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= 007901
         (585 letters)

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

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



>pdb|1ZU1|A Chain A, Solution Structure Of The N-Terminal Zinc Fingers Of The
           Xenopus Laevis Double Stranded Rna Binding Protein Zfa
          Length = 127

 Score = 31.2 bits (69), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 12/28 (42%), Positives = 19/28 (67%)

Query: 338 CELCNVKCESQVVFDSHLVGKKHLANVK 365
           C +CN+   S VV +SH +GK H+ N++
Sbjct: 96  CPVCNMTFSSPVVAESHYIGKTHIKNLR 123


>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 = 30.4 bits (67), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 24/82 (29%), Positives = 42/82 (51%), Gaps = 4/82 (4%)

Query: 209 KRNLRTHADLQNLNKCIAGQQNIQMPNSGSQPEVSQPEKVEECREKQPLESLPSQTLL-- 266
           + N  T  DL+ + K +    +I  PN  ++ +++     +    K+ +E+LPS+  L  
Sbjct: 84  RSNKMTATDLKEIAKKLLTYVSISSPNL-TERQLADYYLADPEIYKKTVEALPSEKRLDS 142

Query: 267 -GNASNETEMQKNTVDSVKEPQ 287
            GN  +E+E+  N VDSV   Q
Sbjct: 143 DGNRLSESELYNNAVDSVPTSQ 164


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

 Score = 30.4 bits (67), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 24/82 (29%), Positives = 42/82 (51%), Gaps = 4/82 (4%)

Query: 209 KRNLRTHADLQNLNKCIAGQQNIQMPNSGSQPEVSQPEKVEECREKQPLESLPSQTLL-- 266
           + N  T  DL+ + K +    +I  PN  ++ +++     +    K+ +E+LPS+  L  
Sbjct: 84  RSNKMTATDLKEIAKKLLTYVSISSPNL-TERQLADYYLADPEIYKKTVEALPSEKRLDS 142

Query: 267 -GNASNETEMQKNTVDSVKEPQ 287
            GN  +E+E+  N VDSV   Q
Sbjct: 143 DGNRLSESELYNNAVDSVPTSQ 164


>pdb|2WAF|A Chain A, Penicillin-Binding Protein 2b (Pbp-2b) From Streptococcus
           Pneumoniae (Strain R6)
          Length = 682

 Score = 29.6 bits (65), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 24/82 (29%), Positives = 42/82 (51%), Gaps = 4/82 (4%)

Query: 209 KRNLRTHADLQNLNKCIAGQQNIQMPNSGSQPEVSQPEKVEECREKQPLESLPSQTLL-- 266
           + N  T  DL+   K +    +I  PN  ++ +++     +    K+ +E+LPS+  L  
Sbjct: 84  RSNKMTATDLKETAKKLLTYVSISSPNL-TERQLADYYLADPEIYKKIVEALPSEKRLDS 142

Query: 267 -GNASNETEMQKNTVDSVKEPQ 287
            GN  +E+E+  N VDSV+  Q
Sbjct: 143 DGNRLSESELYNNAVDSVQTSQ 164


  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
   0.309    0.126    0.360 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,601,432
Number of Sequences: 62578
Number of extensions: 523957
Number of successful extensions: 1054
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1043
Number of HSP's gapped (non-prelim): 13
length of query: 585
length of database: 14,973,337
effective HSP length: 104
effective length of query: 481
effective length of database: 8,465,225
effective search space: 4071773225
effective search space used: 4071773225
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: 54 (25.4 bits)