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= psy3671
         (266 letters)

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

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



>pdb|2F1E|A Chain A, Solution Structure Of Apag Protein
          Length = 127

 Score = 63.5 bits (153), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 34/90 (37%), Positives = 50/90 (55%), Gaps = 1/90 (1%)

Query: 177 VRVTVIPFYMGCRDSPTSSVYWWRYCIRLENLGELTVQLRERHWRIFSLSGTLETVRGRG 236
           V V V P ++  + +P    Y + Y IR++N G +  +L  RHW+I   +G  E V G G
Sbjct: 9   VEVEVSPRFLAHQSTPDEGRYAFAYSIRIQNAGAVPARLVARHWQITDGNGRTEQVDGEG 68

Query: 237 VVGQEPVLSKSLPAFQYSSHVSLQAPSGHM 266
           VVG++P L +   AF Y+S V L+   G M
Sbjct: 69  VVGEQPWL-RPGEAFHYTSGVLLETEQGQM 97


>pdb|1TZA|A Chain A, X-Ray Structure Of Northeast Structural Genomics
           Consortium Target Sor45
 pdb|1TZA|B Chain B, X-Ray Structure Of Northeast Structural Genomics
           Consortium Target Sor45
          Length = 134

 Score = 61.2 bits (147), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 33/89 (37%), Positives = 47/89 (52%), Gaps = 1/89 (1%)

Query: 176 NVRVTVIPFYMGCRDSPTSSVYWWRYCIRLENLGELTVQLRERHWRIFSLSGTLETVRGR 235
           ++RV V   Y+  + SP    Y + Y I + NLGE   +L  RHW I   +G    V+G 
Sbjct: 7   SIRVEVKTEYIEQQSSPEDEKYLFSYTITIINLGEQAAKLETRHWIITDANGKTSEVQGA 66

Query: 236 GVVGQEPVLSKSLPAFQYSSHVSLQAPSG 264
           GVVG+ P +  +  A+QY+S   L  P G
Sbjct: 67  GVVGETPTIPPNT-AYQYTSGTVLDTPFG 94


>pdb|1XQ4|A Chain A, Crystal Structure Of The Putative Apaa Protein From
           Bordetella Pertussis, Northeast Structural Genomics
           Target Ber40
 pdb|1XQ4|B Chain B, Crystal Structure Of The Putative Apaa Protein From
           Bordetella Pertussis, Northeast Structural Genomics
           Target Ber40
 pdb|1XQ4|C Chain C, Crystal Structure Of The Putative Apaa Protein From
           Bordetella Pertussis, Northeast Structural Genomics
           Target Ber40
 pdb|1XQ4|D Chain D, Crystal Structure Of The Putative Apaa Protein From
           Bordetella Pertussis, Northeast Structural Genomics
           Target Ber40
          Length = 139

 Score = 57.4 bits (137), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 31/89 (34%), Positives = 48/89 (53%), Gaps = 1/89 (1%)

Query: 176 NVRVTVIPFYMGCRDSPTSSVYWWRYCIRLENLGELTVQLRERHWRIFSLSGTLETVRGR 235
           ++ V+V P Y+  +  P+   Y + Y +R+ N G    Q+  RHW I      ++ VRG 
Sbjct: 12  DLTVSVTPRYVPEQSDPSQQQYVFAYTVRITNTGSHPAQVISRHWIITDGEERVQEVRGL 71

Query: 236 GVVGQEPVLSKSLPAFQYSSHVSLQAPSG 264
           GVVGQ+P+L+     F+Y+S   L  P G
Sbjct: 72  GVVGQQPLLAPGE-TFEYTSGCPLPTPIG 99


>pdb|1XVS|A Chain A, Crystal Structure Of Apag Protein From Vibrio Cholerae
 pdb|1XVS|B Chain B, Crystal Structure Of Apag Protein From Vibrio Cholerae
          Length = 126

 Score = 52.0 bits (123), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 29/88 (32%), Positives = 45/88 (51%), Gaps = 1/88 (1%)

Query: 177 VRVTVIPFYMGCRDSPTSSVYWWRYCIRLENLGELTVQLRERHWRIFSLSGTLETVRGRG 236
           +++ V   Y+  + +P    + + Y I ++NL   TVQL  R W I    G    V G G
Sbjct: 8   IKIQVQTRYIEEQSNPEYQRFVFAYLITIKNLSSQTVQLXSRRWLITDADGKQTVVEGDG 67

Query: 237 VVGQEPVLSKSLPAFQYSSHVSLQAPSG 264
           VVG++P + K+   + YSS  +L  P G
Sbjct: 68  VVGEQPRI-KANDEYTYSSGTALDTPVG 94


>pdb|1U7H|A Chain A, Structure And A Proposed Mechanism For Ornithine
           Cyclodeaminase From Pseudomonas Putida
 pdb|1U7H|B Chain B, Structure And A Proposed Mechanism For Ornithine
           Cyclodeaminase From Pseudomonas Putida
 pdb|1X7D|A Chain A, Crystal Structure Analysis Of Ornithine Cyclodeaminase
           Complexed With Nad And Ornithine To 1.6 Angstroms
 pdb|1X7D|B Chain B, Crystal Structure Analysis Of Ornithine Cyclodeaminase
           Complexed With Nad And Ornithine To 1.6 Angstroms
          Length = 350

 Score = 30.0 bits (66), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 2/48 (4%)

Query: 208 LGELTVQLRE--RHWRIFSLSGTLETVRGRGVVGQEPVLSKSLPAFQY 253
           +GEL   LR+  + W+ F  S  + +    GV+   PV  KS  AF+Y
Sbjct: 23  IGELAAALRDDFKRWQAFDKSARVASHSEVGVIELXPVADKSRYAFKY 70


  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
   0.321    0.137    0.432 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,406,289
Number of Sequences: 62578
Number of extensions: 346897
Number of successful extensions: 622
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 618
Number of HSP's gapped (non-prelim): 5
length of query: 266
length of database: 14,973,337
effective HSP length: 97
effective length of query: 169
effective length of database: 8,903,271
effective search space: 1504652799
effective search space used: 1504652799
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: 50 (23.9 bits)