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= 021432
         (312 letters)

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

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



>pdb|3HXR|A Chain A, Nucleoporin Nup120 From S.Cerevisiae (Aa 1-757)
          Length = 761

 Score = 28.9 bits (63), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 27/92 (29%), Positives = 39/92 (42%), Gaps = 12/92 (13%)

Query: 117 LSNEFDASRSKGYL---------CAATVNNFEQLLDNILEGKTVPSNLSRILIRVNSKSL 167
           LSN+   S SK +L            TV  F  +  N LE +   +NL  +   +NS  +
Sbjct: 524 LSNDVLRSISKKFLDIITGELPDSXTTVEKFTDIFKNCLENQFEITNLKILFDELNSFDI 583

Query: 168 PTFALNDILIAHPCPAMVSRFSF--KIKSDGM 197
           P   LND++     P +  +  F   IK DG 
Sbjct: 584 PV-VLNDLINNQXKPGIFWKKDFISAIKFDGF 614


>pdb|3F7F|A Chain A, Structure Of Nup120
 pdb|3F7F|B Chain B, Structure Of Nup120
 pdb|3F7F|C Chain C, Structure Of Nup120
 pdb|3F7F|D Chain D, Structure Of Nup120
          Length = 729

 Score = 28.5 bits (62), Expect = 5.4,   Method: Compositional matrix adjust.
 Identities = 27/92 (29%), Positives = 39/92 (42%), Gaps = 12/92 (13%)

Query: 117 LSNEFDASRSKGYL---------CAATVNNFEQLLDNILEGKTVPSNLSRILIRVNSKSL 167
           LSN+   S SK +L            TV  F  +  N LE +   +NL  +   +NS  +
Sbjct: 520 LSNDVLRSISKKFLDIITGELPDSMTTVEKFTDIFKNCLENQFEITNLKILFDELNSFDI 579

Query: 168 PTFALNDILIAHPCPAMVSRFSF--KIKSDGM 197
           P   LND++     P +  +  F   IK DG 
Sbjct: 580 PV-VLNDLINNQMKPGIFWKKDFISAIKFDGF 610


>pdb|3H7N|A Chain A, Structure Of Nup120
 pdb|3H7N|B Chain B, Structure Of Nup120
 pdb|3H7N|C Chain C, Structure Of Nup120
 pdb|3H7N|D Chain D, Structure Of Nup120
          Length = 729

 Score = 28.5 bits (62), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 27/92 (29%), Positives = 39/92 (42%), Gaps = 12/92 (13%)

Query: 117 LSNEFDASRSKGYL---------CAATVNNFEQLLDNILEGKTVPSNLSRILIRVNSKSL 167
           LSN+   S SK +L            TV  F  +  N LE +   +NL  +   +NS  +
Sbjct: 520 LSNDVLRSISKKFLDIITGELPDSMTTVEKFTDIFKNCLENQFEITNLKILFDELNSFDI 579

Query: 168 PTFALNDILIAHPCPAMVSRFSF--KIKSDGM 197
           P   LND++     P +  +  F   IK DG 
Sbjct: 580 PV-VLNDLINNQMKPGIFWKKDFISAIKFDGF 610


>pdb|3UVV|A Chain A, Crystal Structure Of The Ligand Binding Domains Of The
           Thyroid Receptor:retinoid X Receptor Complexed With
           3,3',5 Triiodo-L- Thyronine And 9-Cis Retinoic Acid
          Length = 265

 Score = 27.7 bits (60), Expect = 8.5,   Method: Compositional matrix adjust.
 Identities = 20/78 (25%), Positives = 38/78 (48%), Gaps = 4/78 (5%)

Query: 234 SHDLQYMVREPISPAAATSSLIHGLVKSDQSMEAM---WFCKEGFVYID-GSHVFVSIQN 289
           SH++   ++   SP+A    LIH + ++ +S  A    W  K  F+  D G     S+ +
Sbjct: 2   SHEMIKSLQHRPSPSAEEWELIHVVTEAHRSTNAQGSHWKQKRKFLPEDIGQSPMASMPD 61

Query: 290 GDVIEISSKAPALKVFLP 307
           GD +++ + +   K+  P
Sbjct: 62  GDKVDLEAFSEFTKIITP 79


  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
   0.321    0.137    0.407 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,990,907
Number of Sequences: 62578
Number of extensions: 280396
Number of successful extensions: 506
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 506
Number of HSP's gapped (non-prelim): 4
length of query: 312
length of database: 14,973,337
effective HSP length: 99
effective length of query: 213
effective length of database: 8,778,115
effective search space: 1869738495
effective search space used: 1869738495
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: 51 (24.3 bits)