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= 037045
(424 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 27/72 (37%), Positives = 40/72 (55%), Gaps = 2/72 (2%)
Query: 314 LDLHETNIGCLPPSISRLINLNALFLRSSCSLLLQLPAEIGRLQKLEILDVSHTKVQCLP 373
LDL I + +I + L L+L + L +LPAEI L L +LD+SH ++ LP
Sbjct: 229 LDLSNLQIFNISANIFKYDFLTRLYLNGNS--LTELPAEIKNLSNLRVLDLSHNRLTSLP 286
Query: 374 SEIGQLIELKYL 385
+E+G +LKY
Sbjct: 287 AELGSCFQLKYF 298
Score = 35.4 bits (80), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 28/83 (33%), Positives = 40/83 (48%), Gaps = 5/83 (6%)
Query: 305 FDYMCHLQLLDLHETNIGCLPPSISRLINLNALFLRSSCSLLLQLPAEIGRLQKLEILDV 364
+D++ L L + ++ LP I L NL L L S + L LPAE+G +L+
Sbjct: 246 YDFLTRLYL---NGNSLTELPAEIKNLSNLRVLDL--SHNRLTSLPAELGSCFQLKYFYF 300
Query: 365 SHTKVQCLPSEIGQLIELKYLRV 387
V LP E G L L++L V
Sbjct: 301 FDNMVTTLPWEFGNLCNLQFLGV 323
>pdb|3RFS|A Chain A, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
pdb|3RFS|B Chain B, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
Length = 272
Score = 46.2 bits (108), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 35/101 (34%), Positives = 56/101 (55%), Gaps = 5/101 (4%)
Query: 290 LILEGKRLEKLPTSFFDYMCHLQLLDLHETNIGCLPPSI-SRLINLNALFLRSSCSLLLQ 348
LIL G +L+ LP FD + +L+ L L E + LP + +L NL +L + + L
Sbjct: 90 LILTGNQLQSLPNGVFDKLTNLKELVLVENQLQSLPDGVFDKLTNLT--YLNLAHNQLQS 147
Query: 349 LPAEI-GRLQKLEILDVSHTKVQCLPSEI-GQLIELKYLRV 387
LP + +L L LD+S+ ++Q LP + +L +LK LR+
Sbjct: 148 LPKGVFDKLTNLTELDLSYNQLQSLPEGVFDKLTQLKDLRL 188
>pdb|3RFJ|A Chain A, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
Length = 279
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 34/102 (33%), Positives = 55/102 (53%), Gaps = 5/102 (4%)
Query: 290 LILEGKRLEKLPTSFFDYMCHLQLLDLHETNIGCLPPSI-SRLINLNALFLRSSCSLLLQ 348
LIL G +L+ LP FD + +L+ L L E + LP + +L NL L+L + L
Sbjct: 90 LILTGNQLQSLPNGVFDKLTNLKELVLVENQLQSLPDGVFDKLTNLTYLYLYHNQ--LQS 147
Query: 349 LPAEI-GRLQKLEILDVSHTKVQCLPSEI-GQLIELKYLRVS 388
LP + +L L LD+ + ++Q LP + +L +LK L ++
Sbjct: 148 LPKGVFDKLTNLTRLDLDNNQLQSLPEGVFDKLTQLKQLSLN 189
>pdb|3E6J|A Chain A, Crystal Structure Of Variable Lymphocyte Receptor (Vlr)
Rbc36 In Complex With H-Trisaccharide
Length = 229
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 28/85 (32%), Positives = 44/85 (51%), Gaps = 3/85 (3%)
Query: 290 LILEGKRLEKLPTSFFDYMCHLQLLDLHETNIGCLPPSI-SRLINLNALFLRSSCSLLLQ 348
L L +L LP FD + L +LDL + LP ++ RL++L LF+ C+ L +
Sbjct: 69 LYLGSNQLGALPVGVFDSLTQLTVLDLGTNQLTVLPSAVFDRLVHLKELFM--CCNKLTE 126
Query: 349 LPAEIGRLQKLEILDVSHTKVQCLP 373
LP I RL L L + +++ +P
Sbjct: 127 LPRGIERLTHLTHLALDQNQLKSIP 151
>pdb|2Z63|A Chain A, Crystal Structure Of The Tv8 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
Length = 570
Score = 37.4 bits (85), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 38/131 (29%), Positives = 52/131 (39%), Gaps = 16/131 (12%)
Query: 256 SFNKIGDAHTKRLSLFGFPSSTLPDMPNC-------------CEILTLILEGKRLEKLPT 302
SFN + H S F FP + D+ C + TLIL G ++ L
Sbjct: 36 SFNPL--RHLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPIQSLAL 93
Query: 303 SFFDYMCHLQLLDLHETNIGCLPP-SISRLINLNALFLRSSCSLLLQLPAEIGRLQKLEI 361
F + LQ L ETN+ L I L L L + + +LP L LE
Sbjct: 94 GAFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEH 153
Query: 362 LDVSHTKVQCL 372
LD+S K+Q +
Sbjct: 154 LDLSSNKIQSI 164
>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 = 0.017, Method: Compositional matrix adjust.
