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= 004909
         (724 letters)

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

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



>pdb|2J7N|A Chain A, Structure Of The Rnai Polymerase From Neurospora Crassa
 pdb|2J7N|B Chain B, Structure Of The Rnai Polymerase From Neurospora Crassa
 pdb|2J7O|A Chain A, Structure Of The Rnai Polymerase From Neurospora Crassa
          Length = 1022

 Score = 57.0 bits (136), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 75/306 (24%), Positives = 122/306 (39%), Gaps = 49/306 (16%)

Query: 426 TKYVFSDGIGKVSAEFARKVASKCGLKDNPPSAFQIRYGGYKG--VVAADPTSSKK-LSL 482
           T  V +DG+G++S   A+++    GL D  PSA Q R+G  KG  V+  D T  +  +  
Sbjct: 323 TGEVMNDGVGRMSRSVAKRIRDVLGLGDV-PSAVQGRFGSAKGMWVIDVDDTGDEDWIET 381

Query: 483 RDSMRKYESELTK-----LDVLA-WSKYQPCFLNRQLISLLST---------LGIWDEIF 527
             S RK+E +        L+V +  S+ +   LN QL+ +L             I D + 
Sbjct: 382 YPSQRKWECDFVDKHQRTLEVRSVASELKSAGLNLQLLPVLEDRARDKVKMRQAIGDRLI 441

Query: 528 EKKQREAVRQLDAILTDPLK-AQEALELMS-----------------PGENTNILKELLI 569
              QR+   Q  A L  P++  Q   E  S                 P      L  L+ 
Sbjct: 442 NDLQRQFSEQKHA-LNRPVEFRQWVYESYSSRATRVSHGRVPFLAGLPDSQEETLNFLMN 500

Query: 570 CGYKPDAEPFLSMMLQTFRASKLLELRTKTRIFIPNGRSMMGCLDETRTLNYGQVFVQIS 629
            G+ P  + +L  +    +  K   L++K  I +     +    D    L   +V V  S
Sbjct: 501 SGFDPKKQKYLQDIAWDLQKRKCDTLKSKLNIRVGRSAYIYMIADFWGVLEENEVHVGFS 560

Query: 630 GAGYRQLHGEXXXXXXXXXXXXXIVQGLVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCV 689
            + +R                  +    V+VA++P   P D++ ++AV  P LH + D +
Sbjct: 561 -SKFRD----------EEESFTLLSDCDVLVARSPAHFPSDIQRVRAVFKPELHSLKDVI 609

Query: 690 VFPQKG 695
           +F  KG
Sbjct: 610 IFSTKG 615


>pdb|2LDK|A Chain A, Solution Nmr Structure Of Protein Aaur_3427 From
           Arthrobacter Aurescens, Northeast Structural Genomics
           Consortium Target Aar96
          Length = 172

 Score = 30.4 bits (67), Expect = 3.7,   Method: Composition-based stats.
 Identities = 15/48 (31%), Positives = 28/48 (58%), Gaps = 7/48 (14%)

Query: 510 NRQLISLLSTLGIWDEI-------FEKKQREAVRQLDAILTDPLKAQE 550
           NR  ++++ST    +++        E+  REA+ Q+DA+L++P  A E
Sbjct: 119 NRTRMTIISTFESEEQMQKMAEMGMEEGMREAIEQIDAVLSEPANALE 166


  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
   0.322    0.139    0.420 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,058,386
Number of Sequences: 62578
Number of extensions: 869506
Number of successful extensions: 1732
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1729
Number of HSP's gapped (non-prelim): 6
length of query: 724
length of database: 14,973,337
effective HSP length: 106
effective length of query: 618
effective length of database: 8,340,069
effective search space: 5154162642
effective search space used: 5154162642
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.8 bits)