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= 037930
         (361 letters)

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

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



>pdb|1W26|A Chain A, Trigger Factor In Complex With The Ribosome Forms A
           Molecular Cradle For Nascent Proteins
 pdb|1W26|B Chain B, Trigger Factor In Complex With The Ribosome Forms A
           Molecular Cradle For Nascent Proteins
 pdb|2VRH|A Chain A, Structure Of The E. Coli Trigger Factor Bound To A
           Translating Ribosome
          Length = 432

 Score = 30.4 bits (67), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 12/36 (33%), Positives = 23/36 (63%)

Query: 63  KDKSAMVDYVLGVSDPQQWHSENLKMNADHYALWLR 98
           K   A  ++ + V+ P+++H+ENLK  A  +A+ L+
Sbjct: 203 KGHKAGEEFTIDVTFPEEYHAENLKGKAAKFAINLK 238


>pdb|1T11|A Chain A, Trigger Factor
 pdb|1T11|B Chain B, Trigger Factor
          Length = 392

 Score = 30.4 bits (67), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 11/31 (35%), Positives = 22/31 (70%)

Query: 65  KSAMVDYVLGVSDPQQWHSENLKMNADHYAL 95
           K+  +++V+ V+ P+ +H+ENLK  A  +A+
Sbjct: 208 KTKGMEFVIDVTFPEDYHAENLKGKAAKFAI 238


>pdb|3QP1|A Chain A, Crystal Structure Of Cvir Ligand-Binding Domain Bound To
          The Native Ligand C6-Hsl
 pdb|3QP2|A Chain A, Crystal Structure Of Cvir Ligand-Binding Domain Bound To
          C8-Hsl
 pdb|3QP4|A Chain A, Crystal Structure Of Cvir Ligand-Binding Domain Bound To
          C10-Hsl
          Length = 182

 Score = 29.6 bits (65), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 21/78 (26%), Positives = 34/78 (43%), Gaps = 3/78 (3%)

Query: 22 IYLTPSLRMENDKKAELASFLKVIPPVEFCCVYGSSLHPNNKDKSAMVDYVLGVSDPQQW 81
          I++   +  EN+ KA L   L   P        G     NN+++   ++ VL VS P  W
Sbjct: 23 IHMAGHIETENELKAFLDQVLSQAPSERLLLALGRL---NNQNQIQRLERVLNVSYPSDW 79

Query: 82 HSENLKMNADHYALWLRL 99
            + +K N   +   LR+
Sbjct: 80 LDQYMKENYAQHDPILRI 97


>pdb|3QP5|A Chain A, Crystal Structure Of Cvir Bound To Antagonist
           Chlorolactone (Cl)
 pdb|3QP5|B Chain B, Crystal Structure Of Cvir Bound To Antagonist
           Chlorolactone (Cl)
 pdb|3QP5|C Chain C, Crystal Structure Of Cvir Bound To Antagonist
           Chlorolactone (Cl)
 pdb|3QP5|D Chain D, Crystal Structure Of Cvir Bound To Antagonist
           Chlorolactone (Cl)
          Length = 265

 Score = 28.9 bits (63), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 22/81 (27%), Positives = 35/81 (43%), Gaps = 3/81 (3%)

Query: 22  IYLTPSLRMENDKKAELASFLKVIPPVEFCCVYGSSLHPNNKDKSAMVDYVLGVSDPQQW 81
           I++   +  EN+ KA L   L   P        G     NN+++   ++ VL VS P  W
Sbjct: 28  IHMAGHIETENELKAFLDQVLSQAPSERLLLALGRL---NNQNQIQRLERVLNVSYPSDW 84

Query: 82  HSENLKMNADHYALWLRLLGG 102
             + +K N   +   LR+  G
Sbjct: 85  LDQYMKENYAQHDPILRIHLG 105


>pdb|1L1P|A Chain A, Solution Structure Of The Ppiase Domain From E. Coli
          Trigger Factor
          Length = 106

 Score = 28.5 bits (62), Expect = 5.5,   Method: Composition-based stats.
 Identities = 12/36 (33%), Positives = 23/36 (63%)

Query: 63 KDKSAMVDYVLGVSDPQQWHSENLKMNADHYALWLR 98
          K   A  ++ + V+ P+++H+ENLK  A  +A+ L+
Sbjct: 60 KGHKAGEEFTIDVTFPEEYHAENLKGKAAKFAINLK 95


  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
   0.319    0.135    0.399 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,026,865
Number of Sequences: 62578
Number of extensions: 378943
Number of successful extensions: 917
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: 914
Number of HSP's gapped (non-prelim): 5
length of query: 361
length of database: 14,973,337
effective HSP length: 100
effective length of query: 261
effective length of database: 8,715,537
effective search space: 2274755157
effective search space used: 2274755157
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)