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= 039390
         (263 letters)

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

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



>pdb|2GCC|A Chain A, Solution Structure Of The Gcc-Box Binding Domain, Nmr,
           Minimized Mean Structure
 pdb|3GCC|A Chain A, Solution Structure Of The Gcc-Box Binding Domain, Nmr, 46
           Structures
          Length = 70

 Score = 73.6 bits (179), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 37/63 (58%), Positives = 42/63 (66%), Gaps = 1/63 (1%)

Query: 154 RKYRGVRQRPWGKWAAEIRDPFK-AARVWLGTFDTXXXXXXXXXXXXLRFRGNKAKLNFP 212
           + YRGVRQRPWGK+AAEIRDP K  ARVWLGTF+T             R RG++A LNFP
Sbjct: 4   KHYRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFP 63

Query: 213 ENV 215
             V
Sbjct: 64  LRV 66


>pdb|1GCC|A Chain A, Solution Nmr Structure Of The Complex Of Gcc-Box Binding
           Domain Of Aterf1 And Gcc-Box Dna, Minimized Average
           Structure
          Length = 63

 Score = 73.2 bits (178), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 37/63 (58%), Positives = 42/63 (66%), Gaps = 1/63 (1%)

Query: 154 RKYRGVRQRPWGKWAAEIRDPFK-AARVWLGTFDTXXXXXXXXXXXXLRFRGNKAKLNFP 212
           + YRGVRQRPWGK+AAEIRDP K  ARVWLGTF+T             R RG++A LNFP
Sbjct: 1   KHYRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFP 60

Query: 213 ENV 215
             V
Sbjct: 61  LRV 63


>pdb|2EPK|X Chain X, N-Acetyl-B-D-Glucosaminidase (Gcna) From Streptococcus
           Gordonii
          Length = 627

 Score = 27.3 bits (59), Expect = 10.0,   Method: Compositional matrix adjust.
 Identities = 21/85 (24%), Positives = 36/85 (42%), Gaps = 18/85 (21%)

Query: 11  KKKKEGDQHHEERLSEVDQGMNYQPLMQYSDDQRRRW-KEREMSAMVSA----------- 58
           K  + GD+ H   L+E D    YQ +  +SD   R+W +E ++  + +            
Sbjct: 511 KAYRNGDKEHLSALAEKDFPQLYQXVEDFSDQFSRQWQQENKIFGLDTIDIRFGGLLKRI 570

Query: 59  ------LKHVVAGDIDVVASQPQQI 77
                 L+  ++G ID V    Q+I
Sbjct: 571 KRAQERLEQFISGQIDCVEELEQEI 595


  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
   0.316    0.131    0.386 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,503,333
Number of Sequences: 62578
Number of extensions: 162332
Number of successful extensions: 264
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 258
Number of HSP's gapped (non-prelim): 4
length of query: 263
length of database: 14,973,337
effective HSP length: 97
effective length of query: 166
effective length of database: 8,903,271
effective search space: 1477942986
effective search space used: 1477942986
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)