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= 028404
         (209 letters)

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

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



>pdb|1WDC|B Chain B, Scallop Myosin Regulatory Domain
 pdb|1B7T|Y Chain Y, Myosin Digested By Papain
 pdb|1KK7|Y Chain Y, Scallop Myosin In The Near Rigor Conformation
 pdb|1L2O|B Chain B, Scallop Myosin S1-Adp-P-Pdm In The Actin-Detached
           Conformation
 pdb|1KQM|B Chain B, Scallop Myosin S1-Amppnp In The Actin-Detached
           Conformation
 pdb|1KWO|B Chain B, Scallop Myosin S1-Atpgammas-P-Pdm In The Actin-Detached
           Conformation
 pdb|1QVI|Y Chain Y, Crystal Structure Of Scallop Myosin S1 In The Pre-Power
           Stroke State To 2.6 Angstrom Resolution: Flexibility And
           Function In The Head
 pdb|1S5G|Y Chain Y, Structure Of Scallop Myosin S1 Reveals A Novel Nucleotide
           Conformation
 pdb|1SR6|B Chain B, Structure Of Nucleotide-free Scallop Myosin S1
 pdb|3JTD|B Chain B, Calcium-Free Scallop Myosin Regulatory Domain With
           Elc-D19a Point Mutation
 pdb|3JVT|B Chain B, Calcium-Bound Scallop Myosin Regulatory Domain (Lever Arm)
           With Reconstituted Complete Light Chains
          Length = 156

 Score = 28.1 bits (61), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 19/47 (40%), Positives = 27/47 (57%), Gaps = 4/47 (8%)

Query: 160 PQDLPLELKHAFSVVVVD-PPYLSKECLEKVSETVSFLARPGDSKLL 205
           PQ    E+K AFS++ VD   ++SKE ++ +SE    L R  D K L
Sbjct: 13  PQKQIQEMKEAFSMIDVDRDGFVSKEDIKAISEQ---LGRAPDDKEL 56


>pdb|1KK8|B Chain B, Scallop Myosin (S1-Adp-Befx) In The Actin-Detached
           Conformation
          Length = 139

 Score = 28.1 bits (61), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 19/47 (40%), Positives = 27/47 (57%), Gaps = 4/47 (8%)

Query: 160 PQDLPLELKHAFSVVVVD-PPYLSKECLEKVSETVSFLARPGDSKLL 205
           PQ    E+K AFS++ VD   ++SKE ++ +SE    L R  D K L
Sbjct: 1   PQKQIQEMKEAFSMIDVDRDGFVSKEDIKAISEQ---LGRAPDDKEL 44


>pdb|1SCM|B Chain B, Structure Of The Regulatory Domain Of Scallop Myosin At
           2.8 Angstroms Resolution
          Length = 145

 Score = 28.1 bits (61), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 19/47 (40%), Positives = 27/47 (57%), Gaps = 4/47 (8%)

Query: 160 PQDLPLELKHAFSVVVVD-PPYLSKECLEKVSETVSFLARPGDSKLL 205
           PQ    E+K AFS++ VD   ++SKE ++ +SE    L R  D K L
Sbjct: 2   PQKQIQEMKEAFSMIDVDRDGFVSKEDIKAISEQ---LGRAPDDKEL 45


>pdb|1DFK|Y Chain Y, Nucleotide-Free Scallop Myosin S1-Near Rigor State
 pdb|1DFL|Y Chain Y, Scallop Myosin S1 Complexed With Mgadp:vanadate-Transition
           State
 pdb|1DFL|W Chain W, Scallop Myosin S1 Complexed With Mgadp:vanadate-Transition
           State
          Length = 139

 Score = 27.7 bits (60), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 19/47 (40%), Positives = 27/47 (57%), Gaps = 4/47 (8%)

Query: 160 PQDLPLELKHAFSVVVVD-PPYLSKECLEKVSETVSFLARPGDSKLL 205
           PQ    E+K AFS++ VD   ++SKE ++ +SE    L R  D K L
Sbjct: 2   PQKQIQEMKEAFSMIDVDRDGFVSKEDIKAISEQ---LGRAPDDKEL 45


>pdb|3KEZ|A Chain A, Crystal Structure Of Putative Sugar Binding Protein
           (Yp_001299726.1) From Bacteroides Vulgatus Atcc 8482 At
           1.90 A Resolution
 pdb|3KEZ|B Chain B, Crystal Structure Of Putative Sugar Binding Protein
           (Yp_001299726.1) From Bacteroides Vulgatus Atcc 8482 At
           1.90 A Resolution
          Length = 461

 Score = 27.3 bits (59), Expect = 6.8,   Method: Compositional matrix adjust.
 Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 7/45 (15%)

Query: 117 CIACPTLYAYLKKIRPEVSPKILEYDMRFEQYGSDFAFYDYNQPQ 161
           CI C + Y  LKK   +V  KIL +D ++      +A+ +  QPQ
Sbjct: 285 CITC-SFYQLLKKDPKDVRLKILSFDKKY------YAYVNKYQPQ 322


  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
   0.315    0.129    0.379 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,061,287
Number of Sequences: 62578
Number of extensions: 168581
Number of successful extensions: 399
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 399
Number of HSP's gapped (non-prelim): 5
length of query: 209
length of database: 14,973,337
effective HSP length: 94
effective length of query: 115
effective length of database: 9,091,005
effective search space: 1045465575
effective search space used: 1045465575
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)