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= 047314
(173 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 = 37.0 bits (84), Expect = 0.006, Method: Composition-based stats.
Identities = 37/118 (31%), Positives = 53/118 (44%), Gaps = 12/118 (10%)
Query: 52 RLLQVLDLEGVYMALLDSSVGNLIHLRYLDLRKTWLKKLPSSMGNLFNLQSLDLSSTLVD 111
+L LDL + + + +++ L L L L +LP+ + NL NL+ LDLS +
Sbjct: 224 QLWHALDLSNLQIFNISANIFKYDFLTRLYLNGNSLTELPAEIKNLSNLRVLDLSHNRLT 283
Query: 112 PIPLLKHVCFNE-----FREMVVNPPVE-ASLPNLQKLIGTEMVCSSGRFSHLQFLKL 163
+P CF F MV P E +L NLQ +G E G QFLK+
Sbjct: 284 SLPAELGSCFQLKYFYFFDNMVTTLPWEFGNLCNLQ-FLGVE-----GNPLEKQFLKI 335
>pdb|2KIW|A Chain A, Solution Nmr Structure Of The Domain N-Terminal To The
Integrase Domain Of Sh1003 From Staphylococcus
Haemolyticus. Northeast Structural Genomics Consortium
Target Shr105f (64-166)
Length = 111
Score = 31.6 bits (70), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 33/61 (54%), Gaps = 2/61 (3%)
Query: 4 IERSMVQPIKTIQVHDLLREL-AISKAKEDRFLDIIHEDSNARF-LAKECRLLQVLDLEG 61
IER +PI+TI+ HD R + IS ++D I +N F A + RL++ + EG
Sbjct: 33 IERFNTKPIQTIKKHDYQRFVDDISAQYSKNYVDSIVASTNMIFKYAYDTRLIKAMPSEG 92
Query: 62 V 62
+
Sbjct: 93 I 93
>pdb|2CSE|A Chain A, Features Of Reovirus Outer-Capsid Protein Mu1 Revealed By
Electron And Image Reconstruction Of The Virion At 7.0-A
Resolution
pdb|2CSE|B Chain B, Features Of Reovirus Outer-Capsid Protein Mu1 Revealed By
Electron And Image Reconstruction Of The Virion At 7.0-A
Resolution
pdb|2CSE|C Chain C, Features Of Reovirus Outer-Capsid Protein Mu1 Revealed By
Electron And Image Reconstruction Of The Virion At 7.0-A
Resolution
pdb|2CSE|P Chain P, Features Of Reovirus Outer-Capsid Protein Mu1 Revealed By
Electron And Image Reconstruction Of The Virion At 7.0-A
Resolution
pdb|2CSE|Q Chain Q, Features Of Reovirus Outer-Capsid Protein Mu1 Revealed By
Electron And Image Reconstruction Of The Virion At 7.0-A
Resolution
pdb|2CSE|R Chain R, Features Of Reovirus Outer-Capsid Protein Mu1 Revealed By
Electron And Image Reconstruction Of The Virion At 7.0-A
Resolution
pdb|2CSE|J Chain J, Features Of Reovirus Outer-Capsid Protein Mu1 Revealed By
Electron And Image Reconstruction Of The Virion At 7.0-A
Resolution
pdb|2CSE|K Chain K, Features Of Reovirus Outer-Capsid Protein Mu1 Revealed By
Electron And Image Reconstruction Of The Virion At 7.0-A
Resolution
pdb|2CSE|L Chain L, Features Of Reovirus Outer-Capsid Protein Mu1 Revealed By
Electron And Image Reconstruction Of The Virion At 7.0-A
Resolution
pdb|2CSE|T Chain T, Features Of Reovirus Outer-Capsid Protein Mu1 Revealed By
Electron And Image Reconstruction Of The Virion At 7.0-A
Resolution
Length = 708
Score = 30.8 bits (68), Expect = 0.38, Method: Composition-based stats.
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 85 TWLKKLPSSMGNLFNLQSLDLSST 108
TWL+ +P +MG LF +Q D + T
Sbjct: 332 TWLRMIPKTMGTLFQIQVTDNTGT 355
>pdb|1JMU|B Chain B, Crystal Structure Of The Reovirus Mu1SIGMA3 COMPLEX
pdb|1JMU|D Chain D, Crystal Structure Of The Reovirus Mu1SIGMA3 COMPLEX
pdb|1JMU|F Chain F, Crystal Structure Of The Reovirus Mu1SIGMA3 COMPLEX
Length = 666
Score = 30.8 bits (68), Expect = 0.38, Method: Composition-based stats.
