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= 041570
(394 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2A0Z|A Chain A, The Molecular Structure Of Toll-like Receptor 3 Ligand
Binding Domain
Length = 705
Score = 33.5 bits (75), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 32/122 (26%), Positives = 53/122 (43%), Gaps = 14/122 (11%)
Query: 267 SMGSFPSLKTLFLEANNFTATTTQELHNFTNLEFLNLRHS----SLDINLLKTIASFT-- 320
S P L+ FLE NN + LH N+ +LNL+ S S+ + L I F+
Sbjct: 272 SFAWLPQLEYFFLEYNNIQHLFSHSLHGLFNVRYLNLKRSFTKQSISLASLPKIDDFSFQ 331
Query: 321 ---SLKNLSMVSCEVNGVLDGQGFLNFKSLERLDMGGARNALNASFLQIIGESMASLKHL 377
L++L+M ++ G+ F +L+ L + + +L + E+ SL H
Sbjct: 332 WLKCLEHLNMEDNDIPGI-KSNMFTGLINLKYLSLSNSFTSLRT----LTNETFVSLAHS 386
Query: 378 SL 379
L
Sbjct: 387 PL 388
>pdb|1ZIW|A Chain A, Human Toll-Like Receptor 3 Extracellular Domain Structure
Length = 680
Score = 33.1 bits (74), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 32/122 (26%), Positives = 53/122 (43%), Gaps = 14/122 (11%)
Query: 267 SMGSFPSLKTLFLEANNFTATTTQELHNFTNLEFLNLRHS----SLDINLLKTIASFT-- 320
S P L+ FLE NN + LH N+ +LNL+ S S+ + L I F+
Sbjct: 267 SFAWLPQLEYFFLEYNNIQHLFSHSLHGLFNVRYLNLKRSFTKQSISLASLPKIDDFSFQ 326
Query: 321 ---SLKNLSMVSCEVNGVLDGQGFLNFKSLERLDMGGARNALNASFLQIIGESMASLKHL 377
L++L+M ++ G+ F +L+ L + + +L + E+ SL H
Sbjct: 327 WLKCLEHLNMEDNDIPGI-KSNMFTGLINLKYLSLSNSFTSLRT----LTNETFVSLAHS 381
Query: 378 SL 379
L
Sbjct: 382 PL 383
>pdb|4FHO|A Chain A, Crystal Structure Of An Internalin C2 (Inlc2) From
Listeria Monocytogenes Str. 4b F2365 At 1.90 A
Resolution
pdb|4FHO|B Chain B, Crystal Structure Of An Internalin C2 (Inlc2) From
Listeria Monocytogenes Str. 4b F2365 At 1.90 A
Resolution
Length = 231
Score = 33.1 bits (74), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 32/108 (29%), Positives = 49/108 (45%), Gaps = 11/108 (10%)
Query: 243 RGLSKLKRLDLSGVGIRDGSELLRSMGSFPSLKTLFLEANNFTATTTQELHNFTNLEFLN 302
+ L+K+ L+LSG +++ S ++ S+KTL L + T T L +NL+ L
Sbjct: 88 KNLTKITELELSGNPLKNVS----AIAGLQSIKTLDLTSTQITDVT--PLAGLSNLQVL- 140
Query: 303 LRHSSLDINLLKTIASFTSLKNLSMVSCEVNGVLDGQGFLNFKSLERL 350
LD+N + I+ L NL +S N V D N L L
Sbjct: 141 ----YLDLNQITNISPLAGLTNLQYLSIGNNQVNDLTPLANLSKLTTL 184
>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 = 33.1 bits (74), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 32/122 (26%), Positives = 53/122 (43%), Gaps = 14/122 (11%)
Query: 267 SMGSFPSLKTLFLEANNFTATTTQELHNFTNLEFLNLRHS----SLDINLLKTIASFT-- 320
S P L+ FLE NN + LH N+ +LNL+ S S+ + L I F+
Sbjct: 277 SFAWLPQLEYFFLEYNNIQHLFSHSLHGLFNVRYLNLKRSFTKQSISLASLPKIDDFSFQ 336
Query: 321 ---SLKNLSMVSCEVNGVLDGQGFLNFKSLERLDMGGARNALNASFLQIIGESMASLKHL 377
L++L+M ++ G+ F +L+ L + + +L + E+ SL H
