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= 004741
         (732 letters)

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

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



>pdb|1O5I|A Chain A, Crystal Structure Of 3-Oxoacyl-(Acyl Carrier Protein)
           Reductase (Tm1169) From Thermotoga Maritima At 2.50 A
           Resolution
 pdb|1O5I|B Chain B, Crystal Structure Of 3-Oxoacyl-(Acyl Carrier Protein)
           Reductase (Tm1169) From Thermotoga Maritima At 2.50 A
           Resolution
 pdb|1O5I|C Chain C, Crystal Structure Of 3-Oxoacyl-(Acyl Carrier Protein)
           Reductase (Tm1169) From Thermotoga Maritima At 2.50 A
           Resolution
 pdb|1O5I|D Chain D, Crystal Structure Of 3-Oxoacyl-(Acyl Carrier Protein)
           Reductase (Tm1169) From Thermotoga Maritima At 2.50 A
           Resolution
          Length = 249

 Score = 31.2 bits (69), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 17/68 (25%), Positives = 33/68 (48%)

Query: 132 VQDSKHRKTLAELEKGVDGLFDSFARLDSRISSVGQTAAKIGDHLQSADAQRVTASQTID 191
           ++ S HR  + +L K +D LF+    +D  + + G   A   D L + D +    S  ++
Sbjct: 56  LKRSGHRYVVCDLRKDLDLLFEKVKEVDILVLNAGGPKAGFFDELTNEDFKEAIDSLFLN 115

Query: 192 LIKYLMEF 199
           +IK +  +
Sbjct: 116 MIKIVRNY 123


>pdb|4GYZ|A Chain A, Mus Musculus Tdp2 Bound To Damp And Mg2+
 pdb|4GYZ|B Chain B, Mus Musculus Tdp2 Bound To Damp And Mg2+
 pdb|4GYZ|C Chain C, Mus Musculus Tdp2 Bound To Damp And Mg2+
 pdb|4GYZ|D Chain D, Mus Musculus Tdp2 Bound To Damp And Mg2+
 pdb|4GYZ|E Chain E, Mus Musculus Tdp2 Bound To Damp And Mg2+
 pdb|4GYZ|F Chain F, Mus Musculus Tdp2 Bound To Damp And Mg2+
 pdb|4GYZ|G Chain G, Mus Musculus Tdp2 Bound To Damp And Mg2+
 pdb|4GYZ|H Chain H, Mus Musculus Tdp2 Bound To Damp And Mg2+
 pdb|4GYZ|I Chain I, Mus Musculus Tdp2 Bound To Damp And Mg2+
 pdb|4GZ0|A Chain A, Mus Musculus Tdp2-Dna Substrate Analog (5'-6-Aminohexanol)
           Complex
 pdb|4GZ0|B Chain B, Mus Musculus Tdp2-Dna Substrate Analog (5'-6-Aminohexanol)
           Complex
 pdb|4GZ0|E Chain E, Mus Musculus Tdp2-Dna Substrate Analog (5'-6-Aminohexanol)
           Complex
 pdb|4GZ0|K Chain K, Mus Musculus Tdp2-Dna Substrate Analog (5'-6-Aminohexanol)
           Complex
 pdb|4GZ0|G Chain G, Mus Musculus Tdp2-Dna Substrate Analog (5'-6-Aminohexanol)
           Complex
 pdb|4GZ0|I Chain I, Mus Musculus Tdp2-Dna Substrate Analog (5'-6-Aminohexanol)
           Complex
 pdb|4GZ1|A Chain A, Mus Musculus Tdp2 Reaction Product (5'-Phosphorylated
           Dna)-Mg2+ Complex At 1.5 Angstroms Resolution
 pdb|4GZ1|B Chain B, Mus Musculus Tdp2 Reaction Product (5'-Phosphorylated
           Dna)-Mg2+ Complex At 1.5 Angstroms Resolution
          Length = 256

 Score = 30.0 bits (66), Expect = 4.5,   Method: Compositional matrix adjust.
 Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 5/50 (10%)

Query: 423 KTQEL-----ARDLRTVGCGDLDIEGVTECLFTSHKEEYPEHEQASLRQL 467
           K+QE+      + +R + C ++ + G   CL TSH E   EH    +RQL
Sbjct: 88  KSQEIIPFPNTKMMRNLLCVNVSLGGNEFCLMTSHLESTREHSAERIRQL 137


>pdb|4GZ2|A Chain A, Mus Musculus Tdp2 Excluded Ssdna Complex
 pdb|4GZ2|B Chain B, Mus Musculus Tdp2 Excluded Ssdna Complex
          Length = 255

 Score = 30.0 bits (66), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 5/50 (10%)

Query: 423 KTQEL-----ARDLRTVGCGDLDIEGVTECLFTSHKEEYPEHEQASLRQL 467
           K+QE+      + +R + C ++ + G   CL TSH E   EH    +RQL
Sbjct: 88  KSQEIIPFPNTKMMRNLLCVNVSLGGNEFCLMTSHLESTREHSAERIRQL 137


  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
   0.317    0.132    0.363 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,693,323
Number of Sequences: 62578
Number of extensions: 586646
Number of successful extensions: 1635
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 1632
Number of HSP's gapped (non-prelim): 14
length of query: 732
length of database: 14,973,337
effective HSP length: 106
effective length of query: 626
effective length of database: 8,340,069
effective search space: 5220883194
effective search space used: 5220883194
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)