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 85 TWLKKLPSSMGNLFNLQSLDLSST 108
TWL+ +P +MG LF +Q D + T
Sbjct: 290 TWLRMIPKTMGTLFQIQVTDNTGT 313
>pdb|2Z64|A Chain A, Crystal Structure Of Mouse Tlr4 And Mouse Md-2 Complex
Length = 599
Score = 30.0 bits (66), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 35/69 (50%), Gaps = 8/69 (11%)
Query: 71 VGNLIHLRYLDLRKTWLK--KLPSSMGNLFNLQSLDLSSTLVDPIPLLKHVCFNEFREMV 128
+G LI L+ L++ ++ KLP+ NL NL +DLS + I + N+ + +
Sbjct: 119 IGQLITLKKLNVAHNFIHSCKLPAYFSNLTNLVHVDLSYNYIQTITV------NDLQFLR 172
Query: 129 VNPPVEASL 137
NP V SL
Sbjct: 173 ENPQVNLSL 181
>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 = 30.0 bits (66), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 35/69 (50%), Gaps = 8/69 (11%)
Query: 71 VGNLIHLRYLDLRKTWLK--KLPSSMGNLFNLQSLDLSSTLVDPIPLLKHVCFNEFREMV 128
+G LI L+ L++ ++ KLP+ NL NL +DLS + I + N+ + +
Sbjct: 124 IGQLITLKKLNVAHNFIHSCKLPAYFSNLTNLVHVDLSYNYIQTITV------NDLQFLR 177
Query: 129 VNPPVEASL 137
NP V SL
Sbjct: 178 ENPQVNLSL 186
>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 = 29.3 bits (64), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 44/150 (29%), Positives = 61/150 (40%), Gaps = 19/150 (12%)
Query: 34 FLDIIHEDSNARFLAKECRL-LQVLDL-EGVYMALLDSSVGNLIHLRYLDLRKTWLKKLP 91
F DI ED ++ L C + ++ L+L E + + ++ L+ LDL T LK LP
Sbjct: 232 FEDIDDEDISSAMLKGLCEMSVESLNLQEHRFSDISSTTFQCFTQLQELDLTATHLKGLP 291
Query: 92 SSMGNLFNLQSLDLSSTLVDPIPLLKHVCFNEFREMVVNPPVEA---------SLPNLQK 142
S M L L+ L LS D + + F + + V+ L NLQ
Sbjct: 292 SGMKGLNLLKKLVLSVNHFDQLCQISAANFPSLTHLYIRGNVKKLHLGVGCLEKLGNLQT 351
Query: 143 L------IGTEMVCS--SGRFSHLQFLKLS 164
L I CS SHLQ L LS
Sbjct: 352 LDLSHNDIEASDCCSLQLKNLSHLQTLNLS 381
>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type
Iii Effector Xcv3220 (Xopl)
Length = 328
Score = 28.9 bits (63), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 31/48 (64%), Gaps = 1/48 (2%)
Query: 73 NLIHLRYLDLRKTWLKKLPSSMGNLFNLQSLDLSSTLVDPI-PLLKHV 119
L++L+ L L T ++ LP+S+ NL NL+SL + ++ + + P + H+
Sbjct: 181 GLVNLQSLRLEWTGIRSLPASIANLQNLKSLKIRNSPLSALGPAIHHL 228
>pdb|3UL8|A Chain A, Crystal Structure Of The Tv3 Mutant V134l
Length = 279
Score = 28.5 bits (62), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 2/63 (3%)
Query: 53 LLQVLDLEGVYMALLDSSVGNLIHLRYLDLRKTWLK--KLPSSMGNLFNLQSLDLSSTLV 110
L +++ LE +L + +G+L L+ L++ ++ KLP NL NL+ LDLSS +
Sbjct: 104 LQKLVALETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKI 163
Query: 111 DPI 113
I
Sbjct: 164 QSI 166
>pdb|3DZZ|A Chain A, Crystal Structure Of A Putative Plp-Dependent
Aminotransferase (Lbul_1103) From Lactobacillus
Delbrueckii Subsp. At 1.61 A Resolution
pdb|3DZZ|B Chain B, Crystal Structure Of A Putative Plp-Dependent
Aminotransferase (Lbul_1103) From Lactobacillus
Delbrueckii Subsp. At 1.61 A Resolution
Length = 391
Score = 28.1 bits (61), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 28/55 (50%), Gaps = 10/55 (18%)
Query: 18 HDLLRELAISKAKEDRFLDIIHEDSNAR-FLAKECRLLQVLDLEGVYMALLDSSV 71
HD LREL + D F + AR FLAKE ++VLD Y+A +D S
Sbjct: 285 HDWLREL--KQVLRDNF-------AYAREFLAKEVPEVKVLDSNASYLAWVDISA 330
>pdb|2QO6|A Chain A, Crystal Structure Of The Glycine 55 Arginine Mutant Of
Zebrafish Liver Bile Acid-Binding Protein Complexed With
Cholic Acid
Length = 126
Score = 28.1 bits (61), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 142 KLIGTEMVCSSGRFSHLQFLKLSNI 166
KL G ++VC + RFSH+Q +K +
Sbjct: 84 KLDGGKLVCRTDRFSHIQEIKAGEM 108
>pdb|2QO4|A Chain A, Crystal Structure Of Zebrafish Liver Bile Acid-Binding
Protein Complexed With Cholic Acid
Length = 126
Score = 28.1 bits (61), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 142 KLIGTEMVCSSGRFSHLQFLKLSNI 166
KL G ++VC + RFSH+Q +K +
Sbjct: 84 KLDGGKLVCRTDRFSHIQEIKAGEM 108
>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 = 27.7 bits (60), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 26/45 (57%), Gaps = 2/45 (4%)
