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= 008004
         (581 letters)

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

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



>pdb|2RD7|A Chain A, Human Complement Membrane Attack Proteins Share A Common
           Fold With Bacterial Cytolysins
          Length = 367

 Score = 32.3 bits (72), Expect = 0.79,   Method: Compositional matrix adjust.
 Identities = 15/45 (33%), Positives = 27/45 (60%), Gaps = 3/45 (6%)

Query: 141 KSPLVLQENVKRAI---PASWDPPSLASFIENFGTHVITSVTIGG 182
           K  ++L E + +++   P  ++    A FI ++GTH ITS ++GG
Sbjct: 180 KDDIMLDEGMLQSLMELPDQYNYGMYAKFINDYGTHYITSGSMGG 224


>pdb|2QQH|A Chain A, Structure Of C8a-Macpf Reveals Mechanism Of Membrane
           Attack In Complement Immune Defense
          Length = 334

 Score = 32.0 bits (71), Expect = 0.95,   Method: Compositional matrix adjust.
 Identities = 15/45 (33%), Positives = 27/45 (60%), Gaps = 3/45 (6%)

Query: 141 KSPLVLQENVKRAI---PASWDPPSLASFIENFGTHVITSVTIGG 182
           K  ++L E + +++   P  ++    A FI ++GTH ITS ++GG
Sbjct: 175 KDDIMLDEGMLQSLMELPDQYNYGMYAKFINDYGTHYITSGSMGG 219


>pdb|3OJY|A Chain A, Crystal Structure Of Human Complement Component C8
          Length = 554

 Score = 31.6 bits (70), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 15/45 (33%), Positives = 27/45 (60%), Gaps = 3/45 (6%)

Query: 141 KSPLVLQENVKRAI---PASWDPPSLASFIENFGTHVITSVTIGG 182
           K  ++L E + +++   P  ++    A FI ++GTH ITS ++GG
Sbjct: 275 KDDIMLDEGMLQSLMELPDQYNYGMYAKFINDYGTHYITSGSMGG 319


>pdb|2XZM|R Chain R, Crystal Structure Of The Eukaryotic 40s Ribosomal Subunit
           In Complex With Initiation Factor 1. This File Contains
           The 40s Subunit And Initiation Factor For Molecule 1
 pdb|2XZN|R Chain R, Crystal Structure Of The Eukaryotic 40s Ribosomal Subunit
           In Complex With Initiation Factor 1. This File Contains
           The 40s Subunit And Initiation Factor For Molecule 2
          Length = 343

 Score = 30.4 bits (67), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 12/26 (46%), Positives = 18/26 (69%)

Query: 342 TKIPGQQRKEPVCPSLQFSMMGQKLY 367
           TK  GQ+ K P C SL ++ +G+KL+
Sbjct: 300 TKAEGQKGKNPQCTSLAWNALGKKLF 325


  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
   0.317    0.134    0.402 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,540,786
Number of Sequences: 62578
Number of extensions: 735302
Number of successful extensions: 1801
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1796
Number of HSP's gapped (non-prelim): 6
length of query: 581
length of database: 14,973,337
effective HSP length: 104
effective length of query: 477
effective length of database: 8,465,225
effective search space: 4037912325
effective search space used: 4037912325
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)