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= psy16364
         (276 letters)

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

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



>pdb|2JKR|A Chain A, Ap2 Clathrin Adaptor Core With Dileucine Peptide Rm(
           Phosphos)qikrllse
 pdb|2JKR|L Chain L, Ap2 Clathrin Adaptor Core With Dileucine Peptide Rm(
           Phosphos)qikrllse
 pdb|2JKT|A Chain A, Ap2 Clathrin Adaptor Core With Cd4 Dileucine Peptide Rm(
           Phosphos)eikrllse  Q To E Mutant
 pdb|2JKT|L Chain L, Ap2 Clathrin Adaptor Core With Cd4 Dileucine Peptide Rm(
           Phosphos)eikrllse  Q To E Mutant
          Length = 623

 Score = 52.0 bits (123), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 30/121 (24%), Positives = 69/121 (57%), Gaps = 6/121 (4%)

Query: 10  KSVQSHRDLIMQCL-DDKDESIRLRALDLLYGMVSKKTLMEIVKKLMVHMDKAEGTMYRD 68
           ++V++H + ++  L  ++D S+R RA+DLLY M  +    +IV +++ +++ A+ ++ R+
Sbjct: 364 EAVKTHIETVINALKTERDVSVRQRAVDLLYAMCDRSNAQQIVAEMLSYLETADYSI-RE 422

Query: 69  ELLSKVIDICSQNNYQYITNFEWYMTVLVELTRMEGTRHGALVAAQMMDVAIRVSAVRAF 128
           E++ KV  +      +Y  ++ WY+  ++ L R+ G      V  +++ + I    V+ +
Sbjct: 423 EIVLKVAILAE----KYAVDYTWYVDTILNLIRIAGDYVSEEVWYRVIQIVINRDDVQGY 478

Query: 129 A 129
           A
Sbjct: 479 A 479



 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/86 (27%), Positives = 55/86 (63%), Gaps = 4/86 (4%)

Query: 178 HMKYLGLLAMSKILKTH--PKSVQSHRDLIMQCL-DDKDESIRLRALDLLYGMVSKKTLM 234
           +++YL L +M  +  +    ++V++H + ++  L  ++D S+R RA+DLLY M  +    
Sbjct: 344 NLRYLALESMCTLASSEFSHEAVKTHIETVINALKTERDVSVRQRAVDLLYAMCDRSNAQ 403

Query: 235 EIVKKLMVHMDKAEGTMYRDELLSKV 260
           +IV +++ +++ A+ ++ R+E++ KV
Sbjct: 404 QIVAEMLSYLETADYSI-REEIVLKV 428


>pdb|2VGL|A Chain A, Ap2 Clathrin Adaptor Core
 pdb|2XA7|A Chain A, Ap2 Clathrin Adaptor Core In Active Complex With Cargo
           Peptides
          Length = 621

 Score = 51.6 bits (122), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 30/121 (24%), Positives = 69/121 (57%), Gaps = 6/121 (4%)

Query: 10  KSVQSHRDLIMQCL-DDKDESIRLRALDLLYGMVSKKTLMEIVKKLMVHMDKAEGTMYRD 68
           ++V++H + ++  L  ++D S+R RA+DLLY M  +    +IV +++ +++ A+ ++ R+
Sbjct: 364 EAVKTHIETVINALKTERDVSVRQRAVDLLYAMCDRSNAQQIVAEMLSYLETADYSI-RE 422

Query: 69  ELLSKVIDICSQNNYQYITNFEWYMTVLVELTRMEGTRHGALVAAQMMDVAIRVSAVRAF 128
           E++ KV  +      +Y  ++ WY+  ++ L R+ G      V  +++ + I    V+ +
Sbjct: 423 EIVLKVAILAE----KYAVDYTWYVDTILNLIRIAGDYVSEEVWYRVIQIVINRDDVQGY 478

Query: 129 A 129
           A
Sbjct: 479 A 479



 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/86 (27%), Positives = 55/86 (63%), Gaps = 4/86 (4%)

Query: 178 HMKYLGLLAMSKILKTH--PKSVQSHRDLIMQCL-DDKDESIRLRALDLLYGMVSKKTLM 234
           +++YL L +M  +  +    ++V++H + ++  L  ++D S+R RA+DLLY M  +    
Sbjct: 344 NLRYLALESMCTLASSEFSHEAVKTHIETVINALKTERDVSVRQRAVDLLYAMCDRSNAQ 403

Query: 235 EIVKKLMVHMDKAEGTMYRDELLSKV 260
           +IV +++ +++ A+ ++ R+E++ KV
Sbjct: 404 QIVAEMLSYLETADYSI-REEIVLKV 428


>pdb|1W63|A Chain A, Ap1 Clathrin Adaptor Core
 pdb|1W63|C Chain C, Ap1 Clathrin Adaptor Core
 pdb|1W63|E Chain E, Ap1 Clathrin Adaptor Core
 pdb|1W63|G Chain G, Ap1 Clathrin Adaptor Core
 pdb|1W63|I Chain I, Ap1 Clathrin Adaptor Core
 pdb|1W63|K Chain K, Ap1 Clathrin Adaptor Core
          Length = 618

 Score = 50.1 bits (118), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/77 (31%), Positives = 46/77 (59%)

Query: 178 HMKYLGLLAMSKILKTHPKSVQSHRDLIMQCLDDKDESIRLRALDLLYGMVSKKTLMEIV 237
           +++Y+ L ++ K ++T   +VQ HR  I+ CL D D SI+ RA++L + +V+   +  ++
Sbjct: 328 NIRYVALTSLLKTVQTDHNAVQRHRSTIVDCLKDLDVSIKRRAMELSFALVNGNNIRGMM 387

Query: 238 KKLMVHMDKAEGTMYRD 254
           K+L+  +D  E     D
Sbjct: 388 KELLYFLDSCEPEFKAD 404



 Score = 44.3 bits (103), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 22/66 (33%), Positives = 38/66 (57%)

Query: 3   KILKTHPKSVQSHRDLIMQCLDDKDESIRLRALDLLYGMVSKKTLMEIVKKLMVHMDKAE 62
           K ++T   +VQ HR  I+ CL D D SI+ RA++L + +V+   +  ++K+L+  +D  E
Sbjct: 339 KTVQTDHNAVQRHRSTIVDCLKDLDVSIKRRAMELSFALVNGNNIRGMMKELLYFLDSCE 398

Query: 63  GTMYRD 68
                D
Sbjct: 399 PEFKAD 404


  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
   0.323    0.134    0.373 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,333,387
Number of Sequences: 62578
Number of extensions: 207709
Number of successful extensions: 852
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 843
Number of HSP's gapped (non-prelim): 12
length of query: 276
length of database: 14,973,337
effective HSP length: 97
effective length of query: 179
effective length of database: 8,903,271
effective search space: 1593685509
effective search space used: 1593685509
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (24.3 bits)