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= psy17736
         (99 letters)

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

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



>pdb|1N0W|A Chain A, Crystal Structure Of A Rad51-Brca2 Brc Repeat Complex
          Length = 243

 Score = 58.2 bits (139), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 27/30 (90%), Positives = 28/30 (93%)

Query: 2   KYALLIVDSAMALYRTDYSGRGELSARQMH 31
           +YALLIVDSA ALYRTDYSGRGELSARQ H
Sbjct: 119 RYALLIVDSATALYRTDYSGRGELSARQXH 148


>pdb|1SZP|A Chain A, A Crystal Structure Of The Rad51 Filament
 pdb|1SZP|B Chain B, A Crystal Structure Of The Rad51 Filament
 pdb|1SZP|C Chain C, A Crystal Structure Of The Rad51 Filament
 pdb|1SZP|D Chain D, A Crystal Structure Of The Rad51 Filament
 pdb|1SZP|E Chain E, A Crystal Structure Of The Rad51 Filament
 pdb|1SZP|F Chain F, A Crystal Structure Of The Rad51 Filament
          Length = 321

 Score = 57.0 bits (136), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 23/30 (76%), Positives = 29/30 (96%)

Query: 2   KYALLIVDSAMALYRTDYSGRGELSARQMH 31
           +++L++VDS MALYRTD+SGRGELSARQMH
Sbjct: 194 RFSLIVVDSVMALYRTDFSGRGELSARQMH 223


>pdb|3LDA|A Chain A, Yeast Rad51 H352y Filament Interface Mutant
          Length = 400

 Score = 57.0 bits (136), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 23/30 (76%), Positives = 29/30 (96%)

Query: 2   KYALLIVDSAMALYRTDYSGRGELSARQMH 31
           +++L++VDS MALYRTD+SGRGELSARQMH
Sbjct: 273 RFSLIVVDSVMALYRTDFSGRGELSARQMH 302


>pdb|2ZJB|A Chain A, Crystal Structure Of The Human Dmc1-M200v Polymorphic
           Variant
 pdb|2ZJB|B Chain B, Crystal Structure Of The Human Dmc1-M200v Polymorphic
           Variant
          Length = 343

 Score = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 18/27 (66%), Positives = 23/27 (85%)

Query: 3   YALLIVDSAMALYRTDYSGRGELSARQ 29
           + LLI+DS MAL+R D+SGRGEL+ RQ
Sbjct: 220 FKLLIIDSIMALFRVDFSGRGELAERQ 246


>pdb|1V5W|A Chain A, Crystal Structure Of The Human Dmc1 Protein
 pdb|1V5W|B Chain B, Crystal Structure Of The Human Dmc1 Protein
          Length = 343

 Score = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 18/27 (66%), Positives = 23/27 (85%)

Query: 3   YALLIVDSAMALYRTDYSGRGELSARQ 29
           + LLI+DS MAL+R D+SGRGEL+ RQ
Sbjct: 220 FKLLIIDSIMALFRVDFSGRGELAERQ 246


>pdb|2GDJ|A Chain A, Delta-62 Rada Recombinase In Complex With Amp-Pnp And
           Magnesium
          Length = 264

 Score = 32.0 bits (71), Expect = 0.080,   Method: Compositional matrix adjust.
 Identities = 11/25 (44%), Positives = 20/25 (80%)

Query: 5   LLIVDSAMALYRTDYSGRGELSARQ 29
           L+++DS  + +R +Y+GRG+L+ RQ
Sbjct: 149 LVVIDSLTSTFRNEYTGRGKLAERQ 173


>pdb|4DC9|A Chain A, Hexameric Ring Of Methanococcus Voltae Rada
 pdb|4DC9|B Chain B, Hexameric Ring Of Methanococcus Voltae Rada
 pdb|4DC9|C Chain C, Hexameric Ring Of Methanococcus Voltae Rada
 pdb|4DC9|D Chain D, Hexameric Ring Of Methanococcus Voltae Rada
 pdb|4DC9|E Chain E, Hexameric Ring Of Methanococcus Voltae Rada
 pdb|4DC9|F Chain F, Hexameric Ring Of Methanococcus Voltae Rada
          Length = 266

 Score = 32.0 bits (71), Expect = 0.084,   Method: Compositional matrix adjust.
 Identities = 11/25 (44%), Positives = 20/25 (80%)

