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= 038576
(411 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 30/109 (27%), Positives = 50/109 (45%), Gaps = 20/109 (18%)
Query: 259 STSFQNLTTLTVWGCHGMINVLTSSTARSLVRLRQMTIKVCVMITEIVADEDDEGDNYAA 318
+ SF+N L + C G ++ A + L+++ ++ +D DD ++ +
Sbjct: 126 AKSFKNFKVLVLSSCEGFSTDGLAAIAATCRNLKELDLRE--------SDVDDVSGHWLS 177
Query: 319 QDEIVFSELKELNLSNLQSLTSFSCSGNNCAFKFPSLERLVVNRCPNMK 367
++ L LN+S L S SFS +LERL V RCPN+K
Sbjct: 178 HFPDTYTSLVSLNISCLASEVSFS-----------ALERL-VTRCPNLK 214
>pdb|1H6U|A Chain A, Internalin H: Crystal Structure Of Fused N-Terminal
Domains
Length = 308
Score = 33.9 bits (76), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 31/116 (26%), Positives = 58/116 (50%), Gaps = 20/116 (17%)
Query: 23 DCELGDMAIIGDLKKLVILALRGSDMEELAGEIGQLTQLRLLNLSKCFELKVIPPNVISS 82
D ++ D+A + +L K+ L L G+ ++ ++ I L ++ L+L+ V P ++
Sbjct: 72 DNQITDLAPLKNLTKITELELSGNPLKNVSA-IAGLQSIKTLDLTSTQITDVTP---LAG 127
Query: 83 LSRLEELYI------------GQSPIQWGKVEGVDGERRNASLDELNNLSKLTSLE 126
LS L+ LY+ G + +Q+ + G + + L L NLSKLT+L+
Sbjct: 128 LSNLQVLYLDLNQITNISPLAGLTNLQYLSI----GNAQVSDLTPLANLSKLTTLK 179
>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type
Iii Effector Xcv3220 (Xopl)
Length = 328
Score = 32.0 bits (71), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 34/126 (26%), Positives = 58/126 (46%), Gaps = 20/126 (15%)
Query: 262 FQNLTTLTVWGCHGMINVLTSSTARSLVRLRQMTIKVCVMITEI---VADEDDEGDNYAA 318
F L TLT+ + L +S A SL RLR+++I+ C +TE+ +A D G++
Sbjct: 126 FAGLETLTL--ARNPLRALPASIA-SLNRLRELSIRACPELTELPEPLASTDASGEHQGL 182
Query: 319 QD----EIVFSELKEL-----NLSNLQSL----TSFSCSGNNCAFKFPSLERLVVNRCPN 365
+ + ++ ++ L NL NL+SL + S G P LE L + C
Sbjct: 183 VNLQSLRLEWTGIRSLPASIANLQNLKSLKIRNSPLSALG-PAIHHLPKLEELDLRGCTA 241
Query: 366 MKIFSE 371
++ +
Sbjct: 242 LRNYPP 247
>pdb|2O6Q|A Chain A, Structural Diversity Of The Hagfish Variable Lymphocyte
Receptors A29
Length = 270
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 36/69 (52%), Gaps = 2/69 (2%)
Query: 30 AIIGDLKKLVILALRGSDMEELA-GEIGQLTQLRLLNLSKCFELKVIPPNVISSLSRLEE 88
I +LK L L + + ++ L G QL L L L + +LK +PP V SL++L
Sbjct: 79 GIFKELKNLETLWVTDNKLQALPIGVFDQLVNLAELRLDR-NQLKSLPPRVFDSLTKLTY 137
Query: 89 LYIGQSPIQ 97
L +G + +Q
Sbjct: 138 LSLGYNELQ 146
>pdb|3ZYI|A Chain A, Netring2 In Complex With Ngl2
Length = 452
Score = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 34/66 (51%), Gaps = 4/66 (6%)
Query: 34 DLKKLVILALRGSDMEELAGEIGQLTQLRLLNLSKCFE--LKVIPPNVISSLSRLEELYI 91
L L +L L + + ++ E+G L LN + F+ L VIP LS+L EL++
Sbjct: 97 HLHHLEVLQLGRNSIRQI--EVGAFNGLASLNTLELFDNWLTVIPSGAFEYLSKLRELWL 154
Query: 92 GQSPIQ 97
+PI+
Sbjct: 155 RNNPIE 160
>pdb|3ZYJ|A Chain A, Netring1 In Complex With Ngl1
pdb|3ZYJ|C Chain C, Netring1 In Complex With Ngl1
Length = 440
Score = 28.9 bits (63), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 34/65 (52%), Gaps = 4/65 (6%)
Query: 35 LKKLVILALRGSDMEELAGEIGQLTQLRLLNLSKCFE--LKVIPPNVISSLSRLEELYIG 92
L+ L IL L + + + EIG L LN + F+ L IP LS+L+EL++
Sbjct: 87 LRHLEILQLSRNHIRTI--EIGAFNGLANLNTLELFDNRLTTIPNGAFVYLSKLKELWLR 144
Query: 93 QSPIQ 97
+PI+
Sbjct: 145 NNPIE 149
>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 = 28.9 bits (63), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 10/79 (12%)
