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= 011834
         (476 letters)

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

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



>pdb|1M06|F Chain F, Structural Studies Of Bacteriophage Alpha3 Assembly, X-Ray
           Crystallography
 pdb|1M0F|F Chain F, Structural Studies Of Bacteriophage Alpha3 Assembly, Cryo-
           Electron Microscopy
 pdb|1RB8|F Chain F, The Phix174 Dna Binding Protein J In Two Different Capsid
           Environments
          Length = 431

 Score = 30.8 bits (68), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 10/62 (16%)

Query: 124 YHEQHSFPLVDQCKNSSSGVHSTAINNLEGSTLLDYHHFDL----HQEFEQNFYAGYNVS 179
           YH+ H FP +D    +S+G      +NL+ + L+ +  +D      Q  + N  A YNVS
Sbjct: 363 YHDLHGFPFLDDAPGTSTG------DNLQEAILVRHQDYDACFQSQQLLQWNKQARYNVS 416

Query: 180 NF 181
            +
Sbjct: 417 VY 418


>pdb|2ZUY|A Chain A, Crystal Structure Of Exotype Rhamnogalacturonan Lyase Yesx
          Length = 620

 Score = 30.0 bits (66), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 12/48 (25%), Positives = 21/48 (43%)

Query: 366 HLYEYEINKCDACALYRLELKLVDGKKSAKGKLANDSVADLQKQMGRL 413
           H  ++ +   D      + +K  DG    KG +  D  AD + + GR+
Sbjct: 181 HYTQFMVYDLDGDGKAEIAMKTADGTTDGKGHIIGDEQADFRNEQGRI 228


  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
   0.316    0.134    0.413 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,710,773
Number of Sequences: 62578
Number of extensions: 707008
Number of successful extensions: 1474
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1473
Number of HSP's gapped (non-prelim): 3
length of query: 476
length of database: 14,973,337
effective HSP length: 102
effective length of query: 374
effective length of database: 8,590,381
effective search space: 3212802494
effective search space used: 3212802494
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)