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= 038454
         (359 letters)

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

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



>pdb|1VLC|A Chain A, Crystal Structure Of 3-isopropylmalate Dehydrogenase
           (tm0556) From Thermotoga Maritima At 1.90 A Resolution
          Length = 366

 Score = 32.0 bits (71), Expect = 0.62,   Method: Compositional matrix adjust.
 Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 4/59 (6%)

Query: 242 LSKEEALNLFLD----KVGRNILHVPTLNEEIINSVVEECAGLQLAIFTVVGCMRGVDE 296
           L+  + LNL+ +    KV R+++HV  L E++I S V+     +L+     G  RG+DE
Sbjct: 104 LALRKMLNLYANIRPIKVYRSLVHVSPLKEKVIGSGVDLVTVRELSYGVYYGQPRGLDE 162


>pdb|3FBT|A Chain A, Crystal Structure Of A Chorismate MutaseSHIKIMATE 5-
           Dehydrogenase Fusion Protein From Clostridium
           Acetobutylicum
 pdb|3FBT|B Chain B, Crystal Structure Of A Chorismate MutaseSHIKIMATE 5-
           Dehydrogenase Fusion Protein From Clostridium
           Acetobutylicum
 pdb|3FBT|C Chain C, Crystal Structure Of A Chorismate MutaseSHIKIMATE 5-
           Dehydrogenase Fusion Protein From Clostridium
           Acetobutylicum
 pdb|3FBT|D Chain D, Crystal Structure Of A Chorismate MutaseSHIKIMATE 5-
           Dehydrogenase Fusion Protein From Clostridium
           Acetobutylicum
          Length = 282

 Score = 30.8 bits (68), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 26/83 (31%), Positives = 37/83 (44%), Gaps = 9/83 (10%)

Query: 250 LFLDKVG----RNILHVPT--LNEEIINSVVEECAGLQLAIFTVVGCMRGVDEIHEWR-- 301
           L  +KVG     N+  VP   L E +    + +C GL + I   V  M+ + EI E    
Sbjct: 26  LIFEKVGIKGIYNLFEVPKEKLKESVDTFKIIKCGGLNVTIPYKVEVMKELYEISEKARK 85

Query: 302 -NALNELRGLVRSFSGINADVLG 323
             A+N L+      SG N D +G
Sbjct: 86  IGAVNTLKFSREGISGFNTDYIG 108


>pdb|3L6G|A Chain A, Crystal Structure Of Lactococcal Opuac In Its Open
           Conformation
 pdb|3L6H|A Chain A, Crystal Structure Of Lactococcal Opuac In Its
           Closed-Ligande Conformation Complexed With Glycine
           Betaine
          Length = 256

 Score = 29.6 bits (65), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 14/40 (35%), Positives = 24/40 (60%), Gaps = 1/40 (2%)

Query: 6   RVLQEFNSQKEDIEATLKAEGDRGKKPRTEVKNWLQNVQR 45
           +VL +FN   +D+EA +  +   GK P    KNW+++ Q+
Sbjct: 209 KVLDKFNWTTKDMEAVM-LDIQNGKTPEEAAKNWIKDHQK 247


>pdb|2F8S|A Chain A, Crystal Structure Of Aa-Ago With Externally-Bound Sirna
 pdb|2F8S|B Chain B, Crystal Structure Of Aa-Ago With Externally-Bound Sirna
 pdb|2F8T|A Chain A, Crystal Structure Of Aa-Ago With Externally-Bound Sirna
 pdb|2F8T|B Chain B, Crystal Structure Of Aa-Ago With Externally-Bound Sirna
 pdb|2NUB|A Chain A, Structure Of Aquifex Aeolicus Argonuate
          Length = 706

 Score = 28.1 bits (61), Expect = 8.1,   Method: Compositional matrix adjust.
 Identities = 25/117 (21%), Positives = 51/117 (43%), Gaps = 23/117 (19%)

Query: 68  LGKDVDAKIQEMKDCHQKGCSFISLVIDAPPSSGLILPTTTLVGENTKKIVKKVWEDLMG 127
           +G D   ++Q++    +KG  F  L ++                 +T K  KK WE+L+ 
Sbjct: 188 IGIDFVGRVQDVFKAKEKGEEFFRLCME----------------RSTHKSSKKAWEELLK 231

Query: 128 DKVTK----IGVWGMGGFGKTAIMRHI---NNRPQEETNEFSDVIWVTVSQPLDLVK 177
           ++  +    + V   G      I++ +    N   EE NE +D++ +   + L+L++
Sbjct: 232 NRELREKAFLVVLEKGYTYPATILKPVLTYENLEDEERNEVADIVRMEPGKRLNLIR 288


  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    0.401 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,716,868
Number of Sequences: 62578
Number of extensions: 374032
Number of successful extensions: 1096
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1095
Number of HSP's gapped (non-prelim): 7
length of query: 359
length of database: 14,973,337
effective HSP length: 100
effective length of query: 259
effective length of database: 8,715,537
effective search space: 2257324083
effective search space used: 2257324083
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: 52 (24.6 bits)