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= psy16666
         (167 letters)

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

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



>pdb|3S4U|A Chain A, Crystal Structure Of Open, Unliganded E. Coli Phnd H157a
          Length = 321

 Score = 33.9 bits (76), Expect = 0.042,   Method: Compositional matrix adjust.
 Identities = 13/35 (37%), Positives = 21/35 (60%)

Query: 129 TEEHERSLAYGLVSSETNQYSSPSLTPFYYYCNNK 163
           +EE E++L +G++S+E+ Q   P  TPF      K
Sbjct: 9   SEEQEKALNFGIISTESQQNLKPQWTPFLQDMEKK 43


>pdb|3P7I|A Chain A, Crystal Structure Of Escherichia Coli Phnd In Complex With
           2- Aminoethyl Phosphonate
          Length = 321

 Score = 33.9 bits (76), Expect = 0.043,   Method: Compositional matrix adjust.
 Identities = 13/35 (37%), Positives = 21/35 (60%)

Query: 129 TEEHERSLAYGLVSSETNQYSSPSLTPFYYYCNNK 163
           +EE E++L +G++S+E+ Q   P  TPF      K
Sbjct: 9   SEEQEKALNFGIISTESQQNLKPQWTPFLQDMEKK 43


>pdb|3QK6|A Chain A, Crystal Structure Of Escherichia Coli Phnd
 pdb|3QK6|B Chain B, Crystal Structure Of Escherichia Coli Phnd
 pdb|3QUJ|A Chain A, Crystal Structure Of The Phosphonate Binding Protein,
           Phnd, From Escherichia Coli
 pdb|3QUJ|B Chain B, Crystal Structure Of The Phosphonate Binding Protein,
           Phnd, From Escherichia Coli
 pdb|3QUJ|C Chain C, Crystal Structure Of The Phosphonate Binding Protein,
           Phnd, From Escherichia Coli
 pdb|3QUJ|D Chain D, Crystal Structure Of The Phosphonate Binding Protein,
           Phnd, From Escherichia Coli
          Length = 321

 Score = 33.5 bits (75), Expect = 0.055,   Method: Compositional matrix adjust.
 Identities = 13/35 (37%), Positives = 21/35 (60%)

Query: 129 TEEHERSLAYGLVSSETNQYSSPSLTPFYYYCNNK 163
           +EE E++L +G++S+E+ Q   P  TPF      K
Sbjct: 9   SEEQEKALNFGIISTESQQNLKPQWTPFLQDXEKK 43


>pdb|2CZL|A Chain A, Crystal Structure Of Mqnd (Ttha1568), A Menaquinone
           Biosynthetic Enzyme From Thermus Thermophilus Hb8 (Cys11
           Modified With Beta- Mercaptoethanol)
          Length = 272

 Score = 28.5 bits (62), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 20/68 (29%), Positives = 31/68 (45%), Gaps = 1/68 (1%)

Query: 91  CLPIPLMTLDTWWFFAM-ISISGVFAVTFSVVFAYVADVTEEHERSLAYGLVSSETNQYS 149
            L  P   LD     A  +S   ++A   + V A+  DV EE ER++A     +E    +
Sbjct: 204 ALAHPEEALDYMRAHAQELSDEVIWAHVHTYVNAFSLDVGEEGERAVARLFAEAEARGLA 263

Query: 150 SPSLTPFY 157
           +PS  P +
Sbjct: 264 APSPRPLF 271


>pdb|3A3U|A Chain A, Crystal Structure Of Mqnd (Ttha1568), A Menaquinone
           Biosynthetic Enzyme From Thermus Thermophilus Hb8
          Length = 272

 Score = 28.5 bits (62), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 20/68 (29%), Positives = 31/68 (45%), Gaps = 1/68 (1%)

Query: 91  CLPIPLMTLDTWWFFAM-ISISGVFAVTFSVVFAYVADVTEEHERSLAYGLVSSETNQYS 149
            L  P   LD     A  +S   ++A   + V A+  DV EE ER++A     +E    +
Sbjct: 204 ALAHPEEALDYMRAHAQELSDEVIWAHVHTYVNAFSLDVGEEGERAVARLFAEAEARGLA 263

Query: 150 SPSLTPFY 157
           +PS  P +
Sbjct: 264 APSPRPLF 271


>pdb|2RMR|A Chain A, Solution Structure Of Msin3a Pah1 Domain
 pdb|2RMS|A Chain A, Solution Structure Of The Msin3a Pah1-Sap25 Sid Complex
          Length = 71

 Score = 27.7 bits (60), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 4/51 (7%)

Query: 12 EPSVYHALVVIFLEFFAWGLLTMPIISVLNRTFPDHTFLMNGLIMGIKGFL 62
          +P VY+  + I  EF +  + T  +IS +++ F  H      LIMG   FL
Sbjct: 22 QPQVYNDFLDIMKEFKSQSIDTPGVISRVSQLFKGHP----DLIMGFNTFL 68


  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
   0.327    0.141    0.445 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,735,308
Number of Sequences: 62578
Number of extensions: 170326
Number of successful extensions: 441
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 436
Number of HSP's gapped (non-prelim): 6
length of query: 167
length of database: 14,973,337
effective HSP length: 92
effective length of query: 75
effective length of database: 9,216,161
effective search space: 691212075
effective search space used: 691212075
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: 48 (23.1 bits)