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= 027131
         (227 letters)

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

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



>pdb|1L9A|A Chain A, Crystal Structure Of Srp19 In Complex With The S Domain Of
           Signal Recognition Particle Rna
          Length = 87

 Score = 30.0 bits (66), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 16/63 (25%), Positives = 33/63 (52%), Gaps = 5/63 (7%)

Query: 102 MPFAMMMQFPSFSAYDNAFRLIGRKGRLYRLERAEQSEWDIV----MPYNG-KTVLLQNV 156
           +P  + ++ PS    + A + +G + ++YR +R  +  W+I     + Y G K  LL+ +
Sbjct: 20  VPEELAIEKPSLKDIEKALKKLGLEPKIYRDKRYPRQHWEIAGRVEVDYKGNKLCLLKEI 79

Query: 157 PRI 159
            +I
Sbjct: 80  AKI 82


>pdb|1LNG|A Chain A, Crystal Structure Of The Srp19-7s.S Srp Rna Complex Of M.
           Jannaschii
 pdb|2V3C|A Chain A, Crystal Structure Of The Srp54-Srp19-7s.S Srp Rna Complex
           Of M. Jannaschii
 pdb|2V3C|B Chain B, Crystal Structure Of The Srp54-Srp19-7s.S Srp Rna Complex
           Of M. Jannaschii
 pdb|3NDB|A Chain A, Crystal Structure Of A Signal Sequence Bound To The Signal
           Recognition Particle
          Length = 87

 Score = 29.3 bits (64), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 16/63 (25%), Positives = 33/63 (52%), Gaps = 5/63 (7%)

Query: 102 MPFAMMMQFPSFSAYDNAFRLIGRKGRLYRLERAEQSEWDIV----MPYNG-KTVLLQNV 156
           +P  + ++ PS    + A + +G + ++YR +R  +  W+I     + Y G K  LL+ +
Sbjct: 20  VPEELAIEKPSLKDIEKALKKLGLEPKIYRDKRYPRQHWEICGCVEVDYKGNKLQLLKEI 79

Query: 157 PRI 159
            +I
Sbjct: 80  CKI 82


>pdb|3H4P|A Chain A, Proteasome 20s Core Particle From Methanocaldococcus
           Jannaschii
 pdb|3H4P|B Chain B, Proteasome 20s Core Particle From Methanocaldococcus
           Jannaschii
 pdb|3H4P|C Chain C, Proteasome 20s Core Particle From Methanocaldococcus
           Jannaschii
 pdb|3H4P|D Chain D, Proteasome 20s Core Particle From Methanocaldococcus
           Jannaschii
 pdb|3H4P|E Chain E, Proteasome 20s Core Particle From Methanocaldococcus
           Jannaschii
 pdb|3H4P|F Chain F, Proteasome 20s Core Particle From Methanocaldococcus
           Jannaschii
 pdb|3H4P|G Chain G, Proteasome 20s Core Particle From Methanocaldococcus
           Jannaschii
 pdb|3H4P|H Chain H, Proteasome 20s Core Particle From Methanocaldococcus
           Jannaschii
 pdb|3H4P|I Chain I, Proteasome 20s Core Particle From Methanocaldococcus
           Jannaschii
 pdb|3H4P|J Chain J, Proteasome 20s Core Particle From Methanocaldococcus
           Jannaschii
 pdb|3H4P|K Chain K, Proteasome 20s Core Particle From Methanocaldococcus
           Jannaschii
 pdb|3H4P|L Chain L, Proteasome 20s Core Particle From Methanocaldococcus
           Jannaschii
 pdb|3H4P|M Chain M, Proteasome 20s Core Particle From Methanocaldococcus
           Jannaschii
 pdb|3H4P|N Chain N, Proteasome 20s Core Particle From Methanocaldococcus
           Jannaschii
          Length = 264

 Score = 28.1 bits (61), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 13/31 (41%), Positives = 19/31 (61%)

Query: 108 MQFPSFSAYDNAFRLIGRKGRLYRLERAEQS 138
           MQ    SAYD A  +   +GRLY++E A ++
Sbjct: 4   MQMVPPSAYDRAITVFSPEGRLYQVEYAREA 34


  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    0.390 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,913,576
Number of Sequences: 62578
Number of extensions: 216241
Number of successful extensions: 405
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: 404
Number of HSP's gapped (non-prelim): 3
length of query: 227
length of database: 14,973,337
effective HSP length: 95
effective length of query: 132
effective length of database: 9,028,427
effective search space: 1191752364
effective search space used: 1191752364
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)