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= 029015
         (200 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 = 40.4 bits (93), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 21/57 (36%), Positives = 28/57 (49%), Gaps = 1/57 (1%)

Query: 45  FRGVRMRNNNKWVCELREPNKK-SRIWLGTYPTPEMXXXXXXXXXXXXXGKSTCLNF 100
           +RGVR R   K+  E+R+P K  +R+WLGT+ T E              G    LNF
Sbjct: 6   YRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNF 62


>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 = 38.5 bits (88), Expect = 0.002,   Method: Composition-based stats.
 Identities = 21/57 (36%), Positives = 28/57 (49%), Gaps = 1/57 (1%)

Query: 45  FRGVRMRNNNKWVCELREPNKK-SRIWLGTYPTPEMXXXXXXXXXXXXXGKSTCLNF 100
           +RGVR R   K+  E+R+P K  +R+WLGT+ T E              G    LNF
Sbjct: 3   YRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNF 59


>pdb|3JTZ|A Chain A, Structure Of The Arm-type Binding Domain Of Hpi
          Integrase
 pdb|3RMP|A Chain A, Structural Basis For The Recognition Of Attp Substrates
          By P4-Like Integrases
 pdb|3RMP|C Chain C, Structural Basis For The Recognition Of Attp Substrates
          By P4-Like Integrases
          Length = 88

 Score = 26.9 bits (58), Expect = 7.5,   Method: Compositional matrix adjust.
 Identities = 12/38 (31%), Positives = 19/38 (50%)

Query: 42 HPIFRGVRMRNNNKWVCELREPNKKSRIWLGTYPTPEM 79
          H ++  V+   +  W  + R   K+SRI LG YP   +
Sbjct: 24 HGLYLLVKPGGSRHWYLKYRISGKESRIALGAYPAISL 61


  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
   0.320    0.136    0.445 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,935,969
Number of Sequences: 62578
Number of extensions: 148341
Number of successful extensions: 183
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 168
Number of HSP's gapped (non-prelim): 15
length of query: 200
length of database: 14,973,337
effective HSP length: 94
effective length of query: 106
effective length of database: 9,091,005
effective search space: 963646530
effective search space used: 963646530
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)