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= psy5112
         (184 letters)

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

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



>pdb|3KF9|A Chain A, Crystal Structure Of The SdcenSKMLCK COMPLEX
 pdb|3KF9|C Chain C, Crystal Structure Of The SdcenSKMLCK COMPLEX
          Length = 149

 Score = 30.8 bits (68), Expect = 0.51,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 24/42 (57%), Gaps = 5/42 (11%)

Query: 35 DGSTTI--EEFLQTLNSEIDCRDSN---VSGFALFSDDPIDK 71
          DGS TI  EEFLQ + +++  RDS    +  F LF DD   K
Sbjct: 56 DGSGTIDFEEFLQMMTAKMGERDSREEIMKAFRLFDDDETGK 97


>pdb|4FP4|A Chain A, Crystal Structure Of Isoprenoid Synthase A3mx09 (Target
           Efi-501993) From Pyrobaculum Calidifontis
 pdb|4FP4|B Chain B, Crystal Structure Of Isoprenoid Synthase A3mx09 (Target
           Efi-501993) From Pyrobaculum Calidifontis
          Length = 285

 Score = 29.6 bits (65), Expect = 0.99,   Method: Compositional matrix adjust.
 Identities = 22/72 (30%), Positives = 34/72 (47%), Gaps = 4/72 (5%)

Query: 64  FSDDPIDKNLEHYLEPELK-VSQTKGKYPLKIYVMLCDVISKWETALREKGTGKFENNRC 122
           +SDD  D+N+E    PE K ++   G+Y LKI   + D I+ +E  ++       E    
Sbjct: 202 YSDDYSDENVER---PETKSIANEIGRYLLKIKEHVGDAIAPFERLIKYLIGKALEGTLT 258

Query: 123 VQFIYKNRLYFR 134
           V       LYF+
Sbjct: 259 VSRTIAENLYFQ 270


>pdb|1I7O|A Chain A, Crystal Structure Of Hpce
 pdb|1I7O|B Chain B, Crystal Structure Of Hpce
 pdb|1I7O|C Chain C, Crystal Structure Of Hpce
 pdb|1I7O|D Chain D, Crystal Structure Of Hpce
 pdb|1GTT|A Chain A, Crystal Structure Of Hpce
 pdb|1GTT|B Chain B, Crystal Structure Of Hpce
 pdb|1GTT|C Chain C, Crystal Structure Of Hpce
 pdb|1GTT|D Chain D, Crystal Structure Of Hpce
          Length = 429

 Score = 28.1 bits (61), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 19/56 (33%), Positives = 27/56 (48%), Gaps = 6/56 (10%)

Query: 49  SEIDCRDSNVSGFALFSDDPIDKNLEHYLEPELKVSQTKGKYPLKIYVMLCDVISK 104
           SE D  D  V+G+ + +D  I   LE+Y  P L+V    G  P     ML  ++ K
Sbjct: 291 SEADAMDY-VAGYTVCNDYAIRDYLENYYRPNLRVKSRDGLTP-----MLSTIVPK 340


>pdb|1XJ5|A Chain A, X-Ray Structure Of Spermidine Synthase From Arabidopsis
           Thaliana Gene At1g23820
 pdb|1XJ5|B Chain B, X-Ray Structure Of Spermidine Synthase From Arabidopsis
           Thaliana Gene At1g23820
 pdb|1XJ5|C Chain C, X-Ray Structure Of Spermidine Synthase From Arabidopsis
           Thaliana Gene At1g23820
 pdb|1XJ5|D Chain D, X-Ray Structure Of Spermidine Synthase From Arabidopsis
           Thaliana Gene At1g23820
 pdb|2Q41|A Chain A, Ensemble Refinement Of The Protein Crystal Structure Of
           Spermidine Synthase From Arabidopsis Thaliana Gene
           At1g23820
 pdb|2Q41|D Chain D, Ensemble Refinement Of The Protein Crystal Structure Of
           Spermidine Synthase From Arabidopsis Thaliana Gene
           At1g23820
 pdb|2Q41|B Chain B, Ensemble Refinement Of The Protein Crystal Structure Of
           Spermidine Synthase From Arabidopsis Thaliana Gene
           At1g23820
 pdb|2Q41|C Chain C, Ensemble Refinement Of The Protein Crystal Structure Of
           Spermidine Synthase From Arabidopsis Thaliana Gene
           At1g23820
          Length = 334

 Score = 26.6 bits (57), Expect = 9.4,   Method: Compositional matrix adjust.
 Identities = 16/40 (40%), Positives = 21/40 (52%), Gaps = 1/40 (2%)

Query: 56  SNVSGFALFSDDPIDKNLEHYLEPELKVSQTKGKYPLKIY 95
           S V GF L S +  D + +H L P +  S +K   PLK Y
Sbjct: 272 SGVIGFXLCSTEGPDVDFKHPLNP-IDESSSKSNGPLKFY 310


  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    0.137    0.409 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,283,638
Number of Sequences: 62578
Number of extensions: 208828
Number of successful extensions: 478
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 475
Number of HSP's gapped (non-prelim): 12
length of query: 184
length of database: 14,973,337
effective HSP length: 93
effective length of query: 91
effective length of database: 9,153,583
effective search space: 832976053
effective search space used: 832976053
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: 48 (23.1 bits)