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= 025444
(252 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 27/102 (26%), Positives = 47/102 (46%), Gaps = 3/102 (2%)
Query: 1 MVEMLITRSSGSLRKLCVSGLHNDMMFSLIAENAGSLQTLRLPRSEMSDSIVAQIAGRLS 60
M E + S +L L +S H + F+ I SL+ L++ + ++ + I L
Sbjct: 435 MSEFSVFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELR 494
Query: 61 AVTFLDLSYCS--KIGAPALEAIGKHCKLLVVLCRNMHPLDT 100
+TFLDLS C ++ A ++ ++L + N LDT
Sbjct: 495 NLTFLDLSQCQLEQLSPTAFNSLSS-LQVLNMSHNNFFSLDT 535
>pdb|1FS2|A Chain A, Insights Into Scf Ubiquitin Ligases From The Structure Of
The Skp1-Skp2 Complex
pdb|1FS2|C Chain C, Insights Into Scf Ubiquitin Ligases From The Structure Of
The Skp1-Skp2 Complex
Length = 272
Score = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 45/181 (24%), Positives = 67/181 (37%), Gaps = 29/181 (16%)
Query: 18 VSGLHNDMMFSLIAENAGSLQTLRLPRSEMSDSIVAQIAGRLSAVTFLDLSYCSKIGAPA 77
VS LH I LQ L L +SD IV +A S + L+LS CS A
Sbjct: 69 VSTLHG------ILSQCSKLQNLSLEGLRLSDPIVNTLAKN-SNLVRLNLSGCSGFSEFA 121
Query: 78 LEAIGKHCKLLVVL----CRNM----------HPLDTADKLS--------QDDEANAIAS 115
L+ + C L L C + H +T +L+ Q + + +
Sbjct: 122 LQTLLSSCSRLDELNLSWCFDFTEKHVQVAVAHVSETITQLNLSGYRKNLQKSDLSTLVR 181
Query: 116 TMPKLKRLEMAYHVISTEIVLKILSSCALLEFLDLRGCWDVKLDDKFMKGNFPNLKVLGP 175
P L L+++ V+ + L+ L L C+D+ + G P LK L
Sbjct: 182 RCPNLVHLDLSDSVMLKNDCFQEFFQLNYLQHLSLSRCYDIIPETLLELGEIPTLKTLQV 241
Query: 176 F 176
F
Sbjct: 242 F 242
>pdb|2Z63|A Chain A, Crystal Structure Of The Tv8 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
Length = 570
Score = 33.1 bits (74), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 34/70 (48%)
Query: 1 MVEMLITRSSGSLRKLCVSGLHNDMMFSLIAENAGSLQTLRLPRSEMSDSIVAQIAGRLS 60
M E + S +L L +S H + F+ I SL+ L++ + ++ + I L
Sbjct: 411 MSEFSVFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELR 470
Query: 61 AVTFLDLSYC 70
+TFLDLS C
Sbjct: 471 NLTFLDLSQC 480
>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 = 32.7 bits (73), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 27/102 (26%), Positives = 47/102 (46%), Gaps = 3/102 (2%)
Query: 1 MVEMLITRSSGSLRKLCVSGLHNDMMFSLIAENAGSLQTLRLPRSEMSDSIVAQIAGRLS 60
M E + S +L L +S H + F+ I SL+ L++ + ++ + I L
Sbjct: 411 MSEFSVFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELR 470
Query: 61 AVTFLDLSYCS--KIGAPALEAIGKHCKLLVVLCRNMHPLDT 100
+TFLDLS C ++ A ++ ++L + N LDT
Sbjct: 471 NLTFLDLSQCQLEQLSPTAFNSLSS-LQVLNMSHNNFFSLDT 511
>pdb|1FQV|A Chain A, Insights Into Scf Ubiquitin Ligases From The Structure Of
The Skp1-Skp2 Complex
pdb|1FQV|C Chain C, Insights Into Scf Ubiquitin Ligases From The Structure Of
The Skp1-Skp2 Complex
pdb|1FQV|E Chain E, Insights Into Scf Ubiquitin Ligases From The Structure Of
The Skp1-Skp2 Complex
pdb|1FQV|G Chain G, Insights Into Scf Ubiquitin Ligases From The Structure Of
The Skp1-Skp2 Complex
pdb|1FQV|I Chain I, Insights Into Scf Ubiquitin Ligases From The Structure Of
The Skp1-Skp2 Complex
pdb|1FQV|K Chain K, Insights Into Scf Ubiquitin Ligases From The Structure Of
The Skp1-Skp2 Complex
pdb|1FQV|M Chain M, Insights Into Scf Ubiquitin Ligases From The Structure Of
The Skp1-Skp2 Complex
pdb|1FQV|O Chain O, Insights Into Scf Ubiquitin Ligases From The Structure Of
The Skp1-Skp2 Complex
pdb|2ASS|B Chain B, Crystal Structure Of The Skp1-Skp2-Cks1 Complex
