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= 009053
(545 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type
Iii Effector Xcv3220 (Xopl)
Length = 328
Score = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 43/128 (33%), Positives = 60/128 (46%), Gaps = 6/128 (4%)
Query: 55 PLKTLDIHAE-----NLVSLKMPGSKVKQLWDDVQNLVNLKKIDLWYSKLLTKLPDLSLA 109
PL + D E NL SL++ + ++ L + NL NLK + + S L P +
Sbjct: 169 PLASTDASGEHQGLVNLQSLRLEWTGIRSLPASIANLQNLKSLKIRNSPLSALGPAIHHL 228
Query: 110 QNLEILDLGGCSSLTETHSSIQYLNKLEVLDLDRCESLRTLPTSIQS-KYLKRLVLRGCS 168
LE LDL GC++L L+ L L C +L TLP I L++L LRGC
Sbjct: 229 PKLEELDLRGCTALRNYPPIFGGRAPLKRLILKDCSNLLTLPLDIHRLTQLEKLDLRGCV 288
Query: 169 NLKNFPEI 176
NL P +
Sbjct: 289 NLSRLPSL 296
Score = 52.0 bits (123), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 53/205 (25%), Positives = 79/205 (38%), Gaps = 40/205 (19%)
Query: 170 LKNFPEISS--SGIHRLDLTHVGIKELPSSIDRLSKLDTLKIHDCTSLESLPSSLSMFKS 227
L FP+ + S + + G+ ELP + + + L+TL + L +LP+S++
Sbjct: 93 LPQFPDQAFRLSHLQHXTIDAAGLXELPDTXQQFAGLETLTLAR-NPLRALPASIASLNR 151
Query: 228 LTSLEIIYCPKLKRLPDELGNLKA---------LEELRVEGTAIRRPPEXXXXXXXXXXX 278
L L I CP+L LP+ L + A L+ LR+E T IR P
Sbjct: 152 LRELSIRACPELTELPEPLASTDASGEHQGLVNLQSLRLEWTGIRSLPASIANLQNLKSL 211
Query: 279 XXXXXXXXERAPESIRHLSKLTSLFISDCKMLQTLPE---------------------LP 317
P +I HL KL L + C L+ P LP
Sbjct: 212 KIRNSPLSALGP-AIHHLPKLEELDLRGCTALRNYPPIFGGRAPLKRLILKDCSNLLTLP 270
Query: 318 CNLH------DLDASGCTSLEALPA 336
++H LD GC +L LP+
Sbjct: 271 LDIHRLTQLEKLDLRGCVNLSRLPS 295
Score = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 52/175 (29%), Positives = 69/175 (39%), Gaps = 36/175 (20%)
Query: 120 CSSLTETHSSIQYLNKLEVLDLDRCESLRTLPTSIQS-KYLKRLVLRGCSNLKNFPE--- 175
+ L E + Q LE L L R LR LP SI S L+ L +R C L PE
Sbjct: 113 AAGLXELPDTXQQFAGLETLTLAR-NPLRALPASIASLNRLRELSIRACPELTELPEPLA 171
Query: 176 -ISSSGIHR-------LDLTHVGIKELPSSIDRLSKLDTLK------------------- 208
+SG H+ L L GI+ LP+SI L L +LK
Sbjct: 172 STDASGEHQGLVNLQSLRLEWTGIRSLPASIANLQNLKSLKIRNSPLSALGPAIHHLPKL 231
Query: 209 ----IHDCTSLESLPSSLSMFKSLTSLEIIYCPKLKRLPDELGNLKALEELRVEG 259
+ CT+L + P L L + C L LP ++ L LE+L + G
Sbjct: 232 EELDLRGCTALRNYPPIFGGRAPLKRLILKDCSNLLTLPLDIHRLTQLEKLDLRG 286
>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 = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 61/244 (25%), Positives = 99/244 (40%), Gaps = 69/244 (28%)
Query: 32 KCMVSSLEGVPFTEVRYFEWHQYPLKTLDIHA-------------ENLVSLKMPGSKVKQ 78
K V+ EG+P TE R + + +KTL+ EN+VS PG+
