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= psy1160
         (121 letters)

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

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



>pdb|1G7S|A Chain A, X-Ray Structure Of Translation Initiation Factor If2EIF5B
           Complexed With Gdp
 pdb|1G7T|A Chain A, X-Ray Structure Of Translation Initiation Factor If2EIF5B
           Complexed With Gdpnp
          Length = 594

 Score = 31.2 bits (69), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 22/74 (29%), Positives = 42/74 (56%), Gaps = 11/74 (14%)

Query: 10  TGLAVSPDPKHSLTVLYNKILRLLAKMPDDAAYKKYTKEIVDTRIKVVQQAKSIDEM-ET 68
           TGL ++ D      V+Y+ ILR      DD      +K+++ TRI+ + + + ++EM E+
Sbjct: 243 TGLGMTID-----AVIYDGILR-----KDDTIAMMTSKDVISTRIRSLLKPRPLEEMRES 292

Query: 69  KIKSGQIEEVIIQA 82
           + K  +++EV+  A
Sbjct: 293 RKKFQKVDEVVAAA 306


>pdb|1G7R|A Chain A, X-Ray Structure Of Translation Initiation Factor If2EIF5B
          Length = 594

 Score = 30.0 bits (66), Expect = 0.35,   Method: Composition-based stats.
 Identities = 21/74 (28%), Positives = 40/74 (54%), Gaps = 11/74 (14%)

Query: 10  TGLAVSPDPKHSLTVLYNKILRLLAKMPDDAAYKKYTKEIVDTRIKVVQQAKSIDEM-ET 68
           TGL  + D      V+Y+ ILR      DD      +K+++ TRI+ + + + ++E  E+
Sbjct: 243 TGLGXTID-----AVIYDGILR-----KDDTIAXXTSKDVISTRIRSLLKPRPLEEXRES 292

Query: 69  KIKSGQIEEVIIQA 82
           + K  +++EV+  A
Sbjct: 293 RKKFQKVDEVVAAA 306


>pdb|3K01|A Chain A, Crystal Structures Of The Gach Receptor Of Streptomyces
           Glaucescens Gla.O In The Unliganded Form And In Complex
           With Acarbose And An Acarbose Homolog. Comparison With
           Acarbose-Loaded Maltose Binding Protein Of Salmonella
           Typhimurium
          Length = 412

 Score = 29.6 bits (65), Expect = 0.45,   Method: Compositional matrix adjust.
 Identities = 21/84 (25%), Positives = 41/84 (48%), Gaps = 9/84 (10%)

Query: 5   QTTGLTGLAV-SPDPKHSLTVLYNKILRLLAK------MPDDAAYKKY--TKEIVDTRIK 55
           + TG TGL +   DP   L  LY +   L+ +      + D+A  + Y   K++VD++  
Sbjct: 175 EKTGATGLYLRGDDPYWFLPYLYGEGGDLVDEKNKTVTVDDEAGVRAYRVIKDLVDSKAA 234

Query: 56  VVQQAKSIDEMETKIKSGQIEEVI 79
           +   +   + M+   KSG++  ++
Sbjct: 235 ITDASDGWNNMQNAFKSGKVAMMV 258


>pdb|3JZJ|A Chain A, Crystal Structures Of The Gach Receptor Of Streptomyces
           Glaucescens Gla.o In The Unliganded Form And In Complex
           With Acarbose And An Acarbose Homolog. Comparison With
           Acarbose-loaded Maltose Binding Protein Of Salmonella
           Typhimurium.
 pdb|3K00|A Chain A, Crystal Structures Of The Gach Receptor Of Streptomyces
           Glaucescens Gla.O In The Unliganded Form And In Complex
           With Acarbose And An Acarbose Homolog. Comparison With
           Acarbose-Loaded Maltose Binding Protein Of Salmonella
           Typhimurium.
 pdb|3K02|A Chain A, Crystal Structures Of The Gach Receptor Of Streptomyces
           Glaucescens Gla.O In The Unliganded Form And In Complex
           With Acarbose And An Acarbose Homolog. Comparison With
           Acarbose-Loaded Maltose Binding Protein Of Salmonella
           Typhimurium
          Length = 409

 Score = 29.6 bits (65), Expect = 0.47,   Method: Compositional matrix adjust.
 Identities = 21/84 (25%), Positives = 41/84 (48%), Gaps = 9/84 (10%)

Query: 5   QTTGLTGLAV-SPDPKHSLTVLYNKILRLLAK------MPDDAAYKKY--TKEIVDTRIK 55
           + TG TGL +   DP   L  LY +   L+ +      + D+A  + Y   K++VD++  
Sbjct: 172 EKTGATGLYLRGDDPYWFLPYLYGEGGDLVDEKNKTVTVDDEAGVRAYRVIKDLVDSKAA 231

Query: 56  VVQQAKSIDEMETKIKSGQIEEVI 79
           +   +   + M+   KSG++  ++
Sbjct: 232 ITDASDGWNNMQNAFKSGKVAMMV 255


>pdb|4HBC|L Chain L, Crystal Structure Of A Conformation-Dependent Rabbit Igg
           Fab Specific For Amyloid Prefibrillar Oligomers
          Length = 213

 Score = 26.2 bits (56), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 17/61 (27%), Positives = 27/61 (44%)

Query: 4   EQTTGLTGLAVSPDPKHSLTVLYNKILRLLAKMPDDAAYKKYTKEIVDTRIKVVQQAKSI 63
           + TT  TG+  S  P++S    YN    L     +  ++K+YT ++      VVQ     
Sbjct: 152 DGTTQTTGIENSKTPQNSADCTYNLSSTLTLTSTEYNSHKEYTCKVTQGTTSVVQSFNRG 211

Query: 64  D 64
           D
Sbjct: 212 D 212


  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    0.129    0.380 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,426,569
Number of Sequences: 62578
Number of extensions: 113529
Number of successful extensions: 277
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 267
Number of HSP's gapped (non-prelim): 21
length of query: 121
length of database: 14,973,337
effective HSP length: 83
effective length of query: 38
effective length of database: 9,779,363
effective search space: 371615794
effective search space used: 371615794
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: 45 (21.9 bits)