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= 047440
         (619 letters)

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

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



>pdb|3J27|A Chain A, Cryoem Structure Of Dengue Virus
 pdb|3J27|C Chain C, Cryoem Structure Of Dengue Virus
 pdb|3J27|E Chain E, Cryoem Structure Of Dengue Virus
 pdb|3J2P|A Chain A, Cryoem Structure Of Dengue Virus Capsid Protein
           Heterotetramer
 pdb|3J2P|C Chain C, Cryoem Structure Of Dengue Virus Capsid Protein
           Heterotetramer
          Length = 495

 Score = 29.6 bits (65), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 20/60 (33%), Positives = 32/60 (53%), Gaps = 6/60 (10%)

Query: 266 IIVPTADDYSMSLGAAATVCGIVIGAMAIAQVFSSVYFSAWSNRSYFKPLVFSSIVLFIG 325
           I+  TA D+  SLG   T  G      A+ QVF ++Y +A+S  S+   ++   I+ +IG
Sbjct: 414 ILGDTAWDFG-SLGGVFTSIG-----KALHQVFGAIYGAAFSGVSWIMKILIGVIITWIG 467


>pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact
           Activator-Dependent Transcription Initiation Complex
          Length = 613

 Score = 29.6 bits (65), Expect = 5.0,   Method: Compositional matrix adjust.
 Identities = 13/32 (40%), Positives = 20/32 (62%)

Query: 111 LKLLFFVEINAIGLRKILKKFDKRFGYRFTDY 142
           L+ L  ++   IGL K + KF+ R GY+F+ Y
Sbjct: 399 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 430


>pdb|4IGC|X Chain X, X-ray Crystal Structure Of Escherichia Coli Sigma70
           Holoenzyme
 pdb|4IGC|Y Chain Y, X-ray Crystal Structure Of Escherichia Coli Sigma70
           Holoenzyme
          Length = 613

 Score = 29.6 bits (65), Expect = 5.0,   Method: Compositional matrix adjust.
 Identities = 13/32 (40%), Positives = 20/32 (62%)

Query: 111 LKLLFFVEINAIGLRKILKKFDKRFGYRFTDY 142
           L+ L  ++   IGL K + KF+ R GY+F+ Y
Sbjct: 399 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 430


>pdb|1SIG|A Chain A, Crystal Structure Of A Sigma70 Subunit Fragment From
           Escherichia Coli Rna Polymerase
          Length = 339

 Score = 29.6 bits (65), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 13/32 (40%), Positives = 20/32 (62%)

Query: 111 LKLLFFVEINAIGLRKILKKFDKRFGYRFTDY 142
           L+ L  ++   IGL K + KF+ R GY+F+ Y
Sbjct: 290 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 321


  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    0.137    0.400 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,987,638
Number of Sequences: 62578
Number of extensions: 672282
Number of successful extensions: 1533
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1524
Number of HSP's gapped (non-prelim): 13
length of query: 619
length of database: 14,973,337
effective HSP length: 105
effective length of query: 514
effective length of database: 8,402,647
effective search space: 4318960558
effective search space used: 4318960558
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: 54 (25.4 bits)