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= 041168
         (177 letters)

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

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



>pdb|3RIZ|A Chain A, Crystal Structure Of The Plant Steroid Receptor Bri1
           Ectodomain
 pdb|3RJ0|A Chain A, Plant Steroid Receptor Bri1 Ectodomain In Complex With
           Brassinolide
          Length = 772

 Score = 32.7 bits (73), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 23/50 (46%), Positives = 25/50 (50%), Gaps = 3/50 (6%)

Query: 73  SSLFQLVHLEWLVLSNNHFNFSEIPSEIKNLSRLT--ALSNPSFFGQIPA 120
           S L    +L W+ LSNN     EIP  I  L  L    LSN SF G IPA
Sbjct: 481 SGLSNCTNLNWISLSNNRLT-GEIPKWIGRLENLAILKLSNNSFSGNIPA 529


>pdb|3RGX|A Chain A, Structural Insight Into Brassinosteroid Perception By Bri1
 pdb|3RGZ|A Chain A, Structural Insight Into Brassinosteroid Perception By Bri1
          Length = 768

 Score = 32.3 bits (72), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 23/50 (46%), Positives = 25/50 (50%), Gaps = 3/50 (6%)

Query: 73  SSLFQLVHLEWLVLSNNHFNFSEIPSEIKNLSRLT--ALSNPSFFGQIPA 120
           S L    +L W+ LSNN     EIP  I  L  L    LSN SF G IPA
Sbjct: 484 SGLSNCTNLNWISLSNNRLT-GEIPKWIGRLENLAILKLSNNSFSGNIPA 532


>pdb|4B8C|D Chain D, Nuclease Module Of The Yeast Ccr4-Not Complex
 pdb|4B8C|J Chain J, Nuclease Module Of The Yeast Ccr4-Not Complex
 pdb|4B8C|K Chain K, Nuclease Module Of The Yeast Ccr4-Not Complex
 pdb|4B8C|L Chain L, Nuclease Module Of The Yeast Ccr4-Not Complex
          Length = 727

 Score = 29.6 bits (65), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 20/52 (38%), Positives = 33/52 (63%), Gaps = 5/52 (9%)

Query: 58  LDLTSSCLYGSINSSSSLFQLVHLEWLVLSNNHFNFSEIPSEIKNLSRLTAL 109
           LDL++  ++   N S+++F+   L  L L+ N  + +E+P+EIKNLS L  L
Sbjct: 229 LDLSNLQIF---NISANIFKYDFLTRLYLNGN--SLTELPAEIKNLSNLRVL 275


>pdb|3DSM|A Chain A, Crystal Structure Of The Surface Layer Protein
           Bacuni_02894 From Bacteroides Uniformis, Northeast
           Structural Genomics Consortium Target Btr193d
          Length = 328

 Score = 27.3 bits (59), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 9/34 (26%), Positives = 21/34 (61%)

Query: 81  LEWLVLSNNHFNFSEIPSEIKNLSRLTALSNPSF 114
           + W+V++N+H  F+   +  K + R+T  ++P +
Sbjct: 55  IGWIVVNNSHVIFAIDINTFKEVGRITGFTSPRY 88


  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    0.132    0.407 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,322,021
Number of Sequences: 62578
Number of extensions: 142616
Number of successful extensions: 281
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 269
Number of HSP's gapped (non-prelim): 9
length of query: 177
length of database: 14,973,337
effective HSP length: 92
effective length of query: 85
effective length of database: 9,216,161
effective search space: 783373685
effective search space used: 783373685
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)