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= psy16329
         (215 letters)

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

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



>pdb|1WWY|A Chain A, Solution Structure Of The Duf1000 Domain Of A
           Thioredoxin-Li 1
          Length = 171

 Score = 51.6 bits (122), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 37/105 (35%), Positives = 55/105 (52%), Gaps = 10/105 (9%)

Query: 104 LYKHIDTENVECLNETVDGSGKTIFKPWEDRLNKEK-FVESDVDSELLINIPFTSNIKLK 162
           L   I+    ECLNE+ D  G      +++ L K+  F+ESD D +LLI + F   +KL 
Sbjct: 12  LMPFINKAGCECLNES-DEHG------FDNCLRKDTTFLESDCDEQLLITVAFNQPVKLY 64

Query: 163 GLRLIGGDSDSHPNRIKLFKNRP-GMTFDDVNAS-PDQEFELNQD 205
            ++  G D+   P  +K+F N P  M F++   S P Q  EL +D
Sbjct: 65  SMKFQGPDNGQGPKYVKIFINLPRSMDFEEAERSEPTQALELTED 109


>pdb|1XOY|A Chain A, Solution Structure Of At3g04780.1, An Arabidopsis Ortholog
           Of The C-Terminal Domain Of Human Thioredoxin-Like
           Protein
          Length = 161

 Score = 50.4 bits (119), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 37/99 (37%), Positives = 47/99 (47%), Gaps = 8/99 (8%)

Query: 101 QYSLYKHIDTENVECLNETVDGSGKTIFKPW---EDRLNKEKFVESDVDSELLINIPFTS 157
           Q  L   ID   VECLN++   S     K     ++ LN    +ESD D +LLI IPF  
Sbjct: 13  QVDLLDFIDWSGVECLNQSSSHSLPNALKQGYREDEGLN----LESDADEQLLIYIPFNQ 68

Query: 158 NIKLKGLRLIGGDSDSHPNRIKLFKNRPGMTFDDVNASP 196
            IKL     I G  +  P  +K F N+  M F +VN  P
Sbjct: 69  VIKLHSFA-IKGPEEEGPKTVKFFSNKEHMCFSNVNDFP 106


>pdb|1RM8|A Chain A, Crystal Structure Of The Catalytic Domain Of Mmp-16MT3-
           Mmp: Characterization Of Mt-Mmp Specific Features
          Length = 169

 Score = 30.8 bits (68), Expect = 0.53,   Method: Compositional matrix adjust.
 Identities = 32/114 (28%), Positives = 51/114 (44%), Gaps = 18/114 (15%)

Query: 31  DNTCLYYLGFRGESSPLHRHGVTICN-YETTPSL-ADHKVDNMNSFPVMAHNHG------ 82
           D T ++  GF G+SSP    G  + + Y   P +  D   D+   + +   NH       
Sbjct: 60  DITIIFASGFHGDSSPFDGEGGFLAHAYFPGPGIGGDTHFDSDEPWTLGNPNHDGNDLFL 119

Query: 83  ------GHCCGEEDHSHDDTELGIQYSLYKHIDTENVECLNETVDGSGKTIFKP 130
                 GH  G E HS+D T   I    Y++++T+N +  N+ + G  K I+ P
Sbjct: 120 VAVHELGHALGLE-HSNDPT--AIMAPFYQYMETDNFKLPNDDLQGIQK-IYGP 169


>pdb|4E4Y|A Chain A, The Crystal Structure Of A Short Chain Dehydrogenase
           Family Protein From Francisella Tularensis Subsp.
           Tularensis Schu S4
          Length = 244

 Score = 30.4 bits (67), Expect = 0.83,   Method: Compositional matrix adjust.
 Identities = 12/35 (34%), Positives = 22/35 (62%)

Query: 170 DSDSHPNRIKLFKNRPGMTFDDVNASPDQEFELNQ 204
           D+D + N I+ + N  G++FD+     ++EF LN+
Sbjct: 174 DTDLYRNLIQKYANNVGISFDEAQKQEEKEFPLNR 208


>pdb|3F40|A Chain A, Crystal Structure Of Ntf2-Like Protein Of Unknown Function
           (Yp_677363.1) From Cytophaga Hutchinsonii Atcc 33406 At
           1.27 A Resolution
          Length = 114

 Score = 26.9 bits (58), Expect = 8.4,   Method: Compositional matrix adjust.
 Identities = 14/45 (31%), Positives = 24/45 (53%)

Query: 83  GHCCGEEDHSHDDTELGIQYSLYKHIDTENVECLNETVDGSGKTI 127
           GH  G E + +D  +   +Y ++K  +  N  CL   ++ +GKTI
Sbjct: 42  GHREGSERYXNDXEKXKFKYVVHKXFEEGNDVCLIYDINXNGKTI 86


  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
   0.319    0.138    0.427 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,198,559
Number of Sequences: 62578
Number of extensions: 310052
Number of successful extensions: 635
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 629
Number of HSP's gapped (non-prelim): 6
length of query: 215
length of database: 14,973,337
effective HSP length: 95
effective length of query: 120
effective length of database: 9,028,427
effective search space: 1083411240
effective search space used: 1083411240
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)