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= 034908
         (79 letters)

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

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



>pdb|1VMB|A Chain A, Crystal Structure Of 30s Ribosomal Protein S6 (tm0603)
          From Thermotoga Maritima At 1.70 A Resolution
          Length = 140

 Score = 35.0 bits (79), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 1/62 (1%)

Query: 3  LYDCMLLLKPHVRKESLMELVARVGKHVYGR-NGVLTDITSFGTVQLGYGIKKLDGRYYQ 61
          +Y+ M ++ P+V +E    LV RV K +  R  G +  +   G  +  Y IKK +   Y 
Sbjct: 20 IYESMFIIAPNVPEEERENLVERVKKIIEERVKGKIDKVERMGMRKFAYEIKKFNEGDYT 79

Query: 62 LI 63
          +I
Sbjct: 80 VI 81


>pdb|2J5A|A Chain A, Folding Of S6 Structures With Divergent Amino-Acid
          Composition: Pathway Flexibility Within Partly
          Overlapping Foldons
          Length = 110

 Score = 28.9 bits (63), Expect = 0.84,   Method: Compositional matrix adjust.
 Identities = 14/60 (23%), Positives = 30/60 (50%)

Query: 4  YDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQLI 63
          Y+ +  +KP + +E + +   +V + +  + G +     +G  QL Y I+K +   Y L+
Sbjct: 10 YETVFAVKPTLSEEEMKKKFEQVKEFIKQKGGEILYEEDWGMRQLAYPIQKFNNARYFLV 69


>pdb|3MGW|A Chain A, Thermodynamics And Structure Of A Salmon Cold-Active
           Goose-T Lysozyme
          Length = 181

 Score = 25.4 bits (54), Expect = 8.3,   Method: Compositional matrix adjust.
 Identities = 19/77 (24%), Positives = 33/77 (42%), Gaps = 14/77 (18%)

Query: 5   DCMLLLKPH--VRKESLMELVARVGKHVYGRNGVLTDITS------------FGTVQLGY 50
           D    L  H  VR     EL+ RVG+       ++  I S            +G    G+
Sbjct: 28  DASHKLAEHDLVRMNKYKELITRVGQKHGLDPAIIAGIISRESRAGSALDHGWGDHGKGF 87

Query: 51  GIKKLDGRYYQLIPTWE 67
           G+ ++D RY++++  W+
Sbjct: 88  GLMQVDKRYHKIVGAWD 104


>pdb|4G9S|A Chain A, Crystal Structure Of Escherichia Coli Plig In Complex With
           Atlantic Salmon G-Type Lysozyme
          Length = 187

 Score = 25.4 bits (54), Expect = 8.8,   Method: Compositional matrix adjust.
 Identities = 19/77 (24%), Positives = 33/77 (42%), Gaps = 14/77 (18%)

Query: 5   DCMLLLKPH--VRKESLMELVARVGKHVYGRNGVLTDITS------------FGTVQLGY 50
           D    L  H  VR     EL+ RVG+       ++  I S            +G    G+
Sbjct: 34  DASHKLAEHDLVRMNKYKELITRVGQKHGLDPAIIAGIISRESRAGSALDHGWGDHGKGF 93

Query: 51  GIKKLDGRYYQLIPTWE 67
           G+ ++D RY++++  W+
Sbjct: 94  GLMQVDKRYHKIVGAWD 110


  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
   0.325    0.144    0.462 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,481,838
Number of Sequences: 62578
Number of extensions: 87256
Number of successful extensions: 220
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 217
Number of HSP's gapped (non-prelim): 6
length of query: 79
length of database: 14,973,337
effective HSP length: 48
effective length of query: 31
effective length of database: 11,969,593
effective search space: 371057383
effective search space used: 371057383
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 45 (21.9 bits)