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= psy16812
         (359 letters)

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

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



>pdb|1COY|A Chain A, Crystal Structure Of Cholesterol Oxidase Complexed With A
           Steroid Substrate. Implications For Fad Dependent
           Alcohol Oxidases
 pdb|3COX|A Chain A, Crystal Structure Of Cholesterol Oxidase Complexed With A
           Steroid Substrate. Implications For Fad Dependent
           Alcohol Oxidases
          Length = 507

 Score = 35.4 bits (80), Expect = 0.051,   Method: Compositional matrix adjust.
 Identities = 27/99 (27%), Positives = 39/99 (39%), Gaps = 14/99 (14%)

Query: 253 HGTFLINSVAHMW---GNKP-------YDKNINPTENLFVSVASFGDGWHNYHHVFPWDY 302
           +G  ++    HMW   G+K         D   +PT  +F  +A    G   Y  ++    
Sbjct: 321 NGNIMVGRANHMWDATGSKQATIPTMGIDNWADPTAPIFAEIAPLPAGLETYVSLYLAIT 380

Query: 303 KNAELWNYKFNISTAFVDLCALIGWAYDLKTVPTDMIQK 341
           KN E   ++FN  T  VDL     WA        DM +K
Sbjct: 381 KNPERARFQFNSGTGKVDLT----WAQSQNQKGIDMAKK 415



 Score = 33.5 bits (75), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 20/67 (29%), Positives = 28/67 (41%), Gaps = 4/67 (5%)

Query: 120 NPTENLFVSVASFGDGWHNYHHVFPWDYKNAELWNYKFNISTAFVDLCALIGWAYDLKTV 179
           +PT  +F  +A    G   Y  ++    KN E   ++FN  T  VDL     WA      
Sbjct: 353 DPTAPIFAEIAPLPAGLETYVSLYLAITKNPERARFQFNSGTGKVDLT----WAQSQNQK 408

Query: 180 PTDMIQK 186
             DM +K
Sbjct: 409 GIDMAKK 415


>pdb|1Z2W|A Chain A, Crystal Structure Of Mouse Vps29 Complexed With Mn2+
 pdb|1Z2W|B Chain B, Crystal Structure Of Mouse Vps29 Complexed With Mn2+
 pdb|1Z2X|A Chain A, Crystal Structure Of Mouse Vps29
 pdb|1Z2X|B Chain B, Crystal Structure Of Mouse Vps29
 pdb|3PSN|A Chain A, Crystal Structure Of Mouse Vps29 Complexed With Mn2+
 pdb|3PSN|B Chain B, Crystal Structure Of Mouse Vps29 Complexed With Mn2+
 pdb|3PSO|A Chain A, Crystal Structure Of Mouse Vps29 Complexed With Zn2+
 pdb|3PSO|B Chain B, Crystal Structure Of Mouse Vps29 Complexed With Zn2+
          Length = 192

 Score = 30.4 bits (67), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 15/46 (32%), Positives = 24/46 (52%), Gaps = 1/46 (2%)

Query: 270 YDKNINPTENLFVSVASFGDGWHNYHHVFPW-DYKNAELWNYKFNI 314
           +D+N+N  E   V+V  F  G  + H V PW D  +  L   +F++
Sbjct: 73  FDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDV 118


>pdb|1W24|A Chain A, Crystal Structure Of Human Vps29
          Length = 182

 Score = 30.4 bits (67), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 1/47 (2%)

Query: 270 YDKNINPTENLFVSVASFGDGWHNYHHVFPW-DYKNAELWNYKFNIS 315
           +D+N+N  E   V+V  F  G  + H V PW D  +  L   +F++ 
Sbjct: 63  FDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVD 109


>pdb|3LV4|A Chain A, Crystal Structure Of The Glycoside Hydrolase, Family 43
           Yxia Protein From Bacillus Licheniformis. Northeast
           Structural Genomics Consortium Target Bir14.
 pdb|3LV4|B Chain B, Crystal Structure Of The Glycoside Hydrolase, Family 43
           Yxia Protein From Bacillus Licheniformis. Northeast
           Structural Genomics Consortium Target Bir14
          Length = 456

 Score = 30.0 bits (66), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 13/37 (35%), Positives = 22/37 (59%)

Query: 84  GWSLILPHPEVTEKVKVIDTSDVEKDWVVVWQYKNIN 120
           GW ++ PH    EK++ +  SDV  D+ +V   K+I+
Sbjct: 331 GWPVVAPHRYAGEKLEKVKKSDVIGDYELVRHGKDIS 367


>pdb|2R17|A Chain A, Functional Architecture Of The Retromer Cargo-Recognition
           Complex
 pdb|2R17|B Chain B, Functional Architecture Of The Retromer Cargo-Recognition
           Complex
          Length = 183

 Score = 29.6 bits (65), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 1/47 (2%)

Query: 270 YDKNINPTENLFVSVASFGDGWHNYHHVFPW-DYKNAELWNYKFNIS 315
           +D+N+N  E   V+V  F  G  + H V PW D  +  L   +F++ 
Sbjct: 64  FDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDXASLALLQRQFDVD 110


  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
   0.325    0.138    0.483 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,867,775
Number of Sequences: 62578
Number of extensions: 530935
Number of successful extensions: 1379
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1365
Number of HSP's gapped (non-prelim): 18
length of query: 359
length of database: 14,973,337
effective HSP length: 100
effective length of query: 259
effective length of database: 8,715,537
effective search space: 2257324083
effective search space used: 2257324083
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 bits)