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= 024302
         (269 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 = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 32/95 (33%), Positives = 45/95 (47%), Gaps = 6/95 (6%)

Query: 148 QVVKRRRIKNNLSRKNLMYRDNFT---CQYCSS---RENLTIDHVVPASRGGEWKWENLV 201
           Q VKR + K    R++  +++      C YC      E LT DH+VP  RGG+    N+V
Sbjct: 11  QEVKREKEKARELRRSQWWKNRIARGICHYCGEIFPPEELTXDHLVPVVRGGKSTRGNVV 70

Query: 202 AACFKCNSRKGKKTLEEANMQLSRVPKAPKDYDIL 236
            AC +CN+RK      E    L  +   P D + L
Sbjct: 71  PACKECNNRKKYLLPVEWEEYLDSLESEPSDGEGL 105


>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 = 28.1 bits (61), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 26/98 (26%), Positives = 46/98 (46%), Gaps = 8/98 (8%)

Query: 102 VLDISYRPVNVV-----CWKRAICLEFMEKTINSPNGSFYIPAVLRVRHLLQVVKRRRIK 156
           +LD+SY  +NVV      W   +   F+E        S  +  +  VR+L   +KR   K
Sbjct: 262 MLDLSYNNLNVVGNDSFAWLPQLEYFFLEYNNIQHLFSHSLHGLFNVRYL--NLKRSFTK 319

Query: 157 NNLSRKNLMYRDNFTCQYCSSRENLTI-DHVVPASRGG 193
            ++S  +L   D+F+ Q+    E+L + D+ +P  +  
Sbjct: 320 QSISLASLPKIDDFSFQWLKCLEHLNMEDNDIPGIKSN 357


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

 Score = 28.1 bits (61), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 26/98 (26%), Positives = 46/98 (46%), Gaps = 8/98 (8%)

Query: 102 VLDISYRPVNVV-----CWKRAICLEFMEKTINSPNGSFYIPAVLRVRHLLQVVKRRRIK 156
           +LD+SY  +NVV      W   +   F+E        S  +  +  VR+L   +KR   K
Sbjct: 252 MLDLSYNNLNVVGNDSFAWLPQLEYFFLEYNNIQHLFSHSLHGLFNVRYL--NLKRSFTK 309

Query: 157 NNLSRKNLMYRDNFTCQYCSSRENLTI-DHVVPASRGG 193
            ++S  +L   D+F+ Q+    E+L + D+ +P  +  
Sbjct: 310 QSISLASLPKIDDFSFQWLKCLEHLNMEDNDIPGIKSN 347


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

 Score = 28.1 bits (61), Expect = 5.6,   Method: Compositional matrix adjust.
 Identities = 26/98 (26%), Positives = 46/98 (46%), Gaps = 8/98 (8%)

Query: 102 VLDISYRPVNVV-----CWKRAICLEFMEKTINSPNGSFYIPAVLRVRHLLQVVKRRRIK 156
           +LD+SY  +NVV      W   +   F+E        S  +  +  VR+L   +KR   K
Sbjct: 257 MLDLSYNNLNVVGNDSFAWLPQLEYFFLEYNNIQHLFSHSLHGLFNVRYL--NLKRSFTK 314

Query: 157 NNLSRKNLMYRDNFTCQYCSSRENLTI-DHVVPASRGG 193
            ++S  +L   D+F+ Q+    E+L + D+ +P  +  
Sbjct: 315 QSISLASLPKIDDFSFQWLKCLEHLNMEDNDIPGIKSN 352


  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
   0.322    0.137    0.426 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,235,762
Number of Sequences: 62578
Number of extensions: 263320
Number of successful extensions: 508
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: 507
Number of HSP's gapped (non-prelim): 4
length of query: 269
length of database: 14,973,337
effective HSP length: 97
effective length of query: 172
effective length of database: 8,903,271
effective search space: 1531362612
effective search space used: 1531362612
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)