Query: 71 VGNLIHLRYLDLRKTWLK--KLPSSMGNLFNLQSLDLSSTLVDPI 113
+G+L L+ L++ ++ KLP NL NL+ LDLSS + I
Sbjct: 120 IGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKIQSI 164
>pdb|3UL9|A Chain A, Structure Of The Tv3 Mutant M41e
Length = 278
Score = 27.7 bits (60), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 35/63 (55%), Gaps = 2/63 (3%)
Query: 53 LLQVLDLEGVYMALLDSSVGNLIHLRYLDLRKTWLK--KLPSSMGNLFNLQSLDLSSTLV 110
L +++ +E +L + +G+L L+ L++ ++ KLP NL NL+ LDLSS +
Sbjct: 103 LQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKI 162
Query: 111 DPI 113
I
Sbjct: 163 QSI 165
>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 = 27.7 bits (60), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 35/63 (55%), Gaps = 2/63 (3%)
Query: 53 LLQVLDLEGVYMALLDSSVGNLIHLRYLDLRKTWLK--KLPSSMGNLFNLQSLDLSSTLV 110
L +++ +E +L + +G+L L+ L++ ++ KLP NL NL+ LDLSS +
Sbjct: 102 LQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKI 161
Query: 111 DPI 113
I
Sbjct: 162 QSI 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 = 27.3 bits (59), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 26/45 (57%), Gaps = 2/45 (4%)
Query: 71 VGNLIHLRYLDLRKTWLK--KLPSSMGNLFNLQSLDLSSTLVDPI 113
+G+L L+ L++ ++ KLP NL NL+ LDLSS + I
Sbjct: 144 IGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKIQSI 188
>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 = 27.3 bits (59), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 35/63 (55%), Gaps = 2/63 (3%)
Query: 53 LLQVLDLEGVYMALLDSSVGNLIHLRYLDLRKTWLK--KLPSSMGNLFNLQSLDLSSTLV 110
L +++ +E +L + +G+L L+ L++ ++ KLP NL NL+ LDLSS +
Sbjct: 104 LQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKI 163
Query: 111 DPI 113
I
Sbjct: 164 QSI 166
>pdb|3UL7|A Chain A, Crystal Structure Of The Tv3 Mutant F63w
Length = 278
Score = 27.3 bits (59), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 35/63 (55%), Gaps = 2/63 (3%)
Query: 53 LLQVLDLEGVYMALLDSSVGNLIHLRYLDLRKTWLK--KLPSSMGNLFNLQSLDLSSTLV 110
L +++ +E +L + +G+L L+ L++ ++ KLP NL NL+ LDLSS +
Sbjct: 103 LQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKI 162
Query: 111 DPI 113
I
Sbjct: 163 QSI 165
>pdb|2Z63|A Chain A, Crystal Structure Of The Tv8 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
Length = 570
Score = 27.3 bits (59), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 35/63 (55%), Gaps = 2/63 (3%)
Query: 53 LLQVLDLEGVYMALLDSSVGNLIHLRYLDLRKTWLK--KLPSSMGNLFNLQSLDLSSTLV 110
L +++ +E +L + +G+L L+ L++ ++ KLP NL NL+ LDLSS +
Sbjct: 102 LQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKI 161
Query: 111 DPI 113
I
Sbjct: 162 QSI 164
>pdb|2ID5|A Chain A, Crystal Structure Of The Lingo-1 Ectodomain
pdb|2ID5|B Chain B, Crystal Structure Of The Lingo-1 Ectodomain
pdb|2ID5|C Chain C, Crystal Structure Of The Lingo-1 Ectodomain
pdb|2ID5|D Chain D, Crystal Structure Of The Lingo-1 Ectodomain
Length = 477
Score = 27.3 bits (59), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 24/41 (58%), Gaps = 1/41 (2%)
Query: 76 HLRYLDLRKTWLKKL-PSSMGNLFNLQSLDLSSTLVDPIPL 115
HL L+L + + + P + NLFNL++L L S + IPL
Sbjct: 57 HLEELELNENIVSAVEPGAFNNLFNLRTLGLRSNRLKLIPL 97
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 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,587,469
Number of Sequences: 62578
Number of extensions: 169872
Number of successful extensions: 375
Number of sequences better than 100.0: 29
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 355
Number of HSP's gapped (non-prelim): 31
length of query: 173
length of database: 14,973,337
effective HSP length: 92
effective length of query: 81
effective length of database: 9,216,161
effective search space: 746509041
effective search space used: 746509041
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: 48 (23.1 bits)