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= 023231
         (285 letters)

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

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



>pdb|3PBP|A Chain A, Structure Of The Yeast Heterotrimeric Nup82-Nup159-Nup116
           Nucleoporin Complex
 pdb|3PBP|D Chain D, Structure Of The Yeast Heterotrimeric Nup82-Nup159-Nup116
           Nucleoporin Complex
 pdb|3PBP|G Chain G, Structure Of The Yeast Heterotrimeric Nup82-Nup159-Nup116
           Nucleoporin Complex
 pdb|3PBP|J Chain J, Structure Of The Yeast Heterotrimeric Nup82-Nup159-Nup116
           Nucleoporin Complex
          Length = 452

 Score = 31.2 bits (69), Expect = 0.61,   Method: Compositional matrix adjust.
 Identities = 19/67 (28%), Positives = 33/67 (49%)

Query: 216 IIRAEGESEAAQLISEATSKFGLGLIELRRIEASREIAATLARSPHVAYLPGGKNSNMLL 275
           II+       A  +S++ ++  L  +   + E+  E  AT+ R P++AY+     SN+ L
Sbjct: 380 IIQQVNFXSWASTLSKSINESDLNPLAGLKFESKLEDIATIERIPNLAYINWNDQSNLAL 439

Query: 276 ALNPALT 282
             N  LT
Sbjct: 440 XSNKTLT 446


>pdb|3TKN|A Chain A, Structure Of The Nup82-Nup159-Nup98 Heterotrimer
 pdb|3TKN|D Chain D, Structure Of The Nup82-Nup159-Nup98 Heterotrimer
 pdb|3TKN|G Chain G, Structure Of The Nup82-Nup159-Nup98 Heterotrimer
          Length = 452

 Score = 30.8 bits (68), Expect = 0.88,   Method: Compositional matrix adjust.
 Identities = 19/67 (28%), Positives = 33/67 (49%)

Query: 216 IIRAEGESEAAQLISEATSKFGLGLIELRRIEASREIAATLARSPHVAYLPGGKNSNMLL 275
           II+       A  +S++ ++  L  +   + E+  E  AT+ R P++AY+     SN+ L
Sbjct: 380 IIQQVNFMSWASTLSKSINESDLNPLAGLKFESKLEDIATIERIPNLAYINWNDQSNLAL 439

Query: 276 ALNPALT 282
             N  LT
Sbjct: 440 MSNKTLT 446


>pdb|4DDQ|A Chain A, Structural Plasticity Of The Bacillus Subtilis Gyra
           Homodimer
 pdb|4DDQ|B Chain B, Structural Plasticity Of The Bacillus Subtilis Gyra
           Homodimer
 pdb|4DDQ|C Chain C, Structural Plasticity Of The Bacillus Subtilis Gyra
           Homodimer
 pdb|4DDQ|D Chain D, Structural Plasticity Of The Bacillus Subtilis Gyra
           Homodimer
 pdb|4DDQ|E Chain E, Structural Plasticity Of The Bacillus Subtilis Gyra
           Homodimer
 pdb|4DDQ|F Chain F, Structural Plasticity Of The Bacillus Subtilis Gyra
           Homodimer
          Length = 502

 Score = 27.3 bits (59), Expect = 9.4,   Method: Compositional matrix adjust.
 Identities = 17/66 (25%), Positives = 32/66 (48%), Gaps = 10/66 (15%)

Query: 102 RPEVSRLPYIFQHLGLEYDEKVLPSIGNEVLKAVVAQFNADQLLTERPHVSALVRESLIK 161
           +P   R+ Y    LG+  D+    S    ++  V+ +++        PH  + V ES+++
Sbjct: 43  KPVHRRILYAMNDLGMTSDKPYKKSA--RIVGEVIGKYH--------PHGDSAVYESMVR 92

Query: 162 RARDFN 167
            A+DFN
Sbjct: 93  MAQDFN 98


  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
   0.320    0.136    0.377 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,765,995
Number of Sequences: 62578
Number of extensions: 241099
Number of successful extensions: 519
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 515
Number of HSP's gapped (non-prelim): 6
length of query: 285
length of database: 14,973,337
effective HSP length: 98
effective length of query: 187
effective length of database: 8,840,693
effective search space: 1653209591
effective search space used: 1653209591
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)