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= 008314
         (570 letters)

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

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



>pdb|3D6T|B Chain B, Structure Of The Roc Domain From The Parkinson's
           Disease-Associated Leucine-Rich Repeat Kinase 2 Reveals
           A Dimeric Gtpase
          Length = 171

 Score = 31.2 bits (69), Expect = 1.5,   Method: Composition-based stats.
 Identities = 17/54 (31%), Positives = 29/54 (53%), Gaps = 1/54 (1%)

Query: 204 DMSKTPFQVYSTRPWIRGMFARGVSVGSFVCGTYLN-SEEELDIACLKNLNSSL 256
           D+SK   +V + +PW+  + AR  S    + GT+L+ S+E+   AC   +   L
Sbjct: 86  DLSKGQAEVDAXKPWLFNIKARASSSPVILVGTHLDVSDEKQRKACXSKITKEL 139


>pdb|2ZEJ|A Chain A, Structure Of The Roc Domain From The Parkinson's
           Disease-associated Leucine-rich Repeat Kinase 2 Reveals
           A Dimeric Gtpase
 pdb|2ZEJ|B Chain B, Structure Of The Roc Domain From The Parkinson's
           Disease-associated Leucine-rich Repeat Kinase 2 Reveals
           A Dimeric Gtpase
          Length = 184

 Score = 31.2 bits (69), Expect = 1.5,   Method: Composition-based stats.
 Identities = 17/54 (31%), Positives = 29/54 (53%), Gaps = 1/54 (1%)

Query: 204 DMSKTPFQVYSTRPWIRGMFARGVSVGSFVCGTYLN-SEEELDIACLKNLNSSL 256
           D+SK   +V + +PW+  + AR  S    + GT+L+ S+E+   AC   +   L
Sbjct: 88  DLSKGQAEVDAXKPWLFNIKARASSSPVILVGTHLDVSDEKQRKACXSKITKEL 141


>pdb|4A0L|E Chain E, Structure Of Ddb1-Ddb2-Cul4b-Rbx1 Bound To A 12 Bp Abasic
           Site Containing Dna-Duplex
 pdb|4A0L|H Chain H, Structure Of Ddb1-Ddb2-Cul4b-Rbx1 Bound To A 12 Bp Abasic
           Site Containing Dna-Duplex
          Length = 726

 Score = 28.9 bits (63), Expect = 7.9,   Method: Compositional matrix adjust.
 Identities = 19/74 (25%), Positives = 39/74 (52%), Gaps = 3/74 (4%)

Query: 471 NDTAKSNFFVDSSTKYQIIAAEYLGDGVVTEPCWLQFMREWGPTIVYDSKSEIDKILNLL 530
           N+    N   D S  YQ+ +    G  V+ +  W+++++ +G TIV + + +   +  LL
Sbjct: 275 NNLLDENRIQDLSLLYQLFSRVRGGVQVLLQQ-WIEYIKAFGSTIVINPEKDKTMVQELL 333

Query: 531 PFFMRFSVENLIDL 544
            F  +  V+++ID+
Sbjct: 334 DF--KDKVDHIIDI 345


>pdb|4A0C|C Chain C, Structure Of The Cand1-Cul4b-Rbx1 Complex
 pdb|4A0C|E Chain E, Structure Of The Cand1-Cul4b-Rbx1 Complex
          Length = 741

 Score = 28.9 bits (63), Expect = 8.2,   Method: Compositional matrix adjust.
 Identities = 19/74 (25%), Positives = 39/74 (52%), Gaps = 3/74 (4%)

Query: 471 NDTAKSNFFVDSSTKYQIIAAEYLGDGVVTEPCWLQFMREWGPTIVYDSKSEIDKILNLL 530
           N+    N   D S  YQ+ +    G  V+ +  W+++++ +G TIV + + +   +  LL
Sbjct: 290 NNLLDENRIQDLSLLYQLFSRVRGGVQVLLQQ-WIEYIKAFGSTIVINPEKDKTMVQELL 348

Query: 531 PFFMRFSVENLIDL 544
            F  +  V+++ID+
Sbjct: 349 DF--KDKVDHIIDI 360


  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
   0.319    0.138    0.450 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,983,012
Number of Sequences: 62578
Number of extensions: 925982
Number of successful extensions: 1850
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1850
Number of HSP's gapped (non-prelim): 4
length of query: 570
length of database: 14,973,337
effective HSP length: 104
effective length of query: 466
effective length of database: 8,465,225
effective search space: 3944794850
effective search space used: 3944794850
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)