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= 028336
         (210 letters)

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

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



>pdb|4H9D|A Chain A, Crystal Structure Of Mn-Dependent Gme Hnh Nicking
           Endonuclease From Geobacter Metallireducens Gs-15,
           Northeast Structural Genomics Consortium (Nesg) Target
           Gmr87
 pdb|4H9D|B Chain B, Crystal Structure Of Mn-Dependent Gme Hnh Nicking
           Endonuclease From Geobacter Metallireducens Gs-15,
           Northeast Structural Genomics Consortium (Nesg) Target
           Gmr87
 pdb|4H9D|C Chain C, Crystal Structure Of Mn-Dependent Gme Hnh Nicking
           Endonuclease From Geobacter Metallireducens Gs-15,
           Northeast Structural Genomics Consortium (Nesg) Target
           Gmr87
          Length = 112

 Score = 32.7 bits (73), Expect = 0.16,   Method: Compositional matrix adjust.
 Identities = 19/52 (36%), Positives = 26/52 (50%), Gaps = 6/52 (11%)

Query: 157 QVVKRRRIKNNLSRKNLMYRDNFT---CQYCSS---RENLTIDHVVPASRGG 202
           Q VKR + K    R++  +++      C YC      E LT DH+VP  RGG
Sbjct: 11  QEVKREKEKARELRRSQWWKNRIARGICHYCGEIFPPEELTXDHLVPVVRGG 62


>pdb|2A0Z|A Chain A, The Molecular Structure Of Toll-like Receptor 3 Ligand
           Binding Domain
          Length = 705

 Score = 27.7 bits (60), Expect = 4.8,   Method: Composition-based stats.
 Identities = 25/103 (24%), Positives = 49/103 (47%), Gaps = 17/103 (16%)

Query: 102 VLDISYRPVNVV-----CWKRAICLEFMEKADVLEYYDQTINSPNGSFYIPAVLRVRHLL 156
           +LD+SY  +NVV      W   +   F+E  ++   +  +++          +  VR+L 
Sbjct: 257 MLDLSYNNLNVVGNDSFAWLPQLEYFFLEYNNIQHLFSHSLH---------GLFNVRYL- 306

Query: 157 QVVKRRRIKNNLSRKNLMYRDNFTCQYCSSRENLTI-DHVVPA 198
             +KR   K ++S  +L   D+F+ Q+    E+L + D+ +P 
Sbjct: 307 -NLKRSFTKQSISLASLPKIDDFSFQWLKCLEHLNMEDNDIPG 348


>pdb|3ULU|A Chain A, Structure Of Quaternary Complex Of Human Tlr3ecd With
           Three Fabs (Form1)
 pdb|3ULV|A Chain A, Structure Of Quaternary Complex Of Human Tlr3ecd With
           Three Fabs (Form2)
          Length = 694

 Score = 27.7 bits (60), Expect = 4.8,   Method: Composition-based stats.
 Identities = 25/103 (24%), Positives = 49/103 (47%), Gaps = 17/103 (16%)

Query: 102 VLDISYRPVNVV-----CWKRAICLEFMEKADVLEYYDQTINSPNGSFYIPAVLRVRHLL 156
           +LD+SY  +NVV      W   +   F+E  ++   +  +++          +  VR+L 
Sbjct: 262 MLDLSYNNLNVVGNDSFAWLPQLEYFFLEYNNIQHLFSHSLH---------GLFNVRYL- 311

Query: 157 QVVKRRRIKNNLSRKNLMYRDNFTCQYCSSRENLTI-DHVVPA 198
             +KR   K ++S  +L   D+F+ Q+    E+L + D+ +P 
Sbjct: 312 -NLKRSFTKQSISLASLPKIDDFSFQWLKCLEHLNMEDNDIPG 353


>pdb|1ZIW|A Chain A, Human Toll-Like Receptor 3 Extracellular Domain Structure
          Length = 680

 Score = 27.7 bits (60), Expect = 5.1,   Method: Composition-based stats.
 Identities = 25/103 (24%), Positives = 49/103 (47%), Gaps = 17/103 (16%)

Query: 102 VLDISYRPVNVV-----CWKRAICLEFMEKADVLEYYDQTINSPNGSFYIPAVLRVRHLL 156
           +LD+SY  +NVV      W   +   F+E  ++   +  +++          +  VR+L 
Sbjct: 252 MLDLSYNNLNVVGNDSFAWLPQLEYFFLEYNNIQHLFSHSLH---------GLFNVRYL- 301

Query: 157 QVVKRRRIKNNLSRKNLMYRDNFTCQYCSSRENLTI-DHVVPA 198
             +KR   K ++S  +L   D+F+ Q+    E+L + D+ +P 
Sbjct: 302 -NLKRSFTKQSISLASLPKIDDFSFQWLKCLEHLNMEDNDIPG 343


  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
   0.323    0.139    0.435 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,688,797
Number of Sequences: 62578
Number of extensions: 198316
Number of successful extensions: 361
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 361
Number of HSP's gapped (non-prelim): 4
length of query: 210
length of database: 14,973,337
effective HSP length: 95
effective length of query: 115
effective length of database: 9,028,427
effective search space: 1038269105
effective search space used: 1038269105
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 49 (23.5 bits)