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= psy17141
         (141 letters)

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

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



>pdb|2RR7|A Chain A, Microtubule Binding Domain Of Dynein-C
          Length = 155

 Score = 56.2 bits (134), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 40/60 (66%)

Query: 31  SLYEYDKDHIPEKILKKITNYVNLPDFDPEEIGMVSVAAKSLSKWVMAIEKYAQLFKDIQ 90
           SL ++DKDHIP +++ KI  +   P+F P+ I   SVA   L  WV+A+EKY ++ K+++
Sbjct: 87  SLRKFDKDHIPPEVIVKIRPFAQDPEFQPKVIEKQSVACAGLCSWVIALEKYDKVIKEVE 146


>pdb|3ERR|A Chain A, Microtubule Binding Domain From Mouse Cytoplasmic Dynein
           As A Fusion With Seryl-Trna Synthetase
 pdb|3ERR|B Chain B, Microtubule Binding Domain From Mouse Cytoplasmic Dynein
           As A Fusion With Seryl-Trna Synthetase
          Length = 536

 Score = 33.9 bits (76), Expect = 0.035,   Method: Composition-based stats.
 Identities = 18/53 (33%), Positives = 30/53 (56%), Gaps = 3/53 (5%)

Query: 38  DHIPEKILKKITNYVNLPDFDPEEIGMVSVAAKSLSKWVMAIEKYAQLFKDIQ 90
           D I EK+ K   NY++ P ++ E +   S+AA  + KW +A   YA + K ++
Sbjct: 134 DAIREKMKK---NYMSNPSYNYEIVNRASLAAGPMVKWAIAQLNYADMLKRVE 183


>pdb|2GYQ|A Chain A, Ycfi, A Putative Structural Protein From Rhodopseudomonas
           Palustris.
 pdb|2GYQ|B Chain B, Ycfi, A Putative Structural Protein From Rhodopseudomonas
           Palustris
          Length = 173

 Score = 30.4 bits (67), Expect = 0.38,   Method: Compositional matrix adjust.
 Identities = 13/41 (31%), Positives = 26/41 (63%), Gaps = 1/41 (2%)

Query: 79  IEKYAQLFKDIQRQYPSIIDCTTIDWILDCPEQSLMEVAER 119
           IE+  Q+FK +  Q PS ++C  ID ++   +++  E+A++
Sbjct: 62  IERLDQVFKKLG-QKPSGVNCPAIDGLIKEADETAGEIADK 101


>pdb|3VKH|A Chain A, X-Ray Structure Of A Functional Full-Length Dynein Motor
            Domain
 pdb|3VKH|B Chain B, X-Ray Structure Of A Functional Full-Length Dynein Motor
            Domain
          Length = 3367

 Score = 30.0 bits (66), Expect = 0.46,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 35/75 (46%), Gaps = 5/75 (6%)

Query: 17   KVRFPNYRKNCTRISLYEYDKDHIPEKILKKIT-NYVNLPDFDPEEIGMVSVAAKSLSKW 75
            K+  PN+    T I  Y+  K   P KI + IT  Y+  P FD E +   S A   L KW
Sbjct: 2062 KIMEPNF---ITSIINYDTKKMMTP-KIREAITKGYLEDPGFDYETVNRASKACGPLVKW 2117

Query: 76   VMAIEKYAQLFKDIQ 90
              A   Y+++   I+
Sbjct: 2118 ATAQTYYSEILDRIK 2132


>pdb|3J1T|A Chain A, High Affinity Dynein Microtubule Binding Domain - Tubulin
           Complex
 pdb|3J1U|A Chain A, Low Affinity Dynein Microtubule Binding Domain - Tubulin
           Complex
          Length = 164

 Score = 29.6 bits (65), Expect = 0.64,   Method: Compositional matrix adjust.
 Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 3/53 (5%)

Query: 38  DHIPEKILKKITNYVNLPDFDPEEIGMVSVAAKSLSKWVMAIEKYAQLFKDIQ 90
           D I EK+ K   NY++ P ++ E +   S+A   + KW +A   YA + K ++
Sbjct: 96  DAIREKMKK---NYMSNPSYNYEIVNRASLACGPMVKWAIAQLNYADMLKRVE 145


>pdb|3PFE|A Chain A, Crystal Structure Of A M20a Metallo Peptidase (Dape,
          Lpg0809) From Legionella Pneumophila Subsp. Pneumophila
          Str. Philadelphia 1 At 1.50 A Resolution
          Length = 472

 Score = 27.3 bits (59), Expect = 3.2,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 6/50 (12%)

Query: 32 LYEYDKDHIPEKILKKITNYVNLPDFDP------EEIGMVSVAAKSLSKW 75
          LY+Y      E+IL  + +Y+ +P+  P      EE G    A   ++ W
Sbjct: 8  LYDYICQQWQEEILPSLCDYIKIPNKSPHFDAKWEEHGYXEQAVNHIANW 57


  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
   0.323    0.137    0.407 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,018,170
Number of Sequences: 62578
Number of extensions: 144879
Number of successful extensions: 361
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 352
Number of HSP's gapped (non-prelim): 16
length of query: 141
length of database: 14,973,337
effective HSP length: 89
effective length of query: 52
effective length of database: 9,403,895
effective search space: 489002540
effective search space used: 489002540
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 46 (22.3 bits)