Sbjct: 21 KRFVAVPEGIP-TETRLLDLGKNRIKTLNQDEFASFPHLEELELNENIVSAVEPGA---- 75
Query: 79 LWDDVQNLVNLKKIDLWYSKL----------LTKLPDLSLAQN---------------LE 113
NL NL+ + L ++L L+ L L +++N L+
Sbjct: 76 ----FNNLFNLRTLGLRSNRLKLIPLGVFTGLSNLTKLDISENKIVILLDYMFQDLYNLK 131
Query: 114 ILDLGGCSSLTETHSSIQYLNKLEVLDLDRCESLRTLPTSIQSKYLKRLVLRGCSNLKNF 173
L++G + +H + LN LE L L++C +L ++PT S +VLR
Sbjct: 132 SLEVGDNDLVYISHRAFSGLNSLEQLTLEKC-NLTSIPTEALSHLHGLIVLR-------- 182
Query: 174 PEISSSGIHRLDLTHVGIKELPS-SIDRLSKLDTLKIHDCTSLESLPSSLSMFKSLTSLE 232
L H+ I + S RL +L L+I L+++ + +LTSL
Sbjct: 183 ------------LRHLNINAIRDYSFKRLYRLKVLEISHWPYLDTMTPNCLYGLNLTSLS 230
Query: 233 IIYC 236
I +C
Sbjct: 231 ITHC 234
>pdb|1G9U|A Chain A, Crystal Structure Of Yopm-leucine Rich Effector Protein
From Yersinia Pestis
pdb|1JL5|A Chain A, Novel Molecular Architecture Of Yopm-A Leucine-Rich
Effector Protein From Yersinia Pestis
Length = 454
Score = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 72/247 (29%), Positives = 116/247 (46%), Gaps = 56/247 (22%)
Query: 100 LTKLPDLSLAQNLEILDLGGCSSLTETHSSIQYLNKLEVLDLDRCESLRTLPTSIQSKYL 159
L+ LP+L +LE L + C+SLTE Q L L ++D + ++L LP ++ YL
Sbjct: 83 LSSLPEL--PPHLESL-VASCNSLTELPELPQSLKSL-LVDNNNLKALSDLPPLLE--YL 136
Query: 160 KRLVLRGCSN--LKNFPEISSSGIHRL-DLTHVGIKELPSSIDRLSKLDTLKIHDCTSLE 216
G SN L+ PE+ +S ++ D+ + +K+LP D L+ + + LE
Sbjct: 137 ------GVSNNQLEKLPELQNSSFLKIIDVDNNSLKKLP---DLPPSLEFIAAGN-NQLE 186
Query: 217 SLPSSLSMFKSLTSLEIIYCPK--LKRLPDELGNLKALEELRVEGTAIRRPPEXXXXXXX 274
LP ++L L IY LK+LPD +L+++ V G I
Sbjct: 187 ELPE----LQNLPFLTAIYADNNSLKKLPDLPLSLESI----VAGNNI------------ 226
Query: 275 XXXXXXXXXXXXERAPESIRHLSKLTSLFISDCKMLQTLPELPCNLHDLDASG--CTSLE 332
E PE +++L LT+++ +D +L+TLP+LP +L L+ T L
Sbjct: 227 -----------LEELPE-LQNLPFLTTIY-ADNNLLKTLPDLPPSLEALNVRDNYLTDLP 273
Query: 333 ALPASLS 339
LP SL+
Sbjct: 274 ELPQSLT 280
Score = 32.3 bits (72), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 50/204 (24%), Positives = 91/204 (44%), Gaps = 22/204 (10%)
Query: 182 HRLDLTHVGIKELPSSIDRLSKLDTLKIHDCTSLESLPSSL-------SMFKSLTSLEI- 233
H L+L ++G+ LP L L + T L LP SL + K+L+ L
Sbjct: 74 HELELNNLGLSSLPELPPHLESL-VASCNSLTELPELPQSLKSLLVDNNNLKALSDLPPL 132
Query: 234 -----IYCPKLKRLPDELGNLKALEELRVEGTAIRRPPEXXXXXXXXXXXXXXXXXXXER 288
+ +L++LP EL N L+ + V+ ++++ P+ E
Sbjct: 133 LEYLGVSNNQLEKLP-ELQNSSFLKIIDVDNNSLKKLPD----LPPSLEFIAAGNNQLEE 187
Query: 289 APESIRHLSKLTSLFISDCKMLQTLPELPCNLHDLDASGCTSLEALPASLSSKFYLSVDL 348
PE +++L LT+++ +D L+ LP+LP +L + +G LE LP + F ++
