
Sbjct: 250 ISFNESQRGEDDLTFKLADILKANISLETLEH 281


>pdb|1I3Q|A Chain A, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
 pdb|1I50|A Chain A, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
 pdb|1I6H|A Chain A, Rna Polymerase Ii Elongation Complex
 pdb|1K83|A Chain A, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
           With The Inhibitor Alpha Amanitin
 pdb|1NIK|A Chain A, Wild Type Rna Polymerase Ii
 pdb|1NT9|A Chain A, Complete 12-Subunit Rna Polymerase Ii
 pdb|1PQV|A Chain A, Rna Polymerase Ii-Tfiis Complex
 pdb|1R5U|A Chain A, Rna Polymerase Ii Tfiib Complex
 pdb|1SFO|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex
 pdb|1R9S|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex,
           Matched Nucleotide
 pdb|1R9T|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex,
           Mismatched Nucleotide
 pdb|1TWA|A Chain A, Rna Polymerase Ii Complexed With Atp
 pdb|1TWC|A Chain A, Rna Polymerase Ii Complexed With Gtp
 pdb|1TWF|A Chain A, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
 pdb|1TWG|A Chain A, Rna Polymerase Ii Complexed With Ctp
 pdb|1TWH|A Chain A, Rna Polymerase Ii Complexed With 2'datp
 pdb|1WCM|A Chain A, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
 pdb|1Y1W|A Chain A, Complete Rna Polymerase Ii Elongation Complex
 pdb|1Y77|A Chain A, Complete Rna Polymerase Ii Elongation Complex With
           Substrate Analogue Gmpcpp
 pdb|1Y1V|A Chain A, Refined Rna Polymerase Ii-tfiis Complex
 pdb|1Y1Y|A Chain A, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
 pdb|2B63|A Chain A, Complete Rna Polymerase Ii-Rna Inhibitor Complex
 pdb|2B8K|A Chain A, 12-Subunit Rna Polymerase Ii
 pdb|2E2H|A Chain A, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With Gtp
 pdb|2E2I|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
           Dgtp
 pdb|2E2J|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
           Gmpcpp
 pdb|2NVQ|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
           2'dutp
 pdb|2NVT|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
           Gmpcpp
 pdb|2NVX|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
           Dutp
 pdb|2NVY|A Chain A, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
 pdb|2NVZ|A Chain A, Rna Polymerase Ii Elongation Complex With Utp, Updated
           112006
 pdb|2JA5|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           A
 pdb|2JA6|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           B
 pdb|2JA7|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           C
 pdb|2JA7|M Chain M, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           C
 pdb|2JA8|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           D
 pdb|2YU9|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
           Utp
 pdb|2R7Z|A Chain A, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
           Complex
 pdb|2R92|A Chain A, Elongation Complex Of Rna Polymerase Ii With Artificial
           Rdrp Scaffold
 pdb|2R93|A Chain A, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
           Delta Virus-Derived Rna Stem Loop
 pdb|2VUM|A Chain A, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
           Elongation Complex
 pdb|3CQZ|A Chain A, Crystal Structure Of 10 Subunit Rna Polymerase Ii In
           Complex With The Inhibitor Alpha-Amanitin
 pdb|3FKI|A Chain A, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
 pdb|3GTG|A Chain A, Backtracked Rna Polymerase Ii Complex With 12mer Rna
 pdb|3GTJ|A Chain A, Backtracked Rna Polymerase Ii Complex With 13mer Rna
 pdb|3GTK|A Chain A, Backtracked Rna Polymerase Ii Complex With 18mer Rna
 pdb|3GTL|A Chain A, Backtracked Rna Polymerase Ii Complex With 13mer With G<>u
           Mismatch
 pdb|3GTM|A Chain A, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
 pdb|3GTO|A Chain A, Backtracked Rna Polymerase Ii Complex With 15mer Rna
 pdb|3GTP|A Chain A, Backtracked Rna Polymerase Ii Complex With 24mer Rna
 pdb|3GTQ|A Chain A, Backtracked Rna Polymerase Ii Complex Induced By Damage
 pdb|3H3V|B Chain B, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
           Active Site
 pdb|3HOU|A Chain A, Complete Rna Polymerase Ii Elongation Complex I With A T-U
           Mismatch
 pdb|3HOU|M Chain M, Complete Rna Polymerase Ii Elongation Complex I With A T-U
           Mismatch
 pdb|3HOV|A Chain A, Complete Rna Polymerase Ii Elongation Complex Ii
 pdb|3HOW|A Chain A, Complete Rna Polymerase Ii Elongation Complex Iii With A
           T-U Mismatch And A Frayed Rna 3'-Uridine
 pdb|3HOX|A Chain A, Complete Rna Polymerase Ii Elongation Complex V
 pdb|3HOY|A Chain A, Complete Rna Polymerase Ii Elongation Complex Vi
 pdb|3HOZ|A Chain A, Complete Rna Polymerase Ii Elongation Complex Iv With A
           T-U Mismatch And A Frayed Rna 3'-Guanine
 pdb|3I4M|A Chain A, 8-oxoguanine Containing Rna Polymerase Ii Elongation
           Complex D
 pdb|3I4N|A Chain A, 8-oxoguanine Containing Rna Polymerase Ii Elongation
           Complex E
 pdb|3K1F|A Chain A, Crystal Structure Of Rna Polymerase Ii In Complex With
           Tfiib
 pdb|3K7A|A Chain A, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
 pdb|3M3Y|A Chain A, Rna Polymerase Ii Elongation Complex C
 pdb|3M4O|A Chain A, Rna Polymerase Ii Elongation Complex B
 pdb|3PO2|A Chain A, Arrested Rna Polymerase Ii Elongation Complex
 pdb|3PO3|A Chain A, Arrested Rna Polymerase Ii Reactivation Intermediate
 pdb|3QT1|A Chain A, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
           Subunit
 pdb|3RZD|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
 pdb|3RZO|A Chain A, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
 pdb|3S14|A Chain A, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
 pdb|3S15|A Chain A, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
 pdb|3S16|A Chain A, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
 pdb|3S17|A Chain A, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
 pdb|3S1M|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
           (Variant 1)
 pdb|3S1N|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
           (Variant 2)
 pdb|3S1Q|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
           Rna Soaked With Atp
 pdb|3S1R|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
           Rna Soaked With Gtp
 pdb|3S2D|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
           Containing A 5br- U
 pdb|3S2H|A Chain A, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
           Containing A 2[prime]-Iodo Atp
 pdb|4BBR|A Chain A, Structure Of Rna Polymerase Ii-tfiib Complex
 pdb|4BBS|A Chain A, Structure Of An Initially Transcribing Rna Polymerase Ii-
           Tfiib Complex
          Length = 1733

