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= 027021
         (229 letters)

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

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



>pdb|3SAE|A Chain A, Structure Of A Three-Domain Sesquiterpene Synthase: A
           Prospective Target For Advanced Biofuels Production
 pdb|3SDQ|A Chain A, Structure Of A Three-Domain Sesquiterpene Synthase: A
           Prospective Target For Advanced Biofuels Production
 pdb|3SDR|A Chain A, Structure Of A Three-Domain Sesquiterpene Synthase: A
           Prospective Target For Advanced Biofuels Production
 pdb|3SDT|A Chain A, Structure Of A Three-Domain Sesquiterpene Synthase: A
           Prospective Target For Advanced Biofuels Production
 pdb|3SDU|A Chain A, Structure Of A Three-Domain Sesquiterpene Synthase: A
           Prospective Target For Advanced Biofuels Production
 pdb|3SDV|A Chain A, Structure Of A Three-Domain Sesquiterpene Synthase: A
           Prospective Target For Advanced Biofuels Production
          Length = 817

 Score = 28.9 bits (63), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 2/48 (4%)

Query: 95  SGASMMEQLVPEITTHALSYLDYPSLCRLSMTNSLMRKAANDDNAWKA 142
           SG  +M+  +  ++  AL  +DYP    L+  NSL+ + A+D   +KA
Sbjct: 675 SGVLIMDGQL--LSQEALEKVDYPGRRVLTELNSLISRLADDTKTYKA 720


>pdb|3L2O|B Chain B, Structure-Based Mechanism Of Dimerization-Dependent
           Ubiquitination By The Scffbx4 Ubiquitin Ligase
          Length = 312

 Score = 28.1 bits (61), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 14/53 (26%), Positives = 24/53 (45%)

Query: 96  GASMMEQLVPEITTHALSYLDYPSLCRLSMTNSLMRKAANDDNAWKALYHKDF 148
            AS + +L  ++  + LS+L    LC+L  TN    +   D   W+    +D 
Sbjct: 1   AASTLTRLPIDVQLYILSFLSPHDLCQLGSTNHYWNETVRDPILWRYFLLRDL 53


>pdb|2Y8N|A Chain A, Crystal Structure Of Glycyl Radical Enzyme
 pdb|2Y8N|C Chain C, Crystal Structure Of Glycyl Radical Enzyme
 pdb|2YAJ|A Chain A, Crystal Structure Of Glycyl Radical Enzyme With Bound
           Substrate
 pdb|2YAJ|C Chain C, Crystal Structure Of Glycyl Radical Enzyme With Bound
           Substrate
          Length = 897

 Score = 27.7 bits (60), Expect = 5.4,   Method: Compositional matrix adjust.
 Identities = 28/106 (26%), Positives = 43/106 (40%), Gaps = 8/106 (7%)

Query: 111 ALSYLDYPSLCRLSMTNSLMRKAANDDNAWKALYHKDFTLEQDSVIPVNGWKAYYAATRA 170
            + ++  P +  L +TN L      D    K +Y             VN WK Y   T  
Sbjct: 534 GVHFIGMPKVLELVLTNGL------DKRTGKQVYPPHNKKLDSYETMVNQWKEYMELTTD 587

Query: 171 VVN-VNAEFFNIIRERSLPAMSRFWLNADYVKCIHASGELFSGYDS 215
           VVN  N    +I R+ ++PA++   L  D  K     G + + Y+S
Sbjct: 588 VVNRCNNIQMDIWRKYNMPAVNSL-LKPDCFKKGKHIGTMGARYNS 632


  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
   0.321    0.130    0.395 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,766,681
Number of Sequences: 62578
Number of extensions: 188238
Number of successful extensions: 295
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 292
Number of HSP's gapped (non-prelim): 5
length of query: 229
length of database: 14,973,337
effective HSP length: 95
effective length of query: 134
effective length of database: 9,028,427
effective search space: 1209809218
effective search space used: 1209809218
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 50 (23.9 bits)