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= psy1701
         (270 letters)

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

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



>pdb|3BRZ|A Chain A, Crystal Structure Of The Pseudomonas Putida Toluene
           Transporter Todx
 pdb|3BS0|A Chain A, Crystal Structure Of The P. Putida Toluene Transporter
           Todx
 pdb|3BS0|B Chain B, Crystal Structure Of The P. Putida Toluene Transporter
           Todx
          Length = 439

 Score = 32.3 bits (72), Expect = 0.27,   Method: Compositional matrix adjust.
 Identities = 25/103 (24%), Positives = 43/103 (41%), Gaps = 11/103 (10%)

Query: 112 KYGEDTKGSITLNLPKDPFSESIKILV-----ALSILFTYGLQFGVPSEIVWERIKHRVP 166
           +YG  +  S T N  +  F  S +++V       S   T  L FG   ++VW  +   + 
Sbjct: 108 EYGSKSFLSQTENGIQTSFDNSSRLIVLRAPIGFSYQATSKLTFGASVDLVWTSLNLELL 167

Query: 167 IPRHNMGYYIMRGLMIIGTVLVAAIIPNLGPIISLVGAICFSM 209
           +P   +G    +G       L   ++P+L   +   GA  FS+
Sbjct: 168 LPSSQVGALTAQG------NLSGGLVPSLAGFVGTGGAAHFSL 204


>pdb|4DDO|A Chain A, Crystal Structure Of 3-Oxoacyl-[acyl-Carrier-Protein]
           Synthase Ii From Burkholderia Vietnamiensis
          Length = 451

 Score = 27.7 bits (60), Expect = 7.6,   Method: Compositional matrix adjust.
 Identities = 31/143 (21%), Positives = 61/143 (42%), Gaps = 9/143 (6%)

Query: 21  DNHSGHFMYLLCTYAVTDLPDTSTRHNVAPFTQFPLFFSTVLFAME---GIGTVLPIENS 77
           D+ SG    +     + D+      +  A  T  P+  +  + A++   G+G    I ++
Sbjct: 305 DDGSGAMRAMKLALRMGDVAPEQVDYVNAHATSTPVGDAGEIEALKTVFGVGAGPAISST 364

Query: 78  MKKPGHFLGKFGVLNIAMAVVISFYGMVGYCGYLKYGEDTKGSITLNLPKDPFSESIKIL 137
               GH LG  G +  A +++    G++   G L        +  L+L   P +  + + 
Sbjct: 365 KSATGHLLGAAGAIEAAFSILALRDGVL--PGTLNLEHPDPAADGLDL-IGPAARHVPVE 421

Query: 138 VALSILFTYGLQFGVPSEIVWER 160
           +ALS  F +G   GV + +++ R
Sbjct: 422 IALSNGFGFG---GVNASVLFRR 441


>pdb|4F32|A Chain A, Crystal Structure Of 3-Oxoacyl-[acyl-Carrier-Protein]
           Synthase Ii From Burkholderia Vietnamiensis In Complex
           With Platencin
 pdb|4F32|B Chain B, Crystal Structure Of 3-Oxoacyl-[acyl-Carrier-Protein]
           Synthase Ii From Burkholderia Vietnamiensis In Complex
           With Platencin
          Length = 451

 Score = 27.3 bits (59), Expect = 8.0,   Method: Compositional matrix adjust.
 Identities = 31/143 (21%), Positives = 61/143 (42%), Gaps = 9/143 (6%)

Query: 21  DNHSGHFMYLLCTYAVTDLPDTSTRHNVAPFTQFPLFFSTVLFAME---GIGTVLPIENS 77
           D+ SG    +     + D+      +  A  T  P+  +  + A++   G+G    I ++
Sbjct: 305 DDGSGAMRAMKLALRMGDVAPEQVDYVNAHATSTPVGDAGEIEALKTVFGVGAGPAISST 364

Query: 78  MKKPGHFLGKFGVLNIAMAVVISFYGMVGYCGYLKYGEDTKGSITLNLPKDPFSESIKIL 137
               GH LG  G +  A +++    G++   G L        +  L+L   P +  + + 
Sbjct: 365 KSATGHLLGAAGAIEAAFSILALRDGVL--PGTLNLEHPDPAADGLDL-IGPAARHVPVE 421

Query: 138 VALSILFTYGLQFGVPSEIVWER 160
           +ALS  F +G   GV + +++ R
Sbjct: 422 IALSNGFGFG---GVNASVLFRR 441


  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
   0.328    0.144    0.453 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,816,963
Number of Sequences: 62578
Number of extensions: 303424
Number of successful extensions: 623
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 623
Number of HSP's gapped (non-prelim): 3
length of query: 270
length of database: 14,973,337
effective HSP length: 97
effective length of query: 173
effective length of database: 8,903,271
effective search space: 1540265883
effective search space used: 1540265883
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: 51 (24.3 bits)