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= 020727
(322 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 = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 72/260 (27%), Positives = 100/260 (38%), Gaps = 49/260 (18%)
Query: 10 WDELIPDALGL-IFRNLSLQEVLTVIPGVCKSWRRAVIGPYCWQEIDIEEWSNRCQPDHL 68
WD L PD L L IF L L E+L V GVCK W R WQ +D + H+
Sbjct: 9 WDSL-PDELLLGIFSCLCLPELLKV-SGVCKRWYRLASDESLWQTLD------EFRVQHM 60
Query: 69 DRMVEMLITRSSGSLRKLCVSGLHNDMMFSLIAENAGSLQTLRLPRSEMSDSIVAQIAGR 128
D S S+ + VS LH I LQ L L +SD IV +A
Sbjct: 61 DL---------SNSVIE--VSTLHG------ILSQCSKLQNLSLEGLRLSDPIVNTLAKN 103
Query: 129 LSAVTFLDLSYCSKIGAPALEAIGKHCKLLVVL----CRNM----------HPLDTADKL 174
S + L+LS CS AL+ + C L L C + H +T +L
Sbjct: 104 -SNLVRLNLSGCSGFSEFALQTLLSSCSRLDELNLSWCFDFTEKHVQVAVAHVSETITQL 162
Query: 175 S--------QDDEANAIASTMPKLKRLEMAYHVISTEIVLKILSSCALLEFLDLRGCWDV 226
+ Q + + + P L L+++ V+ + L+ L L C+D+
Sbjct: 163 NLSGYRKNLQKSDLSTLVRRCPNLVHLDLSDSVMLKNDCFQEFFQLNYLQHLSLSRCYDI 222
Query: 227 KLDDKFMKGNFPNLKVLGPF 246
+ G P LK L F
Sbjct: 223 IPETLLELGEIPTLKTLQVF 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 = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 73/283 (25%), Positives = 103/283 (36%), Gaps = 57/283 (20%)
Query: 10 WDELIPDALGL-IFRNLSLQEVLTVIPGVCKSWRRAVIGPYCWQEIDIEEWSNRCQPDHL 68
WD L PD L L IF L L E+L V GVCK W R WQ +D+ PD
Sbjct: 9 WDSL-PDELLLGIFSCLCLPELLKV-SGVCKRWYRLASDESLWQTLDLT--GKNLHPDVT 64
Query: 69 DRMVEMLITRSSGSLRKLCVSGL---------------HNDMMFSLIA--------ENAG 105
R++ S G + C H D+ S+I
Sbjct: 65 GRLL------SQGVIAFRCPRSFMDQPLAEHFSPFRVQHMDLSNSVIEVSTLHGILSQCS 118
Query: 106 SLQTLRLPRSEMSDSIVAQIAGRLSAVTFLDLSYCSKIGAPALEAIGKHCKLLVVL---- 161
LQ L L +SD IV +A S + L+LS CS AL+ + C L L
Sbjct: 119 KLQNLSLEGLRLSDPIVNTLAKN-SNLVRLNLSGCSGFSEFALQTLLSSCSRLDELNLSW 177
Query: 162 CRNM----------HPLDTADKLS--------QDDEANAIASTMPKLKRLEMAYHVISTE 203
C + H +T +L+ Q + + + P L L+++ V+
Sbjct: 178 CFDFTEKHVQVAVAHVSETITQLNLSGYRKNLQKSDLSTLVRRCPNLVHLDLSDSVMLKN 237
Query: 204 IVLKILSSCALLEFLDLRGCWDVKLDDKFMKGNFPNLKVLGPF 246
+ L+ L L C+D+ + G P LK L F
Sbjct: 238 DCFQEFFQLNYLQHLSLSRCYDIIPETLLELGEIPTLKTLQVF 280
>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 = 37.4 bits (85), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 29/109 (26%), Positives = 51/109 (46%), Gaps = 3/109 (2%)
Query: 64 QPDHLDRMVEMLITRSSGSLRKLCVSGLHNDMMFSLIAENAGSLQTLRLPRSEMSDSIVA 123
Q +L +M E + S +L L +S H + F+ I SL+ L++ + ++ +
Sbjct: 428 QHSNLKQMSEFSVFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLP 487
Query: 124 QIAGRLSAVTFLDLSYCS--KIGAPALEAIGKHCKLLVVLCRNMHPLDT 170
I L +TFLDLS C ++ A ++ ++L + N LDT
Sbjct: 488 DIFTELRNLTFLDLSQCQLEQLSPTAFNSLSS-LQVLNMSHNNFFSLDT 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 = 37.0 bits (84), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 29/109 (26%), Positives = 51/109 (46%), Gaps = 3/109 (2%)
Query: 64 QPDHLDRMVEMLITRSSGSLRKLCVSGLHNDMMFSLIAENAGSLQTLRLPRSEMSDSIVA 123
Q +L +M E + S +L L +S H + F+ I SL+ L++ + ++ +
Sbjct: 404 QHSNLKQMSEFSVFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLP 463
Query: 124 QIAGRLSAVTFLDLSYCS--KIGAPALEAIGKHCKLLVVLCRNMHPLDT 170
I L +TFLDLS C ++ A ++ ++L + N LDT
Sbjct: 464 DIFTELRNLTFLDLSQCQLEQLSPTAFNSLSS-LQVLNMSHNNFFSLDT 511
