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= psy489
         (99 letters)

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

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



>pdb|2NPS|C Chain C, Crystal Structure Of The Early Endosomal Snare Complex
          Length = 81

 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 18/36 (50%), Positives = 29/36 (80%)

Query: 46 LLDTSEEIERTGKHLETGYRIAIETEKIATDVLKDL 81
          LLD +E +ER+ + LE GY+IA+ETE+I  ++L++L
Sbjct: 7  LLDNTERLERSSRRLEAGYQIAVETEQIGQEMLENL 42


>pdb|1GL2|C Chain C, Crystal Structure Of An Endosomal Snare Core Complex
          Length = 65

 Score = 26.2 bits (56), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 10/29 (34%), Positives = 21/29 (72%)

Query: 53 IERTGKHLETGYRIAIETEKIATDVLKDL 81
          + R  + +E  +RIA ET++I T+++++L
Sbjct: 4  MNRATQSIERSHRIATETDQIGTEIIEEL 32


>pdb|3U2H|A Chain A, Crystal Structure Of The C-Terminal Duf1608 Domain Of The
           Methanosarcina Acetivorans S-Layer (Ma0829) Protein
          Length = 286

 Score = 25.4 bits (54), Expect = 8.8,   Method: Compositional matrix adjust.
 Identities = 15/52 (28%), Positives = 30/52 (57%), Gaps = 5/52 (9%)

Query: 30  YFSENSTNINEEQSQRL----LDTSEEIE-RTGKHLETGYRIAIETEKIATD 76
           +F+E    IN +++ ++    LD+ ++   RTG+ L+ G   AIE +++  D
Sbjct: 83  FFAEEYIPINPDKADKIAKLVLDSDDKYTIRTGEMLDLGEGYAIEAKQVDVD 134


>pdb|3U2G|A Chain A, Crystal Structure Of The C-Terminal Duf1608 Domain Of The
           Methanosarcina Acetivorans S-Layer (Ma0829) Protein
          Length = 286

 Score = 25.0 bits (53), Expect = 9.9,   Method: Compositional matrix adjust.
 Identities = 15/52 (28%), Positives = 30/52 (57%), Gaps = 5/52 (9%)

Query: 30  YFSENSTNINEEQSQRL----LDTSEEIE-RTGKHLETGYRIAIETEKIATD 76
           +F+E    IN +++ ++    LD+ ++   RTG+ L+ G   AIE +++  D
Sbjct: 83  FFAEEYIPINPDKADKIAKLVLDSDDKYTIRTGEXLDLGEGYAIEAKQVDVD 134


  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
   0.308    0.126    0.337 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,362,736
Number of Sequences: 62578
Number of extensions: 78293
Number of successful extensions: 210
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: 207
Number of HSP's gapped (non-prelim): 5
length of query: 99
length of database: 14,973,337
effective HSP length: 65
effective length of query: 34
effective length of database: 10,905,767
effective search space: 370796078
effective search space used: 370796078
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 45 (21.9 bits)