Sbjct: 337 WLKCLEHLNMEDNDIPGI-KSNMFTGLINLKYLSLSNSFTSLRT----LTNETFVSLAHS 391
Query: 378 SL 379
L
Sbjct: 392 PL 393
>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type
Iii Effector Xcv3220 (Xopl)
Length = 328
Score = 32.3 bits (72), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 40/151 (26%), Positives = 60/151 (39%), Gaps = 21/151 (13%)
Query: 241 DYRGLSKLKRLDLSGVGIRDGSELLRSMGSFPSLKTLFLEANNFTATTTQELHNFTNLEF 300
+++GL L+ L L GIR L S+ + +LK+L + + +A +H+ LE
Sbjct: 178 EHQGLVNLQSLRLEWTGIRS---LPASIANLQNLKSLKIRNSPLSALGP-AIHHLPKLEE 233
Query: 301 LNLRHSSLDINLLKTIASFTSLKNLSMVSCEVNGVLDGQGFLNFKSLERLDMGGARNALN 360
L+LR + N LK L + C N + LE+LD+ G N
Sbjct: 234 LDLRGCTALRNYPPIFGGRAPLKRLILKDCS-NLLTLPLDIHRLTQLEKLDLRGCVN--- 289
Query: 361 ASFLQIIGESMASLKHLSLSYSILNANCTIL 391
L L + L ANC IL
Sbjct: 290 -------------LSRLPSLIAQLPANCIIL 307
>pdb|1OGQ|A Chain A, The Crystal Structure Of Pgip (Polygalacturonase
Inhibiting Protein), A Leucine Rich Repeat Protein
Involved In Plant Defense
Length = 313
Score = 31.2 bits (69), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 5/70 (7%)
Query: 240 QDYRGLSKLKRLDLSGVGIRDGSELLRSMGSFPSLKTLFLEA-NNFTATTTQELHNFTNL 298
Q YR + LDLSG+ + + S+ + P L L++ NN + T L
Sbjct: 48 QTYR----VNNLDLSGLNLPKPYPIPSSLANLPYLNFLYIGGINNLVGPIPPAIAKLTQL 103
Query: 299 EFLNLRHSSL 308
+L + H+++
Sbjct: 104 HYLYITHTNV 113
>pdb|2OMU|A Chain A, Crystal Structure Of Inla G194s+s Y369s/hec1 Complex
Length = 462
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 31/66 (46%), Gaps = 5/66 (7%)
Query: 291 ELHNFTNLEFLNLRHSSLDINLLKTIASFTSLKNLSMVSCEVNGVLDGQGFLNFKSLERL 350
L N TNL L L N + I++ + L +L +S N V D + N +LERL
Sbjct: 124 PLKNLTNLNRLELSS-----NTISDISALSGLTSLQQLSFSSNQVTDLKPLANLTTLERL 178
Query: 351 DMGGAR 356
D+ +
Sbjct: 179 DISSNK 184
>pdb|2OMT|A Chain A, Crystal Structure Of Inla G194s+sHEC1 COMPLEX
Length = 462
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 31/66 (46%), Gaps = 5/66 (7%)
Query: 291 ELHNFTNLEFLNLRHSSLDINLLKTIASFTSLKNLSMVSCEVNGVLDGQGFLNFKSLERL 350
L N TNL L L N + I++ + L +L +S N V D + N +LERL
Sbjct: 124 PLKNLTNLNRLELSS-----NTISDISALSGLTSLQQLSFSSNQVTDLKPLANLTTLERL 178
Query: 351 DMGGAR 356
D+ +
Sbjct: 179 DISSNK 184
>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 = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 37/142 (26%), Positives = 61/142 (42%), Gaps = 14/142 (9%)
Query: 246 SKLKRLDLSGVGIRDGSELLRSMGSFPSLKTLFLEANNFTATTTQELHNFTNLEFLNLRH 305
+ L +LDLS + D S PSL+ L LE NN + + + +NL +L+L+
Sbjct: 248 TNLTQLDLSYNNLHDVGN--GSFSYLPSLRYLSLEYNNIQRLSPRSFYGLSNLRYLSLKR 305
Query: 306 S----SLDINLLKTIA--SFTSLKNLSMVSCEVNGVLDGQG--FLNFKSLERLDMGGARN 357
+ S+ + I SF LK L ++ + N + + F SL+ L +
Sbjct: 306 AFTKQSVSLASHPNIDDFSFQWLKYLEYLNMDDNNIPSTKSNTFTGLVSLKYLSLSKTFT 365
Query: 358 ALNASFLQIIGESMASLKHLSL 379
