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= 025493
         (252 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 = 40.4 bits (93), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 24/65 (36%), Positives = 40/65 (61%), Gaps = 3/65 (4%)

Query: 36  DHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKG 95
           + E+L+Y +I  +  + GIW+RD++   K NLP   + K +K+L++K LIK V ++    
Sbjct: 20  NQEKLVYQIIE-DAGNKGIWSRDVR--YKSNLPLTEINKILKNLESKKLIKAVKSVAASK 76

Query: 96  KKHLM 100
           KK  M
Sbjct: 77  KKVYM 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 = 38.9 bits (89), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 45/77 (58%), Gaps = 4/77 (5%)

Query: 13 LAKGSGMSKRKRPDSNAPSDSLTDH-ERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNI 71
          L   +G+  R +   NA     +D+ E+L+Y +I  +  + GIW+RD++   K NLP   
Sbjct: 13 LRSNTGLLYRIKDSQNAGKMKGSDNQEKLVYQIIE-DAGNKGIWSRDVR--YKSNLPLTE 69

Query: 72 VTKSIKSLQNKSLIKEV 88
          + K +K+L++K LIK V
Sbjct: 70 INKILKNLESKKLIKAV 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 = 29.3 bits (64), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 32/118 (27%), Positives = 53/118 (44%), Gaps = 16/118 (13%)

Query: 32  DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNI 91
           D  +  E L+YD IR  K  + I+    ++  +V L    ++K +KSL  K  I+ +  +
Sbjct: 221 DRFSSWEELVYDAIRKKKGAL-IFVNMRRKAERVALE---LSKKVKSLLTKPEIRALNEL 276

Query: 92  HNKGKKHLMAVEFEP-----SKDISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVAT 144
            +       ++E  P     +K I GG  +    L  +   +V+    K IIK  VAT
Sbjct: 277 AD-------SLEENPTNEKLAKAIRGGVAFHHAGLGRDERVLVEENFRKGIIKAVVAT 327


>pdb|1FW1|A Chain A, Glutathione Transferase ZetaMALEYLACETOACETATE ISOMERASE
          Length = 216

 Score = 28.5 bits (62), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 15/58 (25%), Positives = 31/58 (53%), Gaps = 1/58 (1%)

Query: 32  DSLTDHERL-IYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV 88
           D +T H+ L I + +   +    +  +D K+   V +  +++   I+ LQN S++K+V
Sbjct: 65  DGITIHQSLAIIEYLEETRPTPRLLPQDPKKRASVRMISDLIAGGIQPLQNLSVLKQV 122


  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    0.384 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,298,689
Number of Sequences: 62578
Number of extensions: 276523
Number of successful extensions: 634
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 631
Number of HSP's gapped (non-prelim): 17
length of query: 252
length of database: 14,973,337
effective HSP length: 97
effective length of query: 155
effective length of database: 8,903,271
effective search space: 1380007005
effective search space used: 1380007005
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)