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= psy8635
         (177 letters)

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

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



>pdb|3FBI|B Chain B, Structure Of The Mediator Submodule Med7n31
 pdb|3FBI|D Chain D, Structure Of The Mediator Submodule Med7n31
          Length = 130

 Score = 64.3 bits (155), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 37/80 (46%), Positives = 47/80 (58%), Gaps = 3/80 (3%)

Query: 2  ANKGGPETEDQQRL--RFQIELEFIQCLANPNYLNFL-AQRGYLKDEAFVNYLKYLLYWK 58
           N     + DQ  L  RF++ELEFIQ LAN  Y+ +L  Q+   K   F NYLKYL YW 
Sbjct: 9  GNAPATPSSDQNPLPTRFEVELEFIQSLANIQYVTYLLTQQQIWKSPNFKNYLKYLEYWC 68

Query: 59 EPQYAKYLKYPMCLYFLDLL 78
           P Y++ + YP CL+ L LL
Sbjct: 69 NPPYSQCIVYPNCLFILKLL 88


>pdb|3FBN|B Chain B, Structure Of The Mediator Submodule Med7n31
 pdb|3FBN|D Chain D, Structure Of The Mediator Submodule Med7n31
          Length = 130

 Score = 64.3 bits (155), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 37/80 (46%), Positives = 47/80 (58%), Gaps = 3/80 (3%)

Query: 2  ANKGGPETEDQQRL--RFQIELEFIQCLANPNYLNFL-AQRGYLKDEAFVNYLKYLLYWK 58
           N     + DQ  L  RF++ELEFIQ LAN  Y+ +L  Q+   K   F NYLKYL YW 
Sbjct: 9  GNAPATPSSDQNPLPTRFEVELEFIQSLANIQYVTYLLTQQQIWKSPNFKNYLKYLEYWC 68

Query: 59 EPQYAKYLKYPMCLYFLDLL 78
           P Y++ + YP CL+ L LL
Sbjct: 69 NPPYSQCIVYPNCLFILKLL 88


>pdb|4FHM|B Chain B, Nup37-Nup120(Aa1-961) Complex From Schizosaccharomyces
           Pombe
          Length = 964

 Score = 26.6 bits (57), Expect = 8.2,   Method: Composition-based stats.
 Identities = 22/82 (26%), Positives = 35/82 (42%), Gaps = 5/82 (6%)

Query: 40  GYLKDEAFVNYLKYLLYWKEPQYAKYLKYPMCLYFLDLLQYEHFRREIVNSQCAKFIDD- 98
           G+L  +    YLK L+Y K  +  K ++   C     L+ Y H  +  V  +  +  +  
Sbjct: 836 GWLNSDPIAVYLKALIYLKSKEAVKAVR---CFKTTSLVLYSHTSQFAVLREFQEIAEKY 892

Query: 99  -QQVLLWQHYTRKRTKLLNEAA 119
             Q LL  +Y     KL  E+A
Sbjct: 893 HHQNLLSCYYLHLSKKLFEESA 914


>pdb|4GQ2|M Chain M, S. Pombe Nup120-Nup37 Complex
          Length = 950

 Score = 26.6 bits (57), Expect = 8.7,   Method: Composition-based stats.
 Identities = 22/82 (26%), Positives = 35/82 (42%), Gaps = 5/82 (6%)

Query: 40  GYLKDEAFVNYLKYLLYWKEPQYAKYLKYPMCLYFLDLLQYEHFRREIVNSQCAKFIDD- 98
           G+L  +    YLK L+Y K  +  K ++   C     L+ Y H  +  V  +  +  +  
Sbjct: 834 GWLNSDPIAVYLKALIYLKSKEAVKAVR---CFKTTSLVLYSHTSQFAVLREFQEIAEKY 890

Query: 99  -QQVLLWQHYTRKRTKLLNEAA 119
             Q LL  +Y     KL  E+A
Sbjct: 891 HHQNLLSCYYLHLSKKLFEESA 912


  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    0.137    0.431 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,806,758
Number of Sequences: 62578
Number of extensions: 230696
Number of successful extensions: 365
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 359
Number of HSP's gapped (non-prelim): 7
length of query: 177
length of database: 14,973,337
effective HSP length: 92
effective length of query: 85
effective length of database: 9,216,161
effective search space: 783373685
effective search space used: 783373685
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: 48 (23.1 bits)