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= 008858
         (551 letters)

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

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



>pdb|2K27|A Chain A, Solution Structure Of Human Pax8 Paired Box Domain
          Length = 159

 Score = 29.6 bits (65), Expect = 4.2,   Method: Composition-based stats.
 Identities = 15/38 (39%), Positives = 21/38 (55%)

Query: 338 IRQGLIEPPKPKVKMSNLMKVLGSEATQDPTRLEKEIR 375
           IR G+I   KPKV    +++ +G    Q+PT    EIR
Sbjct: 71  IRPGVIGGSKPKVATPKVVEKIGDYKRQNPTMFAWEIR 108


>pdb|3FIK|T Chain T, Ternary Complex-Bound E.Coli 70s Ribosome. This Entry
           Consists Of The 50s Subunit.
 pdb|2WWQ|T Chain T, E.Coli 70s Ribosome Stalled During Translation Of Tnac
           Leader Peptide. This File Contains The 50s, The P-Site
           Trna And The Tnac Leader Peptide (Part 2 Of 2).
 pdb|3OFQ|T Chain T, Crystal Structure Of The E. Coli Ribosome Bound To
           Erythromycin. This File Contains The 50s Subunit Of The
           Second 70s Ribosome.
 pdb|3OFR|T Chain T, Crystal Structure Of The E. Coli Ribosome Bound To
           Erythromycin. This File Contains The 50s Subunit Of The
           First 70s Ribosome With Erthromycin Bound.
 pdb|3OFC|T Chain T, Crystal Structure Of The E. Coli Ribosome Bound To
           Chloramphenicol. This File Contains The 50s Subunit Of
           The First 70s Ribosome With Chloramphenicol Bound.
 pdb|3OFD|T Chain T, Crystal Structure Of The E. Coli Ribosome Bound To
           Chloramphenicol. This File Contains The 50s Subunit Of
           The Second 70s Ribosome.
 pdb|3OFZ|T Chain T, Crystal Structure Of The E. Coli Ribosome Bound To
           Clindamycin. This File Contains The 50s Subunit Of The
           First 70s Ribosome Bound To Clindamycin.
 pdb|3OG0|T Chain T, Crystal Structure Of The E. Coli Ribosome Bound To
           Clindamycin. This File Contains The 50s Subunit Of The
           Second 70s Ribosome.
 pdb|3OAS|T Chain T, Crystal Structure Of The E. Coli Ribosome Bound To
           Telithromycin. This File Contains The 50s Subunit Of The
           Second 70s Ribosome.
 pdb|3OAT|T Chain T, Crystal Structure Of The E. Coli Ribosome Bound To
           Telithromycin. This File Contains The 50s Subunit Of The
           First 70s Ribosome With Telithromycin Bound.
 pdb|3R8S|T Chain T, Structures Of The Bacterial Ribosome In Classical And
           Hybrid States Of Trna Binding
 pdb|3R8T|T Chain T, Structures Of The Bacterial Ribosome In Classical And
           Hybrid States Of Trna Binding
 pdb|3J19|T Chain T, Structure Of The Bacterial Ribosome Complexed By
           Tmrna-Smpb And Ef-G During Translocation And Mld-Loading
           (50s Subunit)
          Length = 93

 Score = 28.5 bits (62), Expect = 9.0,   Method: Compositional matrix adjust.
 Identities = 14/32 (43%), Positives = 21/32 (65%), Gaps = 3/32 (9%)

Query: 451 CEGINVVVVEGGSKSIKRYGKLMLRRIDWAKA 482
            E +N +VV+G    +KR+G+ + RR DW KA
Sbjct: 55  VEVVNTLVVKG---KVKRHGQRIGRRSDWKKA 83


  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
   0.316    0.134    0.389 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,400,157
Number of Sequences: 62578
Number of extensions: 498502
Number of successful extensions: 1150
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 1149
Number of HSP's gapped (non-prelim): 9
length of query: 551
length of database: 14,973,337
effective HSP length: 104
effective length of query: 447
effective length of database: 8,465,225
effective search space: 3783955575
effective search space used: 3783955575
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: 54 (25.4 bits)