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= 008751
         (555 letters)

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

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



>pdb|1SXJ|A Chain A, Crystal Structure Of The Eukaryotic Clamp Loader
           (Replication Factor C, Rfc) Bound To The Dna Sliding
           Clamp (Proliferating Cell Nuclear Antigen, Pcna)
          Length = 516

 Score = 55.8 bits (133), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 39/136 (28%), Positives = 66/136 (48%), Gaps = 7/136 (5%)

Query: 9   LCEAAQHADDEVVEVIHIPDDENSHGVMGKSDNHVKPLILIEDVDVFFPEDRGFIAGIQQ 68
           L    ++A D +  V +   +E +  + GK   H   +I++++VD     DRG +  + Q
Sbjct: 119 LNAGVKNALDNMSVVGYFKHNEEAQNLNGK---HF--VIIMDEVDGMSGGDRGGVGQLAQ 173

Query: 69  IAEKAKGPVILTSNSNNITLPDSLDR--LEVSFTMPMPKDLLSHLQMICAAEKVELQQHL 126
              K   P+IL  N  N+      DR  L++ F  P    + S L  I   EK +L  ++
Sbjct: 174 FCRKTSTPLILICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLDPNV 233

Query: 127 LVQLIESCRADIRKTI 142
           + +LI++ R DIR+ I
Sbjct: 234 IDRLIQTTRGDIRQVI 249


  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    0.132    0.383 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,369,613
Number of Sequences: 62578
Number of extensions: 669009
Number of successful extensions: 1573
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1572
Number of HSP's gapped (non-prelim): 2
length of query: 555
length of database: 14,973,337
effective HSP length: 104
effective length of query: 451
effective length of database: 8,465,225
effective search space: 3817816475
effective search space used: 3817816475
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 bits)
S2: 54 (25.4 bits)