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= psy4341
         (211 letters)

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

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



>pdb|3BBO|I Chain I, Homology Model For The Spinach Chloroplast 50s Subunit
           Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome
          Length = 223

 Score = 27.3 bits (59), Expect = 7.0,   Method: Compositional matrix adjust.
 Identities = 15/64 (23%), Positives = 31/64 (48%), Gaps = 3/64 (4%)

Query: 17  VLMCLGDTIQQTIELYTKVDKTGYDLKRVAHMGIIGLVMGPPQHF---FYKYLDKYLPKR 73
           V M + D+++  +E  T++  +GYD   +           PP+ +     KY D+ + ++
Sbjct: 156 VKMQIPDSLKVKVEENTRITVSGYDKSEIGQFAATVRKWRPPEPYKGKGVKYSDEIVRRK 215

Query: 74  SGKS 77
            GK+
Sbjct: 216 EGKA 219


>pdb|2R01|A Chain A, Crystal Structure Of A Putative Fmn-Dependent
           Nitroreductase (Ct0345) From Chlorobium Tepidum Tls At
           1.15 A Resolution
          Length = 210

 Score = 26.9 bits (58), Expect = 9.1,   Method: Compositional matrix adjust.
 Identities = 12/36 (33%), Positives = 21/36 (58%)

Query: 160 IMLSYIKYNDDVFGLRGEEIVHHVEKDKIEENLANA 195
           +++  IK  DD+   R +  +HHV K +++E L  A
Sbjct: 168 VVIDQIKPGDDIRYWRDKHGIHHVPKRQVDELLVTA 203


  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
   0.324    0.144    0.434 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,702,441
Number of Sequences: 62578
Number of extensions: 287349
Number of successful extensions: 472
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 471
Number of HSP's gapped (non-prelim): 3
length of query: 211
length of database: 14,973,337
effective HSP length: 95
effective length of query: 116
effective length of database: 9,028,427
effective search space: 1047297532
effective search space used: 1047297532
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 49 (23.5 bits)