Sbjct: 188 LPE-LQNLPFLTAIY-ADNNSLKKLPDLPLSLESI-VAGNNILEELPELQNLPFLTTIYA 244
Query: 349 SNCLKLDLSELSEIIKDRWMKQSY 372
N L L +L ++ ++ +Y
Sbjct: 245 DNNLLKTLPDLPPSLEALNVRDNY 268
>pdb|3T6Q|A Chain A, Crystal Structure Of Mouse Rp105MD-1 Complex
pdb|3T6Q|B Chain B, Crystal Structure Of Mouse Rp105MD-1 Complex
Length = 606
Score = 33.9 bits (76), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 33/79 (41%), Positives = 39/79 (49%), Gaps = 4/79 (5%)
Query: 179 SGIHRLDLTHVGIKELPSSIDRLSKLDTLKIHDCTSLESLPS-SLSMFKSLTSLEIIYCP 237
SG+ LDLT + ELPS + LS L L + E+L S S F SLT L I
Sbjct: 278 SGLQELDLTATHLSELPSGLVGLSTLKKL-VLSANKFENLCQISASNFPSLTHLSIK--G 334
Query: 238 KLKRLPDELGNLKALEELR 256
KRL G L+ LE LR
Sbjct: 335 NTKRLELGTGCLENLENLR 353
>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 = 32.7 bits (73), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 30/84 (35%), Positives = 39/84 (46%), Gaps = 6/84 (7%)
Query: 183 RLDLTHVGIKELPSSIDRLSKLDTLKIHDCTSLESLPSSLSMFKSLTSLEIIYC--PKLK 240
RL L + ELP+ I LS L L + L SLP+ L S L+ Y +
Sbjct: 251 RLYLNGNSLTELPAEIKNLSNLRVLDL-SHNRLTSLPAELG---SCFQLKYFYFFDNMVT 306
Query: 241 RLPDELGNLKALEELRVEGTAIRR 264
LP E GNL L+ L VEG + +
Sbjct: 307 TLPWEFGNLCNLQFLGVEGNPLEK 330
>pdb|4ECN|A Chain A, Crystal Structure Of A Leucine-Rich Repeat Protein
(Bt_0210) From Bacteroides Thetaiotaomicron Vpi-5482 At
2.80 A Resolution
Length = 876
Score = 30.4 bits (67), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 21/37 (56%)
Query: 221 SLSMFKSLTSLEIIYCPKLKRLPDELGNLKALEELRV 257
S S K LT +E+ CP +LPD L +L L+ L +
Sbjct: 486 SWSNLKDLTDVELYNCPNXTQLPDFLYDLPELQSLNI 522
>pdb|2A0Z|A Chain A, The Molecular Structure Of Toll-like Receptor 3 Ligand
Binding Domain
Length = 705
Score = 29.3 bits (64), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 45/160 (28%), Positives = 66/160 (41%), Gaps = 28/160 (17%)
Query: 110 QNLEILDLGGCSSLTETHSSIQYLNKLEVLDLDRCESLRTLPTSIQSKYLKRLVLRGCSN 169
+NL ILDL + ++ L KLE+LDL R + + L+G S+
Sbjct: 485 RNLTILDLSNNNIANINDDMLEGLEKLEILDLQHNNLARLWKHANPGGPI--YFLKGLSH 542
Query: 170 LKNFPEISSSGIHRLDLTHVGIKELPSSIDRLSKLDTLKIHD--CTSLESLPSSLSMFKS 227
L H L+L G E+P ++ L LKI D +L +LP+ S+F +
Sbjct: 543 L-----------HILNLESNGFDEIP--VEVFKDLFELKIIDLGLNNLNTLPA--SVFNN 587
Query: 228 LTSLEIIYCPKLKRLPDELGNLKALEELRVEGTAIRRPPE 267
SL+ + K NL E +V G A R E
Sbjct: 588 QVSLKSLNLQK---------NLITSVEKKVFGPAFRNLTE 618
>pdb|1ZIW|A Chain A, Human Toll-Like Receptor 3 Extracellular Domain Structure
Length = 680
Score = 29.3 bits (64), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 45/160 (28%), Positives = 66/160 (41%), Gaps = 28/160 (17%)
