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= 038877
(298 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 = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 36/80 (45%), Gaps = 8/80 (10%)
Query: 68 KLPSGISNLVSLHHLDLSWTRIRGLPQELKALEKLRYLSLEGTRHLSIIPHQLIS----- 122
+LP L L L+ +R LP + +L +LR LS+ L+ +P L S
Sbjct: 118 ELPDTXQQFAGLETLTLARNPLRALPASIASLNRLRELSIRACPELTELPEPLASTDASG 177
Query: 123 ---GFSKLEVLRLLWCGLWS 139
G L+ LRL W G+ S
Sbjct: 178 EHQGLVNLQSLRLEWTGIRS 197
Score = 32.0 bits (71), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 30/60 (50%), Gaps = 2/60 (3%)
Query: 76 LVSLHHLDLSWTRIRGLPQELKALEKLRYLSLEGTRHLSIIPHQLISGFSKLEVLRLLWC 135
LV+L L L WT IR LP + L+ L+ L + + ++ P I KLE L L C
Sbjct: 182 LVNLQSLRLEWTGIRSLPASIANLQNLKSLKIRNSPLSALGP--AIHHLPKLEELDLRGC 239
>pdb|2Z80|A Chain A, Crystal Structure Of The Tlr1-Tlr2 Heterodimer Induced By
Binding Of A Tri-Acylated Lipopeptide
pdb|2Z80|B Chain B, Crystal Structure Of The Tlr1-Tlr2 Heterodimer Induced By
Binding Of A Tri-Acylated Lipopeptide
Length = 353
Score = 35.0 bits (79), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 35/129 (27%), Positives = 52/129 (40%), Gaps = 27/129 (20%)
Query: 7 EGAKRISLMKTGIQ--SPSEIPTCPRLVTFLLDGNWIEEITDGFFXXXXXXXXXXXXXXX 64
E K + L I S S++ C L +L N I I + F
Sbjct: 52 EAVKSLDLSNNRITYISNSDLQRCVNLQALVLTSNGINTIEEDSF--------------- 96
Query: 65 XXXKLPSGISNLVSLHHLDLSWTRIRGLPQE-LKALEKLRYLSLEGTRHLSIIPHQLISG 123
S+L SL HLDLS+ + L K L L +L+L G + ++ L S
Sbjct: 97 ---------SSLGSLEHLDLSYNYLSNLSSSWFKPLSSLTFLNLLGNPYKTLGETSLFSH 147
Query: 124 FSKLEVLRL 132
+KL++LR+
Sbjct: 148 LTKLQILRV 156
>pdb|2Z7X|A Chain A, Crystal Structure Of The Tlr1-Tlr2 Heterodimer Induced By
Binding Of A Tri-Acylated Lipopeptide
Length = 549
Score = 35.0 bits (79), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 35/129 (27%), Positives = 52/129 (40%), Gaps = 27/129 (20%)
Query: 7 EGAKRISLMKTGIQ--SPSEIPTCPRLVTFLLDGNWIEEITDGFFXXXXXXXXXXXXXXX 64
E K + L I S S++ C L +L N I I + F
Sbjct: 26 EAVKSLDLSNNRITYISNSDLQRCVNLQALVLTSNGINTIEEDSF--------------- 70
Query: 65 XXXKLPSGISNLVSLHHLDLSWTRIRGLPQE-LKALEKLRYLSLEGTRHLSIIPHQLISG 123
S+L SL HLDLS+ + L K L L +L+L G + ++ L S
Sbjct: 71 ---------SSLGSLEHLDLSYNYLSNLSSSWFKPLSSLTFLNLLGNPYKTLGETSLFSH 121
Query: 124 FSKLEVLRL 132
+KL++LR+
Sbjct: 122 LTKLQILRV 130
>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 = 33.5 bits (75), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 17/38 (44%), Positives = 24/38 (63%)
Query: 68 KLPSGISNLVSLHHLDLSWTRIRGLPQELKALEKLRYL 105
+LP+ I NL +L LDLS R+ LP EL + +L+Y
Sbjct: 261 ELPAEIKNLSNLRVLDLSHNRLTSLPAELGSCFQLKYF 298
>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 = 32.0 bits (71), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 30/54 (55%), Gaps = 1/54 (1%)
Query: 68 KLPSGISNLVSLHHLDLSWTRIRG-LPQELKALEKLRYLSLEGTRHLSIIPHQL 120
++PSG+SN +L+ + LS R+ G +P+ + LE L L L IP +L
Sbjct: 481 EIPSGLSNCTNLNWISLSNNRLTGEIPKWIGRLENLAILKLSNNSFSGNIPAEL 534
>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 = 31.6 bits (70), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 30/54 (55%), Gaps = 1/54 (1%)
Query: 68 KLPSGISNLVSLHHLDLSWTRIRG-LPQELKALEKLRYLSLEGTRHLSIIPHQL 120
++PSG+SN +L+ + LS R+ G +P+ + LE L L L IP +L
Sbjct: 478 EIPSGLSNCTNLNWISLSNNRLTGEIPKWIGRLENLAILKLSNNSFSGNIPAEL 531
>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 = 2.8, Method: Compositional matrix adjust.
