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= 037906
         (80 letters)

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

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



>pdb|2XZM|2 Chain 2, Crystal Structure Of The Eukaryotic 40s Ribosomal Subunit
           In Complex With Initiation Factor 1. This File Contains
           The 40s Subunit And Initiation Factor For Molecule 1
 pdb|2XZN|2 Chain 2, Crystal Structure Of The Eukaryotic 40s Ribosomal Subunit
           In Complex With Initiation Factor 1. This File Contains
           The 40s Subunit And Initiation Factor For Molecule 2
          Length = 208

 Score = 73.2 bits (178), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 38/66 (57%), Positives = 49/66 (74%), Gaps = 2/66 (3%)

Query: 9   KRNHVLRKLEKRKKDRTLDPHIEEQFASGRLLACLSSPPSHCGRADGYILE-KELEFYIK 67
           K  HV +++ KR K + L+ +IEEQF S R+LAC++S P   GRADGYILE KELEFYI+
Sbjct: 143 KSRHVQKRV-KRTKAQALEKNIEEQFVSQRILACITSRPGQSGRADGYILEGKELEFYIR 201

Query: 68  NIQRKK 73
            +Q KK
Sbjct: 202 KLQSKK 207


>pdb|3U5C|I Chain I, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 40s
           Subunit, Ribosome A
 pdb|3U5G|I Chain I, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 40s
           Subunit, Ribosome B
          Length = 200

 Score = 59.7 bits (143), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 28/60 (46%), Positives = 38/60 (63%), Gaps = 1/60 (1%)

Query: 15  RKLEKRKKDRTLDPHIEEQFASGRLLACLSSPPSHCGRADGYILE-KELEFYIKNIQRKK 73
           RK   R     ++  +E QF++GRL AC+SS P   GR DGYILE +EL FY++ +  KK
Sbjct: 141 RKWAARAASAKIESSVESQFSAGRLYACISSRPGQSGRCDGYILEGEELAFYLRRLTAKK 200


>pdb|3ZEY|5 Chain 5, High-resolution Cryo-electron Microscopy Structure Of The
           Trypanosoma Brucei Ribosome
          Length = 220

 Score = 53.5 bits (127), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 29/70 (41%), Positives = 43/70 (61%), Gaps = 1/70 (1%)

Query: 5   DEAKKRNHVLRKLEKRKKDRTLDPHIEEQFASGRLLACLSSPPSHCGRADGYILE-KELE 63
           D  K  + + RK E R+K   ++  + +Q   GRLLA ++S P   GRADG +LE  EL+
Sbjct: 150 DVKKASSKLKRKWEYRRKHHKIEKALADQLREGRLLARITSRPGQTGRADGALLEGAELQ 209

Query: 64  FYIKNIQRKK 73
           FY+K + +KK
Sbjct: 210 FYLKKLDKKK 219


  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    0.133    0.381 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,319,532
Number of Sequences: 62578
Number of extensions: 77476
Number of successful extensions: 145
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 139
Number of HSP's gapped (non-prelim): 4
length of query: 80
length of database: 14,973,337
effective HSP length: 49
effective length of query: 31
effective length of database: 11,907,015
effective search space: 369117465
effective search space used: 369117465
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: 45 (21.9 bits)