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= psy5943
         (133 letters)

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

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



>pdb|3VQJ|A Chain A, Crystal Structutre Of Thiobacillus Thioparus Thi115
           Carbonyl Sulfide Hydrolase
 pdb|3VRK|A Chain A, Crystal Structutre Of Thiobacillus Thioparus Thi115
           Carbonyl Sulfide Hydrolase / Thiocyanate Complex
          Length = 219

 Score = 28.9 bits (63), Expect = 0.86,   Method: Compositional matrix adjust.
 Identities = 10/20 (50%), Positives = 16/20 (80%)

Query: 99  VAKNSGGVMNETELGCLILS 118
           + +N+GGV+NE  + CLI+S
Sbjct: 64  IIRNAGGVINEDAIRCLIIS 83


>pdb|2VPW|A Chain A, Polysulfide Reductase With Bound Menaquinone
 pdb|2VPW|E Chain E, Polysulfide Reductase With Bound Menaquinone
 pdb|2VPX|A Chain A, Polysulfide Reductase With Bound Quinone (uq1)
 pdb|2VPX|E Chain E, Polysulfide Reductase With Bound Quinone (uq1)
 pdb|2VPY|A Chain A, Polysulfide Reductase With Bound Quinone Inhibitor,
           Pentachlorophenol (Pcp)
 pdb|2VPY|E Chain E, Polysulfide Reductase With Bound Quinone Inhibitor,
           Pentachlorophenol (Pcp)
 pdb|2VPZ|A Chain A, Polysulfide Reductase Native Structure
 pdb|2VPZ|E Chain E, Polysulfide Reductase Native Structure
          Length = 765

 Score = 26.6 bits (57), Expect = 4.8,   Method: Composition-based stats.
 Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 3/68 (4%)

Query: 34  SGPGLEDEEKEWYYGTSEQSKGPVTFHQIKHLWS---TGELNPKTKVWAHGMESWKSLHQ 90
           SGP   D E E +   +++ K       I+ L     TGE  P   ++A+G+  + S+  
Sbjct: 389 SGPSGGDHEPEGFKPRADKGKFFARSTAIQELIEPMITGEPYPIKGLFAYGINLFHSIPN 448

Query: 91  VPQLKWTL 98
           VP+ K  L
Sbjct: 449 VPRTKEAL 456


>pdb|1W78|A Chain A, E.Coli Folc In Complex With Dhpp And Adp
 pdb|1W7K|A Chain A, E.Coli Folc In Complex With Adp, Without Folate Substrate
          Length = 422

 Score = 26.2 bits (56), Expect = 5.8,   Method: Composition-based stats.
 Identities = 19/83 (22%), Positives = 31/83 (37%), Gaps = 9/83 (10%)

Query: 32  AGSGPGLEDEEKEWYYGTSEQSKGPVTFHQIKHLWSTGELNPKTKVWAHGMESWK----- 86
           AG+   L+    +WY    E  +G      ++HL +    +   + W   M   K     
Sbjct: 339 AGTLAWLKSVVDDWYCAPLEGPRGATAEQLLEHLGNGKSFDSVAQAWDAAMADAKAEDTV 398

Query: 87  ----SLHQVPQLKWTLVAKNSGG 105
               S H V  +   + A+ SGG
Sbjct: 399 LVCGSFHTVAHVMEVIDARRSGG 421


>pdb|2XQV|A Chain A, The X-Ray Structure Of The Zn(Ii) Bound Znua From
           Salmonella Enterica
 pdb|2XY4|A Chain A, X-Ray Structure Of Znua-Wt From Salmonella Enterica
          Length = 288

 Score = 25.8 bits (55), Expect = 7.1,   Method: Compositional matrix adjust.
 Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 7/67 (10%)

Query: 37  GLEDEEKEWYYGTSEQSKGPVTFHQIK---HLWSTGELNPKTKVWAHGMESWKSLHQVPQ 93
           G +D+E E  +  +++ KG V  H  +   HLW + E+   T V  H     K +  +PQ
Sbjct: 91  GADDDEDEHAHTGADEEKGDVHHHHGEYNMHLWLSPEIARATAVAIH----EKLVELMPQ 146

Query: 94  LKWTLVA 100
            +  L A
Sbjct: 147 SRAKLDA 153


>pdb|3VUS|A Chain A, Escherichia Coli Pgab N-terminal Domain
 pdb|3VUS|B Chain B, Escherichia Coli Pgab N-terminal Domain
          Length = 268

 Score = 25.4 bits (54), Expect = 9.6,   Method: Compositional matrix adjust.
 Identities = 14/72 (19%), Positives = 35/72 (48%), Gaps = 3/72 (4%)

Query: 47  YGTSEQSKGPVTFHQIK---HLWSTGELNPKTKVWAHGMESWKSLHQVPQLKWTLVAKNS 103
           Y T+ + +  +    +K   +L +  E+NP   VW +G  +  ++ ++ +L + +     
Sbjct: 175 YETAAEYRERIRLDAVKMTEYLRTKVEVNPHVFVWPYGEANGIAIEELKKLGYDMFFTLE 234

Query: 104 GGVMNETELGCL 115
            G+ N ++L  +
Sbjct: 235 SGLANASQLDSI 246


  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
   0.314    0.131    0.403 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,395,931
Number of Sequences: 62578
Number of extensions: 172779
Number of successful extensions: 248
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 244
Number of HSP's gapped (non-prelim): 12
length of query: 133
length of database: 14,973,337
effective HSP length: 88
effective length of query: 45
effective length of database: 9,466,473
effective search space: 425991285
effective search space used: 425991285
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 46 (22.3 bits)