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= psy4036
         (93 letters)

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

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



>pdb|1BV8|A Chain A, Receptor Domain From Alpha-2-Macroglobulin
          Length = 138

 Score = 26.9 bits (58), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 13/35 (37%), Positives = 20/35 (57%), Gaps = 3/35 (8%)

Query: 62 KRANEVSRISLKKNHVAIF---IIHQDLQVFMKSL 93
          +R+N VSR  +  NHV I+   + +Q L +F   L
Sbjct: 64 ERSNHVSRTEVSSNHVLIYLDKVSNQTLSLFFTVL 98


>pdb|4ACQ|A Chain A, Alpha-2 Macroglobulin
 pdb|4ACQ|B Chain B, Alpha-2 Macroglobulin
 pdb|4ACQ|C Chain C, Alpha-2 Macroglobulin
 pdb|4ACQ|D Chain D, Alpha-2 Macroglobulin
          Length = 1451

 Score = 26.6 bits (57), Expect = 3.9,   Method: Composition-based stats.
 Identities = 13/35 (37%), Positives = 20/35 (57%), Gaps = 3/35 (8%)

Query: 62   KRANEVSRISLKKNHVAIF---IIHQDLQVFMKSL 93
            +R+N VSR  +  NHV I+   + +Q L +F   L
Sbjct: 1377 ERSNHVSRTEVSSNHVLIYLDKVSNQTLSLFFTVL 1411


>pdb|3BMX|A Chain A, Beta-N-Hexosaminidase (Ybbd) From Bacillus Subtilis
 pdb|3BMX|B Chain B, Beta-N-Hexosaminidase (Ybbd) From Bacillus Subtilis
 pdb|3NVD|A Chain A, Structure Of Ybbd In Complex With Pugnac
 pdb|3NVD|B Chain B, Structure Of Ybbd In Complex With Pugnac
          Length = 642

 Score = 26.2 bits (56), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 17/42 (40%), Positives = 30/42 (71%), Gaps = 2/42 (4%)

Query: 33  SSLEKKEEKLRVIRAQKKAIKDAKLAEEKKRANEVSR-ISLK 73
           +SL+++++  RVI+A K+A+K+  + E++   N V R ISLK
Sbjct: 353 TSLKEEQKFARVIQALKEAVKNGDIPEQQIN-NSVERIISLK 393


>pdb|4GYJ|A Chain A, Crystal Structure Of Mutant (D318n) Bacillus Subtilus
           Family 3 Glycoside Hydrolase (Nagz) In Complex With
           Glcnac-Murnac (Space Group P1)
 pdb|4GYJ|B Chain B, Crystal Structure Of Mutant (D318n) Bacillus Subtilus
           Family 3 Glycoside Hydrolase (Nagz) In Complex With
           Glcnac-Murnac (Space Group P1)
 pdb|4GYK|A Chain A, Crystal Structure Of Mutant (D318n) Bacillus Subtilus
           Family 3 Glycoside Hydrolase (Nagz) In Complex With
           Glcnac-Murnac (Space Group P1211)
 pdb|4GYK|B Chain B, Crystal Structure Of Mutant (D318n) Bacillus Subtilus
           Family 3 Glycoside Hydrolase (Nagz) In Complex With
           Glcnac-Murnac (Space Group P1211)
          Length = 648

 Score = 26.2 bits (56), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 17/42 (40%), Positives = 30/42 (71%), Gaps = 2/42 (4%)

Query: 33  SSLEKKEEKLRVIRAQKKAIKDAKLAEEKKRANEVSR-ISLK 73
           +SL+++++  RVI+A K+A+K+  + E++   N V R ISLK
Sbjct: 357 TSLKEEQKFARVIQALKEAVKNGDIPEQQIN-NSVERIISLK 397


>pdb|3LK6|A Chain A, Beta-N-Hexosaminidase N318d Mutant (Ybbd_n318d) From
           Bacillus Subtilis
 pdb|3LK6|B Chain B, Beta-N-Hexosaminidase N318d Mutant (Ybbd_n318d) From
           Bacillus Subtilis
 pdb|3LK6|C Chain C, Beta-N-Hexosaminidase N318d Mutant (Ybbd_n318d) From
           Bacillus Subtilis
 pdb|3LK6|D Chain D, Beta-N-Hexosaminidase N318d Mutant (Ybbd_n318d) From
           Bacillus Subtilis
          Length = 616

 Score = 26.2 bits (56), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 17/42 (40%), Positives = 30/42 (71%), Gaps = 2/42 (4%)

Query: 33  SSLEKKEEKLRVIRAQKKAIKDAKLAEEKKRANEVSR-ISLK 73
           +SL+++++  RVI+A K+A+K+  + E++   N V R ISLK
Sbjct: 327 TSLKEEQKFARVIQALKEAVKNGDIPEQQIN-NSVERIISLK 367


  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
   0.320    0.131    0.343 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,745,387
Number of Sequences: 62578
Number of extensions: 46552
Number of successful extensions: 192
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 185
Number of HSP's gapped (non-prelim): 14
length of query: 93
length of database: 14,973,337
effective HSP length: 60
effective length of query: 33
effective length of database: 11,218,657
effective search space: 370215681
effective search space used: 370215681
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)