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= psy16970
         (257 letters)

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

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



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

 Score = 29.6 bits (65), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 25/81 (30%), Positives = 32/81 (39%), Gaps = 13/81 (16%)

Query: 86  VLGQIYIYIYHMHWTPAQQANVLFSDEPRVNFGDVRIPKGFDFP-----RPQKIGQLAGV 140
           V G     I H      Q    LF DE  V+ G+V  PK          RP++I Q+A  
Sbjct: 103 VFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQMAEH 162

Query: 141 HGVSSDPIVIVDAQTLLVPNF 161
            G        +D QT+L   F
Sbjct: 163 AG--------IDGQTVLDNTF 175


>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 = 29.6 bits (65), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 25/81 (30%), Positives = 32/81 (39%), Gaps = 13/81 (16%)

Query: 86  VLGQIYIYIYHMHWTPAQQANVLFSDEPRVNFGDVRIPKGFDFP-----RPQKIGQLAGV 140
           V G     I H      Q    LF DE  V+ G+V  PK          RP++I Q+A  
Sbjct: 106 VFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQMAEH 165

Query: 141 HGVSSDPIVIVDAQTLLVPNF 161
            G        +D QT+L   F
Sbjct: 166 AG--------IDGQTVLDNTF 178


>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 = 29.6 bits (65), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 25/81 (30%), Positives = 32/81 (39%), Gaps = 13/81 (16%)

Query: 86  VLGQIYIYIYHMHWTPAQQANVLFSDEPRVNFGDVRIPKGFDFP-----RPQKIGQLAGV 140
           V G     I H      Q    LF DE  V+ G+V  PK          RP++I Q+A  
Sbjct: 106 VFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTDGTFRPERIMQMAEH 165

Query: 141 HGVSSDPIVIVDAQTLLVPNF 161
            G        +D QT+L   F
Sbjct: 166 AG--------IDGQTVLDNTF 178


>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 = 29.3 bits (64), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 25/81 (30%), Positives = 32/81 (39%), Gaps = 13/81 (16%)

Query: 86  VLGQIYIYIYHMHWTPAQQANVLFSDEPRVNFGDVRIPKGFDFP-----RPQKIGQLAGV 140
           V G     I H      Q    LF DE  V+ G+V  PK          RP++I Q+A  
Sbjct: 50  VFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQMAEH 109

Query: 141 HGVSSDPIVIVDAQTLLVPNF 161
            G        +D QT+L   F
Sbjct: 110 AG--------IDGQTVLDNTF 122


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

 Score = 29.3 bits (64), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 25/81 (30%), Positives = 32/81 (39%), Gaps = 13/81 (16%)

Query: 86  VLGQIYIYIYHMHWTPAQQANVLFSDEPRVNFGDVRIPKGFDFP-----RPQKIGQLAGV 140
           V G     I H      Q    LF DE  V+ G+V  PK          RP++I Q+A  
Sbjct: 48  VFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQMAEH 107

Query: 141 HGVSSDPIVIVDAQTLLVPNF 161
            G        +D QT+L   F
Sbjct: 108 AG--------IDGQTVLDNTF 120


  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
   0.321    0.139    0.423 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,959,341
Number of Sequences: 62578
Number of extensions: 351186
Number of successful extensions: 617
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 617
Number of HSP's gapped (non-prelim): 7
length of query: 257
length of database: 14,973,337
effective HSP length: 97
effective length of query: 160
effective length of database: 8,903,271
effective search space: 1424523360
effective search space used: 1424523360
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 bits)