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= 046252
         (124 letters)

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

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



>pdb|2GCC|A Chain A, Solution Structure Of The Gcc-Box Binding Domain, Nmr,
           Minimized Mean Structure
 pdb|3GCC|A Chain A, Solution Structure Of The Gcc-Box Binding Domain, Nmr, 46
           Structures
          Length = 70

 Score = 84.0 bits (206), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 38/65 (58%), Positives = 46/65 (70%)

Query: 55  YRGVRPRPWGKWTGEIKNPNKNTAQVWLGTFDMPEDAGSAYDPAPFQIQGQNAELNFPQT 114
           YRGVR RPWGK+  EI++P KN A+VWLGTF+  EDA  AYD A F+++G  A LNFP  
Sbjct: 6   YRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFPLR 65

Query: 115 HESQE 119
             S E
Sbjct: 66  VNSGE 70


>pdb|1GCC|A Chain A, Solution Nmr Structure Of The Complex Of Gcc-Box Binding
           Domain Of Aterf1 And Gcc-Box Dna, Minimized Average
           Structure
          Length = 63

 Score = 83.2 bits (204), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 36/58 (62%), Positives = 44/58 (75%)

Query: 55  YRGVRPRPWGKWTGEIKNPNKNTAQVWLGTFDMPEDAGSAYDPAPFQIQGQNAELNFP 112
           YRGVR RPWGK+  EI++P KN A+VWLGTF+  EDA  AYD A F+++G  A LNFP
Sbjct: 3   YRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFP 60


>pdb|3N3K|A Chain A, The Catalytic Domain Of Usp8 In Complex With A Usp8
           Specific Inhibitor
          Length = 396

 Score = 29.3 bits (64), Expect = 0.60,   Method: Compositional matrix adjust.
 Identities = 16/80 (20%), Positives = 40/80 (50%), Gaps = 2/80 (2%)

Query: 7   NSSSTETVNSCLELISSSNHLDDLFDQSDYESEPTTPDTIRQKAVRSKYRGVRPRPWGKW 66
           N  +T  +NS L+ + ++ HL D F+++ Y+ +    + +  K   ++  G+  +    W
Sbjct: 67  NLGNTCYMNSILQCLCNAPHLADYFNRNCYQDDINRSNLLGHKGEVAEEFGIIMKAL--W 124

Query: 67  TGEIKNPNKNTAQVWLGTFD 86
           TG+ +  +    ++ +G  +
Sbjct: 125 TGQYRYISPKDFKITIGKIN 144


>pdb|2Y6E|A Chain A, Ubiquitin Specific Protease 4 Is Inhibited By Its
          Ubiquitin- Like Domain
 pdb|2Y6E|B Chain B, Ubiquitin Specific Protease 4 Is Inhibited By Its
          Ubiquitin- Like Domain
 pdb|2Y6E|C Chain C, Ubiquitin Specific Protease 4 Is Inhibited By Its
          Ubiquitin- Like Domain
 pdb|2Y6E|D Chain D, Ubiquitin Specific Protease 4 Is Inhibited By Its
          Ubiquitin- Like Domain
 pdb|2Y6E|E Chain E, Ubiquitin Specific Protease 4 Is Inhibited By Its
          Ubiquitin- Like Domain
 pdb|2Y6E|F Chain F, Ubiquitin Specific Protease 4 Is Inhibited By Its
          Ubiquitin- Like Domain
          Length = 367

 Score = 28.9 bits (63), Expect = 0.87,   Method: Compositional matrix adjust.
 Identities = 13/37 (35%), Positives = 22/37 (59%)

Query: 3  ASAGNSSSTETVNSCLELISSSNHLDDLFDQSDYESE 39
             GN  +T  +NS L+ +S++  L D F + +YE+E
Sbjct: 9  CGLGNLGNTXFMNSALQCLSNTAPLTDYFLKDEYEAE 45


>pdb|3I3V|A Chain A, Crystal Structure Of Probable Secreted Solute-Binding
           Lipoprotein From Streptomyces Coelicolor
 pdb|3I3V|B Chain B, Crystal Structure Of Probable Secreted Solute-Binding
           Lipoprotein From Streptomyces Coelicolor
 pdb|3I3V|C Chain C, Crystal Structure Of Probable Secreted Solute-Binding
           Lipoprotein From Streptomyces Coelicolor
 pdb|3I3V|D Chain D, Crystal Structure Of Probable Secreted Solute-Binding
           Lipoprotein From Streptomyces Coelicolor
          Length = 405

 Score = 28.5 bits (62), Expect = 0.97,   Method: Composition-based stats.
 Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 8/77 (10%)

Query: 30  LFDQSDYESEPTTPDTIRQKAVRSKYRGVRPRPWG--KWTGEIKNPNKNTAQVWLGTFDM 87
           L D++  ++ PTT D +   A + + +G+ P   G   WTG+     K  AQ+ + TF  
Sbjct: 134 LLDRAGVDAIPTTGDQLIAAARKLRAKGIAPVTVGGNDWTGQ-----KLLAQI-IQTFLS 187

Query: 88  PEDAGSAYDPAPFQIQG 104
            ++A   Y    F ++G
Sbjct: 188 QDEARHVYSTGDFGVRG 204


>pdb|3JYS|A Chain A, Crystal Structure Of Susd Superfamily Protein
           (Yp_001298690.1) From Bacteroides Vulgatus Atcc 8482 At
           2.00 A Resolution
          Length = 499

 Score = 28.1 bits (61), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 15/59 (25%), Positives = 26/59 (44%)

Query: 6   GNSSSTETVNSCLELISSSNHLDDLFDQSDYESEPTTPDTIRQKAVRSKYRGVRPRPWG 64
           G +  TE +N+C E+I +   L D +           PDT ++      + G + + WG
Sbjct: 206 GKARYTECINACNEVIKAGYQLADNYADLFKADNGENPDTKKEIIYPIIFDGDKTQSWG 264


  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
   0.309    0.126    0.378 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,993,973
Number of Sequences: 62578
Number of extensions: 155361
Number of successful extensions: 168
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 163
Number of HSP's gapped (non-prelim): 12
length of query: 124
length of database: 14,973,337
effective HSP length: 85
effective length of query: 39
effective length of database: 9,654,207
effective search space: 376514073
effective search space used: 376514073
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: 45 (21.9 bits)