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= 004021
         (779 letters)

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

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



>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type
           Iii Effector Xcv3220 (Xopl)
          Length = 328

 Score = 30.4 bits (67), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 30/118 (25%), Positives = 53/118 (44%), Gaps = 20/118 (16%)

Query: 651 LVFVQNLKELEIIVCTEMEEI----------------ICVDKLR-DVSDISEIIGSEHNF 693
           +  +  L+EL I  C E+ E+                + +  LR + + I  +  S  N 
Sbjct: 146 IASLNRLRELSIRACPELTELPEPLASTDASGEHQGLVNLQSLRLEWTGIRSLPASIANL 205

Query: 694 FTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKL-PINSSSAKERRVVIE 750
              L+SL I   P L ++ P   H PKL+++ + GC  L+   PI    A  +R++++
Sbjct: 206 -QNLKSLKIRNSP-LSALGPAIHHLPKLEELDLRGCTALRNYPPIFGGRAPLKRLILK 261


>pdb|2JGU|A Chain A, Crystal Structure Of Dna-directed Dna Polymerase
          Length = 775

 Score = 30.0 bits (66), Expect = 5.8,   Method: Compositional matrix adjust.
 Identities = 18/66 (27%), Positives = 31/66 (46%)

Query: 555 LKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPL 614
           +K  EK  + N+ Y  Y S+ P  +I+  +  + L L  C +  +  + G+  C D    
Sbjct: 390 VKEPEKGLWENIVYLDYKSLYPSIIITHNVSPDTLNLEGCKNYDIAPQVGHKFCKDIPGF 449

Query: 615 MRELLG 620
           +  LLG
Sbjct: 450 IPSLLG 455


  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
   0.319    0.136    0.400 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,957,765
Number of Sequences: 62578
Number of extensions: 872930
Number of successful extensions: 1916
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1912
Number of HSP's gapped (non-prelim): 6
length of query: 779
length of database: 14,973,337
effective HSP length: 106
effective length of query: 673
effective length of database: 8,340,069
effective search space: 5612866437
effective search space used: 5612866437
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)