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= psy16159
         (175 letters)

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

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



>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 = 62.0 bits (149), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 38/138 (27%), Positives = 84/138 (60%), Gaps = 3/138 (2%)

Query: 5   IKKAAKEGDKIAATILAKQLIQIRKQKTRTYAAQGKVHSIGIQNKTMGSNIKMAEAMKNT 64
           +K AAK+G K    +LAK++I+ RK  ++ YA++  ++S+ +  K   + +++A +++ +
Sbjct: 44  VKDAAKKGQKDVCIVLAKEMIRSRKAVSKLYASKAHMNSVLMGMKNQLAVLRVAGSLQKS 103

Query: 65  ADTMKNMNSIMKPEQIAASAQEFQQGITRMNMTDEMIDEALDDMLEGSDDEQESNKIIDQ 124
            + MK M S++K  +I A+ +E  + + +  + +EM+++  + M +  + E+E+   ID+
Sbjct: 104 TEVMKAMQSLVKIPEIQATMRELSKEMMKAGIIEEMLEDTFESMDDQEEMEEEAEMEIDR 163

Query: 125 VLGEIGIEISGKMANAPT 142
           +L EI    +G +  AP+
Sbjct: 164 ILFEI---TAGALGKAPS 178


>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 = 54.7 bits (130), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 36/138 (26%), Positives = 78/138 (56%), Gaps = 3/138 (2%)

Query: 5   IKKAAKEGDKIAATILAKQLIQIRKQKTRTYAAQGKVHSIGIQNKTMGSNIKMAEAMKNT 64
           +K AAK+G K    +LAK+ I+ RK  ++ YA++   +S+    K   + +++A +++ +
Sbjct: 44  VKDAAKKGQKDVCIVLAKEXIRSRKAVSKLYASKAHXNSVLXGXKNQLAVLRVAGSLQKS 103

Query: 65  ADTMKNMNSIMKPEQIAASAQEFQQGITRMNMTDEMIDEALDDMLEGSDDEQESNKIIDQ 124
            +  K   S++K  +I A+ +E  +   +  + +EM+++  + M +  + E+E+   ID+
Sbjct: 104 TEVXKAXQSLVKIPEIQATXRELSKEXXKAGIIEEMLEDTFESMDDQEEXEEEAEXEIDR 163

Query: 125 VLGEIGIEISGKMANAPT 142
           +L EI    +G +  AP+
Sbjct: 164 ILFEI---TAGALGKAPS 178


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

 Score = 52.8 bits (125), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 27/102 (26%), Positives = 64/102 (62%)

Query: 5   IKKAAKEGDKIAATILAKQLIQIRKQKTRTYAAQGKVHSIGIQNKTMGSNIKMAEAMKNT 64
           +K AAK+G K    +LAK++I+ RK  ++ YA++  ++S+ +  K   + +++A +++ +
Sbjct: 50  VKDAAKKGQKDVCIVLAKEMIRSRKAVSKLYASKAHMNSVLMGMKNQLAVLRVAGSLQKS 109

Query: 65  ADTMKNMNSIMKPEQIAASAQEFQQGITRMNMTDEMIDEALD 106
            + MK M S++K  +I A+ +E  + + +  + +EM+++  +
Sbjct: 110 TEVMKAMQSLVKIPEIQATMRELSKEMMKAGIIEEMLEDTFE 151


  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
   0.308    0.124    0.314 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,835,102
Number of Sequences: 62578
Number of extensions: 127584
Number of successful extensions: 302
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 296
Number of HSP's gapped (non-prelim): 11
length of query: 175
length of database: 14,973,337
effective HSP length: 92
effective length of query: 83
effective length of database: 9,216,161
effective search space: 764941363
effective search space used: 764941363
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 48 (23.1 bits)