Identities = 38/131 (29%), Positives = 52/131 (39%), Gaps = 16/131 (12%)
Query: 256 SFNKIGDAHTKRLSLFGFPSSTLPDMPNC-------------CEILTLILEGKRLEKLPT 302
SFN + H S F FP + D+ C + TLIL G ++ L
Sbjct: 60 SFNPL--RHLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPIQSLAL 117
Query: 303 SFFDYMCHLQLLDLHETNIGCLPP-SISRLINLNALFLRSSCSLLLQLPAEIGRLQKLEI 361
F + LQ L ETN+ L I L L L + + +LP L LE
Sbjct: 118 GAFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEH 177
Query: 362 LDVSHTKVQCL 372
LD+S K+Q +
Sbjct: 178 LDLSSNKIQSI 188
>pdb|2O6Q|A Chain A, Structural Diversity Of The Hagfish Variable Lymphocyte
Receptors A29
Length = 270
Score = 37.0 bits (84), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 38/130 (29%), Positives = 62/130 (47%), Gaps = 7/130 (5%)
Query: 263 AHTKRLSLFGFPSSTLPDMP--NCCEILTLILEGKRLEKLPTSFFDYMCHLQLLDLHETN 320
A TK+L L S+LP ++ L L +L+ LP F + +L+ L + +
Sbjct: 37 ADTKKLDLQSNKLSSLPSKAFHRLTKLRLLYLNDNKLQTLPAGIFKELKNLETLWVTDNK 96
Query: 321 IGCLPPSI-SRLINLNALFLRSSCSLLLQLPAEI-GRLQKLEILDVSHTKVQCLPSEI-G 377
+ LP + +L+NL L L + L LP + L KL L + + ++Q LP +
Sbjct: 97 LQALPIGVFDQLVNLAELRLDR--NQLKSLPPRVFDSLTKLTYLSLGYNELQSLPKGVFD 154
Query: 378 QLIELKYLRV 387
+L LK LR+
Sbjct: 155 KLTSLKELRL 164
>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 = 36.6 bits (83), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 38/131 (29%), Positives = 52/131 (39%), Gaps = 16/131 (12%)
Query: 256 SFNKIGDAHTKRLSLFGFPSSTLPDMPNC-------------CEILTLILEGKRLEKLPT 302
SFN + H S F FP + D+ C + TLIL G ++ L
Sbjct: 36 SFNPL--RHLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPIQSLAL 93
Query: 303 SFFDYMCHLQLLDLHETNIGCLPP-SISRLINLNALFLRSSCSLLLQLPAEIGRLQKLEI 361
F + LQ L ETN+ L I L L L + + +LP L LE
Sbjct: 94 GAFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEH 153
Query: 362 LDVSHTKVQCL 372
LD+S K+Q +
Sbjct: 154 LDLSSNKIQSI 164
>pdb|3UL9|A Chain A, Structure Of The Tv3 Mutant M41e
Length = 278
Score = 36.2 bits (82), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 38/131 (29%), Positives = 52/131 (39%), Gaps = 16/131 (12%)
Query: 256 SFNKIGDAHTKRLSLFGFPSSTLPDMPNC-------------CEILTLILEGKRLEKLPT 302
SFN + H S F FP + D+ C + TLIL G ++ L
Sbjct: 37 SFNPL--RHLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPIQSLAL 94
Query: 303 SFFDYMCHLQLLDLHETNIGCLPP-SISRLINLNALFLRSSCSLLLQLPAEIGRLQKLEI 361
F + LQ L ETN+ L I L L L + + +LP L LE
Sbjct: 95 GAFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEH 154
Query: 362 LDVSHTKVQCL 372
LD+S K+Q +
Sbjct: 155 LDLSSNKIQSI 165
>pdb|3UL8|A Chain A, Crystal Structure Of The Tv3 Mutant V134l
Length = 279
Score = 36.2 bits (82), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 38/131 (29%), Positives = 52/131 (39%), Gaps = 16/131 (12%)
Query: 256 SFNKIGDAHTKRLSLFGFPSSTLPDMPNC-------------CEILTLILEGKRLEKLPT 302
SFN + H S F FP + D+ C + TLIL G ++ L
Sbjct: 38 SFNPL--RHLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPIQSLAL 95
Query: 303 SFFDYMCHLQLLDLHETNIGCLPP-SISRLINLNALFLRSSCSLLLQLPAEIGRLQKLEI 361
F + LQ L ETN+ L I L L L + + +LP L LE
Sbjct: 96 GAFSGLSSLQKLVALETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEH 155
Query: 362 LDVSHTKVQCL 372
LD+S K+Q +
Sbjct: 156 LDLSSNKIQSI 166
>pdb|2Z62|A Chain A, Crystal Structure Of The Tv3 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
pdb|2Z65|A Chain A, Crystal Structure Of The Human Tlr4 Tv3
Hybrid-Md-2-Eritoran Complex
pdb|2Z65|B Chain B, Crystal Structure Of The Human Tlr4 Tv3
Hybrid-Md-2-Eritoran Complex
Length = 276
Score = 36.2 bits (82), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 38/131 (29%), Positives = 52/131 (39%), Gaps = 16/131 (12%)
Query: 256 SFNKIGDAHTKRLSLFGFPSSTLPDMPNC-------------CEILTLILEGKRLEKLPT 302
SFN + H S F FP + D+ C + TLIL G ++ L
Sbjct: 36 SFNPL--RHLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPIQSLAL 93
Query: 303 SFFDYMCHLQLLDLHETNIGCLPP-SISRLINLNALFLRSSCSLLLQLPAEIGRLQKLEI 361
F + LQ L ETN+ L I L L L + + +LP L LE
Sbjct: 94 GAFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEH 153
Query: 362 LDVSHTKVQCL 372
LD+S K+Q +
Sbjct: 154 LDLSSNKIQSI 164
>pdb|3ULA|A Chain A, Crystal Structure Of The Tv3 Mutant F63w-Md-2-Eritoran
Complex
pdb|3ULA|C Chain C, Crystal Structure Of The Tv3 Mutant F63w-Md-2-Eritoran
Complex
Length = 279
Score = 35.4 bits (80), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 35/123 (28%), Positives = 48/123 (39%), Gaps = 14/123 (11%)
Query: 264 HTKRLSLFGFPSSTLPDMPNC-------------CEILTLILEGKRLEKLPTSFFDYMCH 310
