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= 014204
         (429 letters)

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

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



>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 = 42.0 bits (97), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 24/68 (35%), Positives = 38/68 (55%), Gaps = 8/68 (11%)

Query: 108 QYRGVTRHRWTGRYEAHLWDNSCRKEGQTRKGRQVYLGGYDKEDKAARAYDLAALKYWGA 167
            YRGV +  W G++ A + D +       + G +V+LG ++  + AA AYD AA +  G+
Sbjct: 2   HYRGVRQRPW-GKFAAEIRDPA-------KNGARVWLGTFETAEDAALAYDRAAFRMRGS 53

Query: 168 TTHINFPL 175
              +NFPL
Sbjct: 54  RALLNFPL 61



 Score = 37.0 bits (84), Expect = 0.019,   Method: Composition-based stats.
 Identities = 24/60 (40%), Positives = 32/60 (53%), Gaps = 2/60 (3%)

Query: 211 YRGVTRHHQHGRWQARIGRVAGN-KDLYLGTFSTQXXXXXXYDIAAIKFRGTSAVTNFDI 269
           YRGV R    G++ A I   A N   ++LGTF T       YD AA + RG+ A+ NF +
Sbjct: 3   YRGV-RQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFPL 61


>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 = 40.8 bits (94), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 24/70 (34%), Positives = 38/70 (54%), Gaps = 8/70 (11%)

Query: 108 QYRGVTRHRWTGRYEAHLWDNSCRKEGQTRKGRQVYLGGYDKEDKAARAYDLAALKYWGA 167
            YRGV +  W G++ A + D +       + G +V+LG ++  + AA AYD AA +  G+
Sbjct: 5   HYRGVRQRPW-GKFAAEIRDPA-------KNGARVWLGTFETAEDAALAYDRAAFRMRGS 56

Query: 168 TTHINFPLST 177
              +NFPL  
Sbjct: 57  RALLNFPLRV 66



 Score = 38.1 bits (87), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 24/60 (40%), Positives = 32/60 (53%), Gaps = 2/60 (3%)

Query: 211 YRGVTRHHQHGRWQARIGRVAGN-KDLYLGTFSTQXXXXXXYDIAAIKFRGTSAVTNFDI 269
           YRGV R    G++ A I   A N   ++LGTF T       YD AA + RG+ A+ NF +
Sbjct: 6   YRGV-RQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFPL 64


>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
           Single-Stranded Interacting Protein 1
          Length = 114

 Score = 34.3 bits (77), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 23/61 (37%), Positives = 27/61 (44%), Gaps = 4/61 (6%)

Query: 172 NFPLSTYEKELEEMKHMTRQEFVANLRRKSSGFSRGASVYRGVTRHHQHGRWQARIGRVA 231
           N PLS  E+ELE M     Q     + R SSG SRG     G  R     + +A IG   
Sbjct: 32  NLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGV----GFARMESTEKCEAVIGHFN 87

Query: 232 G 232
           G
Sbjct: 88  G 88


>pdb|2Q1F|A Chain A, Crystal Structure Of Chondroitin Sulfate Lyase Abc From
           Bacteroides Thetaiotaomicron Wal2926
 pdb|2Q1F|B Chain B, Crystal Structure Of Chondroitin Sulfate Lyase Abc From
           Bacteroides Thetaiotaomicron Wal2926
          Length = 1022

 Score = 30.8 bits (68), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 11/24 (45%), Positives = 16/24 (66%)

Query: 363 PESPKCPVGLTSEFGMSGAEYNEG 386
           P+ P C  G+ S+ G+SGA Y +G
Sbjct: 28  PQLPACITGVQSQLGISGAHYKDG 51


  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
   0.314    0.129    0.389 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,314,730
Number of Sequences: 62578
Number of extensions: 483836
Number of successful extensions: 652
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 628
Number of HSP's gapped (non-prelim): 24
length of query: 429
length of database: 14,973,337
effective HSP length: 102
effective length of query: 327
effective length of database: 8,590,381
effective search space: 2809054587
effective search space used: 2809054587
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 53 (25.0 bits)