+L + E+ SL H L
Sbjct: 366 SLQT----LTNETFVSLAHSPL 383
>pdb|1H6U|A Chain A, Internalin H: Crystal Structure Of Fused N-Terminal
Domains
Length = 308
Score = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 30/108 (27%), Positives = 48/108 (44%), Gaps = 11/108 (10%)
Query: 243 RGLSKLKRLDLSGVGIRDGSELLRSMGSFPSLKTLFLEANNFTATTTQELHNFTNLEFLN 302
+ L+K+ L+LSG +++ + ++ S+KTL L + T T L +NL+ L
Sbjct: 82 KNLTKITELELSGNPLKN----VSAIAGLQSIKTLDLTSTQITDVT--PLAGLSNLQVL- 134
Query: 303 LRHSSLDINLLKTIASFTSLKNLSMVSCEVNGVLDGQGFLNFKSLERL 350
LD+N + I+ L NL +S V D N L L
Sbjct: 135 ----YLDLNQITNISPLAGLTNLQYLSIGNAQVSDLTPLANLSKLTTL 178
>pdb|1XEU|A Chain A, Crystal Structure Of Internalin C From Listeria
Monocytogenes
Length = 263
Score = 30.0 bits (66), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 26/94 (27%), Positives = 44/94 (46%), Gaps = 9/94 (9%)
Query: 265 LRSMGSFPS--LKTLFLEANNFTATTTQELHNFTNLEFLNLRHSSLDINLLKTIASFTSL 322
L+++ PS L LFL+ N T + L + NLE L++R+ N LK+I L
Sbjct: 97 LKNLNGIPSACLSRLFLDNNELRDTDS--LIHLKNLEILSIRN-----NKLKSIVMLGFL 149
Query: 323 KNLSMVSCEVNGVLDGQGFLNFKSLERLDMGGAR 356
L ++ N + + G K + +D+ G +
Sbjct: 150 SKLEVLDLHGNEITNTGGLTRLKKVNWIDLTGQK 183
>pdb|3G4D|A Chain A, Crystal Structure Of (+)-Delta-Cadinene Synthase From
Gossypium Arboreum And Evolutionary Divergence Of Metal
Binding Motifs For Catalysis
pdb|3G4D|B Chain B, Crystal Structure Of (+)-Delta-Cadinene Synthase From
Gossypium Arboreum And Evolutionary Divergence Of Metal
Binding Motifs For Catalysis
pdb|3G4F|A Chain A, Crystal Structure Of (+)- -Cadinene Synthase From
Gossypium Arboreum In Complex With 2-Fluorofarnesyl
Diphosphate
pdb|3G4F|B Chain B, Crystal Structure Of (+)- -Cadinene Synthase From
Gossypium Arboreum In Complex With 2-Fluorofarnesyl
Diphosphate
Length = 554
Score = 30.0 bits (66), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 34/65 (52%), Gaps = 9/65 (13%)
Query: 328 VSCEV-NGVLDGQGFLNFKSLERLDMGGARNALNASFLQIIGESMA------SLKHLSLS 380
VSC+V N D QG NFKS D+ G AS+L++ GE + + HLSL+
Sbjct: 128 VSCDVFNKFKDEQG--NFKSSVTSDVRGLLELYQASYLRVHGEDILDEAISFTTHHLSLA 185
Query: 381 YSILN 385
+ L+
Sbjct: 186 VASLD 190
>pdb|2OMX|A Chain A, Crystal Structure Of Inla S192n G194s+sHEC1 COMPLEX
Length = 462
Score = 29.3 bits (64), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 31/66 (46%), Gaps = 5/66 (7%)
Query: 291 ELHNFTNLEFLNLRHSSLDINLLKTIASFTSLKNLSMVSCEVNGVLDGQGFLNFKSLERL 350
L N TNL L L N + I++ + L +L ++ N V D + N +LERL
Sbjct: 124 PLKNLTNLNRLELSS-----NTISDISALSGLTSLQQLNFSSNQVTDLKPLANLTTLERL 178
Query: 351 DMGGAR 356
D+ +
Sbjct: 179 DISSNK 184
>pdb|2LLF|A Chain A, Sixth Gelsolin-like Domain Of Villin In 5 Mm Cacl2
Length = 107
Score = 28.9 bits (63), Expect = 5.6, Method: Composition-based stats.
