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= psy10872
         (259 letters)

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

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



>pdb|2DFS|A Chain A, 3-D Structure Of Myosin-V Inhibited State
 pdb|2DFS|M Chain M, 3-D Structure Of Myosin-V Inhibited State
          Length = 1080

 Score = 28.9 bits (63), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 12/31 (38%), Positives = 17/31 (54%)

Query: 74  LPAGTGSTTALKFFNTHQLKCHLQRHPSCTS 104
           +P G+  T A K +NTH  KC L   P  ++
Sbjct: 515 MPKGSDDTWAQKLYNTHLNKCALFEKPRLSN 545


>pdb|1R3H|A Chain A, Crystal Structure Of T10
 pdb|1R3H|C Chain C, Crystal Structure Of T10
 pdb|1R3H|E Chain E, Crystal Structure Of T10
 pdb|1R3H|G Chain G, Crystal Structure Of T10
          Length = 260

 Score = 28.9 bits (63), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 33/135 (24%), Positives = 52/135 (38%), Gaps = 18/135 (13%)

Query: 22  LRKFLHVFAKCPLESNVIVEHKDCSAEPLAALIAKLNGCVSQLEQLPVKVHDLPAGTGST 81
           L   +H + K   +S+ +   +DC  EP   L    N       QL     DLP  + + 
Sbjct: 75  LMTLVHFYNKSMDDSHTLQWLQDCDVEPDRHLCLWYN-------QLAYDSEDLPTLSENP 127

Query: 82  TALKFFNTH--QLKCHLQRHPSCTSLKQWKGGTVKIDPLARMCNTHQLKCHLQRHP---S 136
           ++    N+   Q+  HL+ H S    K  + G        R+  +   K H+ RHP    
Sbjct: 128 SSCTVGNSTVPQISQHLEGHCSDVLQKYLEKGK------ERLLRSDPPKAHVTRHPRPEG 181

Query: 137 CTSLKQWKGGTVKID 151
             +L+ W  G    D
Sbjct: 182 DVTLRCWALGFYPAD 196


>pdb|1OE9|A Chain A, Crystal Structure Of Myosin V Motor With Essential Light
           Chain - Nucleotide-Free
 pdb|1W7I|A Chain A, Crystal Structure Of Myosin V Motor Without Nucleotide
           Soaked In 10 Mm Mgadp
 pdb|1W7J|A Chain A, Crystal Structure Of Myosin V Motor With Essential Light
           Chain + Adp-Befx - Near Rigor
          Length = 795

 Score = 28.5 bits (62), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 12/31 (38%), Positives = 17/31 (54%)

Query: 74  LPAGTGSTTALKFFNTHQLKCHLQRHPSCTS 104
           +P G+  T A K +NTH  KC L   P  ++
Sbjct: 515 MPKGSDDTWAQKLYNTHLNKCALFEKPRLSN 545


>pdb|1W8J|A Chain A, Crystal Structure Of Myosin V Motor Domain -
           Nucleotide-Free
 pdb|1W8J|B Chain B, Crystal Structure Of Myosin V Motor Domain -
           Nucleotide-Free
 pdb|1W8J|C Chain C, Crystal Structure Of Myosin V Motor Domain -
           Nucleotide-Free
 pdb|1W8J|D Chain D, Crystal Structure Of Myosin V Motor Domain -
           Nucleotide-Free
          Length = 766

 Score = 28.5 bits (62), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 12/31 (38%), Positives = 17/31 (54%)

Query: 74  LPAGTGSTTALKFFNTHQLKCHLQRHPSCTS 104
           +P G+  T A K +NTH  KC L   P  ++
Sbjct: 515 MPKGSDDTWAQKLYNTHLNKCALFEKPRLSN 545


  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
   0.322    0.134    0.417 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,610,541
Number of Sequences: 62578
Number of extensions: 226742
Number of successful extensions: 397
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 394
Number of HSP's gapped (non-prelim): 4
length of query: 259
length of database: 14,973,337
effective HSP length: 97
effective length of query: 162
effective length of database: 8,903,271
effective search space: 1442329902
effective search space used: 1442329902
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: 50 (23.9 bits)