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= psy13382
         (237 letters)

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

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



>pdb|3FRV|A Chain A, Structure Of Human Chmp3 (Residues 1-150)
          Length = 152

 Score = 54.7 bits (130), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 34/131 (25%), Positives = 78/131 (59%), Gaps = 2/131 (1%)

Query: 4   LFGR--KITPEEMLRKNQRALNKAMRDLDREKQHMEQQEKKLIADIKKMAKEGQMESVKI 61
           LFG+  +  P+E++ +    + K MR +DR+ + ++++E+K+   +K  AK+GQ +   +
Sbjct: 5   LFGKTQEKPPKELVNEWSLKIRKEMRVVDRQIRDIQREEEKVKRSVKDAAKKGQKDVCIV 64

Query: 62  MAKDLVRTRKYAKKFMMMKANIQAVSLKIQTLRSQNAMAEAMKGCSRAMQNMNRQMNLPQ 121
           +AK+++R+RK   K    KA++ +V + ++   +   +A +++  +  M+ M   + +P+
Sbjct: 65  LAKEMIRSRKAVSKLYASKAHMNSVLMGMKNQLAVLRVAGSLQKSTEVMKAMQSLVKIPE 124

Query: 122 IQRILQEFEKQ 132
           IQ  ++E  K+
Sbjct: 125 IQATMRELSKE 135


>pdb|3FRT|A Chain A, The Structure Of Human Chmp3 (Residues 8 - 222).
 pdb|3FRT|B Chain B, The Structure Of Human Chmp3 (Residues 8 - 222)
          Length = 218

 Score = 54.3 bits (129), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 31/122 (25%), Positives = 73/122 (59%)

Query: 11  PEEMLRKNQRALNKAMRDLDREKQHMEQQEKKLIADIKKMAKEGQMESVKIMAKDLVRTR 70
           P+E++ +    + K MR +DR+ + ++++E+K+   +K  AK+GQ +   ++AK+++R+R
Sbjct: 8   PKELVNEWSLKIRKEMRVVDRQIRDIQREEEKVKRSVKDAAKKGQKDVCIVLAKEMIRSR 67

Query: 71  KYAKKFMMMKANIQAVSLKIQTLRSQNAMAEAMKGCSRAMQNMNRQMNLPQIQRILQEFE 130
           K   K    KA++ +V + ++   +   +A +++  +  M+ M   + +P+IQ  ++E  
Sbjct: 68  KAVSKLYASKAHMNSVLMGMKNQLAVLRVAGSLQKSTEVMKAMQSLVKIPEIQATMRELS 127

Query: 131 KQ 132
           K+
Sbjct: 128 KE 129


>pdb|2GD5|A Chain A, Structural Basis For Budding By The Escrtiii Factor Chmp3
 pdb|2GD5|B Chain B, Structural Basis For Budding By The Escrtiii Factor Chmp3
 pdb|2GD5|C Chain C, Structural Basis For Budding By The Escrtiii Factor Chmp3
 pdb|2GD5|D Chain D, Structural Basis For Budding By The Escrtiii Factor Chmp3
          Length = 179

 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 31/126 (24%), Positives = 70/126 (55%), Gaps = 8/126 (6%)

Query: 11  PEEMLRKNQRALNKAMRDLDREKQHMEQQEKKLIADIKKMAKEGQMESVKIMAKDLVRTR 70
           P+E++ +    + K  R +DR+ + ++++E+K+   +K  AK+GQ +   ++AK+ +R+R
Sbjct: 8   PKELVNEWSLKIRKEXRVVDRQIRDIQREEEKVKRSVKDAAKKGQKDVCIVLAKEXIRSR 67

Query: 71  KYAKKFMMMKANIQAVSL----KIQTLRSQNAMAEAMKGCSRAMQNMNRQMNLPQIQRIL 126
           K   K    KA+  +V      ++  LR   ++ ++ +   +A Q++   + +P+IQ   
Sbjct: 68  KAVSKLYASKAHXNSVLXGXKNQLAVLRVAGSLQKSTE-VXKAXQSL---VKIPEIQATX 123

Query: 127 QEFEKQ 132
           +E  K+
Sbjct: 124 RELSKE 129


  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
   0.316    0.125    0.332 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,001,003
Number of Sequences: 62578
Number of extensions: 101223
Number of successful extensions: 426
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 408
Number of HSP's gapped (non-prelim): 23
length of query: 237
length of database: 14,973,337
effective HSP length: 96
effective length of query: 141
effective length of database: 8,965,849
effective search space: 1264184709
effective search space used: 1264184709
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)