Identities = 13/38 (34%), Positives = 21/38 (55%), Gaps = 2/38 (5%)
Query: 65 ECSNTTGRVIGLDLSDTRNEDLGEGYLNAFLFTPFQQL 102
ECSN TGR + ++ D +DL E + +L + Q+
Sbjct: 5 ECSNKTGRFLATEIVDFTQDDLDEN--DVYLLDTWDQI 40
>pdb|4B8C|D Chain D, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|J Chain J, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|K Chain K, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|L Chain L, Nuclease Module Of The Yeast Ccr4-Not Complex
Length = 727
Score = 28.1 bits (61), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 40/137 (29%), Positives = 63/137 (45%), Gaps = 10/137 (7%)
Query: 234 NNFVVPQDYRGLSKL-KRLDLSGVGIRDGSELLRSMGSFPSLKTLFLEANNFTATTTQEL 292
N V+P+D + +L LDLS + I + S ++ + L L+L N+ T E+
Sbjct: 211 NRMVMPKDSKYDDQLWHALDLSNLQIFNISA---NIFKYDFLTRLYLNGNSLTELPA-EI 266
Query: 293 HNFTNLEFLNLRHSSLDINLLKTIASFTSLKNLSMVSCEVNGVLDGQGFLNFKSLERLDM 352
N +NL L+L H+ L +L + S LK V + F N +L+ L +
Sbjct: 267 KNLSNLRVLDLSHNRL-TSLPAELGSCFQLKYFYFFDNMVTTL--PWEFGNLCNLQFLGV 323
Query: 353 GGARNALNASFLQIIGE 369
G N L FL+I+ E
Sbjct: 324 EG--NPLEKQFLKILTE 338
>pdb|3FG7|A Chain A, The Crystal Structure Of Villin Domain 6
pdb|3FG7|B Chain B, The Crystal Structure Of Villin Domain 6
Length = 398
Score = 28.1 bits (61), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 21/38 (55%), Gaps = 2/38 (5%)
Query: 65 ECSNTTGRVIGLDLSDTRNEDLGEGYLNAFLFTPFQQL 102
ECSN TGR + ++ D +DL E + FL + Q+
Sbjct: 287 ECSNKTGRFLATEIPDFNQDDLEED--DVFLLDVWDQV 322
>pdb|2ID5|A Chain A, Crystal Structure Of The Lingo-1 Ectodomain
pdb|2ID5|B Chain B, Crystal Structure Of The Lingo-1 Ectodomain
pdb|2ID5|C Chain C, Crystal Structure Of The Lingo-1 Ectodomain
pdb|2ID5|D Chain D, Crystal Structure Of The Lingo-1 Ectodomain
Length = 477
Score = 28.1 bits (61), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 32/63 (50%), Gaps = 3/63 (4%)
Query: 266 RSMGSFPSLKTLFLEANNFTATTTQELHNFTNLEFLNLRHSSLDINLLKTIASFTSLKNL 325
R+ SL+ L LE N T+ T+ L + L L LRH L+IN ++ SF L L
Sbjct: 146 RAFSGLNSLEQLTLEKCNLTSIPTEALSHLHGLIVLRLRH--LNINAIRDY-SFKRLYRL 202
Query: 326 SMV 328
++
Sbjct: 203 KVL 205
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
0.318 0.135 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,329,907
Number of Sequences: 62578
Number of extensions: 329709
Number of successful extensions: 701
Number of sequences better than 100.0: 43
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 28
Number of HSP's that attempted gapping in prelim test: 625
Number of HSP's gapped (non-prelim): 119
length of query: 394
length of database: 14,973,337
effective HSP length: 101
effective length of query: 293
effective length of database: 8,652,959
effective search space: 2535316987
effective search space used: 2535316987
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)