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= 027792
         (219 letters)

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

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



>pdb|3JRO|C Chain C, Nup84-Nup145c-Sec13 Edge Element Of The Npc Lattice
          Length = 426

 Score = 30.8 bits (68), Expect = 0.65,   Method: Compositional matrix adjust.
 Identities = 18/64 (28%), Positives = 34/64 (53%)

Query: 149 SKDYSLKQYLLFADKLQAKAKELVSEENCFTPFDVERALWSSAIGLKLKASKSNQDSEIK 208
           S  Y  +++  F+D L+    E  +E+N   PF++ R   S+A  L L  + S  +S + 
Sbjct: 6   SPTYQTERFTKFSDTLKEFKIEQNNEQNPIDPFNIIREFRSAAGQLALDLANSGDESNVI 65

Query: 209 TTKN 212
           ++K+
Sbjct: 66  SSKD 69


>pdb|3IKO|C Chain C, Crystal Structure Of The Heterotrimeric
           Sec13-Nup145c-Nup84 Nucleoporin Complex
 pdb|3IKO|F Chain F, Crystal Structure Of The Heterotrimeric
           Sec13-Nup145c-Nup84 Nucleoporin Complex
 pdb|3IKO|I Chain I, Crystal Structure Of The Heterotrimeric
           Sec13-Nup145c-Nup84 Nucleoporin Complex
          Length = 460

 Score = 30.4 bits (67), Expect = 0.78,   Method: Compositional matrix adjust.
 Identities = 18/64 (28%), Positives = 34/64 (53%)

Query: 149 SKDYSLKQYLLFADKLQAKAKELVSEENCFTPFDVERALWSSAIGLKLKASKSNQDSEIK 208
           S  Y  +++  F+D L+    E  +E+N   PF++ R   S+A  L L  + S  +S + 
Sbjct: 4   SPTYQTERFTKFSDTLKEFKIEQNNEQNPIDPFNIIREFRSAAGQLALDLANSGDESNVI 63

Query: 209 TTKN 212
           ++K+
Sbjct: 64  SSKD 67


  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
   0.313    0.127    0.365 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,626,557
Number of Sequences: 62578
Number of extensions: 191335
Number of successful extensions: 350
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 348
Number of HSP's gapped (non-prelim): 2
length of query: 219
length of database: 14,973,337
effective HSP length: 95
effective length of query: 124
effective length of database: 9,028,427
effective search space: 1119524948
effective search space used: 1119524948
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 bits)