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= 040100
         (177 letters)

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

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



>pdb|3NLC|A Chain A, Crystal Structure Of The Vp0956 Protein From Vibrio
           Parahaemolyticus. Northeast Structural Genomics
           Consortium Target Vpr147
          Length = 549

 Score = 30.0 bits (66), Expect = 0.73,   Method: Composition-based stats.
 Identities = 16/40 (40%), Positives = 22/40 (55%), Gaps = 3/40 (7%)

Query: 41  SEEFDYPGCPIAVIAYQKRMNRASYV---PNFIPLKQKIG 77
           S E DYPG P+A I +Q+ +   +Y     N+    QKIG
Sbjct: 385 SPEVDYPGDPLAGIRFQRELESNAYKLGGENYDAPAQKIG 424


>pdb|2PPY|A Chain A, Crystal Structure Of Enoyl-Coa Hydrates (Gk_1992) From
           Geobacillus Kaustophilus Hta426
 pdb|2PPY|B Chain B, Crystal Structure Of Enoyl-Coa Hydrates (Gk_1992) From
           Geobacillus Kaustophilus Hta426
 pdb|2PPY|C Chain C, Crystal Structure Of Enoyl-Coa Hydrates (Gk_1992) From
           Geobacillus Kaustophilus Hta426
 pdb|2PPY|D Chain D, Crystal Structure Of Enoyl-Coa Hydrates (Gk_1992) From
           Geobacillus Kaustophilus Hta426
 pdb|2PPY|E Chain E, Crystal Structure Of Enoyl-Coa Hydrates (Gk_1992) From
           Geobacillus Kaustophilus Hta426
 pdb|2PPY|F Chain F, Crystal Structure Of Enoyl-Coa Hydrates (Gk_1992) From
           Geobacillus Kaustophilus Hta426
          Length = 265

 Score = 29.6 bits (65), Expect = 0.86,   Method: Compositional matrix adjust.
 Identities = 25/92 (27%), Positives = 40/92 (43%), Gaps = 14/92 (15%)

Query: 86  FSPAKDINISGQTAHPSEESELQAVAEFLESDIAAPGFQEYEMSLRLMQMGAAVRNSSSY 145
           +S A D NI+G+T  P E  E+  V            F + E   R  +    + NS++Y
Sbjct: 160 YSRALDXNITGETITPQEALEIGLVNRV---------FPQAETRERTREYARKLANSATY 210

Query: 146 ----LRMKLNPDKMLPSNVLGAMSTGQLSNLM 173
               +++ +   K  P NV      G+L NL+
Sbjct: 211 AVSNIKLAIXNGKEXPLNV-AIRYEGELQNLL 241


>pdb|3DTE|A Chain A, Crystal Structure Of The Irre Protein, A Central Regulator
           Of Dna Damage Repair In Deinococcaceae
          Length = 301

 Score = 27.3 bits (59), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 5/46 (10%)

Query: 1   MAFAPDGLIEGFYDPEAYNPREGKFLVGLQFHSERMRLSSSEEFDY 46
           + F P G  +G YDPE +       L+  Q   ER R + + E  +
Sbjct: 66  LTFXPXGQRDGAYDPEHH-----VILINSQVRPERQRFTLAHEISH 106


  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
   0.317    0.132    0.377 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,184,918
Number of Sequences: 62578
Number of extensions: 193795
Number of successful extensions: 349
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 347
Number of HSP's gapped (non-prelim): 4
length of query: 177
length of database: 14,973,337
effective HSP length: 92
effective length of query: 85
effective length of database: 9,216,161
effective search space: 783373685
effective search space used: 783373685
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: 48 (23.1 bits)