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= 044254
         (312 letters)

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

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



>pdb|3MGG|A Chain A, Crystal Structure Of Methyl Transferase From
           Methanosarcina Mazei
 pdb|3MGG|B Chain B, Crystal Structure Of Methyl Transferase From
           Methanosarcina Mazei
          Length = 276

 Score = 30.0 bits (66), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 1/70 (1%)

Query: 170 MQLRSYMNGHSRQGERPFPFSVEKGFVRSHRMQRKHYRGLSNPQCVHG-IEVVSSPNLKG 228
           +++++Y  G+S  G + +P   E GF +     R  Y   S P+ V G I     P ++G
Sbjct: 165 IRVQAYXKGNSLVGRQIYPLLQESGFEKIRVEPRXVYIDSSKPELVDGFILKTIIPXVEG 224

Query: 229 IDEEEQKRWM 238
           + E+  K  +
Sbjct: 225 VKEQSLKXQI 234


>pdb|1I94|H Chain H, Crystal Structures Of The Small Ribosomal Subunit With
           Tetracycline, Edeine And If3
 pdb|1I95|H Chain H, Crystal Structure Of The 30s Ribosomal Subunit From
           Thermus Thermophilus In Complex With Edeine
 pdb|1I96|H Chain H, Crystal Structure Of The 30s Ribosomal Subunit From
           Thermus Thermophilus In Complex With The Translation
           Initiation Factor If3 (C-Terminal Domain)
 pdb|1I97|H Chain H, Crystal Structure Of The 30s Ribosomal Subunit From
           Thermus Thermophilus In Complex With Tetracycline
          Length = 138

 Score = 28.5 bits (62), Expect = 5.0,   Method: Compositional matrix adjust.
 Identities = 26/79 (32%), Positives = 38/79 (48%), Gaps = 6/79 (7%)

Query: 168 GKMQLRSYMN-GHSRQGERPFPFSVEKGFVRSHRMQRKHYRGLSNPQCVH---GIEVVSS 223
           GK  LR ++  G  RQG  P P  V K   R  R  R+ Y G+     V    GI ++S+
Sbjct: 55  GKPYLRIHLKYGPRRQGPDPRPEQVIKHIRRISRPGRRVYVGVKEIPRVRRGLGIAILST 114

Query: 224 PNLKGIDEEEQKRWMELTG 242
           P  KG+  + + R + + G
Sbjct: 115 P--KGVLTDREARKLGVGG 131


  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
   0.315    0.133    0.401 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,011,119
Number of Sequences: 62578
Number of extensions: 407104
Number of successful extensions: 676
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 672
Number of HSP's gapped (non-prelim): 6
length of query: 312
length of database: 14,973,337
effective HSP length: 99
effective length of query: 213
effective length of database: 8,778,115
effective search space: 1869738495
effective search space used: 1869738495
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: 51 (24.3 bits)