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= 046775
         (771 letters)

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

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



>pdb|3POT|B Chain B, Structural Analysis Of A Ni(Iii)-Methyl Species In
           Methyl-Coenzyme M Reductase From Methanothermobacter
           Marburgensis
 pdb|3POT|E Chain E, Structural Analysis Of A Ni(Iii)-Methyl Species In
           Methyl-Coenzyme M Reductase From Methanothermobacter
           Marburgensis
          Length = 443

 Score = 30.0 bits (66), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 24/88 (27%), Positives = 43/88 (48%), Gaps = 4/88 (4%)

Query: 301 LSTVLKSVASFQ---AIGVCKQVHALSVKTAFESDDYIVNSLIDAYGKCGHVEDAVKIFK 357
           LST+L+  A F+   A+G  +++H L +     + D +V  L+ A GK G V   +    
Sbjct: 214 LSTILEQTAMFEMGDAVGAFERMHLLGLAYQGMNADNLVFDLVKANGKEGTVGSVIADLV 273

Query: 358 ESSAVD-LVACTSMITAYAQFGLGEEAL 384
           E +  D ++     +T Y  +G  + A+
Sbjct: 274 ERALEDGVIKVEKELTDYKVYGTDDLAM 301


>pdb|1MRO|B Chain B, Methyl-Coenzyme M Reductase
 pdb|1MRO|E Chain E, Methyl-Coenzyme M Reductase
 pdb|1HBM|B Chain B, Methyl-Coenzyme M Reductase Enzyme Product Complex
 pdb|1HBM|E Chain E, Methyl-Coenzyme M Reductase Enzyme Product Complex
 pdb|1HBN|B Chain B, Methyl-Coenzyme M Reductase
 pdb|1HBN|E Chain E, Methyl-Coenzyme M Reductase
 pdb|1HBO|B Chain B, Methyl-Coenzyme M Reductase Mcr-Red1-Silent
 pdb|1HBO|E Chain E, Methyl-Coenzyme M Reductase Mcr-Red1-Silent
 pdb|1HBU|B Chain B, Methyl-Coenzyme M Reductase In The Mcr-Red1-Silent State
           In Complex With Coenzyme M
 pdb|1HBU|E Chain E, Methyl-Coenzyme M Reductase In The Mcr-Red1-Silent State
           In Complex With Coenzyme M
 pdb|3M1V|B Chain B, Structural Insight Into Methyl-Coenzyme M Reductase
           Chemistry Using Coenzyme B Analogues
 pdb|3M1V|E Chain E, Structural Insight Into Methyl-Coenzyme M Reductase
           Chemistry Using Coenzyme B Analogues
 pdb|3M2R|B Chain B, Structural Insight Into Methyl-Coenzyme M Reductase
           Chemistry Using Coenzyme B Analogues
 pdb|3M2R|E Chain E, Structural Insight Into Methyl-Coenzyme M Reductase
           Chemistry Using Coenzyme B Analogues
 pdb|3M2U|B Chain B, Structural Insight Into Methyl-Coenzyme M Reductase
           Chemistry Using Coenzyme B Analogues
 pdb|3M2U|E Chain E, Structural Insight Into Methyl-Coenzyme M Reductase
           Chemistry Using Coenzyme B Analogues
 pdb|3M2V|B Chain B, Structural Insight Into Methyl-Coenzyme M Reductase
           Chemistry Using Coenzyme B Analogues
 pdb|3M2V|E Chain E, Structural Insight Into Methyl-Coenzyme M Reductase
           Chemistry Using Coenzyme B Analogues
 pdb|3M30|B Chain B, Structural Insight Into Methyl-Coenzyme M Reductase
           Chemistry Using Coenzyme B Analogues
 pdb|3M30|E Chain E, Structural Insight Into Methyl-Coenzyme M Reductase
           Chemistry Using Coenzyme B Analogues
 pdb|3M32|B Chain B, Structural Insight Into Methyl-Coenzyme M Reductase
           Chemistry Using Coenzyme B Analogues
 pdb|3M32|E Chain E, Structural Insight Into Methyl-Coenzyme M Reductase
           Chemistry Using Coenzyme B Analogues
          Length = 442

 Score = 30.0 bits (66), Expect = 5.0,   Method: Compositional matrix adjust.
 Identities = 24/88 (27%), Positives = 43/88 (48%), Gaps = 4/88 (4%)

Query: 301 LSTVLKSVASFQ---AIGVCKQVHALSVKTAFESDDYIVNSLIDAYGKCGHVEDAVKIFK 357
           LST+L+  A F+   A+G  +++H L +     + D +V  L+ A GK G V   +    
Sbjct: 213 LSTILEQTAMFEMGDAVGAFERMHLLGLAYQGMNADNLVFDLVKANGKEGTVGSVIADLV 272

Query: 358 ESSAVD-LVACTSMITAYAQFGLGEEAL 384
           E +  D ++     +T Y  +G  + A+
Sbjct: 273 ERALEDGVIKVEKELTDYKVYGTDDLAM 300


>pdb|2Q0O|C Chain C, Crystal Structure Of An Anti-activation Complex In
           Bacterial Quorum Sensing
 pdb|2Q0O|D Chain D, Crystal Structure Of An Anti-activation Complex In
           Bacterial Quorum Sensing
          Length = 107

 Score = 30.0 bits (66), Expect = 5.4,   Method: Composition-based stats.
 Identities = 15/36 (41%), Positives = 22/36 (61%)

Query: 652 TVGDRSHARSKEIYAKLDEVSDLLNKAGYVPMVETD 687
           T+ D   AR K   A+ +E+SD+L+  G+VP V  D
Sbjct: 69  TLQDEYVARQKRSEAQQEELSDILDALGFVPDVPFD 104


  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
   0.322    0.135    0.408 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,787,826
Number of Sequences: 62578
Number of extensions: 926112
Number of successful extensions: 2358
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 2357
Number of HSP's gapped (non-prelim): 3
length of query: 771
length of database: 14,973,337
effective HSP length: 106
effective length of query: 665
effective length of database: 8,340,069
effective search space: 5546145885
effective search space used: 5546145885
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.8 bits)