 Score = 28.9 bits (63), Expect = 3.8,   Method: Compositional matrix adjust.
 Identities = 13/32 (40%), Positives = 19/32 (59%)

Query: 119 VSFASAGSGYDDLTANLSSVLSVSRQLEYLKH 150
           +SF  +  G DDLT  L+ +L  +  LE L+H
Sbjct: 250 ISFNESQRGEDDLTFKLADILKANISLETLEH 281


>pdb|4A3C|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
           Dna-Rna Hybrid
 pdb|4A3B|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
           Dna-Rna Hybrid
 pdb|4A3D|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
           Dna-Rna Hybrid
 pdb|4A3E|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
           Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3F|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
           Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3J|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
           Dna-Rna Hybrid And Soaked With Gmpcpp
 pdb|4A3K|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
           Dna-Rna Hybrid
 pdb|4A3L|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
           Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3M|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
           Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3G|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
           Dna-Rna Hybrid
 pdb|4A3I|A Chain A, Rna Polymerase Ii Binary Complex With Dna
 pdb|4A93|A Chain A, Rna Polymerase Ii Elongation Complex Containing A Cpd
           Lesion
          Length = 1732

 Score = 28.9 bits (63), Expect = 3.8,   Method: Compositional matrix adjust.
 Identities = 13/32 (40%), Positives = 19/32 (59%)

