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= 028108
         (213 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 =  127 bits (319), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 70/149 (46%), Positives = 103/149 (69%)

Query: 22  DIQREEKNVQKSIKESAKRNDMGSAKALAKEILMSRKAVNRLYENKAQLNSISMHLGESV 81
           DIQREE+ V++S+K++AK+        LAKE++ SRKAV++LY +KA +NS+ M +   +
Sbjct: 32  DIQREEEKVKRSVKDAAKKGQKDVCIVLAKEMIRSRKAVSKLYASKAHMNSVLMGMKNQL 91

Query: 82  AIARTVGHLSKSTEVMKLVNNLMKAPEVAVTMQEFSKEMTKAGIIEEMVNDTIDTALDSD 141
           A+ R  G L KSTEVMK + +L+K PE+  TM+E SKEM KAGIIEEM+ DT ++  D +
Sbjct: 92  AVLRVAGSLQKSTEVMKAMQSLVKIPEIQATMRELSKEMMKAGIIEEMLEDTFESMDDQE 151

Query: 142 DIEEETEEKVDKVLSEIAGETAAQLPEAV 170
           ++EEE E ++D++L EI      + P  V
Sbjct: 152 EMEEEAEMEIDRILFEITAGALGKAPSKV 180


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

 Score =  119 bits (297), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 59/115 (51%), Positives = 84/115 (73%)

Query: 22  DIQREEKNVQKSIKESAKRNDMGSAKALAKEILMSRKAVNRLYENKAQLNSISMHLGESV 81
           DIQREE+ V++S+K++AK+        LAKE++ SRKAV++LY +KA +NS+ M +   +
Sbjct: 38  DIQREEEKVKRSVKDAAKKGQKDVCIVLAKEMIRSRKAVSKLYASKAHMNSVLMGMKNQL 97

Query: 82  AIARTVGHLSKSTEVMKLVNNLMKAPEVAVTMQEFSKEMTKAGIIEEMVNDTIDT 136
           A+ R  G L KSTEVMK + +L+K PE+  TM+E SKEM KAGIIEEM+ DT ++
Sbjct: 98  AVLRVAGSLQKSTEVMKAMQSLVKIPEIQATMRELSKEMMKAGIIEEMLEDTFES 152


>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 =  111 bits (278), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 65/146 (44%), Positives = 93/146 (63%)

Query: 22  DIQREEKNVQKSIKESAKRNDMGSAKALAKEILMSRKAVNRLYENKAQLNSISMHLGESV 81
           DIQREE+ V++S+K++AK+        LAKE + SRKAV++LY +KA  NS+       +
Sbjct: 32  DIQREEEKVKRSVKDAAKKGQKDVCIVLAKEXIRSRKAVSKLYASKAHXNSVLXGXKNQL 91

Query: 82  AIARTVGHLSKSTEVMKLVNNLMKAPEVAVTMQEFSKEMTKAGIIEEMVNDTIDTALDSD 141
           A+ R  G L KSTEV K   +L+K PE+  T +E SKE  KAGIIEEM+ DT ++  D +
Sbjct: 92  AVLRVAGSLQKSTEVXKAXQSLVKIPEIQATXRELSKEXXKAGIIEEMLEDTFESMDDQE 151

Query: 142 DIEEETEEKVDKVLSEIAGETAAQLP 167
           + EEE E ++D++L EI      + P
Sbjct: 152 EXEEEAEXEIDRILFEITAGALGKAP 177


>pdb|2RDY|A Chain A, Crystal Structure Of A Putative Glycoside Hydrolase Family
           Protein From Bacillus Halodurans
 pdb|2RDY|B Chain B, Crystal Structure Of A Putative Glycoside Hydrolase Family
           Protein From Bacillus Halodurans
          Length = 803

 Score = 28.5 bits (62), Expect = 2.7,   Method: Composition-based stats.
 Identities = 14/29 (48%), Positives = 21/29 (72%), Gaps = 1/29 (3%)

Query: 57  RKAVNRLYENKAQL-NSISMHLGESVAIA 84
           ++ VNR  E+  +L N +S+HLGES+A A
Sbjct: 282 KEIVNRHLEDYTKLFNRVSLHLGESIAPA 310


  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    0.122    0.305 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,178,290
Number of Sequences: 62578
Number of extensions: 134392
Number of successful extensions: 532
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 523
Number of HSP's gapped (non-prelim): 20
length of query: 213
length of database: 14,973,337
effective HSP length: 95
effective length of query: 118
effective length of database: 9,028,427
effective search space: 1065354386
effective search space used: 1065354386
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: 49 (23.5 bits)