Query: 5   LLIVDSAMALYRTDYSGRGELSARQ 29
           L+++DS  + +R +Y+GRG+L+ RQ
Sbjct: 151 LVVIDSLTSTFRNEYTGRGKLAERQ 175


>pdb|4A6P|A Chain A, Rada C-Terminal Atpase Domain From Pyrococcus Furiosus
 pdb|4A6X|A Chain A, Rada C-Terminal Atpase Domain From Pyrococcus Furiosus
           Bound To Atp
 pdb|4A6X|B Chain B, Rada C-Terminal Atpase Domain From Pyrococcus Furiosus
           Bound To Atp
 pdb|4A74|A Chain A, Rada C-Terminal Atpase Domain From Pyrococcus Furiosus
           Bound To Amppnp
 pdb|4A74|B Chain B, Rada C-Terminal Atpase Domain From Pyrococcus Furiosus
           Bound To Amppnp
 pdb|4A7O|A Chain A, Rada C-Terminal Atpase Domain From Pyrococcus Furiosus
           Bound To Adp
          Length = 231

 Score = 32.0 bits (71), Expect = 0.085,   Method: Compositional matrix adjust.
 Identities = 14/25 (56%), Positives = 19/25 (76%)

Query: 5   LLIVDSAMALYRTDYSGRGELSARQ 29
           LLIVDS  + +R++Y GRG L+ RQ
Sbjct: 128 LLIVDSLTSHFRSEYIGRGALAERQ 152


>pdb|4B2I|A Chain A, Humanised Monomeric Rada In Complex With Indazole
 pdb|4B2L|A Chain A, Humanised Monomeric Rada In Complex With L-methylester
           Tryptophan
 pdb|4B32|A Chain A, Humanised Monomeric Rada In Complex With Napht-1-ol
 pdb|4B33|A Chain A, Humanised Monomeric Rada In Complex With Napht-2-ol
 pdb|4B34|A Chain A, Humanised Monomeric Rada In Complex With 2-amino
           Benzothiazole
 pdb|4B35|A Chain A, Humanised Monomeric Rada In Complex With 4-methylester
           Indole
 pdb|4B3C|A Chain A, Humanised Monomeric Rada In Complex With 5-hydroxy Indole
 pdb|4B3D|A Chain A, Humanised Monomeric Rada In Complex With 5-methyl Indole
 pdb|4B3D|C Chain C, Humanised Monomeric Rada In Complex With 5-methyl Indole
 pdb|4B3B|A Chain A, Humanised Monomeric Rada In Complex With Fhta Tetrapeptide
          Length = 231

 Score = 32.0 bits (71), Expect = 0.092,   Method: Compositional matrix adjust.
 Identities = 14/25 (56%), Positives = 19/25 (76%)

Query: 5   LLIVDSAMALYRTDYSGRGELSARQ 29
           LLIVDS  + +R++Y GRG L+ RQ
Sbjct: 128 LLIVDSLTSHFRSEYIGRGALAERQ 152


>pdb|3NTU|A Chain A, Rada Recombinase D302k Mutant In Complex With Amp-Pnp
          Length = 319

 Score = 32.0 bits (71), Expect = 0.093,   Method: Compositional matrix adjust.
 Identities = 11/25 (44%), Positives = 20/25 (80%)

Query: 5   LLIVDSAMALYRTDYSGRGELSARQ 29
           L+++DS  + +R +Y+GRG+L+ RQ
Sbjct: 204 LVVIDSLTSTFRNEYTGRGKLAERQ 228


>pdb|1T4G|A Chain A, Atpase In Complex With Amp-pnp
 pdb|1XU4|A Chain A, Atpase In Complex With Amp-Pnp, Magnesium And Potassium
           Co-F
 pdb|2FPK|A Chain A, Rada Recombinase In Complex With Adp
 pdb|2FPL|A Chain A, Rada Recombinase In Complex With Amp-Pnp And Low
           Concentration Of K+
 pdb|2FPM|A Chain A, Rada Recombinase In Complex With Amp-Pnp And High
           Concentration Of K+
 pdb|2B21|A Chain A, Rada Recombinase In Complex With Amppnp At Ph 6.0
 pdb|2I1Q|A Chain A, Rada Recombinase In Complex With Calcium
 pdb|3FYH|A Chain A, Recombinase In Complex With Adp And Metatungstate
          Length = 322

 Score = 32.0 bits (71), Expect = 0.097,   Method: Compositional matrix adjust.
 Identities = 11/25 (44%), Positives = 20/25 (80%)

