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= 017436
         (371 letters)

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

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



>pdb|2FMM|E Chain E, Crystal Structure Of Emsy-Hp1 Complex
          Length = 133

 Score = 39.3 bits (90), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 21/56 (37%), Positives = 34/56 (60%), Gaps = 1/56 (1%)

Query: 54  IHSVEQDAYSSVLRAFKAQSDAITWEKESLITELRKELRVSDEEHRELLSKVNADD 109
           +  +E +AY+ V+ A +AQ D +T EK+ L+ EL K L +S E HR  + +   D+
Sbjct: 14  LRKLELEAYAGVISALRAQGD-LTKEKKDLLGELSKVLSISTERHRAEVRRAVNDE 68


>pdb|1UTU|A Chain A, Crystal Structure Of Novel Protein Emsy Truncate
 pdb|1UTU|B Chain B, Crystal Structure Of Novel Protein Emsy Truncate
          Length = 108

 Score = 38.5 bits (88), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 20/46 (43%), Positives = 30/46 (65%), Gaps = 1/46 (2%)

Query: 54 IHSVEQDAYSSVLRAFKAQSDAITWEKESLITELRKELRVSDEEHR 99
          +  +E +AY+ V+ A +AQ D +T EK+ L+ EL K L +S E HR
Sbjct: 20 LRKLELEAYAGVISALRAQGD-LTKEKKDLLGELSKVLSISTERHR 64


>pdb|1UZ3|A Chain A, Crystal Structure Of Novel Protein Emsy
 pdb|1UZ3|B Chain B, Crystal Structure Of Novel Protein Emsy
          Length = 102

 Score = 38.5 bits (88), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 20/46 (43%), Positives = 30/46 (65%), Gaps = 1/46 (2%)

Query: 54 IHSVEQDAYSSVLRAFKAQSDAITWEKESLITELRKELRVSDEEHR 99
          +  +E +AY+ V+ A +AQ D +T EK+ L+ EL K L +S E HR
Sbjct: 22 LRKLELEAYAGVISALRAQGD-LTKEKKDLLGELSKVLSISTERHR 66


>pdb|3GN5|B Chain B, Structure Of The E. Coli Protein Mqsa (YgitB3021)
          Length = 133

 Score = 29.6 bits (65), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 25/96 (26%), Positives = 45/96 (46%), Gaps = 5/96 (5%)

Query: 16  PPSHHNRFQRGVRP---TGNGRSAVIGSASLPRMQNDMATQIHSVEQDAYSSVLRAFKAQ 72
           P  H      G++    T  GR  V+         +   + ++  E DA+ + ++AF+A 
Sbjct: 6   PVCHQGEMVSGIKDIPYTFRGRKTVLKGIHGLYCVHCEESIMNKEESDAFMAQVKAFRAS 65

Query: 73  SDAITWEKESLITELRKELRVSDEEHRELL-SKVNA 107
            +A T   E  I ++RK+L ++ +E  E+    VNA
Sbjct: 66  VNAETVAPE-FIVKVRKKLSLTQKEASEIFGGGVNA 100


>pdb|3GN5|A Chain A, Structure Of The E. Coli Protein Mqsa (YgitB3021)
 pdb|3O9X|A Chain A, Structure Of The E. Coli Antitoxin Mqsa (YgitB3021) IN
           COMPLEX WITH Its Gene Promoter
 pdb|3O9X|B Chain B, Structure Of The E. Coli Antitoxin Mqsa (YgitB3021) IN
           COMPLEX WITH Its Gene Promoter
          Length = 133

 Score = 29.3 bits (64), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 25/96 (26%), Positives = 45/96 (46%), Gaps = 5/96 (5%)

Query: 16  PPSHHNRFQRGVRP---TGNGRSAVIGSASLPRMQNDMATQIHSVEQDAYSSVLRAFKAQ 72
           P  H      G++    T  GR  V+         +   + ++  E DA+ + ++AF+A 
Sbjct: 6   PVCHQGEMVSGIKDIPYTFRGRKTVLKGIHGLYCVHCEESIMNKEESDAFMAQVKAFRAS 65

Query: 73  SDAITWEKESLITELRKELRVSDEEHRELL-SKVNA 107
            +A T   E  I ++RK+L ++ +E  E+    VNA
Sbjct: 66  VNAETVAPE-FIVKVRKKLSLTQKEASEIFGGGVNA 100


>pdb|2KZ8|A Chain A, Solution Nmr Structure Of Mqsa, A Protein From E. Coli,
           Containing A Zinc Finger, N-Terminal And A Helix
           Turn-Helix C-Terminal Domain
          Length = 131

 Score = 29.3 bits (64), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 22/90 (24%), Positives = 42/90 (46%), Gaps = 4/90 (4%)

Query: 16  PPSHHNRFQRGVRP---TGNGRSAVIGSASLPRMQNDMATQIHSVEQDAYSSVLRAFKAQ 72
           P  H      G++    T  GR  V+         +   + ++  E DA+ + ++AF+A 
Sbjct: 4   PVCHQGEMVSGIKDIPYTFRGRKTVLKGIHGLYCVHCEESIMNKEESDAFMAQVKAFRAS 63

Query: 73  SDAITWEKESLITELRKELRVSDEEHRELL 102
            +A T   E  I ++RK+L ++ +E  E+ 
Sbjct: 64  VNAETVAPE-FIVKVRKKLSLTQKEASEIF 92


  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
   0.312    0.130    0.389 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,798,391
Number of Sequences: 62578
Number of extensions: 415777
Number of successful extensions: 862
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 854
Number of HSP's gapped (non-prelim): 12
length of query: 371
length of database: 14,973,337
effective HSP length: 100
effective length of query: 271
effective length of database: 8,715,537
effective search space: 2361910527
effective search space used: 2361910527
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 52 (24.6 bits)