H S F FP + D+ C + TLIL G ++ L F +
Sbjct: 44 HLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPIQSLALGAFSGLSS 103
Query: 311 LQLLDLHETNIGCLPP-SISRLINLNALFLRSSCSLLLQLPAEIGRLQKLEILDVSHTKV 369
LQ L ETN+ L I L L L + + +LP L LE LD+S K+
Sbjct: 104 LQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKI 163
Query: 370 QCL 372
Q +
Sbjct: 164 QSI 166
>pdb|3UL7|A Chain A, Crystal Structure Of The Tv3 Mutant F63w
Length = 278
Score = 35.0 bits (79), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 35/123 (28%), Positives = 48/123 (39%), Gaps = 14/123 (11%)
Query: 264 HTKRLSLFGFPSSTLPDMPNC-------------CEILTLILEGKRLEKLPTSFFDYMCH 310
H S F FP + D+ C + TLIL G ++ L F +
Sbjct: 43 HLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPIQSLALGAFSGLSS 102
Query: 311 LQLLDLHETNIGCLPP-SISRLINLNALFLRSSCSLLLQLPAEIGRLQKLEILDVSHTKV 369
LQ L ETN+ L I L L L + + +LP L LE LD+S K+
Sbjct: 103 LQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKI 162
Query: 370 QCL 372
Q +
Sbjct: 163 QSI 165
>pdb|3M19|A Chain A, Crystal Structure Of Variable Lymphocyte Receptor
Vlra.R5.1
pdb|3M19|B Chain B, Crystal Structure Of Variable Lymphocyte Receptor
Vlra.R5.1
Length = 251
Score = 35.0 bits (79), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 28/90 (31%), Positives = 43/90 (47%), Gaps = 4/90 (4%)
Query: 286 EILTLILEGKRLEKLPTSFFDYMCHLQLLDLHETNIGCLPPSI-SRLINLNALFLRSSCS 344
E+ TL L +L LP FD++ L L L + LP + RL L L L + +
Sbjct: 84 ELGTLGLANNQLASLPLGVFDHLTQLDKLYLGGNQLKSLPSGVFDRLTKLKELRLNT--N 141
Query: 345 LLLQLPA-EIGRLQKLEILDVSHTKVQCLP 373
L +PA +L L+ L +S ++Q +P
Sbjct: 142 QLQSIPAGAFDKLTNLQTLSLSTNQLQSVP 171
>pdb|3M18|A Chain A, Crystal Structure Of Variable Lymphocyte Receptor
Vlra.R2.1 In Complex With Hen Egg Lysozyme
Length = 251
Score = 35.0 bits (79), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 28/90 (31%), Positives = 43/90 (47%), Gaps = 4/90 (4%)
Query: 286 EILTLILEGKRLEKLPTSFFDYMCHLQLLDLHETNIGCLPPSI-SRLINLNALFLRSSCS 344
E+ TL L +L LP FD++ L L L + LP + RL L L L + +
Sbjct: 84 ELGTLGLANNQLASLPLGVFDHLTQLDKLYLGGNQLKSLPSGVFDRLTKLKELRLNT--N 141
Query: 345 LLLQLPA-EIGRLQKLEILDVSHTKVQCLP 373
L +PA +L L+ L +S ++Q +P
Sbjct: 142 QLQSIPAGAFDKLTNLQTLSLSTNQLQSVP 171
>pdb|2WFH|A Chain A, The Human Slit 2 Dimerization Domain D4
pdb|2WFH|B Chain B, The Human Slit 2 Dimerization Domain D4
Length = 193
Score = 33.5 bits (75), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 18/43 (41%), Positives = 25/43 (58%)
Query: 283 NCCEILTLILEGKRLEKLPTSFFDYMCHLQLLDLHETNIGCLP 325
N ++LTLIL RL +P FD + L+LL LH +I +P
Sbjct: 76 NMTQLLTLILSYNRLRCIPPRTFDGLKSLRLLSLHGNDISVVP 118
>pdb|1DO2|A Chain A, Trigonal Crystal Form Of Heat Shock Locus U (Hslu) From
Escherichia Coli
pdb|1DO2|B Chain B, Trigonal Crystal Form Of Heat Shock Locus U (Hslu) From
Escherichia Coli
pdb|1DO2|C Chain C, Trigonal Crystal Form Of Heat Shock Locus U (Hslu) From
Escherichia Coli
pdb|1DO2|D Chain D, Trigonal Crystal Form Of Heat Shock Locus U (Hslu) From
Escherichia Coli
pdb|1DO0|A Chain A, Orthorhombic Crystal Form Of Heat Shock Locus U (Hslu)
From Escherichia Coli
pdb|1DO0|B Chain B, Orthorhombic Crystal Form Of Heat Shock Locus U (Hslu)
From Escherichia Coli
pdb|1DO0|C Chain C, Orthorhombic Crystal Form Of Heat Shock Locus U (Hslu)
From Escherichia Coli
pdb|1DO0|D Chain D, Orthorhombic Crystal Form Of Heat Shock Locus U (Hslu)
From Escherichia Coli
pdb|1DO0|E Chain E, Orthorhombic Crystal Form Of Heat Shock Locus U (Hslu)
From Escherichia Coli
pdb|1DO0|F Chain F, Orthorhombic Crystal Form Of Heat Shock Locus U (Hslu)
From Escherichia Coli
Length = 442
Score = 32.7 bits (73), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 7/80 (8%)
Query: 2 KKICIWGPLGVGKTTIMENLHHSIG------ESRRFDIIFWENINTDGNIRDIQEIILER 55
K I + GP GVGKT I L E+ +F + + D IRD+ + ++
Sbjct: 50 KNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDLTDAAVKM 109
Query: 56 LKVNAKELNNDLRADIISKE 75
++V A E N RA+ +++E
Sbjct: 110 VRVQAIE-KNRYRAEELAEE 128
>pdb|1E94|E Chain E, Hslv-Hslu From E.Coli
pdb|1E94|F Chain F, Hslv-Hslu From E.Coli
pdb|1HT2|E Chain E, Nucleotide-dependent Conformational Changes In A
Protease-associated Atpase Hslu
pdb|1HT2|F Chain F, Nucleotide-dependent Conformational Changes In A
Protease-associated Atpase Hslu
pdb|1HT2|G Chain G, Nucleotide-dependent Conformational Changes In A
Protease-associated Atpase Hslu
pdb|1HT2|H Chain H, Nucleotide-dependent Conformational Changes In A
Protease-associated Atpase Hslu
pdb|1HT1|E Chain E, Nucleotide-Dependent Conformational Changes In A
