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= 004114
         (773 letters)

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

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



>pdb|2BA0|F Chain F, Archaeal Exosome Core
 pdb|2BA0|E Chain E, Archaeal Exosome Core
 pdb|2BA0|D Chain D, Archaeal Exosome Core
 pdb|2BA1|D Chain D, Archaeal Exosome Core
 pdb|2BA1|E Chain E, Archaeal Exosome Core
 pdb|2BA1|F Chain F, Archaeal Exosome Core
          Length = 258

 Score = 30.0 bits (66), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 11/71 (15%)

Query: 335 PNEGQYQSYSGNIQNGMMASQVLNNCKHEDDFAEASRSSQ---NNGTLE-----QLDGLV 386
           P +G   S +    +G +   VL+  K ED+F EA         NG +E     Q+DG +
Sbjct: 154 PMKGMITSVAVGKADGQL---VLDPMKEEDNFGEADMPFAFLIRNGKIESIALLQMDGRM 210

Query: 387 KEGKVKEAIEV 397
              +VK+AIE+
Sbjct: 211 TRDEVKQAIEL 221


>pdb|3M7N|D Chain D, Archaeoglobus Fulgidus Exosome With Rna Bound To The
           Active Site
 pdb|3M7N|E Chain E, Archaeoglobus Fulgidus Exosome With Rna Bound To The
           Active Site
 pdb|3M7N|F Chain F, Archaeoglobus Fulgidus Exosome With Rna Bound To The
           Active Site
 pdb|3M85|D Chain D, Archaeoglobus Fulgidus Exosome Y70a With Rna Bound To The
           Active Site
 pdb|3M85|E Chain E, Archaeoglobus Fulgidus Exosome Y70a With Rna Bound To The
           Active Site
 pdb|3M85|F Chain F, Archaeoglobus Fulgidus Exosome Y70a With Rna Bound To The
           Active Site
          Length = 258

 Score = 30.0 bits (66), Expect = 5.6,   Method: Compositional matrix adjust.
 Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 11/71 (15%)

Query: 335 PNEGQYQSYSGNIQNGMMASQVLNNCKHEDDFAEASRSSQ---NNGTLE-----QLDGLV 386
           P +G   S +    +G +   VL+  K ED+F EA         NG +E     Q+DG +
Sbjct: 154 PMKGMITSVAVGKADGQL---VLDPMKEEDNFGEADMPFAFLIRNGKIESIALLQMDGRM 210

Query: 387 KEGKVKEAIEV 397
              +VK+AIE+
Sbjct: 211 TRDEVKQAIEL 221


  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
   0.315    0.133    0.396 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 23,798,576
Number of Sequences: 62578
Number of extensions: 1040598
Number of successful extensions: 2326
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 2326
Number of HSP's gapped (non-prelim): 3
length of query: 773
length of database: 14,973,337
effective HSP length: 106
effective length of query: 667
effective length of database: 8,340,069
effective search space: 5562826023
effective search space used: 5562826023
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: 55 (25.8 bits)