Identities = 13/25 (52%), Positives = 17/25 (68%)
Query: 68 KLPSGISNLVSLHHLDLSWTRIRGL 92
KLP SNL +L HLDLS +I+ +
Sbjct: 140 KLPEYFSNLTNLEHLDLSSNKIQSI 164
>pdb|2Z7X|B Chain B, Crystal Structure Of The Tlr1-Tlr2 Heterodimer Induced By
Binding Of A Tri-Acylated Lipopeptide
Length = 520
Score = 29.3 bits (64), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 40/75 (53%), Gaps = 10/75 (13%)
Query: 77 VSLHHLDLSWTRIRGLP--QELKALEKLRYLSLEGTRHL---SIIPHQLISGFSKLEVLR 131
V+L HLDLS+ LP +E + +L++L L T HL S++P I+ + +VL
Sbjct: 90 VNLKHLDLSFNAFDALPICKEFGNMSQLKFLGL-STTHLEKSSVLP---IAHLNISKVL- 144
Query: 132 LLWCGLWSRKEQEEG 146
L+ + KE EG
Sbjct: 145 LVLGETYGEKEDPEG 159
>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 = 28.9 bits (63), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 13/25 (52%), Positives = 17/25 (68%)
Query: 68 KLPSGISNLVSLHHLDLSWTRIRGL 92
KLP SNL +L HLDLS +I+ +
Sbjct: 164 KLPEYFSNLTNLEHLDLSSNKIQSI 188
>pdb|2Z63|A Chain A, Crystal Structure Of The Tv8 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
Length = 570
Score = 28.9 bits (63), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 13/25 (52%), Positives = 17/25 (68%)
Query: 68 KLPSGISNLVSLHHLDLSWTRIRGL 92
KLP SNL +L HLDLS +I+ +
Sbjct: 140 KLPEYFSNLTNLEHLDLSSNKIQSI 164
>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 = 28.5 bits (62), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 13/25 (52%), Positives = 17/25 (68%)
Query: 68 KLPSGISNLVSLHHLDLSWTRIRGL 92
KLP SNL +L HLDLS +I+ +
Sbjct: 140 KLPEYFSNLTNLEHLDLSSNKIQSI 164
>pdb|3UL9|A Chain A, Structure Of The Tv3 Mutant M41e
Length = 278
Score = 28.5 bits (62), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 13/25 (52%), Positives = 17/25 (68%)
Query: 68 KLPSGISNLVSLHHLDLSWTRIRGL 92
KLP SNL +L HLDLS +I+ +
Sbjct: 141 KLPEYFSNLTNLEHLDLSSNKIQSI 165
>pdb|3UL8|A Chain A, Crystal Structure Of The Tv3 Mutant V134l
Length = 279
Score = 28.5 bits (62), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 13/25 (52%), Positives = 17/25 (68%)
Query: 68 KLPSGISNLVSLHHLDLSWTRIRGL 92
KLP SNL +L HLDLS +I+ +
Sbjct: 142 KLPEYFSNLTNLEHLDLSSNKIQSI 166
>pdb|3B2D|A Chain A, Crystal Structure Of Human Rp105MD-1 Complex
pdb|3B2D|B Chain B, Crystal Structure Of Human Rp105MD-1 Complex
Length = 603
Score = 28.5 bits (62), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 37/76 (48%), Gaps = 3/76 (3%)
Query: 71 SGISNLVSLHHLDLSWTRIRGLPQELKA-LEKLRYLSLEGTRHL--SIIPHQLISGFSKL 127
S NL L L+L++ + Q L A L LR+L+L+G +I L+ L
Sbjct: 416 SPFQNLHFLQVLNLTYCFLDTSNQHLLAGLPVLRHLNLKGNHFQDGTITKTNLLQTVGSL 475
Query: 128 EVLRLLWCGLWSRKEQ 143
EVL L CGL S +Q
Sbjct: 476 EVLILSSCGLLSIDQQ 491
>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 = 28.5 bits (62), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 13/25 (52%), Positives = 17/25 (68%)
Query: 68 KLPSGISNLVSLHHLDLSWTRIRGL 92
KLP SNL +L HLDLS +I+ +
Sbjct: 142 KLPEYFSNLTNLEHLDLSSNKIQSI 166
>pdb|3UL7|A Chain A, Crystal Structure Of The Tv3 Mutant F63w
Length = 278
Score = 28.5 bits (62), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 13/25 (52%), Positives = 17/25 (68%)
Query: 68 KLPSGISNLVSLHHLDLSWTRIRGL 92
KLP SNL +L HLDLS +I+ +
Sbjct: 141 KLPEYFSNLTNLEHLDLSSNKIQSI 165
>pdb|1N5W|B Chain B, Crystal Structure Of The Cu,Mo-Co Dehydrogenase (Codh);
Oxidized Form
pdb|1N5W|E Chain E, Crystal Structure Of The Cu,Mo-Co Dehydrogenase (Codh);
Oxidized Form
pdb|1N60|B Chain B, Crystal Structure Of The Cu,Mo-Co Dehydrogenase (Codh);
