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= 026799
         (233 letters)

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

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



>pdb|2DK5|A Chain A, Solution Structure Of Winged-Helix Domain In Rna
          Polymerase Iii 39kda Polypeptide
          Length = 91

 Score = 44.7 bits (104), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 23/64 (35%), Positives = 40/64 (62%), Gaps = 2/64 (3%)

Query: 18 DHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGK 77
          + E+L+Y +I    + GIW+RD++   + NLP   + K +K+L++K LIK V ++ +  K
Sbjct: 20 NQEKLVYQIIEDAGNKGIWSRDVR--YKSNLPLTEINKILKNLESKKLIKAVKSVAASKK 77

Query: 78 KHLM 81
          K  M
Sbjct: 78 KVYM 81


>pdb|2YU3|A Chain A, Solution Structure Of The Domain Swapped Wingedhelix In
          Dna- Directed Rna Polymerase Iii 39 Kda Polypeptide
          Length = 95

 Score = 41.2 bits (95), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 20/52 (38%), Positives = 34/52 (65%), Gaps = 2/52 (3%)

Query: 18 DHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV 69
          + E+L+Y +I    + GIW+RD++   + NLP   + K +K+L++K LIK V
Sbjct: 37 NQEKLVYQIIEDAGNKGIWSRDVR--YKSNLPLTEINKILKNLESKKLIKAV 86


>pdb|2ZJ2|A Chain A, Archaeal Dna Helicase Hjm Apo State In Form 1
 pdb|2ZJ5|A Chain A, Archaeal Dna Helicase Hjm Complexed With Adp In Form 1
 pdb|2ZJ8|A Chain A, Archaeal Dna Helicase Hjm Apo State In Form 2
 pdb|2ZJA|A Chain A, Archaeal Dna Helicase Hjm Complexed With Amppcp In Form 2
          Length = 720

 Score = 35.0 bits (79), Expect = 0.038,   Method: Composition-based stats.
 Identities = 33/117 (28%), Positives = 52/117 (44%), Gaps = 15/117 (12%)

Query: 14  DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIH 73
           D  +  E L+YD IR K+   I+    ++  RV L    ++K +KSL  K  I+ +  + 
Sbjct: 221 DRFSSWEELVYDAIRKKKGALIFVNMRRKAERVALE---LSKKVKSLLTKPEIRALNELA 277

Query: 74  SKGKKHLMAVEFEPSKE-----ISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVAT 125
                   ++E  P+ E     I GG  +    L  +   +V+    K IIK  VAT
Sbjct: 278 D-------SLEENPTNEKLAKAIRGGVAFHHAGLGRDERVLVEENFRKGIIKAVVAT 327


>pdb|3U3P|A Chain A, The S-Sad Phased Crystal Structure Of The Ecto-Domain Of
           Death Receptor 6 (Dr6)
 pdb|3U3Q|A Chain A, The S-Sad Phased Crystal Structure Of The Ecto-Domain Of
           Death Receptor 6 (Dr6)
 pdb|3U3S|A Chain A, The S-Sad Phased Crystal Structure Of The Ecto-Domain Of
           Death Receptor 6 (Dr6)
 pdb|3U3T|A Chain A, The S-Sad Phased Crystal Structure Of The Ecto-Domain Of
           Death Receptor 6 (Dr6)
 pdb|3U3V|A Chain A, The S-Sad Phased Crystal Structure Of The Ecto-Domain Of
           Death Receptor 6 (Dr6)
          Length = 313

 Score = 28.5 bits (62), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 16/47 (34%), Positives = 23/47 (48%)

Query: 48  LPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGG 94
           +PDN  +   K   NK+L    V  H +G  H   ++  PS E +GG
Sbjct: 234 VPDNTSSARGKEDVNKTLPNLQVVNHQQGPHHRHILKLLPSMEATGG 280


>pdb|3IB5|A Chain A, Crystal Structure Of Sex Pheromone Precursor (Yp_536235.1)
           From Lactobacillus Salivarius Subsp. Salivarius Ucc118
           At 1.35 A Resolution
          Length = 348

 Score = 28.1 bits (61), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 20/63 (31%), Positives = 28/63 (44%), Gaps = 1/63 (1%)

Query: 11  APSDSLTDHERLIYDVIRSKQDMGIWTR-DMKRELRVNLPDNIVTKSIKSLQNKSLIKEV 69
           AP+DSL       Y V +S  D+G WT  ++K  +     DN +     S    +  KEV
Sbjct: 198 APNDSLVGGYFYSYTVSKSGTDIGSWTETNIKSYVLPATEDNKLPNDNDSTSFDNFQKEV 257

Query: 70  VNI 72
            N 
Sbjct: 258 KNF 260


  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
   0.315    0.133    0.383 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,592,053
Number of Sequences: 62578
Number of extensions: 239902
Number of successful extensions: 611
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 603
Number of HSP's gapped (non-prelim): 18
length of query: 233
length of database: 14,973,337
effective HSP length: 96
effective length of query: 137
effective length of database: 8,965,849
effective search space: 1228321313
effective search space used: 1228321313
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)