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= psy7771
         (193 letters)

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

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



>pdb|2BSP|A Chain A, Bacillus Subtilis Pectate Lyase R279k Mutant
          Length = 420

 Score = 26.9 bits (58), Expect = 6.8,   Method: Compositional matrix adjust.
 Identities = 11/26 (42%), Positives = 15/26 (57%)

Query: 78  NYQPSGQNQYYDPSYQPSNYQESYNP 103
           N +P G N Y DP Y    Y ++Y+P
Sbjct: 90  NLKPLGLNDYKDPEYDLDKYLKAYDP 115


>pdb|1BN8|A Chain A, Bacillus Subtilis Pectate Lyase
          Length = 420

 Score = 26.9 bits (58), Expect = 6.8,   Method: Compositional matrix adjust.
 Identities = 11/26 (42%), Positives = 15/26 (57%)

Query: 78  NYQPSGQNQYYDPSYQPSNYQESYNP 103
           N +P G N Y DP Y    Y ++Y+P
Sbjct: 90  NLKPLGLNDYKDPEYDLDKYLKAYDP 115


>pdb|3KRG|A Chain A, Structural Insights Into Substrate Specificity And The
           Anti Beta-Elimination Mechanism Of Pectate Lyase
          Length = 399

 Score = 26.9 bits (58), Expect = 7.9,   Method: Compositional matrix adjust.
 Identities = 11/26 (42%), Positives = 15/26 (57%)

Query: 78  NYQPSGQNQYYDPSYQPSNYQESYNP 103
           N +P G N Y DP Y    Y ++Y+P
Sbjct: 69  NLKPLGLNDYKDPEYDLDKYLKAYDP 94


>pdb|2NZM|A Chain A, Hexasaccharide I Bound To Bacillus Subtilis Pectate Lyase
 pdb|2O04|A Chain A, Pectate Lyase Bound To Hexasaccharide Compound Ii
 pdb|2O0V|A Chain A, Pectate Lyase Bound To Hexasaccharide Compound Iii
 pdb|2O0W|A Chain A, Pectate Lyase Bound To Hexasaccharide Compound Iv
 pdb|2O17|A Chain A, Pectate Lyase Bound To Hexasaccharide
 pdb|2O1D|A Chain A, Pectate Lyase Bound To Trisaccharide
          Length = 399

 Score = 26.6 bits (57), Expect = 8.3,   Method: Compositional matrix adjust.
 Identities = 11/26 (42%), Positives = 15/26 (57%)

Query: 78  NYQPSGQNQYYDPSYQPSNYQESYNP 103
           N +P G N Y DP Y    Y ++Y+P
Sbjct: 69  NLKPLGLNDYKDPEYDLDKYLKAYDP 94


>pdb|4GU1|A Chain A, Crystal Structure Of Lsd2
 pdb|4GU1|B Chain B, Crystal Structure Of Lsd2
          Length = 784

 Score = 26.6 bits (57), Expect = 8.9,   Method: Compositional matrix adjust.
 Identities = 18/60 (30%), Positives = 26/60 (43%), Gaps = 5/60 (8%)

Query: 48  ISPSLRTTRRAAKPNQ--PTSYSHQTAEYYRPNYQPSGQNQYYDPSYQPSNYQESYNPNP 105
           +SPS  +T RAA      P    H  A     +    G N+Y+ P YQP+   ++    P
Sbjct: 192 MSPSCTSTNRAAATGNASPGKLEHSKAAL---SVHVPGMNRYFQPFYQPNECGKALCVRP 248


>pdb|4FWE|A Chain A, Native Structure Of Lsd2 /aof1/kdm1b In Spacegroup Of
           C2221 At 2.13a
 pdb|4FWF|A Chain A, Complex Structure Of Lsd2/aof1/kdm1b With H3k4 Mimic
 pdb|4FWJ|A Chain A, Native Structure Of Lsd2/aof1/kdm1b In Spacegroup Of I222
           At 2.9a
 pdb|4FWJ|B Chain B, Native Structure Of Lsd2/aof1/kdm1b In Spacegroup Of I222
           At 2.9a
          Length = 796

 Score = 26.6 bits (57), Expect = 9.5,   Method: Compositional matrix adjust.
 Identities = 18/60 (30%), Positives = 26/60 (43%), Gaps = 5/60 (8%)

Query: 48  ISPSLRTTRRAAKPNQ--PTSYSHQTAEYYRPNYQPSGQNQYYDPSYQPSNYQESYNPNP 105
           +SPS  +T RAA      P    H  A     +    G N+Y+ P YQP+   ++    P
Sbjct: 204 MSPSCTSTNRAAATGNASPGKLEHSKAAL---SVHVPGMNRYFQPFYQPNECGKALCVRP 260


>pdb|4GUR|A Chain A, Crystal Structure Of Lsd2-npac With H3 In Space Group P21
 pdb|4GUS|A Chain A, Crystal Structure Of Lsd2-npac With H3 In Space Group
           P3221
 pdb|4GUT|A Chain A, Crystal Structure Of Lsd2-npac
 pdb|4GUU|A Chain A, Crystal Structure Of Lsd2-npac With Tranylcypromine
 pdb|4GU0|A Chain A, Crystal Structure Of Lsd2 With H3
 pdb|4GU0|B Chain B, Crystal Structure Of Lsd2 With H3
 pdb|4GU0|C Chain C, Crystal Structure Of Lsd2 With H3
 pdb|4GU0|D Chain D, Crystal Structure Of Lsd2 With H3
 pdb|4HSU|A Chain A, Crystal Structure Of Lsd2-npac With H3(1-26)in Space Group
           P21
          Length = 776

 Score = 26.6 bits (57), Expect = 9.7,   Method: Compositional matrix adjust.
 Identities = 18/60 (30%), Positives = 26/60 (43%), Gaps = 5/60 (8%)

Query: 48  ISPSLRTTRRAAKPNQ--PTSYSHQTAEYYRPNYQPSGQNQYYDPSYQPSNYQESYNPNP 105
           +SPS  +T RAA      P    H  A     +    G N+Y+ P YQP+   ++    P
Sbjct: 184 MSPSCTSTNRAAATGNASPGKLEHSKAAL---SVHVPGMNRYFQPFYQPNECGKALCVRP 240


  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
   0.310    0.128    0.393 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,607,290
Number of Sequences: 62578
Number of extensions: 304116
Number of successful extensions: 650
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 579
Number of HSP's gapped (non-prelim): 36
length of query: 193
length of database: 14,973,337
effective HSP length: 93
effective length of query: 100
effective length of database: 9,153,583
effective search space: 915358300
effective search space used: 915358300
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 49 (23.5 bits)