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= 043373
         (809 letters)

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

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



>pdb|3NVM|A Chain A, Structural Basis For Substrate Placement By An Archaeal
           Box CD Ribonucleoprotein Particle
          Length = 371

 Score = 29.3 bits (64), Expect = 9.0,   Method: Compositional matrix adjust.
 Identities = 29/108 (26%), Positives = 50/108 (46%), Gaps = 15/108 (13%)

Query: 352 KKILKRWGLSEKDMKPALELVDGLSEGSRVNSRKFLESLEEEATKILTLKDLANCF-LNK 410
           +++L+  GLSE+ +K  LE  +  + G+ ++            T I  ++ LA    L K
Sbjct: 194 EEVLRELGLSEEKIKKILEAKEK-TMGAWMDQ-----------TDIEVVRQLAEEIQLRK 241

Query: 411 DLEKYIKKASQNLSPRLEFIKKVSVHLGVHLLSGIVAYASMKMCPPKT 458
            LE YI +A  +++P L+ +  V   L   L+S       + M P  T
Sbjct: 242 KLEDYIDRAMDDVAPNLKAL--VGAKLAARLISLAGGLRELAMMPSST 287


>pdb|3NVK|A Chain A, Structural Basis For Substrate Placement By An Archaeal
           Box CD Ribonucleoprotein Particle
 pdb|3NVK|F Chain F, Structural Basis For Substrate Placement By An Archaeal
           Box CD Ribonucleoprotein Particle
          Length = 376

 Score = 29.3 bits (64), Expect = 9.7,   Method: Compositional matrix adjust.
 Identities = 28/109 (25%), Positives = 52/109 (47%), Gaps = 13/109 (11%)

Query: 352 KKILKRWGLSEKDMKPALELVDGLSEGSRVNSR--KFLESLEEEATKILTLKDLANCFLN 409
           +++L+  GLSE+ +K  LE  +  + G+ ++    + +  L EE  ++  L+        
Sbjct: 198 EEVLRELGLSEEKIKKILEAKEK-TMGAWMDQTDIEVVRQLAEEIDRLYQLR-------- 248

Query: 410 KDLEKYIKKASQNLSPRLEFIKKVSVHLGVHLLSGIVAYASMKMCPPKT 458
           K LE YI +A  +++P L+ +  V   L   L+S       + M P  T
Sbjct: 249 KKLEDYIDRAMDDVAPNLKAL--VGAKLAARLISLAGGLRELAMMPSST 295


  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
   0.321    0.138    0.398 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,431,022
Number of Sequences: 62578
Number of extensions: 846145
Number of successful extensions: 2505
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 2490
Number of HSP's gapped (non-prelim): 25
length of query: 809
length of database: 14,973,337
effective HSP length: 107
effective length of query: 702
effective length of database: 8,277,491
effective search space: 5810798682
effective search space used: 5810798682
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: 55 (25.8 bits)