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= 006478
         (643 letters)

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

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



>pdb|1RRP|B Chain B, Structure Of The Ran-Gppnhp-Ranbd1 Complex
 pdb|1RRP|D Chain D, Structure Of The Ran-Gppnhp-Ranbd1 Complex
          Length = 134

 Score = 29.6 bits (65), Expect = 5.8,   Method: Composition-based stats.
 Identities = 24/91 (26%), Positives = 42/91 (46%), Gaps = 9/91 (9%)

Query: 16  RVKVYRLNDDGK-WDDQGTGHVTVDSMERSEELCLFVIDEEDNETILLHRISPDDIYRKQ 74
           R K++R + + K W ++G G+V +   + S ++ L +  E+  +    H ISPD      
Sbjct: 28  RAKLFRFDVESKEWKERGIGNVKILRHKTSGKIRLLMRREQVLKICANHYISPDMKLTPN 87

Query: 75  --EDTIISWRDPEYSTE------LALSFQEP 97
              D    W   +Y+ E      LA+ F+ P
Sbjct: 88  AGSDRSFVWHALDYADELPKPEQLAIRFKTP 118


>pdb|2MOB|A Chain A, Methane Monooxygenase Component B
          Length = 138

 Score = 28.9 bits (63), Expect = 9.4,   Method: Composition-based stats.
 Identities = 17/74 (22%), Positives = 35/74 (47%), Gaps = 7/74 (9%)

Query: 259 LSKIHQTYRVGYLKDVVLARVLDEATVANLNSIIHGNNAYVVSLLKDDS--TFIQELF-- 314
           +S  H  Y  G ++     +   +   A  N ++H +NA V+ L+K D     I+++   
Sbjct: 1   MSSAHNAYNAGIMQKT--GKAFADEFFAEENQVVHESNAVVLVLMKSDEIDAIIEDIVLK 58

Query: 315 -ARLRSPTTLEESK 327
             + ++P+ + E K
Sbjct: 59  GGKAKNPSIVVEDK 72


  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    0.139    0.406 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,181,583
Number of Sequences: 62578
Number of extensions: 745948
Number of successful extensions: 1659
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1658
Number of HSP's gapped (non-prelim): 3
length of query: 643
length of database: 14,973,337
effective HSP length: 105
effective length of query: 538
effective length of database: 8,402,647
effective search space: 4520624086
effective search space used: 4520624086
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: 55 (25.8 bits)