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= 036677
         (78 letters)

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

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



>pdb|1W63|Q Chain Q, Ap1 Clathrin Adaptor Core
 pdb|1W63|S Chain S, Ap1 Clathrin Adaptor Core
 pdb|1W63|T Chain T, Ap1 Clathrin Adaptor Core
 pdb|1W63|U Chain U, Ap1 Clathrin Adaptor Core
 pdb|1W63|W Chain W, Ap1 Clathrin Adaptor Core
 pdb|1W63|X Chain X, Ap1 Clathrin Adaptor Core
          Length = 158

 Score = 65.9 bits (159), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 30/78 (38%), Positives = 46/78 (58%), Gaps = 13/78 (16%)

Query: 1  VIRELSGIILTRSPKLCNFVEWNGGLPTSIIFNTKCYPRENVIIYSGLYFCMCVDPDDNE 60
          ++REL  ++L R PK+C+F+EW       +++            Y+ LYFC  ++  DNE
Sbjct: 31 MVRELMQVVLARKPKMCSFLEWR---DLKVVYKR----------YASLYFCCAIEGQDNE 77

Query: 61 LEILDIIHHYVEILDLYF 78
          L  L++IH YVE+LD YF
Sbjct: 78 LITLELIHRYVELLDKYF 95


>pdb|2VGL|S Chain S, Ap2 Clathrin Adaptor Core
 pdb|2JKR|I Chain I, Ap2 Clathrin Adaptor Core With Dileucine Peptide Rm(
          Phosphos)qikrllse
 pdb|2JKR|S Chain S, Ap2 Clathrin Adaptor Core With Dileucine Peptide Rm(
          Phosphos)qikrllse
 pdb|2JKT|I Chain I, Ap2 Clathrin Adaptor Core With Cd4 Dileucine Peptide Rm(
          Phosphos)eikrllse  Q To E Mutant
 pdb|2JKT|S Chain S, Ap2 Clathrin Adaptor Core With Cd4 Dileucine Peptide Rm(
          Phosphos)eikrllse  Q To E Mutant
 pdb|2XA7|S Chain S, Ap2 Clathrin Adaptor Core In Active Complex With Cargo
          Peptides
          Length = 142

 Score = 56.6 bits (135), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 31/78 (39%), Positives = 44/78 (56%), Gaps = 13/78 (16%)

Query: 1  VIRELSGIILTRSPKLCNFVEWNGGLPTSIIFNTKCYPRENVIIYSGLYFCMCVDPDDNE 60
          +I E+  ++  R  K  NFVE+          N K   R     Y+GLYFC+CVD +DN 
Sbjct: 31 LIEEVHAVVTVRDAKHTNFVEFR---------NFKIIYRR----YAGLYFCICVDVNDNN 77

Query: 61 LEILDIIHHYVEILDLYF 78
          L  L+ IH++VE+L+ YF
Sbjct: 78 LAYLEAIHNFVEVLNEYF 95


>pdb|1OLT|A Chain A, Coproporphyrinogen Iii Oxidase (Hemn) From Escherichia
           Coli Is A Radical Sam Enzyme
          Length = 457

 Score = 25.4 bits (54), Expect = 8.9,   Method: Composition-based stats.
 Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 4/50 (8%)

Query: 20  VEWNGGLPTSI----IFNTKCYPRENVIIYSGLYFCMCVDPDDNELEILD 65
           + W GG PT +    I       REN    +     + VDP + EL++LD
Sbjct: 108 LHWGGGTPTYLNKAQISRLMKLLRENFQFNADAEISIEVDPREIELDVLD 157


  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
   0.328    0.149    0.484 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,699,525
Number of Sequences: 62578
Number of extensions: 98355
Number of successful extensions: 200
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 197
Number of HSP's gapped (non-prelim): 3
length of query: 78
length of database: 14,973,337
effective HSP length: 47
effective length of query: 31
effective length of database: 12,032,171
effective search space: 372997301
effective search space used: 372997301
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 45 (21.9 bits)