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= 043145
         (134 letters)

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

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



>pdb|1NBW|A Chain A, Glycerol Dehydratase Reactivase
 pdb|1NBW|C Chain C, Glycerol Dehydratase Reactivase
          Length = 607

 Score = 26.2 bits (56), Expect = 5.5,   Method: Composition-based stats.
 Identities = 15/48 (31%), Positives = 21/48 (43%), Gaps = 1/48 (2%)

Query: 48  VKRDDGDFSCEVDPMGKVLIKGVTTTGEKSVYKYSQVFEMQTQNLCPP 95
           +K   GD    V P G + I G    GE  V + ++   MQ  + C P
Sbjct: 249 LKTPQGDVQSRVIPAGNLYISGEKRRGEADVAEGAEAI-MQAMSACAP 295


>pdb|2H5E|A Chain A, Crystal Structure Of E.Coli Polypeptide Release Factor Rf3
 pdb|2H5E|B Chain B, Crystal Structure Of E.Coli Polypeptide Release Factor Rf3
 pdb|2O0F|A Chain A, Docking Of The Modified Rf3 X-Ray Structure Into Cryo-Em
           Map Of E.Coli 70s Ribosome Bound With Rf3
 pdb|3ZVO|Y Chain Y, Crystal Structure Of The Hybrid State Of Ribosome In
           Complex With The Guanosine Triphosphatase Release Factor
           3
 pdb|3SFS|W Chain W, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
           State On A Rotated Conformation Of The Ribosome
          Length = 529

 Score = 25.8 bits (55), Expect = 7.0,   Method: Composition-based stats.
 Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 3/33 (9%)

Query: 98  FSISFQLPGPVNPEQFS---GNFGIDGILEGIV 127
           F     L G + P  F    GNFG+D +L+G+V
Sbjct: 241 FDKELFLAGEITPVFFGTALGNFGVDHMLDGLV 273


>pdb|3UOQ|W Chain W, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
           State On A Rotated Conformation Of The Ribosome (Without
           Viomycin)
          Length = 534

 Score = 25.8 bits (55), Expect = 7.0,   Method: Composition-based stats.
 Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 3/33 (9%)

Query: 98  FSISFQLPGPVNPEQFS---GNFGIDGILEGIV 127
           F     L G + P  F    GNFG+D +L+G+V
Sbjct: 241 FDKELFLAGEITPVFFGTALGNFGVDHMLDGLV 273


  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
   0.317    0.137    0.411 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,361,403
Number of Sequences: 62578
Number of extensions: 175473
Number of successful extensions: 277
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 271
Number of HSP's gapped (non-prelim): 12
length of query: 134
length of database: 14,973,337
effective HSP length: 88
effective length of query: 46
effective length of database: 9,466,473
effective search space: 435457758
effective search space used: 435457758
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: 46 (22.3 bits)