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= psy1643
         (962 letters)

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

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



>pdb|1YVP|A Chain A, Ro Autoantigen Complexed With Rnas
 pdb|1YVP|B Chain B, Ro Autoantigen Complexed With Rnas
 pdb|1YVR|A Chain A, Ro Autoantigen
 pdb|2I91|A Chain A, 60kda Ro Autoantigen In Complex With A Fragment Of
           Misfolded Rna
 pdb|2I91|B Chain B, 60kda Ro Autoantigen In Complex With A Fragment Of
           Misfolded Rna
          Length = 538

 Score = 33.5 bits (75), Expect = 0.62,   Method: Compositional matrix adjust.
 Identities = 43/212 (20%), Positives = 91/212 (42%), Gaps = 29/212 (13%)

Query: 333 AVRKQLQKWYMGKESDQLVVLVAKCSVYQGLSHANVLKLIHFDVFHQSPDKKLALYA--I 390
           A+RK +  WY  K++  L + V K     G SH ++L+L H     +  ++ L + A  +
Sbjct: 147 ALRKAVSDWYNTKDALNLAMAVTKYKQRNGWSHKDLLRLSHI----KPANEGLTMVAKYV 202

Query: 391 AFGFAYVSHRLISGKFLATPRVPPFVTSDDCFDKASDKVKTIVKDVAVVRCNTSHQKVVA 450
           + G+  V       +   +P     +     + +A+++VK    ++ ++     ++    
Sbjct: 203 SKGWKEVQEAYKEKEL--SPETEKVLK----YLEATERVKRTKDELEIIHLIDEYR---- 252

Query: 451 AAVKTHSLGIESVCPKFAKSFKVNTACLEGMTQRGLLQSMHRLRKDNVLSSEDHAIVDES 510
             V+ H L I        KS ++  + L+ M    LL+++ ++  D+VL+     +   S
Sbjct: 253 -LVREHLLTIH------LKSKEIWKSLLQDMPLTALLRNLGKMTADSVLAPASSEV---S 302

Query: 511 TTCGTYVKQLGASPVTEPPLHPAEVLAAYAEY 542
           + C     +     + +  +HP  +L A   Y
Sbjct: 303 SVCERLTNE---KLLKKARIHPFHILVALETY 331


>pdb|1YSL|B Chain B, Crystal Structure Of Hmg-Coa Synthase From Enterococcus
           Faecalis With Acetoacetyl-Coa Ligand
          Length = 384

 Score = 30.0 bits (66), Expect = 5.8,   Method: Compositional matrix adjust.
 Identities = 28/91 (30%), Positives = 42/91 (46%), Gaps = 11/91 (12%)

Query: 435 DVAVVRCNTSHQKVVAAAVKTHSL-GIESVCPKFAKSFKVNTACLEGMTQRGLLQSMHRL 493
           D+ +V   +S  +  AAAV  H L GI+     FA+SF++  AC  G T  GL     +L
Sbjct: 72  DMVIVGTESSIDESKAAAVVLHRLMGIQ----PFARSFEIKEACXYGATA-GL-----QL 121

Query: 494 RKDNVLSSEDHAIVDESTTCGTYVKQLGASP 524
            K++V    D  ++  +     Y    G  P
Sbjct: 122 AKNHVALHPDKKVLVVAADIAKYGLNSGGEP 152


  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
   0.316    0.131    0.373 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 25,769,858
Number of Sequences: 62578
Number of extensions: 1006740
Number of successful extensions: 2153
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 2128
Number of HSP's gapped (non-prelim): 28
length of query: 962
length of database: 14,973,337
effective HSP length: 108
effective length of query: 854
effective length of database: 8,214,913
effective search space: 7015535702
effective search space used: 7015535702
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: 56 (26.2 bits)