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= psy7109
         (236 letters)

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

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



>pdb|1WD3|A Chain A, Crystal Structure Of Arabinofuranosidase
 pdb|1WD4|A Chain A, Crystal Structure Of Arabinofuranosidase Complexed With
           Arabinose
          Length = 482

 Score = 29.3 bits (64), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 22/65 (33%), Positives = 30/65 (46%), Gaps = 12/65 (18%)

Query: 111 TIAVMYSSF-GVLLQTTRGTDDDFNTLTAATATGMLFRSTGNCXXXXXXXXXXHFCDNKT 169
           T   +YSSF G L Q  RG+DD   T++  TA G+   S  +            FC N T
Sbjct: 20  TTRALYSSFSGALYQLQRGSDDTTTTISPLTAGGIADASAQDT-----------FCANTT 68

Query: 170 SAVTV 174
             +T+
Sbjct: 69  CLITI 73


>pdb|2D43|A Chain A, Crystal Structure Of Arabinofuranosidase Complexed With
           Arabinotriose
 pdb|2D44|A Chain A, Crystal Structure Of Arabinofuranosidase Complexed With
           Arabinofuranosyl-alpha-1,2-xylobiose
          Length = 482

 Score = 29.3 bits (64), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 22/65 (33%), Positives = 30/65 (46%), Gaps = 12/65 (18%)

Query: 111 TIAVMYSSF-GVLLQTTRGTDDDFNTLTAATATGMLFRSTGNCXXXXXXXXXXHFCDNKT 169
           T   +YSSF G L Q  RG+DD   T++  TA G+   S  +            FC N T
Sbjct: 20  TTRALYSSFSGALYQLQRGSDDTTTTISPLTAGGIADASAQDT-----------FCANTT 68

Query: 170 SAVTV 174
             +T+
Sbjct: 69  CLITI 73


>pdb|2WAE|A Chain A, Penicillin-Binding Protein 2b (Pbp-2b) From Streptococcus
           Pneumoniae (Strain 5204)
          Length = 680

 Score = 27.3 bits (59), Expect = 6.9,   Method: Compositional matrix adjust.
 Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 68  GGAEGFYKGLRNTTLEGQTGKLRRTQLLNHIMKHGSATASTLGTIAVMY 116
           GGA+ + +G+    L  QTG +     L H +K G  T  +LGT+  ++
Sbjct: 335 GGAK-YSEGVYAVALNPQTGAVLSMSGLKHDLKTGELTPDSLGTVTNVF 382


>pdb|2WAD|A Chain A, Penicillin-Binding Protein 2b (Pbp-2b) From Streptococcus
           Pneumoniae (Strain 5204)
 pdb|2WAD|B Chain B, Penicillin-Binding Protein 2b (Pbp-2b) From Streptococcus
           Pneumoniae (Strain 5204)
 pdb|2WAD|C Chain C, Penicillin-Binding Protein 2b (Pbp-2b) From Streptococcus
           Pneumoniae (Strain 5204)
          Length = 680

 Score = 27.3 bits (59), Expect = 7.2,   Method: Compositional matrix adjust.
 Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 68  GGAEGFYKGLRNTTLEGQTGKLRRTQLLNHIMKHGSATASTLGTIAVMY 116
           GGA+ + +G+    L  QTG +     L H +K G  T  +LGT+  ++
Sbjct: 335 GGAK-YSEGVYAVALNPQTGAVLSMSGLKHDLKTGELTPDSLGTVTNVF 382


  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    0.132    0.386 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,871,576
Number of Sequences: 62578
Number of extensions: 198567
Number of successful extensions: 401
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 399
Number of HSP's gapped (non-prelim): 5
length of query: 236
length of database: 14,973,337
effective HSP length: 96
effective length of query: 140
effective length of database: 8,965,849
effective search space: 1255218860
effective search space used: 1255218860
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: 50 (23.9 bits)