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= psy4906
         (144 letters)

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

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



>pdb|3QKU|A Chain A, Mre11 Rad50 Binding Domain In Complex With Rad50 And
           Amp-Pnp
 pdb|3QKU|B Chain B, Mre11 Rad50 Binding Domain In Complex With Rad50 And
           Amp-Pnp
          Length = 359

 Score = 26.6 bits (57), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 30/101 (29%), Positives = 48/101 (47%), Gaps = 13/101 (12%)

Query: 8   RQGEIDRCLKKVSEGVETFEDIWQKVHNATNSNQKEKYEADLKKEIKKLQRLRDQIKSWI 67
           RQG+ID  L    E  E  E + ++V N        K  ++LKK I       ++IK + 
Sbjct: 139 RQGQIDAIL----ESDEAREKVVREVLNLDKFETAYKKLSELKKTIN------NRIKEYG 188

Query: 68  ASAEIKDKSTLLDYRKLIETQMERFKVVERETKTKAYSKEG 108
            S  IKD     D+ + +  +++++K + RE    A SK G
Sbjct: 189 GSGGIKDLEKAKDFTEELIEKVKKYKALAREA---ALSKIG 226


>pdb|3CSX|A Chain A, Structural Characterization Of A Protein In The Duf683
          Family- Crystal Structure Of Cce_0567 From The
          Cyanobacterium Cyanothece 51142.
 pdb|3CSX|B Chain B, Structural Characterization Of A Protein In The Duf683
          Family- Crystal Structure Of Cce_0567 From The
          Cyanobacterium Cyanothece 51142
          Length = 81

 Score = 26.2 bits (56), Expect = 6.5,   Method: Compositional matrix adjust.
 Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 7/61 (11%)

Query: 36 ATNSNQKEKYEADLKKEIKKLQRLRDQIKSWIASAEIKDKSTLL--DYRKLIETQMERFK 93
          AT++N   +  ADLKK+++KL     Q+K      ++ D +  L  DY  L+ET  + ++
Sbjct: 7  ATDNNPTPEAVADLKKKVRKLNSKAGQMK-----MDLHDLAEGLPTDYENLVETAEKTYE 61

Query: 94 V 94
          +
Sbjct: 62 I 62


>pdb|4DLQ|A Chain A, Crystal Structure Of The Gain And Hormr Domains Of Cirl
           1LATROPHILIN 1 (Cl1)
          Length = 381

 Score = 26.2 bits (56), Expect = 7.0,   Method: Compositional matrix adjust.
 Identities = 16/60 (26%), Positives = 32/60 (53%), Gaps = 5/60 (8%)

Query: 47  ADLKKEIKKLQRLRDQIKSWIASAEIKDKSTLLDYRKLIETQMERFKVVERETKTKAYSK 106
           A++  E+ +    R  I +   S+ +K    LLD   +++ Q++  + +ERE+  K Y+K
Sbjct: 95  ANIASELAR--HTRGSIYAGDVSSSVKLMEQLLD---ILDAQLQALRPIERESAGKNYNK 149


>pdb|2ODR|B Chain B, Methanococcus Maripaludis Phosphoseryl-Trna Synthetase
          Length = 648

 Score = 25.8 bits (55), Expect = 7.9,   Method: Compositional matrix adjust.
 Identities = 17/46 (36%), Positives = 24/46 (52%)

Query: 92  FKVVERETKTKAYSKEGLGAVQKMDPAQKEKEEISTWLVTSIDALN 137
           FK +  E K+K Y+ E    V    P  KE  E++T+ V S  AL+
Sbjct: 281 FKFIPDEKKSKYYTPETQTEVYAYHPKLKEWLEVATFGVYSPVALS 326


>pdb|2ODR|A Chain A, Methanococcus Maripaludis Phosphoseryl-Trna Synthetase
          Length = 665

 Score = 25.8 bits (55), Expect = 7.9,   Method: Compositional matrix adjust.
 Identities = 17/46 (36%), Positives = 24/46 (52%)

Query: 92  FKVVERETKTKAYSKEGLGAVQKMDPAQKEKEEISTWLVTSIDALN 137
           FK +  E K+K Y+ E    V    P  KE  E++T+ V S  AL+
Sbjct: 281 FKFIPDEKKSKYYTPETQTEVYAYHPKLKEWLEVATFGVYSPVALS 326


>pdb|2ODR|C Chain C, Methanococcus Maripaludis Phosphoseryl-Trna Synthetase
          Length = 701

 Score = 25.8 bits (55), Expect = 7.9,   Method: Compositional matrix adjust.
 Identities = 17/46 (36%), Positives = 24/46 (52%)

Query: 92  FKVVERETKTKAYSKEGLGAVQKMDPAQKEKEEISTWLVTSIDALN 137
           FK +  E K+K Y+ E    V    P  KE  E++T+ V S  AL+
Sbjct: 281 FKFIPDEKKSKYYTPETQTEVYAYHPKLKEWLEVATFGVYSPVALS 326


>pdb|2ODR|D Chain D, Methanococcus Maripaludis Phosphoseryl-Trna Synthetase
          Length = 685

 Score = 25.8 bits (55), Expect = 8.0,   Method: Compositional matrix adjust.
 Identities = 17/47 (36%), Positives = 24/47 (51%)

Query: 91  RFKVVERETKTKAYSKEGLGAVQKMDPAQKEKEEISTWLVTSIDALN 137
            FK +  E K+K Y+ E    V    P  KE  E++T+ V S  AL+
Sbjct: 280 NFKFIPDEKKSKYYTPETQTEVYAYHPKLKEWLEVATFGVYSPVALS 326


  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
   0.311    0.126    0.345 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,994,864
Number of Sequences: 62578
Number of extensions: 140812
Number of successful extensions: 417
Number of sequences better than 100.0: 45
Number of HSP's better than 100.0 without gapping: 20
Number of HSP's successfully gapped in prelim test: 25
Number of HSP's that attempted gapping in prelim test: 397
Number of HSP's gapped (non-prelim): 45
length of query: 144
length of database: 14,973,337
effective HSP length: 89
effective length of query: 55
effective length of database: 9,403,895
effective search space: 517214225
effective search space used: 517214225
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 46 (22.3 bits)