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= 003057
         (852 letters)

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

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



>pdb|3KWT|A Chain A, Munc13-1 C2b-Domain, Calcium-Free
 pdb|3KWU|A Chain A, Munc13-1 C2b-Domain, Calcium Bound
          Length = 148

 Score = 36.2 bits (82), Expect = 0.078,   Method: Composition-based stats.
 Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 2/72 (2%)

Query: 68  GKLNVKVTSKIESHLSDKI-TSDPYVTVSICGAVIGRTFVISNSESPVWMQHFNVPVAHS 126
            K+++ V         DK  +SDPYVTV + G    RT  I  + +PVW ++F+    +S
Sbjct: 17  AKISITVVCAQGLQAKDKTGSSDPYVTVQV-GKTKKRTKTIYGNLNPVWEENFHFECHNS 75

Query: 127 AAEVHFVVKDND 138
           +  +   V D D
Sbjct: 76  SDRIKVRVLDED 87


>pdb|3HSI|A Chain A, Crystal Structure Of Phosphatidylserine Synthase
           Haemophilus Influenzae Rd Kw20
 pdb|3HSI|B Chain B, Crystal Structure Of Phosphatidylserine Synthase
           Haemophilus Influenzae Rd Kw20
 pdb|3HSI|C Chain C, Crystal Structure Of Phosphatidylserine Synthase
           Haemophilus Influenzae Rd Kw20
          Length = 458

 Score = 34.7 bits (78), Expect = 0.26,   Method: Compositional matrix adjust.
 Identities = 21/77 (27%), Positives = 36/77 (46%), Gaps = 4/77 (5%)

Query: 703 HSKGMIVDDEYVIIGSANINQRSLEGTRDTEIAMGAYQPRHTWASKLSNPYGQVYGYRMS 762
           H KG+ VDD Y+++   N+N R+     D E  +  Y P+    +++     Q+  +   
Sbjct: 364 HLKGVWVDDRYILLTGNNLNPRAWR--LDAENGLLIYDPQQQLLAQVEKEQNQIRQHTKV 421

Query: 763 LWAEHIGAIEECFNRPE 779
           L  +H   +EE    PE
Sbjct: 422 L--KHYTELEELNQYPE 436


>pdb|2UYR|X Chain X, Crystal Structure Of Bacillus Cereus Sphingomyelinase
           Mutant :n57a
          Length = 306

 Score = 30.4 bits (67), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 21/60 (35%), Positives = 33/60 (55%), Gaps = 4/60 (6%)

Query: 679 AKDSTAANTPQALAKKN--RRFQIYIHSKGMIVDDEYVIIG-SANINQRSLEGTRDTEIA 735
           A+DS    T  A  + N  +  Q +I +K  I ++EYV+IG   N+N+ + E   D+E A
Sbjct: 154 AEDSMCGKTSPASVRTNQLKEIQDFIKNKN-IPNNEYVLIGGDMNVNKINAENNNDSEYA 212


>pdb|2DDR|A Chain A, Crystal Structure Of Sphingomyelinase From Bacillus Cereus
           With Calcium Ion
 pdb|2DDR|B Chain B, Crystal Structure Of Sphingomyelinase From Bacillus Cereus
           With Calcium Ion
 pdb|2DDR|C Chain C, Crystal Structure Of Sphingomyelinase From Bacillus Cereus
           With Calcium Ion
 pdb|2DDR|D Chain D, Crystal Structure Of Sphingomyelinase From Bacillus Cereus
           With Calcium Ion
 pdb|2DDS|A Chain A, Crystal Structure Of Sphingomyelinase From Bacillus Cereus
           With Cobalt Ion
 pdb|2DDS|B Chain B, Crystal Structure Of Sphingomyelinase From Bacillus Cereus
           With Cobalt Ion
 pdb|2DDS|C Chain C, Crystal Structure Of Sphingomyelinase From Bacillus Cereus
           With Cobalt Ion
 pdb|2DDS|D Chain D, Crystal Structure Of Sphingomyelinase From Bacillus Cereus
           With Cobalt Ion
 pdb|2DDT|A Chain A, Crystal Structure Of Sphingomyelinase From Bacillus Cereus
           With Magnesium Ion
 pdb|2DDT|B Chain B, Crystal Structure Of Sphingomyelinase From Bacillus Cereus
           With Magnesium Ion
          Length = 306

 Score = 30.4 bits (67), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 21/60 (35%), Positives = 33/60 (55%), Gaps = 4/60 (6%)

Query: 679 AKDSTAANTPQALAKKN--RRFQIYIHSKGMIVDDEYVIIG-SANINQRSLEGTRDTEIA 735
           A+DS    T  A  + N  +  Q +I +K  I ++EYV+IG   N+N+ + E   D+E A
Sbjct: 154 AEDSMCGKTSPASVRTNQLKEIQDFIKNKN-IPNNEYVLIGGDMNVNKINAENNNDSEYA 212


  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
   0.319    0.136    0.416 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 26,516,443
Number of Sequences: 62578
Number of extensions: 1143247
Number of successful extensions: 2202
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 2201
Number of HSP's gapped (non-prelim): 6
length of query: 852
length of database: 14,973,337
effective HSP length: 107
effective length of query: 745
effective length of database: 8,277,491
effective search space: 6166730795
effective search space used: 6166730795
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (26.2 bits)