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= psy8408
         (393 letters)

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

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



>pdb|2P7N|A Chain A, Crystal Structure Of The Pathogenicity Island 1 Effector
           Protein From Chromobacterium Violaceum. Northeast
           Structural Genomics Consortium (Nesgc) Target Cvr69
          Length = 407

 Score = 30.0 bits (66), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 14/46 (30%), Positives = 23/46 (50%)

Query: 117 QWVPFMLFFQGILFYVPHWIWKNLEENKVRMITDGMRGAIVTSKED 162
           Q+  F   F  IL    +WI    + NKV++  D ++ A+   K+D
Sbjct: 206 QYTDFYKAFSDILSQXANWIKPGGDGNKVKLNVDALKAALEKLKKD 251


>pdb|1JLY|A Chain A, Crystal Structure Of Amaranthus Caudatus Agglutinin
 pdb|1JLY|B Chain B, Crystal Structure Of Amaranthus Caudatus Agglutinin
          Length = 304

 Score = 29.6 bits (65), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 3/61 (4%)

Query: 287 AIMSFGAICYSLSVITLPSIRETILIRRFRFGTPAGVSALIRRTQ-VGDFLLLHL--LGQ 343
           A   F +  +  +VI+L ++++T  I+RF  G P  ++ +   TQ V +  +L +  LGQ
Sbjct: 243 AAALFRSDVHDFNVISLLNMQKTWFIKRFTSGKPGFINCMNAATQNVDETAILEIIELGQ 302

Query: 344 N 344
           N
Sbjct: 303 N 303


>pdb|1JLX|A Chain A, Agglutinin In Complex With T-Disaccharide
 pdb|1JLX|B Chain B, Agglutinin In Complex With T-Disaccharide
          Length = 303

 Score = 29.6 bits (65), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 3/61 (4%)

Query: 287 AIMSFGAICYSLSVITLPSIRETILIRRFRFGTPAGVSALIRRTQ-VGDFLLLHL--LGQ 343
           A   F +  +  +VI+L ++++T  I+RF  G P  ++ +   TQ V +  +L +  LGQ
Sbjct: 242 AAALFRSDVHDFNVISLLNMQKTWFIKRFTSGKPGFINCMNAATQNVDETAILEIIELGQ 301

Query: 344 N 344
           N
Sbjct: 302 N 302


  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
   0.328    0.141    0.443 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,583,106
Number of Sequences: 62578
Number of extensions: 480286
Number of successful extensions: 1127
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1126
Number of HSP's gapped (non-prelim): 4
length of query: 393
length of database: 14,973,337
effective HSP length: 101
effective length of query: 292
effective length of database: 8,652,959
effective search space: 2526664028
effective search space used: 2526664028
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 52 (24.6 bits)