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= 012848
         (455 letters)

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

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



>pdb|4GF6|B Chain B, Crystal Structure Of Gfp With Cuprum Bound At The
           Incorporated Metal Chelating Amino Acid Pyz151
          Length = 246

 Score = 28.5 bits (62), Expect = 8.5,   Method: Compositional matrix adjust.
 Identities = 13/30 (43%), Positives = 19/30 (63%), Gaps = 1/30 (3%)

Query: 408 VLVETYEQG-ECVSRYVDELQGHERLKSAL 436
            LV T+  G +C SRY D ++ H+  KSA+
Sbjct: 59  TLVTTFSYGVQCFSRYPDHMKAHDFFKSAM 88


>pdb|1YHG|A Chain A, Uncyclized Precursor Structure Of S65g Y66s V68g Gfp
           Variant
 pdb|1YHG|B Chain B, Uncyclized Precursor Structure Of S65g Y66s V68g Gfp
           Variant
          Length = 239

 Score = 28.5 bits (62), Expect = 8.9,   Method: Compositional matrix adjust.
 Identities = 12/35 (34%), Positives = 20/35 (57%)

Query: 402 PLVHPAVLVETYEQGECVSRYVDELQGHERLKSAL 436
           P+  P ++      G+C SRY D ++ H+  KSA+
Sbjct: 55  PVPWPTLVTTLGSGGQCFSRYPDHMKQHDFFKSAM 89


  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
   0.326    0.137    0.424 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,661,836
Number of Sequences: 62578
Number of extensions: 478246
Number of successful extensions: 1429
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1428
Number of HSP's gapped (non-prelim): 2
length of query: 455
length of database: 14,973,337
effective HSP length: 102
effective length of query: 353
effective length of database: 8,590,381
effective search space: 3032404493
effective search space used: 3032404493
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (25.0 bits)