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= 043949
         (142 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 = 32.0 bits (71), Expect = 0.12,   Method: Composition-based stats.
 Identities = 19/64 (29%), Positives = 36/64 (56%), Gaps = 2/64 (3%)

Query: 67  KEDSAAIKIQAIFRAHLARRAFKALR-SLVKLQALVRGVCVRRQSRVAMHAMHALVRLQV 125
           +   AAI IQ   R ++ R+ ++ +R + + LQAL+RG  VR + ++ +   H  + +Q 
Sbjct: 814 RRTRAAIIIQKFQRMYVVRKRYQCMRDATIALQALLRGYLVRNKYQMMLRE-HKSIIIQK 872

Query: 126 RIRA 129
            +R 
Sbjct: 873 HVRG 876


>pdb|2DWQ|A Chain A, Thermus Thermophilus Ychf Gtp-Binding Protein
 pdb|2DWQ|B Chain B, Thermus Thermophilus Ychf Gtp-Binding Protein
          Length = 368

 Score = 26.6 bits (57), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 27/85 (31%), Positives = 37/85 (43%), Gaps = 3/85 (3%)

Query: 30  TPSQGATIRKVPEEAANCIDNNTFVSSTLLPLKKEIAKEDSAAIKIQAIFRAHLARRAFK 89
            P   A  RK  EE A  +  +  + + L  L  E A+E  AA  +Q      LAR  ++
Sbjct: 221 NPQVEAVRRKALEEGAEVVVVSARLEAELAELSGEEARELLAAYGLQESGLQRLARAGYR 280

Query: 90  ALRSLVKLQAL---VRGVCVRRQSR 111
           AL  L    A    VR   VRR ++
Sbjct: 281 ALDLLTFFTAGEKEVRAWTVRRGTK 305


>pdb|2DBY|A Chain A, Crystal Structure Of The Gtp-Binding Protein Ychf In
           Complexed With Gdp
          Length = 368

 Score = 26.6 bits (57), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 27/85 (31%), Positives = 37/85 (43%), Gaps = 3/85 (3%)

Query: 30  TPSQGATIRKVPEEAANCIDNNTFVSSTLLPLKKEIAKEDSAAIKIQAIFRAHLARRAFK 89
            P   A  RK  EE A  +  +  + + L  L  E A+E  AA  +Q      LAR  ++
Sbjct: 221 NPQVEAVRRKALEEGAEVVVVSARLEAELAELSGEEARELLAAYGLQESGLQRLARAGYR 280

Query: 90  ALRSLVKLQAL---VRGVCVRRQSR 111
           AL  L    A    VR   VRR ++
Sbjct: 281 ALDLLTFFTAGEKEVRAWTVRRGTK 305


  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
   0.325    0.131    0.366 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,142,331
Number of Sequences: 62578
Number of extensions: 97164
Number of successful extensions: 267
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: 264
Number of HSP's gapped (non-prelim): 5
length of query: 142
length of database: 14,973,337
effective HSP length: 89
effective length of query: 53
effective length of database: 9,403,895
effective search space: 498406435
effective search space used: 498406435
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 46 (22.3 bits)