Protease-Associated Atpase Hslu
pdb|1HT1|F Chain F, Nucleotide-Dependent Conformational Changes In A
Protease-Associated Atpase Hslu
pdb|1HT1|G Chain G, Nucleotide-Dependent Conformational Changes In A
Protease-Associated Atpase Hslu
pdb|1HT1|I Chain I, Nucleotide-Dependent Conformational Changes In A
Protease-Associated Atpase Hslu
pdb|1HQY|E Chain E, Nucleotide-Dependent Conformational Changes In A
Protease-Associated Atpase Hslu
pdb|1HQY|F Chain F, Nucleotide-Dependent Conformational Changes In A
Protease-Associated Atpase Hslu
Length = 449
Score = 32.7 bits (73), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 7/80 (8%)
Query: 2 KKICIWGPLGVGKTTIMENLHHSIG------ESRRFDIIFWENINTDGNIRDIQEIILER 55
K I + GP GVGKT I L E+ +F + + D IRD+ + ++
Sbjct: 57 KNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDLTDAAVKM 116
Query: 56 LKVNAKELNNDLRADIISKE 75
++V A E N RA+ +++E
Sbjct: 117 VRVQAIE-KNRYRAEELAEE 135
>pdb|1G4A|E Chain E, Crystal Structures Of The Hslvu Peptidase-Atpase Complex
Reveal An Atp-Dependent Proteolysis Mechanism
pdb|1G4A|F Chain F, Crystal Structures Of The Hslvu Peptidase-Atpase Complex
Reveal An Atp-Dependent Proteolysis Mechanism
pdb|1G4B|E Chain E, Crystal Structures Of The Hslvu Peptidase-Atpase Complex
Reveal An Atp-Dependent Proteolysis Mechanism
pdb|1G4B|F Chain F, Crystal Structures Of The Hslvu Peptidase-Atpase Complex
Reveal An Atp-Dependent Proteolysis Mechanism
pdb|1G4B|K Chain K, Crystal Structures Of The Hslvu Peptidase-Atpase Complex
Reveal An Atp-Dependent Proteolysis Mechanism
pdb|1G4B|L Chain L, Crystal Structures Of The Hslvu Peptidase-Atpase Complex
Reveal An Atp-Dependent Proteolysis Mechanism
pdb|1YYF|A Chain A, Correction Of X-Ray Intensities From An Hslv-Hslu Co-
Crystal Containing Lattice Translocation Defects
pdb|1YYF|B Chain B, Correction Of X-Ray Intensities From An Hslv-Hslu Co-
Crystal Containing Lattice Translocation Defects
Length = 443
Score = 32.7 bits (73), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 7/80 (8%)
Query: 2 KKICIWGPLGVGKTTIMENLHHSIG------ESRRFDIIFWENINTDGNIRDIQEIILER 55
K I + GP GVGKT I L E+ +F + + D IRD+ + ++
Sbjct: 51 KNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDLTDAAVKM 110
Query: 56 LKVNAKELNNDLRADIISKE 75
++V A E N RA+ +++E
Sbjct: 111 VRVQAIE-KNRYRAEELAEE 129
>pdb|3M6A|A Chain A, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
pdb|3M6A|B Chain B, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
pdb|3M6A|C Chain C, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
pdb|3M6A|D Chain D, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
pdb|3M6A|E Chain E, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
pdb|3M6A|F Chain F, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
Length = 543
Score = 32.3 bits (72), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 26/43 (60%), Gaps = 2/43 (4%)
Query: 4 ICIWGPLGVGKTTIMENLHHSIGESRRFDIIFWENINTDGNIR 46
+C+ GP GVGKT++ +++ S+G R+F I + + IR
Sbjct: 111 LCLAGPPGVGKTSLAKSIAKSLG--RKFVRISLGGVRDESEIR 151
>pdb|3RIZ|A Chain A, Crystal Structure Of The Plant Steroid Receptor Bri1
Ectodomain
pdb|3RJ0|A Chain A, Plant Steroid Receptor Bri1 Ectodomain In Complex With
Brassinolide
Length = 772
Score = 32.3 bits (72), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 38/143 (26%), Positives = 63/143 (44%), Gaps = 27/143 (18%)
Query: 272 GFPSSTLPDMPNCCEILTLILEGKRLE-KLPTSFFD-----------------------Y 307
GF P + NC E+++L L L +P+S Y
Sbjct: 402 GFTGKIPPTLSNCSELVSLHLSFNYLSGTIPSSLGSLSKLRDLKLWLNMLEGEIPQELMY 461
Query: 308 MCHLQLLDLHETNI-GCLPPSISRLINLNALFLRSSCSLLLQLPAEIGRLQKLEILDVSH 366
+ L+ L L ++ G +P +S NLN + L S+ L ++P IGRL+ L IL +S+
Sbjct: 462 VKTLETLILDFNDLTGEIPSGLSNCTNLNWISL-SNNRLTGEIPKWIGRLENLAILKLSN 520
Query: 367 TKVQC-LPSEIGQLIELKYLRVS 388
+P+E+G L +L ++
Sbjct: 521 NSFSGNIPAELGDCRSLIWLDLN 543
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 32.0 bits (71), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 36/131 (27%), Positives = 61/131 (46%), Gaps = 11/131 (8%)
Query: 47 DIQEIILERLKVNAKELNNDLRADIISKELNDRSYVLFLDGVSSEINFKEIGMHDDHGRG 106
D +E +RL +N +E + LR ++ K + RS +L LD V K +
Sbjct: 207 DQEESFSQRLPLNIEEAKDRLRVLMLRK--HPRS-LLILDDVWDPWVLKAFD-----NQC 258
Query: 107 KVVFACRSREFCWQADGVIHVQQLCQREAKKLFWEVVG--VHLKKYPDIELVADSIVKEC 164
+++ R + G HV + ++ E++ V++KK D+ A SI+KEC
Sbjct: 259 QILLTTRDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMKK-EDLPAEAHSIIKEC 317
Query: 165 GGMPYMLKLIG 175
G P ++ LIG
