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= 017146
         (376 letters)

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

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



>pdb|2HX0|A Chain A, Three-Dimensional Structure Of The Hypothetical Protein
           From Salmonella Cholerae-Suis (Aka Salmonella Enterica)
           At The Resolution 1.55 A. Northeast Structural Genomics
           Target Scr59
          Length = 154

 Score = 37.4 bits (85), Expect = 0.014,   Method: Compositional matrix adjust.
 Identities = 25/80 (31%), Positives = 42/80 (52%), Gaps = 2/80 (2%)

Query: 187 GEDISSKIFAFSQQGP-RTVCILSASGAICNVTLRQPTMSGGTVTYEGRFEIISLSGSFL 245
           G+++ S++ AF QQ   R   I   +G++ +V LR       T +  G FE+ISL+G+  
Sbjct: 28  GQEVFSQLHAFVQQNQLRAAWIAGCTGSLTDVALRYAGQEA-TTSLTGTFEVISLNGTLE 86

Query: 246 LSDNNGNRSRSGGLSVSLAG 265
           L+  + + + S    V L G
Sbjct: 87  LTGEHLHLAVSDPYGVXLGG 106


>pdb|2NMU|A Chain A, Crystal Structure Of The Hypothetical Protein From
           Salmonella Typhimurium Lt2. Northeast Structural
           Genomics Consortium Target Str127
          Length = 156

 Score = 37.0 bits (84), Expect = 0.020,   Method: Compositional matrix adjust.
 Identities = 25/80 (31%), Positives = 42/80 (52%), Gaps = 2/80 (2%)

Query: 187 GEDISSKIFAFSQQGP-RTVCILSASGAICNVTLRQPTMSGGTVTYEGRFEIISLSGSFL 245
           G+++ S++ AF QQ   R   I   +G++ +V LR       T +  G FE+ISL+G+  
Sbjct: 28  GQEVFSQLHAFVQQNQLRAAWIAGCTGSLTDVALRYAGQEA-TTSLTGTFEVISLNGTLE 86

Query: 246 LSDNNGNRSRSGGLSVSLAG 265
           L+  + + + S    V L G
Sbjct: 87  LTGEHLHLAVSDPYGVXLGG 106


>pdb|3VTH|A Chain A, Crystal Structure Of Full-Length Hypf In The Phosphate-
           And Nucleotide-Bound Form
 pdb|3VTH|B Chain B, Crystal Structure Of Full-Length Hypf In The Phosphate-
           And Nucleotide-Bound Form
 pdb|3VTI|A Chain A, Crystal Structure Of Hype-Hypf Complex
 pdb|3VTI|B Chain B, Crystal Structure Of Hype-Hypf Complex
          Length = 761

 Score = 30.4 bits (67), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 13/30 (43%), Positives = 17/30 (56%)

Query: 155 RGRPPGSGKKQLDALGGVGGVGFTPHVITV 184
           RGR P    +Q++  G V GVGF P V  +
Sbjct: 3   RGRVPQIQARQINIFGIVQGVGFRPFVFNI 32


>pdb|2XZM|R Chain R, 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|R Chain R, 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 = 343

 Score = 30.0 bits (66), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 14/49 (28%), Positives = 21/49 (42%)

Query: 163 KKQLDALGGVGGVGFTPHVITVKAGEDISSKIFAFSQQGPRTVCILSAS 211
           +++ DA   +  + F P +  V  G D   KIF    Q    VC + A 
Sbjct: 249 QREFDAGSTINQIAFNPKLQWVAVGTDQGVKIFNLMTQSKAPVCTIEAE 297


  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    0.395 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,511,914
Number of Sequences: 62578
Number of extensions: 284598
Number of successful extensions: 619
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 617
Number of HSP's gapped (non-prelim): 8
length of query: 376
length of database: 14,973,337
effective HSP length: 100
effective length of query: 276
effective length of database: 8,715,537
effective search space: 2405488212
effective search space used: 2405488212
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: 52 (24.6 bits)