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= 034037
         (105 letters)

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

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



>pdb|3SHR|A Chain A, Crystal Structure Of Cgmp-Dependent Protein Kinase Reveals
           Novel Site Of Interchain Communication
 pdb|3SHR|B Chain B, Crystal Structure Of Cgmp-Dependent Protein Kinase Reveals
           Novel Site Of Interchain Communication
          Length = 299

 Score = 28.1 bits (61), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 13/29 (44%), Positives = 16/29 (55%)

Query: 52  CKGKGFYICKLCKGNATIEWSPLYDPVFI 80
            +G  F+I    K N T E SP  DPVF+
Sbjct: 196 ARGDTFFIISKGKVNVTREDSPNEDPVFL 224


>pdb|1PY0|A Chain A, Crystal Structure Of E51cE54C PSAZ FROM A.FAECALIS WITH
          Clanp Probe
          Length = 125

 Score = 25.8 bits (55), Expect = 5.9,   Method: Compositional matrix adjust.
 Identities = 14/48 (29%), Positives = 22/48 (45%), Gaps = 1/48 (2%)

Query: 10 GATAAIIFG-GFVTLNVASTITLGALRAASEAKRKKFAMPCGVCKGKG 56
          GA  A++F   ++  N   T+T   +      +  K  +PCG CK K 
Sbjct: 13 GAEGAMVFEPAYIKANPGDTVTFIPVDKGHNVESIKDMIPCGACKFKS 60


>pdb|2YEW|C Chain C, Modeling Barmah Forest Virus Structural Proteins
 pdb|2YEW|F Chain F, Modeling Barmah Forest Virus Structural Proteins
 pdb|2YEW|I Chain I, Modeling Barmah Forest Virus Structural Proteins
 pdb|2YEW|L Chain L, Modeling Barmah Forest Virus Structural Proteins
          Length = 421

 Score = 25.4 bits (54), Expect = 7.8,   Method: Composition-based stats.
 Identities = 19/69 (27%), Positives = 30/69 (43%), Gaps = 7/69 (10%)

Query: 22  TLNVASTITLGALRAASEAKRKKFAM----PCGVCKGKGFYICKLCKGNATIEWSPLYDP 77
           T+N A    +GA     EA+R   ++    PC +    G +I   C+  + +E S   DP
Sbjct: 60  TINHAKIRYMGA-NGVQEAERSTLSVSTTAPCDILATMGHFILARCRPGSQVEVSLSTDP 118

Query: 78  VFINPCLCP 86
             +  C  P
Sbjct: 119 KLL--CRTP 125


>pdb|3U07|A Chain A, Crystal Structure Of The Vpa0106 Protein From Vibrio
           Parahaemolyticus. Northeast Structural Genomics
           Consortium Target Vpr106.
 pdb|3U07|B Chain B, Crystal Structure Of The Vpa0106 Protein From Vibrio
           Parahaemolyticus. Northeast Structural Genomics
           Consortium Target Vpr106.
 pdb|3U07|C Chain C, Crystal Structure Of The Vpa0106 Protein From Vibrio
           Parahaemolyticus. Northeast Structural Genomics
           Consortium Target Vpr106
          Length = 443

 Score = 25.4 bits (54), Expect = 7.9,   Method: Composition-based stats.
 Identities = 9/27 (33%), Positives = 13/27 (48%)

Query: 57  FYICKLCKGNATIEWSPLYDPVFINPC 83
           F +C    GNA  +W   Y  + + PC
Sbjct: 221 FVLCDGSXGNADKQWLDKYQSIGVEPC 247


  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
   0.328    0.143    0.477 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,018,154
Number of Sequences: 62578
Number of extensions: 107904
Number of successful extensions: 219
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 214
Number of HSP's gapped (non-prelim): 7
length of query: 105
length of database: 14,973,337
effective HSP length: 70
effective length of query: 35
effective length of database: 10,592,877
effective search space: 370750695
effective search space used: 370750695
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 45 (21.9 bits)