Sbjct: 318 KGSPLVVSLIG 328
>pdb|3RGX|A Chain A, Structural Insight Into Brassinosteroid Perception By Bri1
pdb|3RGZ|A Chain A, Structural Insight Into Brassinosteroid Perception By Bri1
Length = 768
Score = 31.6 bits (70), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 38/143 (26%), Positives = 63/143 (44%), Gaps = 27/143 (18%)
Query: 272 GFPSSTLPDMPNCCEILTLILEGKRLE-KLPTSFFD-----------------------Y 307
GF P + NC E+++L L L +P+S Y
Sbjct: 405 GFTGKIPPTLSNCSELVSLHLSFNYLSGTIPSSLGSLSKLRDLKLWLNMLEGEIPQELMY 464
Query: 308 MCHLQLLDLHETNI-GCLPPSISRLINLNALFLRSSCSLLLQLPAEIGRLQKLEILDVSH 366
+ L+ L L ++ G +P +S NLN + L S+ L ++P IGRL+ L IL +S+
Sbjct: 465 VKTLETLILDFNDLTGEIPSGLSNCTNLNWISL-SNNRLTGEIPKWIGRLENLAILKLSN 523
Query: 367 TKVQC-LPSEIGQLIELKYLRVS 388
+P+E+G L +L ++
Sbjct: 524 NSFSGNIPAELGDCRSLIWLDLN 546
>pdb|2O6S|A Chain A, Structural Diversity Of The Hagfish Variable Lymphocyte
Receptors B59
pdb|2O6S|B Chain B, Structural Diversity Of The Hagfish Variable Lymphocyte
Receptors B59
Length = 208
Score = 31.6 bits (70), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 31/101 (30%), Positives = 52/101 (51%), Gaps = 5/101 (4%)
Query: 290 LILEGKRLEKLPTSFFDYMCHLQLLDLHETNIGCLPPSI-SRLINLNALFLRSSCSLLLQ 348
L LE L+ LP FD + L L L + LP + ++L +L +L S + L
Sbjct: 33 LDLETNSLKSLPNGVFDELTSLTQLYLGGNKLQSLPNGVFNKLTSLT--YLNLSTNQLQS 90
Query: 349 LPAEI-GRLQKLEILDVSHTKVQCLPSEI-GQLIELKYLRV 387
LP + +L +L+ L ++ ++Q LP + +L +LK LR+
Sbjct: 91 LPNGVFDKLTQLKELALNTNQLQSLPDGVFDKLTQLKDLRL 131
>pdb|2I00|A Chain A, Crystal Structure Of Acetyltransferase (Gnat Family) From
Enterococcus Faecalis
pdb|2I00|B Chain B, Crystal Structure Of Acetyltransferase (Gnat Family) From
Enterococcus Faecalis
pdb|2I00|C Chain C, Crystal Structure Of Acetyltransferase (Gnat Family) From
Enterococcus Faecalis
pdb|2I00|D Chain D, Crystal Structure Of Acetyltransferase (Gnat Family) From
Enterococcus Faecalis
pdb|2I00|E Chain E, Crystal Structure Of Acetyltransferase (Gnat Family) From
Enterococcus Faecalis
pdb|2I00|F Chain F, Crystal Structure Of Acetyltransferase (Gnat Family) From
Enterococcus Faecalis
Length = 406
Score = 31.6 bits (70), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 25/106 (23%), Positives = 45/106 (42%), Gaps = 19/106 (17%)
Query: 88 VSSEINFKEIG-MHDDHGRGKVVFACRSRE-----FCWQADGVIHVQQL--CQREAKKLF 139
+ S N++E ++ R V+ ++E F W AD V H++++ +EA+
Sbjct: 195 IRSAFNWEEYWRFENEEERTAAVYYGANQEPLGVLFYWVADEVFHIKEMFYLNQEARNGL 254
Query: 140 WEVVGVHL-----------KKYPDIELVADSIVKECGGMPYMLKLI 174
W + H K P L+ DS +KE YM +++
Sbjct: 255 WNFITAHFSMVYWVKGDIYKNEPLAFLLEDSQIKESIEPYYMARIV 300
>pdb|2EWV|A Chain A, Crystal Structure Of The Pilus Retraction Motor Pilt And
Bound Adp
Length = 372
Score = 31.6 bits (70), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 42/89 (47%), Gaps = 13/89 (14%)
Query: 1 MKKICIWGPLGVGKTTIMENLHHSIGESRRFDIIFWENINTDGNIRDIQEIILERLK--V 58
M I + GP G GK+T + ++ I +++ + II I D E + + K V
Sbjct: 136 MGLILVTGPTGSGKSTTIASMIDYINQTKSYHII---------TIEDPIEYVFKHKKSIV 186
Query: 59 NAKELNNDLR--ADIISKELNDRSYVLFL 85
N +E+ D + AD + L + V+F+
Sbjct: 187 NQREVGEDTKSFADALRAALREDPDVIFV 215
>pdb|3J0A|A Chain A, Homology Model Of Human Toll-Like Receptor 5 Fitted Into
An Electron Microscopy Single Particle Reconstruction
pdb|3J0A|B Chain B, Homology Model Of Human Toll-Like Receptor 5 Fitted Into
An Electron Microscopy Single Particle Reconstruction
Length = 844
Score = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 28/86 (32%), Positives = 40/86 (46%), Gaps = 19/86 (22%)
Query: 305 FDYMCHLQLLDLHETNIGCLPPSI-SRLINLNALFLRSSCSLLLQ---LPA-----EIGR 355
F+ + HLQ+L L+ + LPP + S L L L L S+ +L LPA +I R
Sbjct: 476 FEGLSHLQVLYLNHNYLNSLPPGVFSHLTALRGLSLNSNRLTVLSHNDLPANLEILDISR 535
Query: 356 LQ----------KLEILDVSHTKVQC 371
Q L +LD++H K C
Sbjct: 536 NQLLAPNPDVFVSLSVLDITHNKFIC 561
>pdb|2O6R|A Chain A, Structural Diversity Of The Hagfish Variable Lymphocyte
Receptors B61
Length = 177
Score = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 29/112 (25%), Positives = 53/112 (47%), Gaps = 11/112 (9%)
Query: 290 LILEGKRLEKLPTSFFDYMCHLQLLDLHETNIGCLPPSI-SRLINLNALFLRSSCSLLLQ 348
L LE +L+ LP FD + L L L + I LP + +L L L+L + L
Sbjct: 33 LELESNKLQSLPHGVFDKLTQLTKLSLSQNQIQSLPDGVFDKLTKLTILYLHE--NKLQS 90
Query: 349 LPAEI-GRLQKLEILDVSHTKVQCLPSEIGQLIELKYLRVSRVENVGNHTHA 399
LP + +L +L+ L + +++ +P I + R++ ++ + HT+
Sbjct: 91 LPNGVFDKLTQLKELALDTNQLKSVPDGI-------FDRLTSLQKIWLHTNP 135
Score = 28.5 bits (62), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 286 EILTLILEGKRLEKLPTSFFDYMCHLQLLDLHETNIGCLPPSI-SRLINLNALFL 339
