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= 019432
         (341 letters)

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

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



>pdb|3NTT|A Chain A, Structural Insights Of Adeno-Associated Virus 5. A Gene
           Therapy Vector For Cystic Fibrosis
          Length = 724

 Score = 32.0 bits (71), Expect = 0.46,   Method: Compositional matrix adjust.
 Identities = 24/91 (26%), Positives = 35/91 (38%), Gaps = 5/91 (5%)

Query: 214 WSYTPHKTISLKGAYFCLQAKHVGKPAKLGIICTDCGSTWEIISDSKMHLSSKADNGTTV 273
           W + P    SL+   F +Q K V        I  +  ST ++ +D    L     NGT  
Sbjct: 295 WGFRPR---SLRVKIFNIQVKEVTVQDSTTTIANNLTSTVQVFTDDDYQLPYVVGNGTEG 351

Query: 274 CLDVDSSN--TIVTNTCKCLSRDKTCDPASQ 302
           CL        T+       L+RD T +P  +
Sbjct: 352 CLPAFPPQVFTLPQYGYATLNRDNTENPTER 382


>pdb|1PQV|S Chain S, Rna Polymerase Ii-Tfiis Complex
          Length = 309

 Score = 28.9 bits (63), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 18/66 (27%), Positives = 26/66 (39%), Gaps = 14/66 (21%)

Query: 189 ATGLCVQRKSFLDPLTLGPCTESEAWSYTPHKTISLKGAYFCLQAKHVGKPAKLGIICTD 248
           A G  ++R S  D  T G C E              K +Y+ LQ +   +P      C  
Sbjct: 256 AQGATIER-SVTDRFTCGKCKEK-------------KVSYYQLQTRSADEPLTTFCTCEA 301

Query: 249 CGSTWE 254
           CG+ W+
Sbjct: 302 CGNRWK 307


>pdb|1Y1V|S Chain S, Refined Rna Polymerase Ii-tfiis Complex
 pdb|1Y1Y|S Chain S, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
          Length = 179

 Score = 28.1 bits (61), Expect = 7.1,   Method: Compositional matrix adjust.
 Identities = 18/66 (27%), Positives = 26/66 (39%), Gaps = 14/66 (21%)

Query: 189 ATGLCVQRKSFLDPLTLGPCTESEAWSYTPHKTISLKGAYFCLQAKHVGKPAKLGIICTD 248
           A G  ++R S  D  T G C E              K +Y+ LQ +   +P      C  
Sbjct: 126 AQGATIER-SVTDRFTCGKCKEK-------------KVSYYQLQTRSADEPLTTFCTCEA 171

Query: 249 CGSTWE 254
           CG+ W+
Sbjct: 172 CGNRWK 177


>pdb|3PO3|S Chain S, Arrested Rna Polymerase Ii Reactivation Intermediate
          Length = 178

 Score = 28.1 bits (61), Expect = 7.3,   Method: Compositional matrix adjust.
 Identities = 18/66 (27%), Positives = 25/66 (37%), Gaps = 14/66 (21%)

Query: 189 ATGLCVQRKSFLDPLTLGPCTESEAWSYTPHKTISLKGAYFCLQAKHVGKPAKLGIICTD 248
           A G  ++R S  D  T G C E              K +Y+ LQ +    P      C  
Sbjct: 125 AQGATIER-SVTDRFTCGKCKEK-------------KVSYYQLQTRSAAAPLTTFCTCEA 170

Query: 249 CGSTWE 254
           CG+ W+
Sbjct: 171 CGNRWK 176


  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    0.466 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,062,974
Number of Sequences: 62578
Number of extensions: 474626
Number of successful extensions: 1046
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1044
Number of HSP's gapped (non-prelim): 8
length of query: 341
length of database: 14,973,337
effective HSP length: 100
effective length of query: 241
effective length of database: 8,715,537
effective search space: 2100444417
effective search space used: 2100444417
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 52 (24.6 bits)