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= psy1736
         (125 letters)

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

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



>pdb|2BTV|A Chain A, Atomic Model For Bluetongue Virus (Btv) Core
 pdb|2BTV|B Chain B, Atomic Model For Bluetongue Virus (Btv) Core
          Length = 901

 Score = 28.1 bits (61), Expect = 1.2,   Method: Composition-based stats.
 Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 9/74 (12%)

Query: 27  GVYCYGLFLDGARWDRTSNQLAEQFPKVLNDALPIIW-------FVPT-KKVELQIG-SR 77
           GV  + LF  G R+   +  +A Q    LND L  ++       + PT + ++ QIG ++
Sbjct: 374 GVVGHLLFTAGGRFTNLTQNMARQLDIALNDYLLYMYNTRVQVNYGPTGEPLDFQIGRNQ 433

Query: 78  YVCPLYKTSERRGT 91
           Y C +++     GT
Sbjct: 434 YDCNVFRADFATGT 447


>pdb|3TGR|A Chain A, Crystal Structure Of Unliganded Hiv-1 Clade C Strain C1086
           Gp120 Core
 pdb|3TGR|B Chain B, Crystal Structure Of Unliganded Hiv-1 Clade C Strain C1086
           Gp120 Core
 pdb|3TGS|A Chain A, Crystal Structure Of Hiv-1 Clade C Strain C1086 Gp120 Core
           In Complex With Nbd-556
 pdb|3TGS|B Chain B, Crystal Structure Of Hiv-1 Clade C Strain C1086 Gp120 Core
           In Complex With Nbd-556
          Length = 358

 Score = 26.9 bits (58), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 13/82 (15%)

Query: 35  LDGARWDRTSNQLAEQFPKVLNDALPIIWFVPTKKVELQI--------GSRYVC---PLY 83
           ++ ++W+ T  ++ E+  K        I F P+   +L+I        G  + C    L+
Sbjct: 201 INESKWNNTLQKVGEELAKHF--PSKTIKFEPSSGGDLEITTHSFNCRGEFFYCNTSDLF 258

Query: 84  KTSERRGTLSTTGHSTNYVIPL 105
             + R GT + TG S+N  I L
Sbjct: 259 NGTYRNGTYNHTGRSSNGTITL 280


>pdb|1WRU|A Chain A, Structure Of Central Hub Elucidated By X-Ray Analysis Of
          Gene Product 44; Baseplate Component Of Bacteriophage
          Mu
          Length = 379

 Score = 26.9 bits (58), Expect = 2.9,   Method: Composition-based stats.
 Identities = 12/26 (46%), Positives = 14/26 (53%)

Query: 64 FVPTKKVELQIGSRYVCPLYKTSERR 89
            P KK  L+IG + VC  Y  S RR
Sbjct: 48 LAPGKKFTLEIGGQIVCTGYIDSRRR 73


>pdb|3RJQ|A Chain A, Crystal Structure Of Anti-Hiv Llama Vhh Antibody A12 In
           Complex With C186 Gp120
          Length = 382

 Score = 26.9 bits (58), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 13/82 (15%)

Query: 35  LDGARWDRTSNQLAEQFPKVLNDALPIIWFVPTKKVELQI--------GSRYVC---PLY 83
           ++ ++W+ T  ++ E+  K        I F P+   +L+I        G  + C    L+
Sbjct: 225 INESKWNNTLQKVGEELAKHFPSK--TIKFEPSSGGDLEITTHSFNCRGEFFYCNTSDLF 282

Query: 84  KTSERRGTLSTTGHSTNYVIPL 105
             + R GT + TG S+N  I L
Sbjct: 283 NGTYRNGTYNHTGRSSNGTITL 304


>pdb|1OZ7|A Chain A, Crystal Structure Of Echicetin From The Venom Of Indian
          Saw- Scaled Viper (Echis Carinatus) At 2.4 Resolution
          Length = 131

 Score = 25.8 bits (55), Expect = 6.6,   Method: Compositional matrix adjust.
 Identities = 10/25 (40%), Positives = 13/25 (52%)

Query: 26 DGVYCYGLFLDGARWDRTSNQLAEQ 50
          +GVYCY LF +   WD       +Q
Sbjct: 9  NGVYCYMLFKEPKTWDEAEKFCNKQ 33


  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
   0.320    0.138    0.438 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,953,293
Number of Sequences: 62578
Number of extensions: 149383
Number of successful extensions: 289
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 286
Number of HSP's gapped (non-prelim): 6
length of query: 125
length of database: 14,973,337
effective HSP length: 86
effective length of query: 39
effective length of database: 9,591,629
effective search space: 374073531
effective search space used: 374073531
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)