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= 047098
         (113 letters)

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

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



>pdb|3THO|A Chain A, Crystal Structure Of Mre11:rad50 In Its AtpADP BOUND STATE
          Length = 382

 Score = 29.3 bits (64), Expect = 0.51,   Method: Composition-based stats.
 Identities = 27/85 (31%), Positives = 38/85 (44%), Gaps = 9/85 (10%)

Query: 11  NPEGWELIKPTLRELQAKMREGGLRAAMFLTRTMELYE--------FCLDQGYKSQIWRK 62
           + +G  +IK    E  A+   GG RA + ++  M L E        F +D+G+ S     
Sbjct: 278 DEKGGFIIKDWGIERPARGLSGGERALISISLAMSLAEVASGRLDAFFIDEGFSSLCTEN 337

Query: 63  KEKVASC-KMNRVLEAVAVMFDIDR 86
           KEK+AS  K    L  V V    DR
Sbjct: 338 KEKIASVLKELERLNKVIVFITCDR 362


>pdb|3QF7|A Chain A, The Mre11:rad50 Complex Forms An Atp Dependent Molecular
           Clamp In Dna Double-Strand Break Repair
 pdb|3QF7|B Chain B, The Mre11:rad50 Complex Forms An Atp Dependent Molecular
           Clamp In Dna Double-Strand Break Repair
          Length = 365

 Score = 28.1 bits (61), Expect = 1.1,   Method: Composition-based stats.
 Identities = 23/78 (29%), Positives = 38/78 (48%), Gaps = 13/78 (16%)

Query: 11  NPEGWELIKPTLRELQAKMREGGLRAAMFLTRTMELYE--------FCLDQGYKSQIWRK 62
           + +G  +IK    E  A+   GG RA + ++  M L E        F +D+G+ S     
Sbjct: 261 DEKGGFIIKDWGIERPARGLSGGERALISISLAMSLAEVASGRLDAFFIDEGFSSLDTEN 320

Query: 63  KEKVASC-----KMNRVL 75
           KEK+AS      ++N+V+
Sbjct: 321 KEKIASVLKELERLNKVI 338


>pdb|1CII|A Chain A, Colicin Ia
          Length = 602

 Score = 26.9 bits (58), Expect = 2.6,   Method: Composition-based stats.
 Identities = 12/35 (34%), Positives = 20/35 (57%)

Query: 4   VKTNRVQNPEGWELIKPTLRELQAKMREGGLRAAM 38
           +KT R  N +  ++ +   R LQA++RE G R  +
Sbjct: 94  LKTLRAGNADAADITRQEFRLLQAELREYGFRTEI 128


>pdb|1JR2|A Chain A, Structure Of Uroporphyrinogen Iii Synthase
 pdb|1JR2|B Chain B, Structure Of Uroporphyrinogen Iii Synthase
          Length = 286

 Score = 26.2 bits (56), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 13/35 (37%), Positives = 21/35 (60%), Gaps = 4/35 (11%)

Query: 32  GGLRAAMFLT-RTMELYEFCLDQGYKSQIWRKKEK 65
           GGL   +F + R +E  E CL+Q  K+++W +  K
Sbjct: 78  GGL---IFTSPRAVEAAELCLEQNNKTEVWERSLK 109


>pdb|3QG5|A Chain A, The Mre11:rad50 Complex Forms An Atp Dependent Molecular
           Clamp In Dna Double-Strand Break Repair
 pdb|3QG5|B Chain B, The Mre11:rad50 Complex Forms An Atp Dependent Molecular
           Clamp In Dna Double-Strand Break Repair
          Length = 365

 Score = 25.8 bits (55), Expect = 7.0,   Method: Composition-based stats.
 Identities = 22/78 (28%), Positives = 37/78 (47%), Gaps = 13/78 (16%)

Query: 11  NPEGWELIKPTLRELQAKMREGGLRAAMFLTRTMELYE--------FCLDQGYKSQIWRK 62
           + +G  +IK    E  A+   GG RA + ++    L E        F +D+G+ S     
Sbjct: 261 DEKGGFIIKDWGIERPARGLSGGERALISISLAXSLAEVASGRLDAFFIDEGFSSLDTEN 320

Query: 63  KEKVASC-----KMNRVL 75
           KEK+AS      ++N+V+
Sbjct: 321 KEKIASVLKELERLNKVI 338


  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
   0.327    0.137    0.433 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,180,672
Number of Sequences: 62578
Number of extensions: 97548
Number of successful extensions: 305
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 302
Number of HSP's gapped (non-prelim): 6
length of query: 113
length of database: 14,973,337
effective HSP length: 77
effective length of query: 36
effective length of database: 10,154,831
effective search space: 365573916
effective search space used: 365573916
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 45 (21.9 bits)