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= 019609
         (338 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 = 37.7 bits (86), Expect = 0.010,   Method: Composition-based stats.
 Identities = 23/57 (40%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 252 YRGVTLHKCGRWEARMGQ-FLGKKYVYLGLFDTEVEAARAYDRAAVKCNGKDAVTNF 307
           YRGV     G++ A +         V+LG F+T  +AA AYDRAA +  G  A+ NF
Sbjct: 3   YRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNF 59



 Score = 29.6 bits (65), Expect = 2.3,   Method: Composition-based stats.
 Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 4/61 (6%)

Query: 159 QYRGVTFYRRTGRWESHIWD---SGKQVYLGGFDTXXXXXXXXXXXXIKFRGAEADINFS 215
            YRGV   R  G++ + I D   +G +V+LG F+T             + RG+ A +NF 
Sbjct: 2   HYRGVR-QRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFP 60

Query: 216 I 216
           +
Sbjct: 61  L 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 = 37.4 bits (85), Expect = 0.012,   Method: Composition-based stats.
 Identities = 23/57 (40%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 252 YRGVTLHKCGRWEARM-GQFLGKKYVYLGLFDTEVEAARAYDRAAVKCNGKDAVTNF 307
           YRGV     G++ A +         V+LG F+T  +AA AYDRAA +  G  A+ NF
Sbjct: 6   YRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNF 62



 Score = 29.6 bits (65), Expect = 2.9,   Method: Composition-based stats.
 Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 4/61 (6%)

Query: 159 QYRGVTFYRRTGRWESHIWD---SGKQVYLGGFDTXXXXXXXXXXXXIKFRGAEADINFS 215
            YRGV   R  G++ + I D   +G +V+LG F+T             + RG+ A +NF 
Sbjct: 5   HYRGVR-QRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFP 63

Query: 216 I 216
           +
Sbjct: 64  L 64


>pdb|3AUX|A Chain A, Crystal Structure Of Rad50 Bound To Adp
 pdb|3AUY|A Chain A, Crystal Structure Of Rad50 Bound To Adp
 pdb|3AUY|B Chain B, Crystal Structure Of Rad50 Bound To Adp
 pdb|3AV0|B Chain B, Crystal Structure Of Mre11-Rad50 Bound To Atp S
          Length = 371

 Score = 27.7 bits (60), Expect = 9.3,   Method: Compositional matrix adjust.
 Identities = 33/135 (24%), Positives = 59/135 (43%), Gaps = 11/135 (8%)

Query: 209 EADINFSIEDYEDDLKQMSNLTKE-----EFVHVLRRQSTGFPRGSSKYRGVTLHKCGRW 263
           E ++N+  E  +  LK+MSNL KE     +FV  L +    F R      G   +   ++
Sbjct: 183 EGELNYKEESLKARLKEMSNLEKEKEKLTKFVEYLDKVRRIFGRN-----GFQAYLREKY 237

Query: 264 EARMGQFLGKKYVYLGLFDTEVEAARAYDRAAVKCNGKDAVTNFDPSLYQDELKASVQLL 323
              + ++L + +    L  + VE  + ++      NG   + N      Q  +  S++L 
Sbjct: 238 VPLIQKYLNEAFSEFDLPYSFVELTKDFEVRVHAPNGVLTIDNLSGG-EQIAVALSLRLA 296

Query: 324 ISKAVRTLLIECNIL 338
           I+ A+    +EC IL
Sbjct: 297 IANALIGNRVECIIL 311


  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
   0.316    0.134    0.396 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,845,120
Number of Sequences: 62578
Number of extensions: 316293
Number of successful extensions: 502
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 498
Number of HSP's gapped (non-prelim): 5
length of query: 338
length of database: 14,973,337
effective HSP length: 99
effective length of query: 239
effective length of database: 8,778,115
effective search space: 2097969485
effective search space used: 2097969485
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)