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= 027923
         (217 letters)

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

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



>pdb|2ZNL|A Chain A, Crystal Structure Of Pa-Pb1 Complex Form Influenza Virus
           Rna Polymerase
          Length = 478

 Score = 27.7 bits (60), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 19/58 (32%), Positives = 30/58 (51%), Gaps = 1/58 (1%)

Query: 108 WVDGHNPGG-GDVSVNIDWKTGIAAKDWESVARKEKLEGVELELRKLEGAVEAIHENL 164
           W  G +P G  + S+    +T +A   + S+    +LEG   E RKL   V+A+ +NL
Sbjct: 381 WPIGESPKGVEESSIGKVCRTLLAKSVFNSLYASPQLEGFSAESRKLLLIVQALRDNL 438


>pdb|3CJI|C Chain C, Structure Of Seneca Valley Virus-001
          Length = 284

 Score = 27.3 bits (59), Expect = 6.7,   Method: Compositional matrix adjust.
 Identities = 23/69 (33%), Positives = 31/69 (44%), Gaps = 6/69 (8%)

Query: 23  INAIVSDAIWLNLPATG-TKCVSEEIQNN---XXXXXXXXXXXXXHSHSP--TISVKVTS 76
           +NA  S ++ +N+P  G T   S E QN+                 +  P  T SV+ TS
Sbjct: 207 LNARTSTSVDINVPYIGETPTQSSETQNSWTLLVMVLVPLDYKEGATTDPEITFSVRPTS 266

Query: 77  PYGNNLHNR 85
           PY N L NR
Sbjct: 267 PYFNGLRNR 275


>pdb|3CM8|A Chain A, A Rna Polymerase Subunit Structure From Virus
          Length = 471

 Score = 27.3 bits (59), Expect = 7.4,   Method: Compositional matrix adjust.
 Identities = 19/58 (32%), Positives = 30/58 (51%), Gaps = 1/58 (1%)

Query: 108 WVDGHNPGGGDV-SVNIDWKTGIAAKDWESVARKEKLEGVELELRKLEGAVEAIHENL 164
           W  G +P G +  S+    +T +A   + S+    +LEG   E RKL   V+A+ +NL
Sbjct: 374 WPIGESPKGMEEGSIGKVCRTLLAKSVFNSLYASPQLEGFSAESRKLLLIVQALRDNL 431


>pdb|4IUJ|A Chain A, Structure Of Polymerase Acid Protein (pa) From
           Influenzavirus A Influenza A Virus A, Wilson-smith/1933
           (h1n1)
          Length = 464

 Score = 26.9 bits (58), Expect = 9.5,   Method: Compositional matrix adjust.
 Identities = 19/58 (32%), Positives = 30/58 (51%), Gaps = 1/58 (1%)

Query: 108 WVDGHNPGG-GDVSVNIDWKTGIAAKDWESVARKEKLEGVELELRKLEGAVEAIHENL 164
           W  G +P G  + S+    +T +A   + S+    +LEG   E RKL   V+A+ +NL
Sbjct: 367 WPVGESPKGVEEGSIGKVCRTLLAKSVFNSLYASPQLEGFSAESRKLLLIVQALRDNL 424


  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
   0.318    0.133    0.409 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,273,333
Number of Sequences: 62578
Number of extensions: 239106
Number of successful extensions: 537
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 535
Number of HSP's gapped (non-prelim): 11
length of query: 217
length of database: 14,973,337
effective HSP length: 95
effective length of query: 122
effective length of database: 9,028,427
effective search space: 1101468094
effective search space used: 1101468094
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)