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= 026286
(240 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 32.3 bits (72), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 39/167 (23%), Positives = 61/167 (36%), Gaps = 23/167 (13%)
Query: 20 ASAGSLQTLRLPRSEMSDSIVAQIAGRLSAVTFLDLSYCSKIGAPALEAIGKHCKLL--- 76
+ LQ L L +SD IV +A S + L+LS CS AL+ + C L
Sbjct: 77 SQCSKLQNLSLEGLRLSDPIVNTLAKN-SNLVRLNLSGCSGFSEFALQTLLSSCSRLDEL 135
Query: 77 -----------VVLCRNMHPLDTADKLS--------QDDEANAIASTMPKLKRLEMAYHV 117
V H +T +L+ Q + + + P L L+++ V
Sbjct: 136 NLSWCFDFTEKHVQVAVAHVSETITQLNLSGYRKNLQKSDLSTLVRRCPNLVHLDLSDSV 195
Query: 118 ISTEIVLKILSSCALLEFLDLRGCWDVKLDDKFMKGNFPNLKVLGPF 164
+ + L+ L L C+D+ + G P LK L F
Sbjct: 196 MLKNDCFQEFFQLNYLQHLSLSRCYDIIPETLLELGEIPTLKTLQVF 242
>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 = 32.0 bits (71), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 39/167 (23%), Positives = 61/167 (36%), Gaps = 23/167 (13%)
Query: 20 ASAGSLQTLRLPRSEMSDSIVAQIAGRLSAVTFLDLSYCSKIGAPALEAIGKHCKLL--- 76
+ LQ L L +SD IV +A S + L+LS CS AL+ + C L
Sbjct: 115 SQCSKLQNLSLEGLRLSDPIVNTLAKN-SNLVRLNLSGCSGFSEFALQTLLSSCSRLDEL 173
Query: 77 -----------VVLCRNMHPLDTADKLS--------QDDEANAIASTMPKLKRLEMAYHV 117
V H +T +L+ Q + + + P L L+++ V
Sbjct: 174 NLSWCFDFTEKHVQVAVAHVSETITQLNLSGYRKNLQKSDLSTLVRRCPNLVHLDLSDSV 233
Query: 118 ISTEIVLKILSSCALLEFLDLRGCWDVKLDDKFMKGNFPNLKVLGPF 164
+ + L+ L L C+D+ + G P LK L F
Sbjct: 234 MLKNDCFQEFFQLNYLQHLSLSRCYDIIPETLLELGEIPTLKTLQVF 280
>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 = 2.1, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 21/35 (60%)
Query: 24 SLQTLRLPRSEMSDSIVAQIAGRLSAVTFLDLSYC 58
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 = 2.1, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 21/35 (60%)
Query: 24 SLQTLRLPRSEMSDSIVAQIAGRLSAVTFLDLSYC 58
SL TL++ + D+ ++ + + +TFLDLS C
Sbjct: 444 SLNTLKMAGNSFKDNTLSNVFANTTNLTFLDLSKC 478
>pdb|2P1M|B Chain B, Tir1-ask1 Complex Structure
pdb|2P1N|B Chain B, Mechanism Of Auxin Perception By The Tir1 Ubiqutin Ligase
pdb|2P1N|E Chain E, Mechanism Of Auxin Perception By The Tir1 Ubiqutin Ligase
pdb|2P1O|B Chain B, Mechanism Of Auxin Perception By The Tir1 Ubiquitin Ligase
pdb|2P1P|B Chain B, Mechanism Of Auxin Perception By The Tir1 Ubiquitin Ligase
pdb|2P1Q|B Chain B, Mechanism Of Auxin Perception By The Tir1 Ubiquitin Ligase
pdb|3C6N|B Chain B, Small Molecule Agonists And Antagonists Of F-Box Protein-
Substrate Interactions In Auxin Perception And Signaling
pdb|3C6O|B Chain B, Small Molecule Agonists And Antagonists Of F-Box
Protein-Substrate Interactions In Auxin Perception And
Signaling
pdb|3C6P|B Chain B, Small Molecule Agonists And Antagonists Of F-Box Protein-
Substrate Interactions In Auxin Perception And Signaling
Length = 594
Score = 27.7 bits (60), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 28/69 (40%), Gaps = 7/69 (10%)
Query: 19 SASAGSLQTLRLPRSEMSDSIVAQIAGRLSAVTFLDLSYCSKIGAPALEAIGKHCKLLVV 78
S+S L+ +RL R ++D + IA L LS C L AI
Sbjct: 101 SSSYTWLEEIRLKRMVVTDDCLELIAKSFKNFKVLVLSSCEGFSTDGLAAIA-------A 153
Query: 79 LCRNMHPLD 87
CRN+ LD
Sbjct: 154 TCRNLKELD 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 = 26.9 bits (58), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 33/68 (48%), Gaps = 3/68 (4%)
Query: 23 GSLQTLRLPRSEMSDSIVAQIAGRLSAVTFLDLSYCS--KIGAPALEAIGKHCKLLVVLC 80
SL+ L++ + ++ + I L +TFLDLS C ++ A ++ ++L +
Sbjct: 469 SSLEVLKMAGNSFQENFLPDIFTELRNLTFLDLSQCQLEQLSPTAFNSLSS-LQVLNMSH 527
Query: 81 RNMHPLDT 88
N LDT
Sbjct: 528 NNFFSLDT 535
>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 = 26.9 bits (58), Expect = 10.0, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 33/68 (48%), Gaps = 3/68 (4%)
Query: 23 GSLQTLRLPRSEMSDSIVAQIAGRLSAVTFLDLSYCS--KIGAPALEAIGKHCKLLVVLC 80
SL+ L++ + ++ + I L +TFLDLS C ++ A ++ ++L +
Sbjct: 445 SSLEVLKMAGNSFQENFLPDIFTELRNLTFLDLSQCQLEQLSPTAFNSLSS-LQVLNMSH 503
Query: 81 RNMHPLDT 88
N LDT
Sbjct: 504 NNFFSLDT 511
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
0.322 0.139 0.437
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,432,915
Number of Sequences: 62578
Number of extensions: 228372
Number of successful extensions: 424
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 415
Number of HSP's gapped (non-prelim): 12
length of query: 240
length of database: 14,973,337
effective HSP length: 96
effective length of query: 144
effective length of database: 8,965,849
effective search space: 1291082256
effective search space used: 1291082256
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)