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= 043839
         (415 letters)

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

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



>pdb|3CIG|A Chain A, Crystal Structure Of Mouse Tlr3 Ectodomain
 pdb|3CIY|A Chain A, Mouse Toll-Like Receptor 3 Ectodomain Complexed With
           Double-Stranded Rna
 pdb|3CIY|B Chain B, Mouse Toll-Like Receptor 3 Ectodomain Complexed With
           Double-Stranded Rna
          Length = 697

 Score = 31.6 bits (70), Expect = 0.78,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 21/34 (61%), Gaps = 1/34 (2%)

Query: 144 NFCKKFKHLRVLNLGSAVLDLYPPGL-ENLFHLK 176
           NF K   HL +LNL S  LD  P G+ +NLF LK
Sbjct: 530 NFLKGLSHLHILNLESNGLDEIPVGVFKNLFELK 563


>pdb|3J0A|A Chain A, Homology Model Of Human Toll-Like Receptor 5 Fitted Into
           An Electron Microscopy Single Particle Reconstruction
 pdb|3J0A|B Chain B, Homology Model Of Human Toll-Like Receptor 5 Fitted Into
           An Electron Microscopy Single Particle Reconstruction
          Length = 844

 Score = 30.0 bits (66), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 18/42 (42%), Positives = 27/42 (64%), Gaps = 2/42 (4%)

Query: 140 IDCENFCKKFKHLRVLNLGSA-VLDLYPPGLENLFHLKYLKL 180
           ID E F +   +LR+L+LGS+ +  L+P   + LFHL  L+L
Sbjct: 64  IDKEAF-RNLPNLRILDLGSSKIYFLHPDAFQGLFHLFELRL 104


>pdb|3HNC|A Chain A, Crystal Structure Of Human Ribonucleotide Reductase 1
           Bound To The Effector Ttp
 pdb|3HNC|B Chain B, Crystal Structure Of Human Ribonucleotide Reductase 1
           Bound To The Effector Ttp
 pdb|3HND|A Chain A, Crystal Structure Of Human Ribonucleotide Reductase 1
           Bound To The Effector Ttp And Substrate Gdp
 pdb|3HND|B Chain B, Crystal Structure Of Human Ribonucleotide Reductase 1
           Bound To The Effector Ttp And Substrate Gdp
 pdb|3HNE|A Chain A, Crystal Structure Of Human Ribonucleotide Reductase 1
           Bound To The Effectors Ttp And Atp
 pdb|3HNE|B Chain B, Crystal Structure Of Human Ribonucleotide Reductase 1
           Bound To The Effectors Ttp And Atp
 pdb|3HNF|A Chain A, Crystal Structure Of Human Ribonucleotide Reductase 1
           Bound To The Effectors Ttp And Datp
 pdb|3HNF|B Chain B, Crystal Structure Of Human Ribonucleotide Reductase 1
           Bound To The Effectors Ttp And Datp
          Length = 792

 Score = 29.6 bits (65), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 8/82 (9%)

Query: 122 MYLQSFLNHSSESDHLAGIDCENFCKKF------KHLRVLNLGSAVLDLYPPGLENLFHL 175
           M  +   N  S   +L  I C N C +         + V NL S  L++Y    E+ +  
Sbjct: 405 MLYKDSCNRKSNQQNLGTIKCSNLCTEIVEYTSKDEVAVCNLASLALNMYVTS-EHTYDF 463

Query: 176 KYLKLITP-LLKLMQKLMHLNF 196
           K L  +T  +++ + K++ +N+
Sbjct: 464 KKLAEVTKVVVRNLNKIIDINY 485


>pdb|2WGH|A Chain A, Human Ribonucleotide Reductase R1 Subunit (Rrm1) In
           Complex With Datp And Mg.
 pdb|2WGH|B Chain B, Human Ribonucleotide Reductase R1 Subunit (Rrm1) In
           Complex With Datp And Mg
          Length = 676

 Score = 29.6 bits (65), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 19/75 (25%), Positives = 35/75 (46%), Gaps = 8/75 (10%)

Query: 129 NHSSESDHLAGIDCENFCKKF------KHLRVLNLGSAVLDLYPPGLENLFHLKYLKLIT 182
           N  S   +L  I C N C +         + V NL S  L++Y    E+ +  K L  +T
Sbjct: 339 NRKSNQQNLGTIKCSNLCTEIVEYTSKDEVAVCNLASLALNMYVTS-EHTYDFKKLAEVT 397

Query: 183 P-LLKLMQKLMHLNF 196
             +++ + K++ +N+
Sbjct: 398 KVVVRNLNKIIDINY 412


  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    0.136    0.420 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,604,647
Number of Sequences: 62578
Number of extensions: 437826
Number of successful extensions: 831
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 831
Number of HSP's gapped (non-prelim): 6
length of query: 415
length of database: 14,973,337
effective HSP length: 101
effective length of query: 314
effective length of database: 8,652,959
effective search space: 2717029126
effective search space used: 2717029126
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: 53 (25.0 bits)