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= 028899
         (202 letters)

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

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



>pdb|1U8K|B Chain B, Crystal Structure Of The Hiv-1 Cross Neutralizing
           Monoclonal Antibody 2f5 In Complex With Gp41 Peptide
           Leldkwasl
          Length = 234

 Score = 26.9 bits (58), Expect = 8.2,   Method: Compositional matrix adjust.
 Identities = 18/63 (28%), Positives = 26/63 (41%), Gaps = 5/63 (7%)

Query: 37  RSKSKAKGPPVQRKPLKHRD-----YVVDLESRLGKTQVVTPIAPLSQQAGYYCSVCECV 91
           R  +   G P+ R P+   D       V + S   K   V P+AP S+      +   C+
Sbjct: 101 RGPTTLFGVPIARGPVNAMDVWGQGITVTISSTSTKGPSVFPLAPCSKSTAGGTAALGCL 160

Query: 92  VKD 94
           VKD
Sbjct: 161 VKD 163


>pdb|4DGW|A Chain A, Crystal Structure Of The Sf3a Splicing Factor Complex Of
           U2 Snrnp
          Length = 402

 Score = 26.9 bits (58), Expect = 8.4,   Method: Compositional matrix adjust.
 Identities = 11/32 (34%), Positives = 17/32 (53%)

Query: 78  SQQAGYYCSVCECVVKDSANYLDHINGKKHQR 109
           S+  G YC  C    K S+ +  H+ GK H++
Sbjct: 288 SEAKGIYCPFCSRWFKTSSVFESHLVGKIHKK 319


  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    0.132    0.383 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,515,185
Number of Sequences: 62578
Number of extensions: 135482
Number of successful extensions: 595
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 594
Number of HSP's gapped (non-prelim): 7
length of query: 202
length of database: 14,973,337
effective HSP length: 94
effective length of query: 108
effective length of database: 9,091,005
effective search space: 981828540
effective search space used: 981828540
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: 49 (23.5 bits)