>pdb|2Z63|A Chain A, Crystal Structure Of The Tv8 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
Length = 570
Score = 36.6 bits (83), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 38/77 (49%)
Query: 64 QPDHLDRMVEMLITRSSGSLRKLCVSGLHNDMMFSLIAENAGSLQTLRLPRSEMSDSIVA 123
Q +L +M E + S +L L +S H + F+ I SL+ L++ + ++ +
Sbjct: 404 QHSNLKQMSEFSVFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLP 463
Query: 124 QIAGRLSAVTFLDLSYC 140
I L +TFLDLS C
Sbjct: 464 DIFTELRNLTFLDLSQC 480
>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 = 35.0 bits (79), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 29/109 (26%), Positives = 51/109 (46%), Gaps = 3/109 (2%)
Query: 64 QPDHLDRMVEMLITRSSGSLRKLCVSGLHNDMMFSLIAENAGSLQTLRLPRSEMSDSIVA 123
Q +L +M E + S +L L +S H + F+ I SL+ L++ + ++ +
Sbjct: 109 QHSNLKQMSEFSVFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLP 168
Query: 124 QIAGRLSAVTFLDLSYCS--KIGAPALEAIGKHCKLLVVLCRNMHPLDT 170
I L +TFLDLS C ++ A ++ ++L + N LDT
Sbjct: 169 DIFTELRNLTFLDLSQCQLEQLSPTAFNSLSS-LQVLNMSHNNFFSLDT 216
>pdb|2Z64|A Chain A, Crystal Structure Of Mouse Tlr4 And Mouse Md-2 Complex
Length = 599
Score = 31.6 bits (70), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 35/77 (45%)
Query: 64 QPDHLDRMVEMLITRSSGSLRKLCVSGLHNDMMFSLIAENAGSLQTLRLPRSEMSDSIVA 123
Q L R+ E S L L +S + + F I SL TL++ + D+ ++
Sbjct: 402 QHSTLKRVTEFSAFLSLEKLLYLDISYTNTKIDFDGIFLGLTSLNTLKMAGNSFKDNTLS 461
Query: 124 QIAGRLSAVTFLDLSYC 140
+ + +TFLDLS C
Sbjct: 462 NVFANTTNLTFLDLSKC 478
>pdb|1FS1|A Chain A, Insights Into Scf Ubiquitin Ligases From The Structure
Of The Skp1-Skp2 Complex
pdb|1FS1|C Chain C, Insights Into Scf Ubiquitin Ligases From The Structure
Of The Skp1-Skp2 Complex
Length = 53
Score = 31.6 bits (70), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 20/46 (43%), Positives = 23/46 (50%), Gaps = 1/46 (2%)
Query: 10 WDELIPDALGLIFRNLSLQEVLTVIPGVCKSWRRAVIGPYCWQEID 55
WD L + L IF L L E+L V GVCK W R WQ +D
Sbjct: 9 WDSLPDELLLGIFSCLCLPELLKV-SGVCKRWYRLASDESLWQTLD 53
>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 = 31.6 bits (70), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 35/77 (45%)
Query: 64 QPDHLDRMVEMLITRSSGSLRKLCVSGLHNDMMFSLIAENAGSLQTLRLPRSEMSDSIVA 123
Q L R+ E S L L +S + + F I SL TL++ + D+ ++
Sbjct: 407 QHSTLKRVTEFSAFLSLEKLLYLDISYTNTKIDFDGIFLGLTSLNTLKMAGNSFKDNTLS 466
Query: 124 QIAGRLSAVTFLDLSYC 140
+ + +TFLDLS C
Sbjct: 467 NVFANTTNLTFLDLSKC 483
>pdb|3PL6|D Chain D, Structure Of Autoimmune Tcr Hy.1b11 In Complex With
Hla-Dq1 And Mbp 85-99
Length = 268
Score = 30.8 bits (68), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 16/34 (47%), Positives = 22/34 (64%), Gaps = 2/34 (5%)
Query: 89 SGLHNDMMFSLIAENAGSLQTLRLPRSEMSDSIV 122
SGL ND F++ E GS+ TL++ R+E DS V
Sbjct: 83 SGLPNDRFFAVRPE--GSVSTLKIQRTERGDSAV 114
>pdb|2YIB|D Chain D, Structure Of The Rna Polymerase Vp1 From Infectious
Pancreatic Necrosis Virus
Length = 770
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 50 CWQEIDIEEWSNRCQPDHLDRMVEMLITR 78
W ID+E+ C P H+ M+ L+TR
Sbjct: 397 TWYSIDLEKGEANCTPQHMQAMMYYLLTR 425
>pdb|2YI8|A Chain A, Structure Of The Rna Polymerase Vp1 From Infectious
Pancreatic Necrosis Virus
pdb|2YI8|B Chain B, Structure Of The Rna Polymerase Vp1 From Infectious
