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= 043117
         (359 letters)

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

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



>pdb|3RM5|A Chain A, Structure Of Trifunctional Thi20 From Yeast
 pdb|3RM5|B Chain B, Structure Of Trifunctional Thi20 From Yeast
          Length = 550

 Score = 30.4 bits (67), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 18/51 (35%), Positives = 29/51 (56%), Gaps = 1/51 (1%)

Query: 175 SEVNHELLIEVIDGTMEIKNVEMFPNDVHISDLVDAAKSFRQSGTQLDSLE 225
           S +NHE + +V DGT+E K  + F    + + LVD A+    +G++   LE
Sbjct: 348 SYINHEFVKKVADGTLERKKFQFFIEQDY-AYLVDYARVHCIAGSKAPCLE 397


>pdb|2PH5|A Chain A, Crystal Structure Of The Homospermidine Synthase Hss From
           Legionella Pneumophila In Complex With Nad, Northeast
           Structural Genomics Target Lgr54
          Length = 480

 Score = 28.1 bits (61), Expect = 7.6,   Method: Compositional matrix adjust.
 Identities = 15/56 (26%), Positives = 28/56 (50%), Gaps = 12/56 (21%)

Query: 163 SFQHKIEDVIEPSEVNHELLIEV------------IDGTMEIKNVEMFPNDVHISD 206
           + +H  E ++EP EV+H+ +I++             D T      E++P +V +SD
Sbjct: 407 AIEHPDEGIVEPEEVDHQYIIDIAKPYLGKVGGYYTDWTPLKNRGELYPEEVDLSD 462


  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
   0.316    0.133    0.368 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,595,676
Number of Sequences: 62578
Number of extensions: 370389
Number of successful extensions: 1011
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1004
Number of HSP's gapped (non-prelim): 14
length of query: 359
length of database: 14,973,337
effective HSP length: 100
effective length of query: 259
effective length of database: 8,715,537
effective search space: 2257324083
effective search space used: 2257324083
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: 52 (24.6 bits)