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= psy460
         (117 letters)

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

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



>pdb|3P96|A Chain A, Crystal Structure Of Phosphoserine Phosphatase Serb From
           Mycobacterium Avium, Native Form
          Length = 415

 Score = 26.6 bits (57), Expect = 3.9,   Method: Composition-based stats.
 Identities = 13/36 (36%), Positives = 23/36 (63%), Gaps = 5/36 (13%)

Query: 55  LELRLQI-----EALTSQLDKISAEQQTAVPLDSYT 85
           LELR+ +     EAL + L+++S+E+   V ++ YT
Sbjct: 144 LELRVSVPPGADEALRTALNRVSSEEHVDVAVEDYT 179


>pdb|2PFS|A Chain A, Crystal Structure Of Universal Stress Protein From
           Nitrosomonas Europaea
          Length = 150

 Score = 25.8 bits (55), Expect = 6.7,   Method: Compositional matrix adjust.
 Identities = 20/68 (29%), Positives = 30/68 (44%), Gaps = 5/68 (7%)

Query: 52  ASQLELRLQIEALTSQLDKISAEQQTAVPLD---SYTRKLVDAQQKISIVGNILQTTQVA 108
           ASQ+  RL +  +   +        TA+PLD   +Y   L   +QK+S +GN L      
Sbjct: 30  ASQIGARLSLIHVLDNIPXPDTPYGTAIPLDTETTYDAXLDVEKQKLSQIGNTLGID--P 87

Query: 109 MHKKFFMG 116
            H+    G
Sbjct: 88  AHRWLVWG 95


>pdb|3TNJ|A Chain A, Crystal Structure Of Universal Stress Protein From
           Nitrosomonas Europaea With Amp Bound
          Length = 150

 Score = 25.4 bits (54), Expect = 9.3,   Method: Compositional matrix adjust.
 Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 3/54 (5%)

Query: 52  ASQLELRLQIEALTSQLDKISAEQQTAVPLD---SYTRKLVDAQQKISIVGNIL 102
           ASQ+  RL +  +   +        TA+PLD   +Y   L   +QK+S +GN L
Sbjct: 30  ASQIGARLSLIHVLDNIPMPDTPYGTAIPLDTETTYDAMLDVEKQKLSQIGNTL 83


>pdb|2LB5|A Chain A, Refined Structural Basis For The Photoconversion Of A
           Phytochrome To The Activated Far-Red Light-Absorbing
           Form
 pdb|2LB9|A Chain A, Refined Solution Structure Of A Cyanobacterial Phytochrome
           Gaf Domain In The Red Light-Absorbing Ground State
           (Corrected Pyrrole Ring Planarity)
          Length = 208

 Score = 25.4 bits (54), Expect = 9.5,   Method: Compositional matrix adjust.
 Identities = 18/60 (30%), Positives = 32/60 (53%), Gaps = 1/60 (1%)

Query: 32  LLGLIKPTVDLLDEKFRATRASQLELRLQIEALTSQLDKISAEQQTA-VPLDSYTRKLVD 90
           LLGL  P  D+ +E  R  R +Q+ + + +EA +  + +  +   +A VPL    ++ VD
Sbjct: 77  LLGLTFPAGDIPEEARRLFRLAQVRVIVDVEAQSRSISQPESWGLSARVPLGEPLQRPVD 136


>pdb|2K2N|A Chain A, Solution Structure Of A Cyanobacterial Phytochrome Gaf
           Domain In The Red Light-Absorbing Ground State
 pdb|2KLI|A Chain A, Structural Basis For The Photoconversion Of A Phytochrome
           To The Activated Far-Red Light-Absorbing Form
 pdb|2KOI|A Chain A, Refined Solution Structure Of A Cyanobacterial Phytochrome
           Gaf Domain In The Red Light-Absorbing Ground State
          Length = 172

 Score = 25.0 bits (53), Expect = 9.8,   Method: Compositional matrix adjust.
 Identities = 18/60 (30%), Positives = 32/60 (53%), Gaps = 1/60 (1%)

Query: 32  LLGLIKPTVDLLDEKFRATRASQLELRLQIEALTSQLDKISAEQQTA-VPLDSYTRKLVD 90
           LLGL  P  D+ +E  R  R +Q+ + + +EA +  + +  +   +A VPL    ++ VD
Sbjct: 47  LLGLTFPAGDIPEEARRLFRLAQVRVIVDVEAQSRSISQPESWGLSARVPLGEPLQRPVD 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
   0.313    0.128    0.339 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,792,193
Number of Sequences: 62578
Number of extensions: 88361
Number of successful extensions: 121
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 120
Number of HSP's gapped (non-prelim): 13
length of query: 117
length of database: 14,973,337
effective HSP length: 80
effective length of query: 37
effective length of database: 9,967,097
effective search space: 368782589
effective search space used: 368782589
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 45 (21.9 bits)