Query: 119 VSFASAGSGYDDLTANLSSVLSVSRQLEYLKH 150
           +SF  +  G DDLT  L+ +L  +  LE L+H
Sbjct: 250 ISFNESQRGEDDLTFKLADILKANISLETLEH 281


>pdb|3SLG|A Chain A, Crystal Structure Of Pbgp3 Protein From Burkholderia
           Pseudomallei
 pdb|3SLG|B Chain B, Crystal Structure Of Pbgp3 Protein From Burkholderia
           Pseudomallei
 pdb|3SLG|C Chain C, Crystal Structure Of Pbgp3 Protein From Burkholderia
           Pseudomallei
 pdb|3SLG|D Chain D, Crystal Structure Of Pbgp3 Protein From Burkholderia
           Pseudomallei
 pdb|3SLG|E Chain E, Crystal Structure Of Pbgp3 Protein From Burkholderia
           Pseudomallei
 pdb|3SLG|F Chain F, Crystal Structure Of Pbgp3 Protein From Burkholderia
           Pseudomallei
          Length = 372

 Score = 28.5 bits (62), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 23/102 (22%), Positives = 44/102 (43%), Gaps = 5/102 (4%)

Query: 50  VDPGNNNRLATTTKGNFLPYGKNFFNGRPTGRFTDGRLATDFIAESFGFTNAIPAFLDPT 109
           VD G +  +      N +  GK +  G P   F+   LA   +  +  F    P + D +
Sbjct: 248 VDDGISALMKIIENSNGVATGKIYNIGNPNNNFSVRELANKMLELAAEF----PEYAD-S 302

Query: 110 IKKIDLLHGVSFASAGSGYDDLTANLSSVLSVSRQLEYLKHY 151
            K++ L+   S A  G+GY D+   +  + +  ++L +   +
Sbjct: 303 AKRVKLVETTSGAYYGNGYQDVQNRVPKIENTMQELGWAPQF 344


>pdb|3EZJ|A Chain A, Crystal Structure Of The N-Terminal Domain Of The Secretin
           Gspd From Etec Determined With The Assistance Of A
           Nanobody
 pdb|3EZJ|C Chain C, Crystal Structure Of The N-Terminal Domain Of The Secretin
           Gspd From Etec Determined With The Assistance Of A
           Nanobody
 pdb|3EZJ|E Chain E, Crystal Structure Of The N-Terminal Domain Of The Secretin
           Gspd From Etec Determined With The Assistance Of A
           Nanobody
 pdb|3EZJ|G Chain G, Crystal Structure Of The N-Terminal Domain Of The Secretin
           Gspd From Etec Determined With The Assistance Of A
           Nanobody
          Length = 241

 Score = 28.1 bits (61), Expect = 6.3,   Method: Compositional matrix adjust.
 Identities = 31/110 (28%), Positives = 43/110 (39%), Gaps = 15/110 (13%)

Query: 170 NSIFLLSMGTNDFLQNYYLEPTRSRQY-----TVEQYENYLVSSMFEDI-KAMKSLGATR 223
           N   ++  G    +    + P   RQY      + + + Y V  M  D+ K +KS  A  
Sbjct: 30  NKTIIMGPGVQGAVSIRTMTPLNERQYYQLFLNLLEAQGYAVVPMENDVLKVVKSSAAK- 88

Query: 224 LVVVGVPPLGCMPIVKTLQDQTACVESYNKVAASLNSKIREKLAILRRTI 273
                V PL   P+V    D  A  E   KV    N  +RE   ILR+ I
Sbjct: 89  -----VEPL---PLVGEGSDNYAGDEMVTKVVPVRNVSVRELAPILRQMI 130


  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
   0.320    0.136    0.388 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,118,389
Number of Sequences: 62578
Number of extensions: 338616
Number of successful extensions: 725
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 721
Number of HSP's gapped (non-prelim): 7
length of query: 314
length of database: 14,973,337
effective HSP length: 99
effective length of query: 215
effective length of database: 8,778,115
effective search space: 1887294725
effective search space used: 1887294725
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)