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= 040436
         (91 letters)

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

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



>pdb|4A1K|A Chain A, Ykud L,D-Transpeptidase
          Length = 165

 Score = 31.6 bits (70), Expect = 0.10,   Method: Compositional matrix adjust.
 Identities = 13/45 (28%), Positives = 25/45 (55%), Gaps = 1/45 (2%)

Query: 45 YGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAG 89
          Y  ++GDT +++  +F +ST   L  NP++    +  GQ + + G
Sbjct: 5  YQVKQGDTLNSIAADFRISTAALLQANPSLQA-GLTAGQSIVIPG 48


>pdb|3ZQD|A Chain A, B. Subtilis L,D-Transpeptidase
 pdb|4A52|A Chain A, Nmr Structure Of The Imipenem-Acylated
          L,D-Transpeptidase From Bacillus Subtilis
          Length = 175

 Score = 31.6 bits (70), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 13/45 (28%), Positives = 25/45 (55%), Gaps = 1/45 (2%)

Query: 45 YGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAG 89
          Y  ++GDT +++  +F +ST   L  NP++    +  GQ + + G
Sbjct: 7  YQVKQGDTLNSIAADFRISTAALLQANPSLQA-GLTAGQSIVIPG 50


>pdb|4A1I|A Chain A, Ykud From B.Subtilis
 pdb|4A1I|B Chain B, Ykud From B.Subtilis
 pdb|4A1I|C Chain C, Ykud From B.Subtilis
 pdb|4A1I|D Chain D, Ykud From B.Subtilis
 pdb|4A1I|E Chain E, Ykud From B.Subtilis
 pdb|4A1I|F Chain F, Ykud From B.Subtilis
 pdb|4A1I|G Chain G, Ykud From B.Subtilis
 pdb|4A1I|H Chain H, Ykud From B.Subtilis
 pdb|4A1J|A Chain A, Ykud L,D-Transpeptidase From B.Subtilis
 pdb|4A1J|B Chain B, Ykud L,D-Transpeptidase From B.Subtilis
          Length = 165

 Score = 31.6 bits (70), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 13/45 (28%), Positives = 25/45 (55%), Gaps = 1/45 (2%)

Query: 45 YGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAG 89
          Y  ++GDT +++  +F +ST   L  NP++    +  GQ + + G
Sbjct: 5  YQVKQGDTLNSIAADFRISTAALLQANPSLQA-GLTAGQSIVIPG 48


>pdb|1Y7M|A Chain A, Crystal Structure Of The B. Subtilis Ykud Protein At 2 A
          Resolution
 pdb|1Y7M|B Chain B, Crystal Structure Of The B. Subtilis Ykud Protein At 2 A
          Resolution
          Length = 164

 Score = 31.6 bits (70), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 13/45 (28%), Positives = 25/45 (55%), Gaps = 1/45 (2%)

Query: 45 YGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAG 89
          Y  ++GDT +++  +F +ST   L  NP++    +  GQ + + G
Sbjct: 4  YQVKQGDTLNSIAADFRISTAALLQANPSLQA-GLTAGQSIVIPG 47


  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
   0.317    0.129    0.391 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,178,027
Number of Sequences: 62578
Number of extensions: 63129
Number of successful extensions: 74
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 69
Number of HSP's gapped (non-prelim): 5
length of query: 91
length of database: 14,973,337
effective HSP length: 58
effective length of query: 33
effective length of database: 11,343,813
effective search space: 374345829
effective search space used: 374345829
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)