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= 025356
         (254 letters)

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

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



>pdb|1IKN|D Chain D, IkappabalphaNF-Kappab Complex
          Length = 236

 Score = 34.3 bits (77), Expect = 0.063,   Method: Compositional matrix adjust.
 Identities = 19/49 (38%), Positives = 22/49 (44%)

Query: 134 GIMSFLNIYNTLLIVRLVLTWFPNSPPAIVSPLSTLCDPYLNIFRGIIP 182
           G ++FLN  N L    L L    N P    + L   CDP L  FRG  P
Sbjct: 33  GDLAFLNFQNNLQQTPLHLAVITNQPEIAEALLGAGCDPELRDFRGNTP 81


>pdb|1NFI|E Chain E, I-Kappa-B-AlphaNF-Kappa-B Complex
 pdb|1NFI|F Chain F, I-Kappa-B-AlphaNF-Kappa-B Complex
          Length = 213

 Score = 33.5 bits (75), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 19/49 (38%), Positives = 22/49 (44%)

Query: 134 GIMSFLNIYNTLLIVRLVLTWFPNSPPAIVSPLSTLCDPYLNIFRGIIP 182
           G ++FLN  N L    L L    N P    + L   CDP L  FRG  P
Sbjct: 30  GDLAFLNFQNNLQQTPLHLAVITNQPEIAEALLGAGCDPELRDFRGNTP 78


>pdb|4F5X|W Chain W, Location Of The Dsrna-dependent Polymerase, Vp1, In
           Rotavirus Particles
          Length = 1089

 Score = 27.3 bits (59), Expect = 9.1,   Method: Composition-based stats.
 Identities = 17/59 (28%), Positives = 32/59 (54%), Gaps = 1/59 (1%)

Query: 43  LARNTVPVASPNIIRDLQNSVISITDKVSKFLNSLASHNPLIQKFLSLSAEFHSFCHQV 101
           L  + V +   N+I+ +Q   ++  +K +K  NS+A+   LI+  LS  +  HSF  ++
Sbjct: 568 LMDSYVQIPDGNVIKKIQYGAVASGEKQTKAANSIANL-ALIKTVLSRISNKHSFATKI 625


>pdb|2R7Q|A Chain A, Crystal Structure Of Vp1 Apoenzyme Of Rotavirus Sa11 (C-
           Terminal Hexahistidine-Tagged)
 pdb|2R7R|A Chain A, Crystal Structure Of Rotavirus Sa11 Vp1RNA (UGUGACC)
           Complex
 pdb|2R7S|A Chain A, Crystal Structure Of Rotavirus Sa11 Vp1  RNA (UGUGCC)
           Complex
 pdb|2R7T|A Chain A, Crystal Structure Of Rotavirus Sa11 Vp1RNA (UGUGAACC)
           Complex
 pdb|2R7U|A Chain A, Crystal Structure Of Rotavirus Sa11 Vp1RNA (AAAAGCC)
           Complex
 pdb|2R7V|A Chain A, Crystal Structure Of Rotavirus Sa11 Vp1RNA (GGCUUU)
           COMPLEX
 pdb|2R7W|A Chain A, Crystal Structure Of Rotavirus Sa11 Vp1RNA (UGUGACC)MRNA
           5'-Cap (M7gpppg) Complex
 pdb|2R7X|A Chain A, Crystal Structure Of Rotavirus Sa11 Vp1RNA (UGUGACC)GTP
           Complex
 pdb|2R7X|B Chain B, Crystal Structure Of Rotavirus Sa11 Vp1RNA (UGUGACC)GTP
           Complex
          Length = 1095

 Score = 27.3 bits (59), Expect = 9.1,   Method: Composition-based stats.
 Identities = 17/59 (28%), Positives = 32/59 (54%), Gaps = 1/59 (1%)

Query: 43  LARNTVPVASPNIIRDLQNSVISITDKVSKFLNSLASHNPLIQKFLSLSAEFHSFCHQV 101
           L  + V +   N+I+ +Q   ++  +K +K  NS+A+   LI+  LS  +  HSF  ++
Sbjct: 568 LMDSYVQIPDGNVIKKIQYGAVASGEKQTKAANSIANL-ALIKTVLSRISNKHSFATKI 625


>pdb|2R7O|A Chain A, Crystal Structure Of Vp1 Apoenzyme Of Rotavirus Sa11 (N-
           Terminal Hexahistidine-Tagged)
 pdb|4AU6|A Chain A, Location Of The Dsrna-dependent Polymerase, Vp1, In
           Rotavirus Particles
 pdb|4AU6|B Chain B, Location Of The Dsrna-dependent Polymerase, Vp1, In
           Rotavirus Particles
 pdb|4AU6|C Chain C, Location Of The Dsrna-dependent Polymerase, Vp1, In
           Rotavirus Particles
 pdb|4AU6|D Chain D, Location Of The Dsrna-dependent Polymerase, Vp1, In
           Rotavirus Particles
 pdb|4AU6|E Chain E, Location Of The Dsrna-dependent Polymerase, Vp1, In
           Rotavirus Particles
          Length = 1095

 Score = 27.3 bits (59), Expect = 9.1,   Method: Composition-based stats.
 Identities = 17/59 (28%), Positives = 32/59 (54%), Gaps = 1/59 (1%)

Query: 43  LARNTVPVASPNIIRDLQNSVISITDKVSKFLNSLASHNPLIQKFLSLSAEFHSFCHQV 101
           L  + V +   N+I+ +Q   ++  +K +K  NS+A+   LI+  LS  +  HSF  ++
Sbjct: 574 LMDSYVQIPDGNVIKKIQYGAVASGEKQTKAANSIANL-ALIKTVLSRISNKHSFATKI 631


  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
   0.322    0.135    0.405 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,483,923
Number of Sequences: 62578
Number of extensions: 228712
Number of successful extensions: 488
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 486
Number of HSP's gapped (non-prelim): 5
length of query: 254
length of database: 14,973,337
effective HSP length: 97
effective length of query: 157
effective length of database: 8,903,271
effective search space: 1397813547
effective search space used: 1397813547
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 bits)