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= 042402
         (523 letters)

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

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



>pdb|1W63|M Chain M, Ap1 Clathrin Adaptor Core
 pdb|1W63|N Chain N, Ap1 Clathrin Adaptor Core
 pdb|1W63|O Chain O, Ap1 Clathrin Adaptor Core
 pdb|1W63|P Chain P, Ap1 Clathrin Adaptor Core
 pdb|1W63|R Chain R, Ap1 Clathrin Adaptor Core
 pdb|1W63|V Chain V, Ap1 Clathrin Adaptor Core
          Length = 423

 Score = 35.0 bits (79), Expect = 0.10,   Method: Compositional matrix adjust.
 Identities = 30/143 (20%), Positives = 60/143 (41%), Gaps = 5/143 (3%)

Query: 1   MVVLAASIVSKSGKILVSRQF---VDMSRIRIEGLLAAFPKLVGTGKQHTYVETENVRYV 57
           M   A  ++   GK+L+ R +   VDMS +  E  +    +    G     +    VR++
Sbjct: 1   MSASAVYVLDLKGKVLICRNYRGDVDMSEV--EHFMPILMEKEEEGMLSPILAHGGVRFM 58

Query: 58  YQPIEALYLLLVTNKQSNILEDLETLRLLSKLVPEYSYSLDEEGICKTAFELLFAFDEVI 117
           +     LYL+  + K + +      L  + ++  EY   L+EE I      +    DE++
Sbjct: 59  WIKHNNLYLVATSKKNACVSLVFSFLYKVVQVFSEYFKELEEESIRDNFVIIYELLDELM 118

Query: 118 SLGHKENVTVAQVKQYCEMESHE 140
             G+ +      ++++   E H+
Sbjct: 119 DFGYPQTTDSKILQEFITQEGHK 141


>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 = 33.1 bits (74), Expect = 0.40,   Method: Composition-based stats.
 Identities = 27/136 (19%), Positives = 60/136 (44%), Gaps = 3/136 (2%)

Query: 8   IVSKSGKILVSRQFVDMSRIRIEGLLAAFPKLVGT--GKQHTYVETENVRYVYQPIEALY 65
           I +++GK  +++ ++       + L+     +V     K   +VE  N + +Y+    LY
Sbjct: 7   IQNRAGKTRLAKWYMQFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIIYRRYAGLY 66

Query: 66  LLLVTNKQSNILEDLETLRLLSKLVPEYSYSLDEEGICKTAFELLFAFDEVISLGH-KEN 124
             +  +   N L  LE +    +++ EY +++ E  +    +++    DE+   G  +E 
Sbjct: 67  FCICVDVNDNNLAYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLAGEIRET 126

Query: 125 VTVAQVKQYCEMESHE 140
                +KQ   ++S E
Sbjct: 127 SQTKVLKQLLMLQSLE 142


>pdb|2KGS|A Chain A, Solution Structure Of The Amino-Terminal Domain Of Ompatb,
           A Pore Forming Protein From Mycobacterium Tuberculosis
          Length = 132

 Score = 32.3 bits (72), Expect = 0.66,   Method: Composition-based stats.
 Identities = 14/27 (51%), Positives = 21/27 (77%)

Query: 481 SVRFSATSTYSDLKVVNIIPLRGGAPP 507
           +V+ +ATST+ D+K+VN I + G APP
Sbjct: 102 AVKRAATSTWPDMKIVNNIEVTGQAPP 128


>pdb|2KSM|A Chain A, Central B Domain Of Rv0899 From Mycobacterium Tuberculosis
          Length = 131

 Score = 32.3 bits (72), Expect = 0.67,   Method: Composition-based stats.
 Identities = 14/27 (51%), Positives = 21/27 (77%)

Query: 481 SVRFSATSTYSDLKVVNIIPLRGGAPP 507
           +V+ +ATST+ D+K+VN I + G APP
Sbjct: 102 AVKRAATSTWPDMKIVNNIEVTGQAPP 128


>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 = 30.4 bits (67), Expect = 2.6,   Method: Composition-based stats.
 Identities = 30/136 (22%), Positives = 60/136 (44%), Gaps = 14/136 (10%)

Query: 8   IVSKSGKILVSRQFV--------DMSRIRIEGLLAAFPKLVGTGKQHTYVETENVRYVYQ 59
           + S+ GK+ + + ++         M R  ++ +LA  PK+       +++E  +++ VY+
Sbjct: 7   LFSRQGKLRLQKWYLATSDKERKKMVRELMQVVLARKPKMC------SFLEWRDLKVVYK 60

Query: 60  PIEALYLLLVTNKQSNILEDLETLRLLSKLVPEYSYSLDEEGICKTAFELLFAFDEVISL 119
              +LY       Q N L  LE +    +L+ +Y  S+ E  I     +  F  DE +  
Sbjct: 61  RYASLYFCCAIEGQDNELITLELIHRYVELLDKYFGSVCELDIIFNFEKAYFILDEFLMG 120

Query: 120 GHKENVTVAQVKQYCE 135
           G  ++ +   V +  E
Sbjct: 121 GDVQDTSKKSVLKAIE 136


  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    0.369 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,663,367
Number of Sequences: 62578
Number of extensions: 535950
Number of successful extensions: 1045
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 1038
Number of HSP's gapped (non-prelim): 22
length of query: 523
length of database: 14,973,337
effective HSP length: 103
effective length of query: 420
effective length of database: 8,527,803
effective search space: 3581677260
effective search space used: 3581677260
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 54 (25.4 bits)