Pancreatic Necrosis Virus
pdb|2YI8|C Chain C, Structure Of The Rna Polymerase Vp1 From Infectious
Pancreatic Necrosis Virus
pdb|2YI8|D Chain D, Structure Of The Rna Polymerase Vp1 From Infectious
Pancreatic Necrosis Virus
pdb|2YI8|E Chain E, Structure Of The Rna Polymerase Vp1 From Infectious
Pancreatic Necrosis Virus
pdb|2YI9|A Chain A, Structure Of The Rna Polymerase Vp1 From Infectious
Pancreatic Necrosis Virus In Complex With Magnesium
pdb|2YI9|B Chain B, Structure Of The Rna Polymerase Vp1 From Infectious
Pancreatic Necrosis Virus In Complex With Magnesium
pdb|2YI9|C Chain C, Structure Of The Rna Polymerase Vp1 From Infectious
Pancreatic Necrosis Virus In Complex With Magnesium
pdb|2YI9|D Chain D, Structure Of The Rna Polymerase Vp1 From Infectious
Pancreatic Necrosis Virus In Complex With Magnesium
pdb|2YI9|E Chain E, Structure Of The Rna Polymerase Vp1 From Infectious
Pancreatic Necrosis Virus In Complex With Magnesium
pdb|2YIA|A Chain A, Structure Of The Rna Polymerase Vp1 From Infectious
Pancreatic Necrosis Virus
pdb|2YIA|B Chain B, Structure Of The Rna Polymerase Vp1 From Infectious
Pancreatic Necrosis Virus
pdb|2YIA|C Chain C, Structure Of The Rna Polymerase Vp1 From Infectious
Pancreatic Necrosis Virus
pdb|2YIA|D Chain D, Structure Of The Rna Polymerase Vp1 From Infectious
Pancreatic Necrosis Virus
pdb|2YIA|E Chain E, Structure Of The Rna Polymerase Vp1 From Infectious
Pancreatic Necrosis Virus
pdb|2YIA|F Chain F, Structure Of The Rna Polymerase Vp1 From Infectious
Pancreatic Necrosis Virus
pdb|2YIA|G Chain G, Structure Of The Rna Polymerase Vp1 From Infectious
Pancreatic Necrosis Virus
pdb|2YIA|H Chain H, Structure Of The Rna Polymerase Vp1 From Infectious
Pancreatic Necrosis Virus
Length = 799
Score = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 50 CWQEIDIEEWSNRCQPDHLDRMVEMLITR 78
W ID+E+ C P H+ M+ L+TR
Sbjct: 397 TWYSIDLEKGEANCTPQHMQAMMYYLLTR 425
>pdb|2YIB|A Chain A, Structure Of The Rna Polymerase Vp1 From Infectious
Pancreatic Necrosis Virus
pdb|2YIB|B Chain B, Structure Of The Rna Polymerase Vp1 From Infectious
Pancreatic Necrosis Virus
pdb|2YIB|C Chain C, Structure Of The Rna Polymerase Vp1 From Infectious
Pancreatic Necrosis Virus
pdb|3ZED|A Chain A, X-ray Structure Of The Birnavirus Vp1-vp3 Complex
pdb|3ZED|B Chain B, X-ray Structure Of The Birnavirus Vp1-vp3 Complex
pdb|3ZED|C Chain C, X-ray Structure Of The Birnavirus Vp1-vp3 Complex
Length = 853
Score = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 50 CWQEIDIEEWSNRCQPDHLDRMVEMLITR 78
W ID+E+ C P H+ M+ L+TR
Sbjct: 397 TWYSIDLEKGEANCTPQHMQAMMYYLLTR 425
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 0.138 0.439
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,088,661
Number of Sequences: 62578
Number of extensions: 337997
Number of successful extensions: 637
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 621
Number of HSP's gapped (non-prelim): 17
length of query: 322
length of database: 14,973,337
effective HSP length: 99
effective length of query: 223
effective length of database: 8,778,115
effective search space: 1957519645
effective search space used: 1957519645
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)