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= 004374
         (758 letters)

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

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



>pdb|2V50|A Chain A, The Missing Part Of The Bacterial Mexab-Oprm System:
           Structural Determination Of The Multidrug Exporter Mexb
 pdb|2V50|B Chain B, The Missing Part Of The Bacterial Mexab-Oprm System:
           Structural Determination Of The Multidrug Exporter Mexb
 pdb|2V50|C Chain C, The Missing Part Of The Bacterial Mexab-Oprm System:
           Structural Determination Of The Multidrug Exporter Mexb
 pdb|2V50|D Chain D, The Missing Part Of The Bacterial Mexab-Oprm System:
           Structural Determination Of The Multidrug Exporter Mexb
 pdb|2V50|E Chain E, The Missing Part Of The Bacterial Mexab-Oprm System:
           Structural Determination Of The Multidrug Exporter Mexb
 pdb|2V50|F Chain F, The Missing Part Of The Bacterial Mexab-Oprm System:
           Structural Determination Of The Multidrug Exporter Mexb
          Length = 1052

 Score = 33.9 bits (76), Expect = 0.33,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 37/81 (45%), Gaps = 2/81 (2%)

Query: 559 VYRHLPKIFSRYTSAEGF-LFLQDDTILNYWNLLQADKNKLWITDKVSKSWSTVSPNGKS 617
           V+   P       +A GF LFLQD   + +  LLQA +NK  +    + +   V PNG S
Sbjct: 663 VFAFAPPSVLELGNATGFDLFLQDQAGVGHEVLLQA-RNKFLMLAAQNPALQRVRPNGMS 721

Query: 618 DWYSKQAEMVKEVVSTMPVHF 638
           D    + E+  E  S + V  
Sbjct: 722 DEPQYKLEIDDEKASALGVSL 742


>pdb|1VSY|4 Chain 4, Proteasome Activator Complex
 pdb|1VSY|7 Chain 7, Proteasome Activator Complex
 pdb|3L5Q|5 Chain 5, Proteasome Activator Complex
 pdb|3L5Q|7 Chain 7, Proteasome Activator Complex
          Length = 799

 Score = 32.3 bits (72), Expect = 0.93,   Method: Compositional matrix adjust.
 Identities = 15/42 (35%), Positives = 26/42 (61%), Gaps = 6/42 (14%)

Query: 408 SNKHRFFEKVLELSHSM------AEEGFWTERDVKFTAAWLQ 443
           S K RFFEK++ L+ ++      +  GFWT+ + KF  A+++
Sbjct: 264 SKKDRFFEKLVSLAKAIETFIHPSNNGFWTKPNAKFVHAFIK 305


>pdb|4J5I|A Chain A, Crystal Structure Of An Alpha-ketoglutarate-dependent
           Taurine Dioxygenase From Mycobacterium Smegmatis
 pdb|4J5I|B Chain B, Crystal Structure Of An Alpha-ketoglutarate-dependent
           Taurine Dioxygenase From Mycobacterium Smegmatis
 pdb|4J5I|C Chain C, Crystal Structure Of An Alpha-ketoglutarate-dependent
           Taurine Dioxygenase From Mycobacterium Smegmatis
 pdb|4J5I|D Chain D, Crystal Structure Of An Alpha-ketoglutarate-dependent
           Taurine Dioxygenase From Mycobacterium Smegmatis
 pdb|4J5I|E Chain E, Crystal Structure Of An Alpha-ketoglutarate-dependent
           Taurine Dioxygenase From Mycobacterium Smegmatis
 pdb|4J5I|F Chain F, Crystal Structure Of An Alpha-ketoglutarate-dependent
           Taurine Dioxygenase From Mycobacterium Smegmatis
 pdb|4J5I|G Chain G, Crystal Structure Of An Alpha-ketoglutarate-dependent
           Taurine Dioxygenase From Mycobacterium Smegmatis
 pdb|4J5I|H Chain H, Crystal Structure Of An Alpha-ketoglutarate-dependent
           Taurine Dioxygenase From Mycobacterium Smegmatis
          Length = 304

 Score = 30.8 bits (68), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 23/98 (23%), Positives = 44/98 (44%), Gaps = 4/98 (4%)

Query: 254 LENVGEISHEEFYTEVFGGKQFIQQGISNGLPDVDSVFYFTRKPSLEAFDIRFDDRVPKV 313
           L++ G++   E           + +G    LP +DS +    K +    D+ F DR+PK 
Sbjct: 56  LDDAGQLEFAELLGTPTVAHPTLAEGAEQLLP-IDSRY---DKANSWHTDVTFVDRIPKA 111

Query: 314 ALPQGMMVPVNSFNTIYQSSAFWALMLPVSVSTMASDV 351
           +L + + +P     T + S+      LP  + T+A ++
Sbjct: 112 SLLRAVTLPSYGGTTAWASTEAAYQQLPAPLRTLADNL 149


>pdb|3LQB|A Chain A, Crystal Structure Of The Hatching Enzyme Zhe1 From The
           Zebrafish Danio Rerio
          Length = 199

 Score = 29.3 bits (64), Expect = 8.7,   Method: Composition-based stats.
 Identities = 15/60 (25%), Positives = 31/60 (51%)

Query: 616 KSDWYSKQAEMVKEVVSTMPVHFQVNYKEAIRSDQSLIICSSELFYIPQHLAADFVDLVN 675
           KS ++ K A  + EV   +   F +N K  I +  S+    + + ++P+ + AD++ + N
Sbjct: 8   KSCFWKKNANNIVEVPYVVSGEFSINDKSVIANAISIFHAQTCIRFVPRSIQADYLSIEN 67


  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
   0.321    0.136    0.416 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,079,783
Number of Sequences: 62578
Number of extensions: 902641
Number of successful extensions: 2303
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 2300
Number of HSP's gapped (non-prelim): 4
length of query: 758
length of database: 14,973,337
effective HSP length: 106
effective length of query: 652
effective length of database: 8,340,069
effective search space: 5437724988
effective search space used: 5437724988
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.8 bits)