Query: 110 QNLEILDLGGCSSLTETHSSIQYLNKLEVLDLDRCESLRTLPTSIQSKYLKRLVLRGCSN 169
+NL ILDL + ++ L KLE+LDL R + + L+G S+
Sbjct: 480 RNLTILDLSNNNIANINDDMLEGLEKLEILDLQHNNLARLWKHANPGGPI--YFLKGLSH 537
Query: 170 LKNFPEISSSGIHRLDLTHVGIKELPSSIDRLSKLDTLKIHD--CTSLESLPSSLSMFKS 227
L H L+L G E+P ++ L LKI D +L +LP+ S+F +
Sbjct: 538 L-----------HILNLESNGFDEIP--VEVFKDLFELKIIDLGLNNLNTLPA--SVFNN 582
Query: 228 LTSLEIIYCPKLKRLPDELGNLKALEELRVEGTAIRRPPE 267
SL+ + K NL E +V G A R E
Sbjct: 583 QVSLKSLNLQK---------NLITSVEKKVFGPAFRNLTE 613
>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 = 29.3 bits (64), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 45/160 (28%), Positives = 66/160 (41%), Gaps = 28/160 (17%)
Query: 110 QNLEILDLGGCSSLTETHSSIQYLNKLEVLDLDRCESLRTLPTSIQSKYLKRLVLRGCSN 169
+NL ILDL + ++ L KLE+LDL R + + L+G S+
Sbjct: 490 RNLTILDLSNNNIANINDDMLEGLEKLEILDLQHNNLARLWKHANPGGPI--YFLKGLSH 547
Query: 170 LKNFPEISSSGIHRLDLTHVGIKELPSSIDRLSKLDTLKIHD--CTSLESLPSSLSMFKS 227
L H L+L G E+P ++ L LKI D +L +LP+ S+F +
Sbjct: 548 L-----------HILNLESNGFDEIP--VEVFKDLFELKIIDLGLNNLNTLPA--SVFNN 592
Query: 228 LTSLEIIYCPKLKRLPDELGNLKALEELRVEGTAIRRPPE 267
SL+ + K NL E +V G A R E
Sbjct: 593 QVSLKSLNLQK---------NLITSVEKKVFGPAFRNLTE 623
>pdb|3FXI|A Chain A, Crystal Structure Of The Human Tlr4-Human Md-2-E.Coli Lps
Ra Complex
pdb|3FXI|B Chain B, Crystal Structure Of The Human Tlr4-Human Md-2-E.Coli Lps
Ra Complex
Length = 605
Score = 29.3 bits (64), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 37/131 (28%), Positives = 58/131 (44%), Gaps = 23/131 (17%)
Query: 135 KLEVLDLDRCESLRTLPTSIQS-KYLKRLVLRGCSNLKNFPEISSSGIHRLDLTHVGIKE 193
+L+VLDL RCE + QS +L L+L G + I L L G
Sbjct: 53 ELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTG------------NPIQSLAL---GAFS 97
Query: 194 LPSSIDRLSKLDTLKIHDCTSLESLPSSLSMFKSLTSLEIIY-CPKLKRLPDELGNLKAL 252
SS+ +L ++T + SLE+ P + K+L L + + + +LP+ NL L
Sbjct: 98 GLSSLQKLVAVET----NLASLENFP--IGHLKTLKELNVAHNLIQSFKLPEYFSNLTNL 151
Query: 253 EELRVEGTAIR 263
E L + I+
Sbjct: 152 EHLDLSSNKIQ 162
>pdb|4G8A|A Chain A, Crystal Structure Of Human Tlr4 Polymorphic Variant D299g
And T399i In Complex With Md-2 And Lps
pdb|4G8A|B Chain B, Crystal Structure Of Human Tlr4 Polymorphic Variant D299g
And T399i In Complex With Md-2 And Lps
Length = 635
Score = 29.3 bits (64), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 37/131 (28%), Positives = 58/131 (44%), Gaps = 23/131 (17%)
Query: 135 KLEVLDLDRCESLRTLPTSIQS-KYLKRLVLRGCSNLKNFPEISSSGIHRLDLTHVGIKE 193