Query: 5   LLIVDSAMALYRTDYSGRGELSARQ 29
           L+++DS  + +R +Y+GRG+L+ RQ
Sbjct: 207 LVVIDSLTSTFRNEYTGRGKLAERQ 231


>pdb|2F1H|A Chain A, Recombinase In Complex With Amp-pnp And Potassium
 pdb|2F1I|A Chain A, Recombinase In Complex With Amp-pnp
 pdb|2F1J|A Chain A, Recombinase In Complex With Adp
          Length = 322

 Score = 32.0 bits (71), Expect = 0.097,   Method: Compositional matrix adjust.
 Identities = 11/25 (44%), Positives = 20/25 (80%)

Query: 5   LLIVDSAMALYRTDYSGRGELSARQ 29
           L+++DS  + +R +Y+GRG+L+ RQ
Sbjct: 207 LVVIDSLTSTFRNEYTGRGKLAERQ 231


>pdb|3ETL|A Chain A, Rada Recombinase From Methanococcus Maripaludis In Complex
           With Amppnp
 pdb|3EW9|A Chain A, Rada Recombinase From Methanococcus Maripaludis In Complex
           With Amppnp And Potassium Ions
 pdb|3EWA|A Chain A, Rada Recombinase From Methanococcus Maripaludis In Complex
           With Amppnp And Ammonium Ions
          Length = 322

 Score = 31.6 bits (70), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 11/25 (44%), Positives = 20/25 (80%)

Query: 5   LLIVDSAMALYRTDYSGRGELSARQ 29
           L+I+DS  + +R +++GRG+L+ RQ
Sbjct: 207 LVIIDSLTSTFRNEFTGRGKLAERQ 231


>pdb|1PZN|A Chain A, Rad51 (Rada)
 pdb|1PZN|B Chain B, Rad51 (Rada)
 pdb|1PZN|C Chain C, Rad51 (Rada)
 pdb|1PZN|D Chain D, Rad51 (Rada)
 pdb|1PZN|E Chain E, Rad51 (Rada)
 pdb|1PZN|F Chain F, Rad51 (Rada)
 pdb|1PZN|G Chain G, Rad51 (Rada)
          Length = 349

 Score = 30.8 bits (68), Expect = 0.20,   Method: Composition-based stats.
 Identities = 14/25 (56%), Positives = 19/25 (76%)

Query: 5   LLIVDSAMALYRTDYSGRGELSARQ 29
           LLIVDS  + +R++Y GRG L+ RQ
Sbjct: 234 LLIVDSLTSHFRSEYIGRGALAERQ 258


>pdb|2BKE|A Chain A, Conformational Flexibility Revealed By The Crystal
           Structure Of A Crenarchaeal Rada
          Length = 324

 Score = 28.1 bits (61), Expect = 1.4,   Method: Composition-based stats.
 Identities = 11/25 (44%), Positives = 17/25 (68%)

Query: 5   LLIVDSAMALYRTDYSGRGELSARQ 29
           L++VDS  + +R +Y GR  L+ RQ
Sbjct: 206 LIVVDSVTSHFRAEYPGRENLAVRQ 230


>pdb|2DFL|A Chain A, Crystal Structure Of Left-Handed Rada Filament
 pdb|2Z43|A Chain A, Structure Of A Twinned Crystal Of Rada
 pdb|2Z43|B Chain B, Structure Of A Twinned Crystal Of Rada
 pdb|2Z43|C Chain C, Structure Of A Twinned Crystal Of Rada
 pdb|2ZUB|A Chain A, Left Handed Rada
 pdb|2ZUB|B Chain B, Left Handed Rada
 pdb|2ZUC|A Chain A, Crystal Structure Of Left-Handed Rada Filament
 pdb|2ZUC|B Chain B, Crystal Structure Of Left-Handed Rada Filament
 pdb|2ZUD|A Chain A, Crystal Structure Of Left-Handed Rada Filament
 pdb|2ZUD|B Chain B, Crystal Structure Of Left-Handed Rada Filament
          Length = 324

 Score = 27.7 bits (60), Expect = 1.5,   Method: Composition-based stats.
 Identities = 11/25 (44%), Positives = 17/25 (68%)

Query: 5   LLIVDSAMALYRTDYSGRGELSARQ 29
           L++VDS  + +R +Y GR  L+ RQ
Sbjct: 206 LIVVDSVTSHFRAEYPGRENLAVRQ 230


  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    0.134    0.369 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,035,712
Number of Sequences: 62578
Number of extensions: 14210
Number of successful extensions: 30
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 14
Number of HSP's gapped (non-prelim): 16
length of query: 99
length of database: 14,973,337
effective HSP length: 65
effective length of query: 34
effective length of database: 10,905,767
effective search space: 370796078
effective search space used: 370796078
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: 45 (21.9 bits)