++ L L +++ LP FD + L +L LHE + LP + +L L L L
Sbjct: 53 QLTKLSLSQNQIQSLPDGVFDKLTKLTILYLHENKLQSLPNGVFDKLTQLKELAL 107
>pdb|1G3I|A Chain A, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|B Chain B, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|C Chain C, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|D Chain D, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|E Chain E, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|F Chain F, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|S Chain S, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|T Chain T, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|U Chain U, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|V Chain V, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|W Chain W, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|X Chain X, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G41|A Chain A, Crystal Structure Of Hslu Haemophilus Influenzae
pdb|1KYI|A Chain A, Hsluv (h. Influenzae)-nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|B Chain B, Hsluv (h. Influenzae)-nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|C Chain C, Hsluv (h. Influenzae)-nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|D Chain D, Hsluv (h. Influenzae)-nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|E Chain E, Hsluv (h. Influenzae)-nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|F Chain F, Hsluv (h. Influenzae)-nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|S Chain S, Hsluv (h. Influenzae)-nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|T Chain T, Hsluv (h. Influenzae)-nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|U Chain U, Hsluv (h. Influenzae)-nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|V Chain V, Hsluv (h. Influenzae)-nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|W Chain W, Hsluv (h. Influenzae)-nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|X Chain X, Hsluv (h. Influenzae)-nlvs Vinyl Sulfone Inhibitor Complex
Length = 444
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 31/123 (25%), Positives = 52/123 (42%), Gaps = 16/123 (13%)
Query: 2 KKICIWGPLGVGKTTIMENLHHSIG------ESRRFDIIFWENINTDGNIRDIQEIILER 55
K I + GP GVGKT I L E+ +F + + D IRD+ + + +
Sbjct: 51 KNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDLTDSAM-K 109
Query: 56 LKVNAKELNNDLRADIISKELNDRSYVLFLDGV--SSEINFKEIGMHDDHGRGKVVFACR 113
L + N RA+ +++E LD + ++ + E+ HD H + F +
Sbjct: 110 LVRQQEIAKNRARAEDVAEE-------RILDALLPPAKNQWGEVENHDSHSSTRQAFRKK 162
Query: 114 SRE 116
RE
Sbjct: 163 LRE 165
>pdb|3RG1|A Chain A, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|E Chain E, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|I Chain I, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|M Chain M, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|B Chain B, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|F Chain F, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|J Chain J, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|N Chain N, Crystal Structure Of The Rp105MD-1 Complex
Length = 612
Score = 30.4 bits (67), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 33/130 (25%), Positives = 55/130 (42%), Gaps = 27/130 (20%)
Query: 292 LEGKRLEKLPTSFFDYMCHLQLLDLHETNIGCLPPSISRLINLNALFLRS-SCSLLLQLP 350
L+ R L +S F +Q LDL ++ LP I + +L L L + S L Q+
Sbjct: 260 LQKHRFSDLSSSTFRCFTRVQELDLTAAHLNGLPSGIEGMNSLKKLVLNANSFDQLCQIN 319
Query: 351 AE-----------------------IGRLQKLEILDVSHTKVQ---CLPSEIGQLIELKY 384
A + +L+ L+ LD+SH+ ++ C ++ L L+Y
Sbjct: 320 AASFPSLRDLYIKGNMRKLDLGTRCLEKLENLQKLDLSHSDIEASDCCNLQLKNLRHLQY 379
Query: 385 LRVSRVENVG 394
L +S E +G
Sbjct: 380 LNLSYNEPLG 389
>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type
Iii Effector Xcv3220 (Xopl)
Length = 328
Score = 30.4 bits (67), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 35/115 (30%), Positives = 49/115 (42%), Gaps = 25/115 (21%)
Query: 289 TLILEGKRLEKLPTSFFDYMCHLQLLDLHETNIGCLPPSISRLINLNALFLRS------- 341
+L LE + LP S + + +L+ L + + + L P+I L L L LR
Sbjct: 187 SLRLEWTGIRSLPASIAN-LQNLKSLKIRNSPLSALGPAIHHLPKLEELDLRGCTALRNY 245
Query: 342 ----------------SCSLLLQLPAEIGRLQKLEILDVSH-TKVQCLPSEIGQL 379
CS LL LP +I RL +LE LD+ + LPS I QL
Sbjct: 246 PPIFGGRAPLKRLILKDCSNLLTLPLDIHRLTQLEKLDLRGCVNLSRLPSLIAQL 300
