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= 034900
         (79 letters)

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

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



>pdb|3NKS|A Chain A, Structure Of Human Protoporphyrinogen Ix Oxidase
          Length = 477

 Score = 28.9 bits (63), Expect = 0.71,   Method: Compositional matrix adjust.
 Identities = 13/46 (28%), Positives = 25/46 (54%)

Query: 6   QELLQQDAPQSNQYRFGFHQPPLNSVNHLHLHCLALPFIPRWKHVK 51
           QEL QQ A ++   + G  + P + + HLH +C+    +  W+ ++
Sbjct: 386 QELFQQRAQEAAATQLGLKEMPSHCLVHLHKNCIPQYTLGHWQKLE 431


>pdb|3DLD|A Chain A, Crystal Structure Of Peptide Deformylase, Xoo1075, From
           Xanthomonas Oryzae Pv. Oryzae Kacc10331
          Length = 171

 Score = 28.5 bits (62), Expect = 0.97,   Method: Compositional matrix adjust.
 Identities = 12/32 (37%), Positives = 19/32 (59%), Gaps = 4/32 (12%)

Query: 38  CLALP----FIPRWKHVKYLSLGPLGGFIEAE 65
           CL++P     IPR+++++Y    P G  IE E
Sbjct: 99  CLSIPGLRAVIPRYRYIRYRGFAPDGSPIERE 130


>pdb|3SPD|A Chain A, Crystal Structure Of Aprataxin Ortholog Hnt3 In Complex
           With Dna
 pdb|3SPD|B Chain B, Crystal Structure Of Aprataxin Ortholog Hnt3 In Complex
           With Dna
 pdb|3SPD|C Chain C, Crystal Structure Of Aprataxin Ortholog Hnt3 In Complex
           With Dna
 pdb|3SPD|D Chain D, Crystal Structure Of Aprataxin Ortholog Hnt3 In Complex
           With Dna
 pdb|3SPL|A Chain A, Crystal Structure Of Aprataxin Ortholog Hnt3 In Complex
           With Dna And Amp
 pdb|3SPL|B Chain B, Crystal Structure Of Aprataxin Ortholog Hnt3 In Complex
           With Dna And Amp
 pdb|3SPL|C Chain C, Crystal Structure Of Aprataxin Ortholog Hnt3 In Complex
           With Dna And Amp
 pdb|3SPL|D Chain D, Crystal Structure Of Aprataxin Ortholog Hnt3 In Complex
           With Dna And Amp
          Length = 204

 Score = 25.8 bits (55), Expect = 6.3,   Method: Compositional matrix adjust.
 Identities = 12/29 (41%), Positives = 18/29 (62%), Gaps = 2/29 (6%)

Query: 16  SNQYRFGFHQPPLNSVNHLHLHCLALPFI 44
           +N  + GFH  P  S+N+LHLH + L  +
Sbjct: 102 ANYIKVGFHAGP--SMNNLHLHIMTLDHV 128


>pdb|3SP4|A Chain A, Crystal Structure Of Aprataxin Ortholog Hnt3 From
           Schizosaccharomyces Pombe
 pdb|3SP4|B Chain B, Crystal Structure Of Aprataxin Ortholog Hnt3 From
           Schizosaccharomyces Pombe
          Length = 204

 Score = 25.4 bits (54), Expect = 9.4,   Method: Compositional matrix adjust.
 Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 2/28 (7%)

Query: 17  NQYRFGFHQPPLNSVNHLHLHCLALPFI 44
           N  + GFH  P  S+N+LHLH + L  +
Sbjct: 103 NYIKVGFHAGP--SMNNLHLHIMTLDHV 128


>pdb|3SZQ|A Chain A, Structure Of An S. Pombe AptxDNAAMPZN COMPLEX
          Length = 206

 Score = 25.4 bits (54), Expect = 9.4,   Method: Compositional matrix adjust.
 Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 2/28 (7%)

Query: 17  NQYRFGFHQPPLNSVNHLHLHCLALPFI 44
           N  + GFH  P  S+N+LHLH + L  +
Sbjct: 105 NYIKVGFHAGP--SMNNLHLHIMTLDHV 130


  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    0.138    0.429 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,478,982
Number of Sequences: 62578
Number of extensions: 88413
Number of successful extensions: 136
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 131
Number of HSP's gapped (non-prelim): 7
length of query: 79
length of database: 14,973,337
effective HSP length: 48
effective length of query: 31
effective length of database: 11,969,593
effective search space: 371057383
effective search space used: 371057383
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)