+L+VLDL RCE + QS +L L+L G + I L L G
Sbjct: 77 ELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTG------------NPIQSLAL---GAFS 121
Query: 194 LPSSIDRLSKLDTLKIHDCTSLESLPSSLSMFKSLTSLEIIY-CPKLKRLPDELGNLKAL 252
SS+ +L ++T + SLE+ P + K+L L + + + +LP+ NL L
Sbjct: 122 GLSSLQKLVAVET----NLASLENFP--IGHLKTLKELNVAHNLIQSFKLPEYFSNLTNL 175
Query: 253 EELRVEGTAIR 263
E L + I+
Sbjct: 176 EHLDLSSNKIQ 186
>pdb|3UL8|A Chain A, Crystal Structure Of The Tv3 Mutant V134l
Length = 279
Score = 28.9 bits (63), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 38/131 (29%), Positives = 58/131 (44%), Gaps = 23/131 (17%)
Query: 135 KLEVLDLDRCESLRTLPTSIQS-KYLKRLVLRGCSNLKNFPEISSSGIHRLDLTHVGIKE 193
+L+VLDL RCE + QS +L L+L G + I L L G
Sbjct: 55 ELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTG------------NPIQSLAL---GAFS 99
Query: 194 LPSSIDRLSKLDTLKIHDCTSLESLPSSLSMFKSLTSLEIIY-CPKLKRLPDELGNLKAL 252
SS+ +L L+T + SLE+ P + K+L L + + + +LP+ NL L
Sbjct: 100 GLSSLQKLVALET----NLASLENFP--IGHLKTLKELNVAHNLIQSFKLPEYFSNLTNL 153
Query: 253 EELRVEGTAIR 263
E L + I+
Sbjct: 154 EHLDLSSNKIQ 164
>pdb|2Z63|A Chain A, Crystal Structure Of The Tv8 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
Length = 570
Score = 28.5 bits (62), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 37/131 (28%), Positives = 58/131 (44%), Gaps = 23/131 (17%)
Query: 135 KLEVLDLDRCESLRTLPTSIQS-KYLKRLVLRGCSNLKNFPEISSSGIHRLDLTHVGIKE 193
+L+VLDL RCE + QS +L L+L G + I L L G
Sbjct: 53 ELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTG------------NPIQSLAL---GAFS 97
Query: 194 LPSSIDRLSKLDTLKIHDCTSLESLPSSLSMFKSLTSLEIIY-CPKLKRLPDELGNLKAL 252
SS+ +L ++T + SLE+ P + K+L L + + + +LP+ NL L
Sbjct: 98 GLSSLQKLVAVET----NLASLENFP--IGHLKTLKELNVAHNLIQSFKLPEYFSNLTNL 151
Query: 253 EELRVEGTAIR 263
E L + I+
Sbjct: 152 EHLDLSSNKIQ 162
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
0.320 0.136 0.409
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,620,696
Number of Sequences: 62578
Number of extensions: 533561
Number of successful extensions: 1211
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 24
Number of HSP's that attempted gapping in prelim test: 1165
Number of HSP's gapped (non-prelim): 56
length of query: 545
length of database: 14,973,337
effective HSP length: 104
effective length of query: 441
effective length of database: 8,465,225
effective search space: 3733164225
effective search space used: 3733164225
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)