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= psy5804
         (113 letters)

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

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



>pdb|2CG6|A Chain A, Second And Third Fibronectin Type I Module Pair (Crystal
          Form I).
 pdb|2CG7|A Chain A, Second And Third Fibronectin Type I Module Pair (Crystal
          Form Ii).
 pdb|2CKU|A Chain A, Solution Structure Of 2f13f1 From Human Fibronectin
 pdb|2RKZ|A Chain A, Crystal Structure Of The Second And Third Fibronectin F1
          Modules In Complex With A Fragment Of Staphylococcus
          Aureus Fnbpa-1
 pdb|2RKZ|B Chain B, Crystal Structure Of The Second And Third Fibronectin F1
          Modules In Complex With A Fragment Of Staphylococcus
          Aureus Fnbpa-1
 pdb|2RKZ|C Chain C, Crystal Structure Of The Second And Third Fibronectin F1
          Modules In Complex With A Fragment Of Staphylococcus
          Aureus Fnbpa-1
 pdb|2RKZ|D Chain D, Crystal Structure Of The Second And Third Fibronectin F1
          Modules In Complex With A Fragment Of Staphylococcus
          Aureus Fnbpa-1
 pdb|2RKZ|E Chain E, Crystal Structure Of The Second And Third Fibronectin F1
          Modules In Complex With A Fragment Of Staphylococcus
          Aureus Fnbpa-1
 pdb|2RKZ|F Chain F, Crystal Structure Of The Second And Third Fibronectin F1
          Modules In Complex With A Fragment Of Staphylococcus
          Aureus Fnbpa-1
 pdb|3CAL|A Chain A, Crystal Structure Of The Second And Third Fibronectin F1
          Modules In Complex With A Fragment Of Staphylococcus
          Aureus Fnbpa-5
 pdb|3CAL|C Chain C, Crystal Structure Of The Second And Third Fibronectin F1
          Modules In Complex With A Fragment Of Staphylococcus
          Aureus Fnbpa-5
 pdb|3ZRZ|A Chain A, Crystal Structure Of The Second And Third Fibronectin F1
          Modules In Complex With A Fragment Of Streptococcus
          Pyogenes Sfbi-5
 pdb|3ZRZ|B Chain B, Crystal Structure Of The Second And Third Fibronectin F1
          Modules In Complex With A Fragment Of Streptococcus
          Pyogenes Sfbi-5
          Length = 90

 Score = 29.6 bits (65), Expect = 0.40,   Method: Compositional matrix adjust.
 Identities = 11/28 (39%), Positives = 16/28 (57%)

Query: 41 QFHEGNFNYKYRDSLKRNYNLGQYFLEI 68
          + HEG  +YK  D+ +R +  G Y LE 
Sbjct: 48 RCHEGGQSYKIGDTWRRPHETGGYMLEC 75


>pdb|3I0P|A Chain A, Crystal Structure Of Malate Dehydrogenase From Entamoeba
           Histolytica
          Length = 365

 Score = 25.4 bits (54), Expect = 7.2,   Method: Composition-based stats.
 Identities = 13/38 (34%), Positives = 21/38 (55%), Gaps = 3/38 (7%)

Query: 77  FINNIDSLKRN---YNLGQYFLEINIEDLTSWRIFKIN 111
           F+N+I+  K     ++LG +F+ IN+E       FK N
Sbjct: 266 FLNHIEEEKEKSGKFSLGHFFIAINVECFRDLNEFKKN 303


>pdb|3B6V|A Chain A, Crystal Structure Of The Motor Domain Of Human Kinesin
           Family Member 3c In Complex With Adp
 pdb|3B6V|B Chain B, Crystal Structure Of The Motor Domain Of Human Kinesin
           Family Member 3c In Complex With Adp
          Length = 395

 Score = 25.4 bits (54), Expect = 7.2,   Method: Composition-based stats.
 Identities = 15/40 (37%), Positives = 20/40 (50%), Gaps = 5/40 (12%)

Query: 52  RDSLKRNYNLGQYFLEINIEDLTSFFINNIDSLKRNYNLG 91
           R  LK N   G Y     I+DL+SF   N+  ++   NLG
Sbjct: 176 RLELKENPETGVY-----IKDLSSFVTKNVKEIEHVMNLG 210


  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    0.141    0.411 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,321,241
Number of Sequences: 62578
Number of extensions: 123980
Number of successful extensions: 346
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 343
Number of HSP's gapped (non-prelim): 8
length of query: 113
length of database: 14,973,337
effective HSP length: 77
effective length of query: 36
effective length of database: 10,154,831
effective search space: 365573916
effective search space used: 365573916
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: 45 (21.9 bits)