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= 011495
         (484 letters)

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

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



>pdb|2JAF|A Chain A, Ground State Of Halorhodopsin T203v
 pdb|2JAG|A Chain A, L1-Intermediate Of Halorhodopsin T203v
          Length = 274

 Score = 31.6 bits (70), Expect = 0.94,   Method: Compositional matrix adjust.
 Identities = 20/70 (28%), Positives = 40/70 (57%), Gaps = 1/70 (1%)

Query: 31  VGAESDSVVAYSWPVFTASLFVLVALILSTYLIIEHLAAYNQPEEQKFLIGLILMVPVYA 90
           +GA+S + V  +  + ++SL+V VAL     L+  ++    +P   + + G  LM+P+ +
Sbjct: 15  LGAQSAAAVREN-ALLSSSLWVNVALAGIAILVFVYMGRTIRPGRPRLIWGATLMIPLVS 73

Query: 91  LESFLSLLNS 100
           + S+L LL+ 
Sbjct: 74  ISSYLGLLSG 83


>pdb|1E12|A Chain A, Halorhodopsin, A Light-Driven Chloride Pump
          Length = 253

 Score = 30.0 bits (66), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 16/57 (28%), Positives = 32/57 (56%)

Query: 44  PVFTASLFVLVALILSTYLIIEHLAAYNQPEEQKFLIGLILMVPVYALESFLSLLNS 100
            + ++SL+V VAL     L+  ++    +P   + + G  LM+P+ ++ S+L LL+ 
Sbjct: 6   ALLSSSLWVNVALAGIAILVFVYMGRTIRPGRPRLIWGATLMIPLVSISSYLGLLSG 62


>pdb|1YFQ|A Chain A, High Resolution S. Cerevisiae Bub3 Mitotic Checkpoint
           Protein
          Length = 342

 Score = 29.3 bits (64), Expect = 5.8,   Method: Compositional matrix adjust.
 Identities = 21/78 (26%), Positives = 34/78 (43%), Gaps = 6/78 (7%)

Query: 240 LVQFYSVTKDKLEPIKPLAKFLTFKSIVFLTWWQGIIVAFLFSIGAFRGSLAQELKTRIQ 299
           +VQ     KD +  IK     +  KS++ +T W G +  + F I A    L Q L  R +
Sbjct: 3   IVQIEQAPKDYISDIK----IIPSKSLLLITSWDGSLTVYKFDIQAKNVDLLQSL--RYK 56

Query: 300 DYIICIEMGIAAVVHLYV 317
             ++C        + +YV
Sbjct: 57  HPLLCCNFIDNTDLQIYV 74


>pdb|1U4C|A Chain A, Structure Of Spindle Checkpoint Protein Bub3
 pdb|1U4C|B Chain B, Structure Of Spindle Checkpoint Protein Bub3
          Length = 349

 Score = 28.9 bits (63), Expect = 6.1,   Method: Compositional matrix adjust.
 Identities = 21/78 (26%), Positives = 34/78 (43%), Gaps = 6/78 (7%)

Query: 240 LVQFYSVTKDKLEPIKPLAKFLTFKSIVFLTWWQGIIVAFLFSIGAFRGSLAQELKTRIQ 299
           +VQ     KD +  IK     +  KS++ +T W G +  + F I A    L Q L  R +
Sbjct: 3   IVQIEQAPKDYISDIK----IIPSKSLLLITSWDGSLTVYKFDIQAKNVDLLQSL--RYK 56

Query: 300 DYIICIEMGIAAVVHLYV 317
             ++C        + +YV
Sbjct: 57  HPLLCCNFIDNTDLQIYV 74


>pdb|2I3T|A Chain A, Bub3 Complex With Mad3 (Bubr1) Glebs Motif
 pdb|2I3T|C Chain C, Bub3 Complex With Mad3 (Bubr1) Glebs Motif
 pdb|2I3T|E Chain E, Bub3 Complex With Mad3 (Bubr1) Glebs Motif
 pdb|2I3T|G Chain G, Bub3 Complex With Mad3 (Bubr1) Glebs Motif
          Length = 341

 Score = 28.9 bits (63), Expect = 6.1,   Method: Compositional matrix adjust.
 Identities = 21/78 (26%), Positives = 34/78 (43%), Gaps = 6/78 (7%)

Query: 240 LVQFYSVTKDKLEPIKPLAKFLTFKSIVFLTWWQGIIVAFLFSIGAFRGSLAQELKTRIQ 299
           +VQ     KD +  IK     +  KS++ +T W G +  + F I A    L Q L  R +
Sbjct: 3   IVQIEQAPKDYISDIK----IIPSKSLLLITSWDGSLTVYKFDIQAKNVDLLQSL--RYK 56

Query: 300 DYIICIEMGIAAVVHLYV 317
             ++C        + +YV
Sbjct: 57  HPLLCCNFIDNTDLQIYV 74


>pdb|2I3S|A Chain A, Bub3 Complex With Bub1 Glebs Motif
 pdb|2I3S|C Chain C, Bub3 Complex With Bub1 Glebs Motif
 pdb|2I3S|E Chain E, Bub3 Complex With Bub1 Glebs Motif
          Length = 349

 Score = 28.9 bits (63), Expect = 6.5,   Method: Compositional matrix adjust.
 Identities = 21/78 (26%), Positives = 34/78 (43%), Gaps = 6/78 (7%)

Query: 240 LVQFYSVTKDKLEPIKPLAKFLTFKSIVFLTWWQGIIVAFLFSIGAFRGSLAQELKTRIQ 299
           +VQ     KD +  IK     +  KS++ +T W G +  + F I A    L Q L  R +
Sbjct: 3   IVQIEQAPKDYISDIK----IIPSKSLLLITSWDGSLTVYKFDIQAKNVDLLQSL--RYK 56

Query: 300 DYIICIEMGIAAVVHLYV 317
             ++C        + +YV
Sbjct: 57  HPLLCCNFIDNTDLQIYV 74


  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
   0.324    0.139    0.424 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,560,819
Number of Sequences: 62578
Number of extensions: 534036
Number of successful extensions: 1216
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1214
Number of HSP's gapped (non-prelim): 6
length of query: 484
length of database: 14,973,337
effective HSP length: 103
effective length of query: 381
effective length of database: 8,527,803
effective search space: 3249092943
effective search space used: 3249092943
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 53 (25.0 bits)