Cyanide- Inactivated Form
pdb|1N60|E Chain E, Crystal Structure Of The Cu,Mo-Co Dehydrogenase (Codh);
Cyanide- Inactivated Form
pdb|1N61|B Chain B, Crystal Structure Of The Cu,Mo-Co Dehydrogenase (Codh);
Dithionite Reduced State
pdb|1N61|E Chain E, Crystal Structure Of The Cu,Mo-Co Dehydrogenase (Codh);
Dithionite Reduced State
pdb|1N62|B Chain B, Crystal Structure Of The Mo,cu-co Dehydrogenase (codh), N-
Butylisocyanide-bound State
pdb|1N62|E Chain E, Crystal Structure Of The Mo,cu-co Dehydrogenase (codh), N-
Butylisocyanide-bound State
pdb|1N63|B Chain B, Crystal Structure Of The Cu,Mo-Co Dehydrogenase (Codh);
Carbon Monoxide Reduced State
pdb|1N63|E Chain E, Crystal Structure Of The Cu,Mo-Co Dehydrogenase (Codh);
Carbon Monoxide Reduced State
Length = 809
Score = 28.5 bits (62), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 11/37 (29%), Positives = 24/37 (64%), Gaps = 4/37 (10%)
Query: 74 SNLVSLHHLDLSWT----RIRGLPQELKALEKLRYLS 106
++++ +H DL W R++GLP++ K +++L + S
Sbjct: 596 AHMLEVHEGDLEWDVDRFRVKGLPEKFKTMKELAWAS 632
>pdb|1ZXI|B Chain B, Reconstituted Co Dehydrogenase From Oligotropha
Carboxidovorans
pdb|1ZXI|E Chain E, Reconstituted Co Dehydrogenase From Oligotropha
Carboxidovorans
Length = 809
Score = 28.5 bits (62), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 11/37 (29%), Positives = 24/37 (64%), Gaps = 4/37 (10%)
Query: 74 SNLVSLHHLDLSWT----RIRGLPQELKALEKLRYLS 106
++++ +H DL W R++GLP++ K +++L + S
Sbjct: 596 AHMLEVHEGDLEWDVDRFRVKGLPEKFKTMKELAWAS 632
>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 = 28.1 bits (61), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 75 NLVSLHHLDLSWTRIRGLPQE-LKALEKLRYLSLEGTRHLSIIPHQLISGFSKLEVLRL 132
+L SL HLDLS + L L L+YL+L G + ++ L + L+ LR+
Sbjct: 72 SLGSLEHLDLSDNHLSSLSSSWFGPLSSLKYLNLMGNPYQTLGVTSLFPNLTNLQTLRI 130
>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 = 28.1 bits (61), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 75 NLVSLHHLDLSWTRIRGLPQE-LKALEKLRYLSLEGTRHLSIIPHQLISGFSKLEVLRL 132
+L SL HLDLS + L L L+YL+L G + ++ L + L+ LR+
Sbjct: 98 SLGSLEHLDLSDNHLSSLSSSWFGPLSSLKYLNLMGNPYQTLGVTSLFPNLTNLQTLRI 156
>pdb|1LTX|A Chain A, Structure Of Rab Escort Protein-1 In Complex With Rab
Geranylgeranyl Transferase And Isoprenoid
Length = 567
Score = 28.1 bits (61), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 19/33 (57%)
Query: 73 ISNLVSLHHLDLSWTRIRGLPQELKALEKLRYL 105
+ L+ + HLDLS R+R LP L AL L L
Sbjct: 459 LEQLLLVTHLDLSHNRLRALPPALAALRCLEVL 491
>pdb|1DCE|A Chain A, Crystal Structure Of Rab Geranylgeranyltransferase From
Rat Brain
pdb|1DCE|C Chain C, Crystal Structure Of Rab Geranylgeranyltransferase From
Rat Brain
Length = 567
Score = 28.1 bits (61), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 19/33 (57%)
Query: 73 ISNLVSLHHLDLSWTRIRGLPQELKALEKLRYL 105
+ L+ + HLDLS R+R LP L AL L L
Sbjct: 459 LEQLLLVTHLDLSHNRLRALPPALAALRCLEVL 491
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
0.319 0.136 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,334,193
Number of Sequences: 62578
Number of extensions: 309554
Number of successful extensions: 753
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 730
Number of HSP's gapped (non-prelim): 35
length of query: 298
length of database: 14,973,337
effective HSP length: 98
effective length of query: 200
effective length of database: 8,840,693
effective search space: 1768138600
effective search space used: 1768138600
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)