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= psy5004
         (173 letters)

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

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



>pdb|3GQ2|A Chain A, Crystal Structure Of The Dimer Of The P115 Tether Globular
           Head Domain
 pdb|3GQ2|B Chain B, Crystal Structure Of The Dimer Of The P115 Tether Globular
           Head Domain
 pdb|3GRL|A Chain A, Crystal Structure Of The Monomer Of The P115 Tether
           Globular Head Domain
          Length = 651

 Score = 28.5 bits (62), Expect = 2.1,   Method: Composition-based stats.
 Identities = 11/27 (40%), Positives = 19/27 (70%), Gaps = 4/27 (14%)

Query: 3   LLVLTLSLIS----FVSRCSALLCYQC 25
           ++VL +S+++    FV RC+ L C+QC
Sbjct: 365 IVVLLMSMVNERQPFVLRCAVLYCFQC 391


>pdb|2W3C|A Chain A, Globular Head Region Of The Human General Vesicular
           Transport Factor P115
          Length = 577

 Score = 28.5 bits (62), Expect = 2.1,   Method: Composition-based stats.
 Identities = 11/27 (40%), Positives = 19/27 (70%), Gaps = 4/27 (14%)

Query: 3   LLVLTLSLIS----FVSRCSALLCYQC 25
           ++VL +S+++    FV RC+ L C+QC
Sbjct: 313 IVVLLMSMVNERQPFVLRCAVLYCFQC 339


>pdb|2OBE|A Chain A, Crystal Structure Of Chimpanzee Adenovirus (Type 68SIMIAN
           25) MAJOR Coat Protein Hexon
 pdb|2OBE|B Chain B, Crystal Structure Of Chimpanzee Adenovirus (Type 68SIMIAN
           25) MAJOR Coat Protein Hexon
 pdb|2OBE|C Chain C, Crystal Structure Of Chimpanzee Adenovirus (Type 68SIMIAN
           25) MAJOR Coat Protein Hexon
          Length = 932

 Score = 28.1 bits (61), Expect = 2.4,   Method: Composition-based stats.
 Identities = 21/75 (28%), Positives = 32/75 (42%), Gaps = 7/75 (9%)

Query: 21  LCYQCVSTQPGCGTPFKWLWYPSISCPEEDDICVKIIERKGAEEIITRDCLSTVKAFRTD 80
           L YQ +    G  T +  +W  ++   + D   V+IIE  G E+ +   C       RTD
Sbjct: 349 LSYQLLLDSLGDRTRYFSMWNQAVDSYDPD---VRIIENHGVEDELPNYCFPLDAVGRTD 405

Query: 81  IPADRYEGCRAAAKD 95
                Y+G +A   D
Sbjct: 406 T----YQGIKANGTD 416


>pdb|3J20|O Chain O, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
           Revealed By Cryo-em: Implications For Evolution Of
           Eukaryotic Ribosomes (30s Ribosomal Subunit)
          Length = 148

 Score = 27.7 bits (60), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 13/30 (43%), Positives = 17/30 (56%)

Query: 98  LANYVNHSIPELDVQRPSELKTGYTEEIIT 127
           LA+ V H IP   V RP + +TG    +IT
Sbjct: 66  LADPVAHGIPRWAVNRPKDYETGRDLHLIT 95


>pdb|3VGP|A Chain A, Crystal Structure Of The C-Terminal Globular Domain Of
           Oligosaccharyltransferase (Af_0329) From Archaeoglobus
           Fulgidus
          Length = 164

 Score = 27.3 bits (59), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 15/59 (25%), Positives = 30/59 (50%), Gaps = 2/59 (3%)

Query: 50  DDICVKIIERKGAEEIITRDCLSTVKAFRTDIPA-DRYEGCRA-AAKDPKLANYVNHSI 106
           +D  +KI +++G   ++T D ++   A  T  PA  R  G       + ++ N+ NH++
Sbjct: 74  EDEAIKIAKKRGVRYVVTADEITXKDANNTKFPAIXRIAGYNVDLXTEGEILNFFNHTV 132


  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    0.136    0.424 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,209,299
Number of Sequences: 62578
Number of extensions: 199879
Number of successful extensions: 274
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 273
Number of HSP's gapped (non-prelim): 5
length of query: 173
length of database: 14,973,337
effective HSP length: 92
effective length of query: 81
effective length of database: 9,216,161
effective search space: 746509041
effective search space used: 746509041
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: 48 (23.1 bits)