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= 042860
         (235 letters)

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

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



>pdb|1JER|A Chain A, Cucumber Stellacyanin, Cu2+, Ph 7.0
          Length = 138

 Score = 28.5 bits (62), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 27/93 (29%), Positives = 39/93 (41%), Gaps = 13/93 (13%)

Query: 26  SEWK-NPSVHVGDTIIFKHKFNNSNLYIFKNKNAFNLCNFSQATLLTNPNSTSYT----W 80
           S+W    +  VGD++ F    N  N++  + K +F+ CNF     + + N    T     
Sbjct: 24  SQWAAGKTFRVGDSLQFNFPANAHNVHEMETKQSFDACNF-----VNSDNDVERTSPVIE 78

Query: 81  HPSRPGFFYFTFNNGSLQTCNKSSQKLSIKVSA 113
                G  YF    G   T   + QKLSI V A
Sbjct: 79  RLDELGMHYFVCTVG---THCSNGQKLSINVVA 108


>pdb|4EJ5|A Chain A, Crystal Structure Of The Catalytic Domain Of Botulinum
           Neurotoxin BontA WILD-Type
          Length = 445

 Score = 27.3 bits (59), Expect = 8.3,   Method: Compositional matrix adjust.
 Identities = 17/55 (30%), Positives = 30/55 (54%), Gaps = 2/55 (3%)

Query: 172 GTVPDKGSGIPFINSNPAVPLPTGEVDSATIRPLPTSGHVNQVEVGVLASQLLVL 226
           G VP +GS +PF+N       P   VD A I+ +P +G +  V+   + +++ V+
Sbjct: 13  GLVP-RGSHMPFVNKQFNYKDPVNGVDIAYIK-IPNAGQMQPVKAFKIHNKIWVI 65


>pdb|4ELC|A Chain A, Crystal Structure Of The Catalytic Domain Of Botulinum
           Neurotoxin BontA C134 MUTANT WITH MTSEA MODIFIED CYS-165
          Length = 445

 Score = 26.9 bits (58), Expect = 9.1,   Method: Compositional matrix adjust.
 Identities = 17/55 (30%), Positives = 30/55 (54%), Gaps = 2/55 (3%)

Query: 172 GTVPDKGSGIPFINSNPAVPLPTGEVDSATIRPLPTSGHVNQVEVGVLASQLLVL 226
           G VP +GS +PF+N       P   VD A I+ +P +G +  V+   + +++ V+
Sbjct: 13  GLVP-RGSHMPFVNKQFNYKDPVNGVDIAYIK-IPNAGQMQPVKAFKIHNKIWVI 65


>pdb|4EL4|A Chain A, Crystal Structure Of The Catalytic Domain Of Botulinum
           Neurotoxin BontA C134SC165S DOUBLE MUTANT
          Length = 445

 Score = 26.9 bits (58), Expect = 9.3,   Method: Compositional matrix adjust.
 Identities = 17/55 (30%), Positives = 30/55 (54%), Gaps = 2/55 (3%)

Query: 172 GTVPDKGSGIPFINSNPAVPLPTGEVDSATIRPLPTSGHVNQVEVGVLASQLLVL 226
           G VP +GS +PF+N       P   VD A I+ +P +G +  V+   + +++ V+
Sbjct: 13  GLVP-RGSHMPFVNKQFNYKDPVNGVDIAYIK-IPNAGQMQPVKAFKIHNKIWVI 65


>pdb|1L6N|A Chain A, Structure Of The N-Terminal 283-Residue Fragment Of The
           Hiv- 1 Gag Polyprotein
          Length = 289

 Score = 26.9 bits (58), Expect = 9.9,   Method: Compositional matrix adjust.
 Identities = 13/28 (46%), Positives = 14/28 (50%)

Query: 149 WPFRPHEKAFSPTPAPMIAATSPGTVPD 176
           W     EKAFSP   PM +A S G  P 
Sbjct: 155 WVKVVEEKAFSPEVIPMFSALSEGATPQ 182


  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
   0.318    0.133    0.405 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,251,777
Number of Sequences: 62578
Number of extensions: 238694
Number of successful extensions: 511
Number of sequences better than 100.0: 31
Number of HSP's better than 100.0 without gapping: 27
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 484
Number of HSP's gapped (non-prelim): 31
length of query: 235
length of database: 14,973,337
effective HSP length: 96
effective length of query: 139
effective length of database: 8,965,849
effective search space: 1246253011
effective search space used: 1246253011
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)