pdb|2AST|B Chain B, Crystal Structure Of Skp1-Skp2-Cks1 In Complex With A P27
Peptide
Length = 336
Score = 32.7 bits (73), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 45/181 (24%), Positives = 67/181 (37%), Gaps = 29/181 (16%)
Query: 18 VSGLHNDMMFSLIAENAGSLQTLRLPRSEMSDSIVAQIAGRLSAVTFLDLSYCSKIGAPA 77
VS LH I LQ L L +SD IV +A S + L+LS CS A
Sbjct: 107 VSTLHG------ILSQCSKLQNLSLEGLRLSDPIVNTLAKN-SNLVRLNLSGCSGFSEFA 159
Query: 78 LEAIGKHCKLLVVL----CRNM----------HPLDTADKLS--------QDDEANAIAS 115
L+ + C L L C + H +T +L+ Q + + +
Sbjct: 160 LQTLLSSCSRLDELNLSWCFDFTEKHVQVAVAHVSETITQLNLSGYRKNLQKSDLSTLVR 219
Query: 116 TMPKLKRLEMAYHVISTEIVLKILSSCALLEFLDLRGCWDVKLDDKFMKGNFPNLKVLGP 175
P L L+++ V+ + L+ L L C+D+ + G P LK L
Sbjct: 220 RCPNLVHLDLSDSVMLKNDCFQEFFQLNYLQHLSLSRCYDIIPETLLELGEIPTLKTLQV 279
Query: 176 F 176
F
Sbjct: 280 F 280
>pdb|2Z66|A Chain A, Crystal Structure Of The Vt3 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
pdb|2Z66|B Chain B, Crystal Structure Of The Vt3 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
pdb|2Z66|C Chain C, Crystal Structure Of The Vt3 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
pdb|2Z66|D Chain D, Crystal Structure Of The Vt3 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
Length = 306
Score = 31.6 bits (70), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 3/62 (4%)
Query: 12 SLRKLC---VSGLHNDMMFSLIAENAGSLQTLRLPRSEMSDSIVAQIAGRLSAVTFLDLS 68
SLR L +S H + F+ I SL+ L++ + ++ + I L +TFLDLS
Sbjct: 124 SLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFLDLS 183
Query: 69 YC 70
C
Sbjct: 184 QC 185
>pdb|3PL6|D Chain D, Structure Of Autoimmune Tcr Hy.1b11 In Complex With
Hla-Dq1 And Mbp 85-99
Length = 268
Score = 31.2 bits (69), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 16/34 (47%), Positives = 22/34 (64%), Gaps = 2/34 (5%)
Query: 19 SGLHNDMMFSLIAENAGSLQTLRLPRSEMSDSIV 52
SGL ND F++ E GS+ TL++ R+E DS V
Sbjct: 83 SGLPNDRFFAVRPE--GSVSTLKIQRTERGDSAV 114
>pdb|3VQ1|A Chain A, Crystal Structure Of Mouse Tlr4MD-2LIPID IVA COMPLEX
pdb|3VQ1|B Chain B, Crystal Structure Of Mouse Tlr4MD-2LIPID IVA COMPLEX
pdb|3VQ2|A Chain A, Crystal Structure Of Mouse Tlr4MD-2LPS COMPLEX
pdb|3VQ2|B Chain B, Crystal Structure Of Mouse Tlr4MD-2LPS COMPLEX
Length = 606
Score = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 21/35 (60%)
Query: 36 SLQTLRLPRSEMSDSIVAQIAGRLSAVTFLDLSYC 70
SL TL++ + D+ ++ + + +TFLDLS C
Sbjct: 449 SLNTLKMAGNSFKDNTLSNVFANTTNLTFLDLSKC 483
>pdb|2Z64|A Chain A, Crystal Structure Of Mouse Tlr4 And Mouse Md-2 Complex
Length = 599
Score = 29.3 bits (64), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 21/35 (60%)
Query: 36 SLQTLRLPRSEMSDSIVAQIAGRLSAVTFLDLSYC 70
SL TL++ + D+ ++ + + +TFLDLS C
Sbjct: 444 SLNTLKMAGNSFKDNTLSNVFANTTNLTFLDLSKC 478
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 0.137 0.423
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,543,528
Number of Sequences: 62578
Number of extensions: 234327
Number of successful extensions: 461
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 453
Number of HSP's gapped (non-prelim): 9
length of query: 252
length of database: 14,973,337
effective HSP length: 97
effective length of query: 155
effective length of database: 8,903,271
effective search space: 1380007005
effective search space used: 1380007005
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: 50 (23.9 bits)