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= 020088
         (331 letters)

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

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



>pdb|1K3R|A Chain A, Crystal Structure Of The Methyltransferase With A Knot
           From Methanobacterium Thermoautotrophicum
 pdb|1K3R|B Chain B, Crystal Structure Of The Methyltransferase With A Knot
           From Methanobacterium Thermoautotrophicum
          Length = 268

 Score = 82.8 bits (203), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 67/249 (26%), Positives = 116/249 (46%), Gaps = 41/249 (16%)

Query: 63  VSVAVPGSIIDNTQSLELATRLAGQIARAVTIFRIDEVVVFDNKXXXXXXXXXXXXXXXX 122
           +S+ +P S+   T  L++ T     IARA +IF +  +V++ +                 
Sbjct: 6   LSLFIPDSLTAETGDLKIKTYKVVLIARAASIFGVKRIVIYHD----------------- 48

Query: 123 XXXENESGAAFLVRLLQYLETPQYLRKALFSMHSSLRFVGMLPPLDAPHH-LRKHEWAPF 181
              + +  A F+  +L Y++TPQYLR+ +F +   L+ VG+LPPL  PHH   K     +
Sbjct: 49  ---DADGEARFIRDILTYMDTPQYLRRKVFPIMRELKHVGILPPLRTPHHPTGKPVTGEY 105

Query: 182 REGVTLKENAPNSVGTLVDVGLNKHVVVDQVLDPGVRVTVAMGTNRNLDADSPRQVVPPS 241
           R+G+T+K       GTLVD+G +K  +  +      ++TV    +  +       ++ P 
Sbjct: 106 RQGLTVKRVKK---GTLVDIGADKLALCRE------KLTVNRIMSFRVVRLGKEILIEPD 156

Query: 242 KPKESGMYWGYKV-RYAPNISSVFKNCSYKGGYDHLIGTSEHG----DIVNSSDLTLPTF 296
           +P++   YWGY+V     N++   K      G D ++ TS +      I++     +   
Sbjct: 157 EPEDR--YWGYEVLDTRRNLAESLKTV----GADVVVATSRNASPITSILDEVKTRMRGA 210

Query: 297 RHLLIAFGG 305
           R   I FGG
Sbjct: 211 REAAILFGG 219


>pdb|1FUX|A Chain A, Crystal Structure Of E.Coli Ybcl, A New Member Of The
           Mammalian Pebp Family
 pdb|1FUX|B Chain B, Crystal Structure Of E.Coli Ybcl, A New Member Of The
           Mammalian Pebp Family
          Length = 166

 Score = 28.5 bits (62), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 19/57 (33%), Positives = 25/57 (43%), Gaps = 4/57 (7%)

Query: 160 FVGMLPPL-DAPHHLRKHEWAPFREGVTLKENAPNSVGTLVDVGLNKHVVVDQVLDP 215
           F G  PP  D PHH +   WA   E + +     NS G LV   LN + +    + P
Sbjct: 106 FGGACPPKGDKPHHYQFKVWALKTEKIPVDS---NSSGALVGYXLNANKIATAEITP 159


  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    0.134    0.389 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,344,018
Number of Sequences: 62578
Number of extensions: 373021
Number of successful extensions: 567
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: 565
Number of HSP's gapped (non-prelim): 4
length of query: 331
length of database: 14,973,337
effective HSP length: 99
effective length of query: 232
effective length of database: 8,778,115
effective search space: 2036522680
effective search space used: 2036522680
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 52 (24.6 bits)