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= psy6082
         (275 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 = 29.6 bits (65), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 24/93 (25%), Positives = 46/93 (49%), Gaps = 8/93 (8%)

Query: 14  LELTNATDALIASATSIIL---GYGIARICSSGFNELRNAVFASVAQRSIRKIAKNVFLH 70
           L+L+ ++ AL+ S   ++L         I  S F  LRN     ++  +I  I +++   
Sbjct: 443 LQLSTSSFALVPSLQRLMLRRVALKNVDISPSPFRPLRNLTILDLSNNNIANINEDLLEG 502

Query: 71  LHNLDLAFHLNRQTGALSKIIDRGSRG--INFV 101
           L NL++   L+ Q   L+++  R + G  +NF+
Sbjct: 503 LENLEI---LDFQHNNLARLWKRANPGGPVNFL 532


>pdb|4AYW|A Chain A, Structure Of The Human Mitochondrial Abc Transporter,
           Abcb10 (plate Form)
          Length = 619

 Score = 27.7 bits (60), Expect = 6.4,   Method: Compositional matrix adjust.
 Identities = 55/231 (23%), Positives = 100/231 (43%), Gaps = 21/231 (9%)

Query: 17  TNATDALIASATSIILGYGIARICSSGFNELRNAVFASVAQRSIRKIAKNVFLHLHNLDL 76
           TN T     + T + LG     +C +  N +R  +  +  QR + ++  ++F  +   ++
Sbjct: 82  TNPTVDYSDNLTRLCLGLSAVFLCGAAANAIRVYLMQTSGQRIVNRLRTSLFSSILRQEV 141

Query: 77  AFHLNRQTGALSKIIDRGSRGINFVLSAMVFNIVPTIFELALIS---SILSYKCGTLISS 133
           AF    +TG L   I+R S     +  ++  N+   +   A  S   S++ +    L + 
Sbjct: 142 AFFDKTRTGEL---INRLSSDTALLGRSVTENLSDGLRAGAQASVGISMMFFVSPNLATF 198

Query: 134 ILSYKCGSEFSLLAVSCVGIYTAYTLSITQWRTQFRVNMNKAENEAGNKAIDSLINYETV 193
           +LS       S++AV    IY  Y   +T+  TQ       +  +A   A + + N  TV
Sbjct: 199 VLSVV--PPVSIIAV----IYGRYLRKLTKV-TQ------DSLAQATQLAEERIGNVRTV 245

Query: 194 KYFNNEKFEADRYEGVLKKYEQAALKTSTSLATLNFGQSAI-GKLMLTLVL 243
           + F  E  E ++Y   +    Q A K + + A   FG + + G L++  VL
Sbjct: 246 RAFGKEMTEIEKYASKVDHVMQLARKEAFARAGF-FGATGLSGNLIVLSVL 295


>pdb|4AYT|A Chain A, Structure Of The Human Mitochondrial Abc Transporter,
           Abcb10
 pdb|4AYX|A Chain A, Structure Of The Human Mitochondrial Abc Transporter,
           Abcb10 (Rod Form B)
 pdb|3ZDQ|A Chain A, Structure Of The Human Mitochondrial Abc Transporter,
           Abcb10 (nucleotide-free Form)
          Length = 595

 Score = 27.7 bits (60), Expect = 6.7,   Method: Compositional matrix adjust.
 Identities = 55/231 (23%), Positives = 100/231 (43%), Gaps = 21/231 (9%)

Query: 17  TNATDALIASATSIILGYGIARICSSGFNELRNAVFASVAQRSIRKIAKNVFLHLHNLDL 76
           TN T     + T + LG     +C +  N +R  +  +  QR + ++  ++F  +   ++
Sbjct: 51  TNPTVDYSDNLTRLCLGLSAVFLCGAAANAIRVYLMQTSGQRIVNRLRTSLFSSILRQEV 110

Query: 77  AFHLNRQTGALSKIIDRGSRGINFVLSAMVFNIVPTIFELALIS---SILSYKCGTLISS 133
           AF    +TG L   I+R S     +  ++  N+   +   A  S   S++ +    L + 
Sbjct: 111 AFFDKTRTGEL---INRLSSDTALLGRSVTENLSDGLRAGAQASVGISMMFFVSPNLATF 167

Query: 134 ILSYKCGSEFSLLAVSCVGIYTAYTLSITQWRTQFRVNMNKAENEAGNKAIDSLINYETV 193
           +LS       S++AV    IY  Y   +T+  TQ       +  +A   A + + N  TV
Sbjct: 168 VLS--VVPPVSIIAV----IYGRYLRKLTKV-TQ------DSLAQATQLAEERIGNVRTV 214

Query: 194 KYFNNEKFEADRYEGVLKKYEQAALKTSTSLATLNFGQSAI-GKLMLTLVL 243
           + F  E  E ++Y   +    Q A K + + A   FG + + G L++  VL
Sbjct: 215 RAFGKEMTEIEKYASKVDHVMQLARKEAFARAGF-FGATGLSGNLIVLSVL 264


  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    0.134    0.382 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,912,085
Number of Sequences: 62578
Number of extensions: 239257
Number of successful extensions: 600
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 591
Number of HSP's gapped (non-prelim): 14
length of query: 275
length of database: 14,973,337
effective HSP length: 97
effective length of query: 178
effective length of database: 8,903,271
effective search space: 1584782238
effective search space used: 1584782238
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)