>pdb|1Z6T|A Chain A, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|B Chain B, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|C Chain C, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|D Chain D, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
Length = 591
Score = 30.4 bits (67), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 36/131 (27%), Positives = 60/131 (45%), Gaps = 11/131 (8%)
Query: 47 DIQEIILERLKVNAKELNNDLRADIISKELNDRSYVLFLDGVSSEINFKEIGMHDDHGRG 106
D E +RL +N +E + LR ++ K + RS +L LD V K +
Sbjct: 207 DQDESFSQRLPLNIEEAKDRLRILMLRK--HPRS-LLILDDVWDSWVLKAFD-----SQC 258
Query: 107 KVVFACRSREFCWQADGVIHVQQLCQREAKKLFWEVVG--VHLKKYPDIELVADSIVKEC 164
+++ R + G +V + K+ E++ V++KK D+ A SI+KEC
Sbjct: 259 QILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKK-ADLPEQAHSIIKEC 317
Query: 165 GGMPYMLKLIG 175
G P ++ LIG
Sbjct: 318 KGSPLVVSLIG 328
>pdb|2EWW|A Chain A, Crystal Structure Of The Pilus Retraction Motor Pilt And
Bound Atp
Length = 372
Score = 30.0 bits (66), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 40/86 (46%), Gaps = 13/86 (15%)
Query: 4 ICIWGPLGVGKTTIMENLHHSIGESRRFDIIFWENINTDGNIRDIQEIILERLK--VNAK 61
I + GP G GK+T + + I +++ + II I D E + + K VN +
Sbjct: 139 ILVTGPTGSGKSTTIASXIDYINQTKSYHII---------TIEDPIEYVFKHKKSIVNQR 189
Query: 62 ELNNDLR--ADIISKELNDRSYVLFL 85
E+ D + AD + L + V+F+
Sbjct: 190 EVGEDTKSFADALRAALREDPDVIFV 215
>pdb|3IZA|A Chain A, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|B Chain B, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|C Chain C, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|D Chain D, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|E Chain E, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|F Chain F, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|G Chain G, Structure Of An Apoptosome-Procaspase-9 Card Complex
Length = 1263
Score = 30.0 bits (66), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 36/131 (27%), Positives = 60/131 (45%), Gaps = 11/131 (8%)
Query: 47 DIQEIILERLKVNAKELNNDLRADIISKELNDRSYVLFLDGVSSEINFKEIGMHDDHGRG 106
D E +RL +N +E + LR ++ K + RS +L LD V K +
Sbjct: 213 DQDESFSQRLPLNIEEAKDRLRILMLRK--HPRS-LLILDDVWDSWVLKAFD-----SQC 264
Query: 107 KVVFACRSREFCWQADGVIHVQQLCQREAKKLFWEVVG--VHLKKYPDIELVADSIVKEC 164
+++ R + G +V + K+ E++ V++KK D+ A SI+KEC
Sbjct: 265 QILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKK-ADLPEQAHSIIKEC 323
Query: 165 GGMPYMLKLIG 175
G P ++ LIG
Sbjct: 324 KGSPLVVSLIG 334
>pdb|2GSZ|A Chain A, Structure Of A. Aeolicus Pilt With 6 Monomers Per
Asymmetric Unit
pdb|2GSZ|B Chain B, Structure Of A. Aeolicus Pilt With 6 Monomers Per
Asymmetric Unit
pdb|2GSZ|C Chain C, Structure Of A. Aeolicus Pilt With 6 Monomers Per
Asymmetric Unit
pdb|2GSZ|D Chain D, Structure Of A. Aeolicus Pilt With 6 Monomers Per
Asymmetric Unit
pdb|2GSZ|E Chain E, Structure Of A. Aeolicus Pilt With 6 Monomers Per
Asymmetric Unit
pdb|2GSZ|F Chain F, Structure Of A. Aeolicus Pilt With 6 Monomers Per
Asymmetric Unit
Length = 363
Score = 30.0 bits (66), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 40/86 (46%), Gaps = 13/86 (15%)
Query: 4 ICIWGPLGVGKTTIMENLHHSIGESRRFDIIFWENINTDGNIRDIQEIILERLK--VNAK 61
I + GP G GK+T + + I +++ + II I D E + + K VN +
Sbjct: 128 ILVTGPTGSGKSTTIASXIDYINQTKSYHII---------TIEDPIEYVFKHKKSIVNQR 178
Query: 62 ELNNDLR--ADIISKELNDRSYVLFL 85
E+ D + AD + L + V+F+
Sbjct: 179 EVGEDTKSFADALRAALREDPDVIFV 204
>pdb|2EYU|A Chain A, The Crystal Structure Of The C-Terminal Domain Of Aquifex
Aeolicus Pilt
pdb|2EYU|B Chain B, The Crystal Structure Of The C-Terminal Domain Of Aquifex
Aeolicus Pilt
Length = 261
Score = 30.0 bits (66), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 40/86 (46%), Gaps = 13/86 (15%)
Query: 4 ICIWGPLGVGKTTIMENLHHSIGESRRFDIIFWENINTDGNIRDIQEIILERLK--VNAK 61
I + GP G GK+T + + I +++ + II I D E + + K VN +
Sbjct: 28 ILVTGPTGSGKSTTIASXIDYINQTKSYHII---------TIEDPIEYVFKHKKSIVNQR 78
Query: 62 ELNNDLR--ADIISKELNDRSYVLFL 85
E+ D + AD + L + V+F+
Sbjct: 79 EVGEDTKSFADALRAALREDPDVIFV 104
>pdb|2Z7X|A Chain A, Crystal Structure Of The Tlr1-Tlr2 Heterodimer Induced By
Binding Of A Tri-Acylated Lipopeptide
Length = 549
Score = 30.0 bits (66), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 30/63 (47%), Gaps = 3/63 (4%)
Query: 277 TLPDMPNCCEILTLILEGKRLEKLPTSFFDYMCHLQLLDLHETNIGCLPPSI---SRLIN 333
TLPD +L L + +L+ +P FD + LQ + LH C P I SR +N
Sbjct: 465 TLPDASLLPMLLVLKISRNQLKSVPDGIFDRLTSLQKIWLHTNPWDCSCPRIDYLSRWLN 524
Query: 334 LNA 336
N+
Sbjct: 525 KNS 527
>pdb|3A79|A Chain A, Crystal Structure Of Tlr2-Tlr6-Pam2csk4 Complex