Query: 58 LTQLRLLNLSKCFELKVIPPNVISSLSRLEELYIGQSPIQWGKVEGVDGERRNASLDELN 117
+L++L+LS+C E++ I SLS L L + +PIQ + G L+
Sbjct: 51 FPELQVLDLSRC-EIQTIEDGAYQSLSHLSTLILTGNPIQSLALGAFSG---------LS 100
Query: 118 NLSKLTSLEILIQDEKTLP 136
+L KL ++E + + P
Sbjct: 101 SLQKLVAVETNLASLENFP 119
>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 = 5.4, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 10/79 (12%)
Query: 58 LTQLRLLNLSKCFELKVIPPNVISSLSRLEELYIGQSPIQWGKVEGVDGERRNASLDELN 117
+L++L+LS+C E++ I SLS L L + +PIQ + G L+
Sbjct: 75 FPELQVLDLSRC-EIQTIEDGAYQSLSHLSTLILTGNPIQSLALGAFSG---------LS 124
Query: 118 NLSKLTSLEILIQDEKTLP 136
+L KL ++E + + P
Sbjct: 125 SLQKLVAVETNLASLENFP 143
>pdb|2Z63|A Chain A, Crystal Structure Of The Tv8 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
Length = 570
Score = 28.5 bits (62), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 10/79 (12%)
Query: 58 LTQLRLLNLSKCFELKVIPPNVISSLSRLEELYIGQSPIQWGKVEGVDGERRNASLDELN 117
+L++L+LS+C E++ I SLS L L + +PIQ + G L+
Sbjct: 51 FPELQVLDLSRC-EIQTIEDGAYQSLSHLSTLILTGNPIQSLALGAFSG---------LS 100
Query: 118 NLSKLTSLEILIQDEKTLP 136
+L KL ++E + + P
Sbjct: 101 SLQKLVAVETNLASLENFP 119
>pdb|3ZYO|A Chain A, Crystal Structure Of The N-Terminal Leucine Rich Repeats
And Immunoglobulin Domain Of Netrin-G Ligand-3
Length = 411
Score = 28.5 bits (62), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 4/65 (6%)
Query: 35 LKKLVILALRGSDMEELAGEIGQLTQLRLLNLSKCFE--LKVIPPNVISSLSRLEELYIG 92
L+ L IL L + + ++ E+G L LN + F+ L +P LS+L EL++
Sbjct: 58 LRHLEILQLSKNLVRKI--EVGAFNGLPSLNTLELFDNRLTTVPTQAFEYLSKLRELWLR 115
Query: 93 QSPIQ 97
+PI+
Sbjct: 116 NNPIE 120
>pdb|3UL8|A Chain A, Crystal Structure Of The Tv3 Mutant V134l
Length = 279
Score = 28.5 bits (62), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 38/79 (48%), Gaps = 10/79 (12%)
Query: 58 LTQLRLLNLSKCFELKVIPPNVISSLSRLEELYIGQSPIQWGKVEGVDGERRNASLDELN 117
+L++L+LS+C E++ I SLS L L + +PIQ + G L+
Sbjct: 53 FPELQVLDLSRC-EIQTIEDGAYQSLSHLSTLILTGNPIQSLALGAFSG---------LS 102
Query: 118 NLSKLTSLEILIQDEKTLP 136
+L KL +LE + + P
Sbjct: 103 SLQKLVALETNLASLENFP 121
>pdb|3ZYN|A Chain A, Crystal Structure Of The N-Terminal Leucine Rich Repeats
Of Netrin-G Ligand-3
pdb|3ZYN|B Chain B, Crystal Structure Of The N-Terminal Leucine Rich Repeats
Of Netrin-G Ligand-3
Length = 321
Score = 28.1 bits (61), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 4/65 (6%)
Query: 35 LKKLVILALRGSDMEELAGEIGQLTQLRLLNLSKCFE--LKVIPPNVISSLSRLEELYIG 92
L+ L IL L + + ++ E+G L LN + F+ L +P LS+L EL++
Sbjct: 58 LRHLEILQLSKNLVRKI--EVGAFNGLPSLNTLELFDNRLTTVPTQAFEYLSKLRELWLR 115
Query: 93 QSPIQ 97
+PI+
Sbjct: 116 NNPIE 120
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
0.318 0.134 0.384
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,558,995
Number of Sequences: 62578
Number of extensions: 400911
Number of successful extensions: 1171
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 20
Number of HSP's that attempted gapping in prelim test: 1162
Number of HSP's gapped (non-prelim): 29
length of query: 411
length of database: 14,973,337
effective HSP length: 101
effective length of query: 310
effective length of database: 8,652,959
effective search space: 2682417290
effective search space used: 2682417290
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)