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= 006008
         (665 letters)

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

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



>pdb|1W63|B Chain B, Ap1 Clathrin Adaptor Core
 pdb|1W63|D Chain D, Ap1 Clathrin Adaptor Core
 pdb|1W63|F Chain F, Ap1 Clathrin Adaptor Core
 pdb|1W63|H Chain H, Ap1 Clathrin Adaptor Core
 pdb|1W63|J Chain J, Ap1 Clathrin Adaptor Core
 pdb|1W63|L Chain L, Ap1 Clathrin Adaptor Core
          Length = 584

 Score = 52.4 bits (124), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 37/117 (31%), Positives = 58/117 (49%), Gaps = 7/117 (5%)

Query: 47  PSCHEKVIIQLFRSLDSIKVPEARVMIIWMVGEYSSVGVKIPRMLTTVLKYLAWCFKSEA 106
           P+ +E VI  L  +LDS   PEAR  +IW+VGEY+        +L + L      F  E+
Sbjct: 422 PNKYESVIATLCENLDSDDEPEARAAMIWIVGEYAERSDNADELLESFLD----GFHDES 477

Query: 107 VETKLQILNTTIKVLLCAKGGDMWTITRLFSYLLELAECDLNYDVRDRARFFKKLFS 163
            + +LQ+L   +K+ L         + ++ S  L   + D N D+RDR   + +L S
Sbjct: 478 TQVQLQLLTAIVKLFLKKPTETQELVQQVLS--LATQDSD-NPDLRDRGYIYWRLLS 531


>pdb|2XA7|B Chain B, Ap2 Clathrin Adaptor Core In Active Complex With Cargo
           Peptides
          Length = 592

 Score = 50.1 bits (118), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 34/117 (29%), Positives = 59/117 (50%), Gaps = 7/117 (5%)

Query: 47  PSCHEKVIIQLFRSLDSIKVPEARVMIIWMVGEYSSVGVKIPRMLTTVLKYLAWCFKSEA 106
           P+ +E +I  L  +LDS+  P+AR  +IW+VGEY+        +L + L+     F  E+
Sbjct: 422 PNKYESIIATLCENLDSLDEPDARAAMIWIVGEYAERIDNADELLESFLE----GFHDES 477

Query: 107 VETKLQILNTTIKVLLCAKGGDMWTITRLFSYLLELAECDLNYDVRDRARFFKKLFS 163
            + +L +L   +K+ L         + ++ S  L   + D N D+RDR   + +L S
Sbjct: 478 TQVQLTLLTAIVKLFLKKPSETQELVQQVLS--LATQDSD-NPDLRDRGYIYWRLLS 531


>pdb|2VGL|B Chain B, Ap2 Clathrin Adaptor Core
 pdb|2JKR|B Chain B, Ap2 Clathrin Adaptor Core With Dileucine Peptide Rm(
           Phosphos)qikrllse
 pdb|2JKR|E Chain E, Ap2 Clathrin Adaptor Core With Dileucine Peptide Rm(
           Phosphos)qikrllse
 pdb|2JKT|B Chain B, Ap2 Clathrin Adaptor Core With Cd4 Dileucine Peptide Rm(
           Phosphos)eikrllse  Q To E Mutant
 pdb|2JKT|E Chain E, Ap2 Clathrin Adaptor Core With Cd4 Dileucine Peptide Rm(
           Phosphos)eikrllse  Q To E Mutant
          Length = 591

 Score = 50.1 bits (118), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 34/117 (29%), Positives = 59/117 (50%), Gaps = 7/117 (5%)

Query: 47  PSCHEKVIIQLFRSLDSIKVPEARVMIIWMVGEYSSVGVKIPRMLTTVLKYLAWCFKSEA 106
           P+ +E +I  L  +LDS+  P+AR  +IW+VGEY+        +L + L+     F  E+
Sbjct: 422 PNKYESIIATLCENLDSLDEPDARAAMIWIVGEYAERIDNADELLESFLE----GFHDES 477

Query: 107 VETKLQILNTTIKVLLCAKGGDMWTITRLFSYLLELAECDLNYDVRDRARFFKKLFS 163
            + +L +L   +K+ L         + ++ S  L   + D N D+RDR   + +L S
Sbjct: 478 TQVQLTLLTAIVKLFLKKPSETQELVQQVLS--LATQDSD-NPDLRDRGYIYWRLLS 531


>pdb|3KEO|A Chain A, Crystal Structure Of A Rex-Family Transcriptional
           Regulatory Protein From Streptococcus Agalactiae
           Complexed With Nad+
 pdb|3KEO|B Chain B, Crystal Structure Of A Rex-Family Transcriptional
           Regulatory Protein From Streptococcus Agalactiae
           Complexed With Nad+
 pdb|3KEQ|A Chain A, Crystal Structure Of A Rex-Family Transcriptional
           Regulatory Protein From Streptococcus Agalactiae
           Complexed With Nad+
 pdb|3KEQ|B Chain B, Crystal Structure Of A Rex-Family Transcriptional
           Regulatory Protein From Streptococcus Agalactiae
           Complexed With Nad+
 pdb|3KET|A Chain A, Crystal Structure Of A Rex-Family Transcriptional
           Regulatory Protein From Streptococcus Agalactiae Bound
           To A Palindromic Operator
          Length = 212

 Score = 29.6 bits (65), Expect = 4.9,   Method: Composition-based stats.
 Identities = 16/47 (34%), Positives = 23/47 (48%)

Query: 124 AKGGDMWTITRLFSYLLELAECDLNYDVRDRARFFKKLFSHNLCSQV 170
           A G D  T+ R FSY  EL      YDV+    FF ++ + +  + V
Sbjct: 41  ALGIDSATVRRDFSYFGELGRRGFGYDVKKLMNFFAEILNDHSTTNV 87


  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
   0.315    0.132    0.382 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,805,964
Number of Sequences: 62578
Number of extensions: 705554
Number of successful extensions: 1328
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 1320
Number of HSP's gapped (non-prelim): 8
length of query: 665
length of database: 14,973,337
effective HSP length: 105
effective length of query: 560
effective length of database: 8,402,647
effective search space: 4705482320
effective search space used: 4705482320
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)