pdb|3A7B|A Chain A, Crystal Structure Of Tlr2-Streptococcus Pneumoniae
Lipoteichoic Acid Complex
pdb|3A7C|A Chain A, Crystal Structure Of Tlr2-Pe-Dtpa Complex
Length = 580
Score = 29.6 bits (65), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 3/63 (4%)
Query: 277 TLPDMPNCCEILTLILEGKRLEKLPTSFFDYMCHLQLLDLHETNIGCLPPSI---SRLIN 333
TLPD +L + + +L+ +P FD + LQ + LH C P I SR +N
Sbjct: 491 TLPDASLFPVLLVMKIASNQLKSVPDGIFDRLTSLQKIWLHTNPWDCSCPRIDYLSRWLN 550
Query: 334 LNA 336
N+
Sbjct: 551 KNS 553
>pdb|3G06|A Chain A, The Salmonella Virulence Effector Ssph2 Functions As A
Novel E3 Ligase
Length = 622
Score = 29.6 bits (65), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 33/112 (29%), Positives = 49/112 (43%), Gaps = 11/112 (9%)
Query: 268 LSLFGFPSSTLPDMPNCCEILTLILEGKRLEKLPTSFFDYMCHLQLLDLHETNIGCLPPS 327
LS+F P + LP +P+ + L + G +L LP LQ L + + + LP
Sbjct: 106 LSIFSNPLTHLPALPSG--LCKLWIFGNQLTSLPV----LPPGLQELSVSDNQLASLPAL 159
Query: 328 ISRLINLNALFLRSSCSLLLQLPAEIGRLQKLEILDVSHTKVQCLPSEIGQL 379
S L L A + L LP LQ+L + D + LPSE+ +L
Sbjct: 160 PSELCKLWAY-----NNQLTSLPMLPSGLQELSVSDNQLASLPTLPSELYKL 206
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 29.6 bits (65), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 15/31 (48%), Positives = 21/31 (67%), Gaps = 1/31 (3%)
Query: 145 VHLKKYPDIELVADSIVKECGGMPYMLKLIG 175
V++KK D+ A SI+KEC G P ++ LIG
Sbjct: 306 VNMKK-EDLPAEAHSIIKECKGSPLVVSLIG 335
>pdb|2Z81|A Chain A, Crystal Structure Of The Tlr1-tlr2 Heterodimer Induced By
Binding Of A Tri-acylated Lipopeptide
pdb|2Z82|A Chain A, Crystal Structure Of The Tlr1-Tlr2 Heterodimer Induced By
Binding Of A Tri-Acylated Lipopeptide
Length = 549
Score = 28.9 bits (63), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 3/63 (4%)
Query: 277 TLPDMPNCCEILTLILEGKRLEKLPTSFFDYMCHLQLLDLHETNIGCLPPSI---SRLIN 333
TLPD +L + + +L+ +P FD + LQ + LH C P I SR +N
Sbjct: 465 TLPDASLFPVLLVMKISRNQLKSVPDGIFDRLTSLQKIWLHTNPWDCSCPRIDYLSRWLN 524
Query: 334 LNA 336
N+
Sbjct: 525 KNS 527
>pdb|3BOB|A Chain A, Carbonic Anhydrase From Marine Diatom Thalassiosira
Weissflo Cadmium Bound Domain 2
pdb|3BOC|A Chain A, Carbonic Anhydrase From Marine Diatom Thalassiosira
Weissflo Bound Domain 2 (Cdca1-R2)
pdb|3BOE|A Chain A, Carbonic Anhydrase From Marine Diatom Thalassiosira
Weissflo Cadmium Bound Domain 2 With Acetate (Cdca1-R2)
Length = 210
Score = 28.5 bits (62), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 19/40 (47%)
Query: 238 ELSQDYIIDGWAAQKFLASFNKIGDAHTKRLSLFGFPSST 277
E Q +I+DGWAA KF K A + + G P +
Sbjct: 166 ENDQRFIVDGWAADKFGLDVPKFLIAAAATVEMLGGPKNA 205
>pdb|1IM2|A Chain A, Hslu, Haemophilus Influenzae, Selenomethionine Variant
Length = 444
Score = 28.5 bits (62), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 31/123 (25%), Positives = 50/123 (40%), Gaps = 16/123 (13%)
Query: 2 KKICIWGPLGVGKTTIMENLHHSIG------ESRRFDIIFWENINTDGNIRDIQEIILER 55
K I GP GVGKT I L E+ +F + + D IRD+ + +
Sbjct: 51 KNILXIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDLTDSAX-K 109
Query: 56 LKVNAKELNNDLRADIISKELNDRSYVLFLDGV--SSEINFKEIGMHDDHGRGKVVFACR 113
L + N RA+ +++E LD + ++ + E+ HD H + F +
Sbjct: 110 LVRQQEIAKNRARAEDVAEE-------RILDALLPPAKNQWGEVENHDSHSSTRQAFRKK 162
Query: 114 SRE 116
RE
Sbjct: 163 LRE 165
>pdb|3V47|A Chain A, Crystal Structure Of The N-Tetminal Fragment Of Zebrafish
Tlr5 In Complex With Salmonella Flagellin
pdb|3V47|B Chain B, Crystal Structure Of The N-Tetminal Fragment Of Zebrafish
Tlr5 In Complex With Salmonella Flagellin
Length = 455
Score = 28.1 bits (61), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 29/59 (49%), Gaps = 6/59 (10%)
Query: 281 MPNCCEILTLILEGKRLEKLPTSFFDYMCHLQLLDLHETNIGCLPPSI---SRLINLNA 336
+PN E L L+ +L+ +P FD + LQ + LH C P I SR +N N+
Sbjct: 370 LPNLKE---LALDTNQLKSVPDGIFDRLTSLQKIWLHTNPWDCSCPRIDYLSRWLNKNS 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
0.323 0.140 0.423
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,876,472
Number of Sequences: 62578
Number of extensions: 466403
Number of successful extensions: 1278
Number of sequences better than 100.0: 68
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 51
Number of HSP's that attempted gapping in prelim test: 1206
Number of HSP's gapped (non-prelim): 114
length of query: 424
length of database: 14,973,337
effective HSP length: 101
effective length of query: 323
effective length of database: 8,652,959
effective search space: 2794905757
effective search space used: 2794905757
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (25.0 bits)