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= 027557
(222 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 = 35.4 bits (80), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 40/76 (52%)
Query: 12 LSRNPIREIGDSLLNMKAITKLSLSNCQVQIIGSSLKSCTELKELRLAHNDIKTLPAELA 71
LS I I ++ +T+L L+ + + + +K+ + L+ L L+HN + +LPAEL
Sbjct: 231 LSNLQIFNISANIFKYDFLTRLYLNGNSLTELPAEIKNLSNLRVLDLSHNRLTSLPAELG 290
Query: 72 FNKKLQNLDLGKNLIT 87
+L+ N++T
Sbjct: 291 SCFQLKYFYFFDNMVT 306
Score = 31.6 bits (70), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 35/74 (47%)
Query: 11 VLSRNPIREIGDSLLNMKAITKLSLSNCQVQIIGSSLKSCTELKELRLAHNDIKTLPAEL 70
L+ N + E+ + N+ + L LS+ ++ + + L SC +LK N + TLP E
Sbjct: 253 YLNGNSLTELPAEIKNLSNLRVLDLSHNRLTSLPAELGSCFQLKYFYFFDNMVTTLPWEF 312
Query: 71 AFNKKLQNLDLGKN 84
LQ L + N
Sbjct: 313 GNLCNLQFLGVEGN 326
Score = 28.9 bits (63), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 28/55 (50%)
Query: 33 LSLSNCQVQIIGSSLKSCTELKELRLAHNDIKTLPAELAFNKKLQNLDLGKNLIT 87
L LSN Q+ I +++ L L L N + LPAE+ L+ LDL N +T
Sbjct: 229 LDLSNLQIFNISANIFKYDFLTRLYLNGNSLTELPAEIKNLSNLRVLDLSHNRLT 283
>pdb|2FT3|A Chain A, Crystal Structure Of The Biglycan Dimer Core Protein
pdb|2FT3|B Chain B, Crystal Structure Of The Biglycan Dimer Core Protein
pdb|2FT3|C Chain C, Crystal Structure Of The Biglycan Dimer Core Protein
pdb|2FT3|D Chain D, Crystal Structure Of The Biglycan Dimer Core Protein
pdb|2FT3|E Chain E, Crystal Structure Of The Biglycan Dimer Core Protein
pdb|2FT3|F Chain F, Crystal Structure Of The Biglycan Dimer Core Protein
Length = 332
Score = 30.8 bits (68), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 36/68 (52%), Gaps = 1/68 (1%)
Query: 22 DSLLNMKAITKLSLSNCQVQII-GSSLKSCTELKELRLAHNDIKTLPAELAFNKKLQNLD 80
+ LL + +L L + Q+++I SL L+EL L +N + +PA L K LQ +
Sbjct: 211 EDLLRYSKLYRLGLGHNQIRMIENGSLSFLPTLRELHLDNNKLSRVPAGLPDLKLLQVVY 270
Query: 81 LGKNLITR 88
L N IT+
Sbjct: 271 LHTNNITK 278
>pdb|2O6Q|A Chain A, Structural Diversity Of The Hagfish Variable Lymphocyte
Receptors A29
Length = 270
Score = 30.4 bits (67), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 28/84 (33%), Positives = 45/84 (53%), Gaps = 5/84 (5%)
Query: 12 LSRNPIREIGDSLLN-MKAITKLSLSNCQVQIIGSS-LKSCTELKELRLAHNDIKTLPAE 69
L RN ++ + + + + +T LSL ++Q + T LKELRL +N +K +P E
Sbjct: 116 LDRNQLKSLPPRVFDSLTKLTYLSLGYNELQSLPKGVFDKLTSLKELRLYNNQLKRVP-E 174
Query: 70 LAFNK--KLQNLDLGKNLITRWSE 91
AF+K +L+ L L N + R E
Sbjct: 175 GAFDKLTELKTLKLDNNQLKRVPE 198
>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 = 0.79, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 40/79 (50%), Gaps = 13/79 (16%)
Query: 11 VLSRNPIREIGDSLLNMKAITKLSLSNC-QVQIIGSSLKSC---------TELKELRLAH 60
L+RNP+R + S+ ++ + +LS+ C ++ + L S L+ LRL
Sbjct: 133 TLARNPLRALPASIASLNRLRELSIRACPELTELPEPLASTDASGEHQGLVNLQSLRLEW 192
Query: 61 NDIKTLPAELAFNKKLQNL 79
I++LPA +A LQNL
Sbjct: 193 TGIRSLPASIA---NLQNL 208
>pdb|2A0Z|A Chain A, The Molecular Structure Of Toll-like Receptor 3 Ligand
Binding Domain
Length = 705
Score = 30.0 bits (66), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 5/72 (6%)
Query: 21 GDSLLNMKAITKLSLSNCQV----QIIGSSLKSCTELKELRLAHNDIKTLPAELAFNK-K 75
G + +K ++ L + N + +I K ELK + L N++ TLPA + N+
Sbjct: 531 GGPIYFLKGLSHLHILNLESNGFDEIPVEVFKDLFELKIIDLGLNNLNTLPASVFNNQVS 590
Query: 76 LQNLDLGKNLIT 87
L++L+L KNLIT
Sbjct: 591 LKSLNLQKNLIT 602
>pdb|1ZIW|A Chain A, Human Toll-Like Receptor 3 Extracellular Domain Structure
Length = 680
Score = 30.0 bits (66), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 5/72 (6%)
Query: 21 GDSLLNMKAITKLSLSNCQV----QIIGSSLKSCTELKELRLAHNDIKTLPAELAFNK-K 75
G + +K ++ L + N + +I K ELK + L N++ TLPA + N+
Sbjct: 526 GGPIYFLKGLSHLHILNLESNGFDEIPVEVFKDLFELKIIDLGLNNLNTLPASVFNNQVS 585
Query: 76 LQNLDLGKNLIT 87
L++L+L KNLIT
Sbjct: 586 LKSLNLQKNLIT 597
>pdb|3ZYI|A Chain A, Netring2 In Complex With Ngl2
Length = 452
Score = 30.0 bits (66), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 33/61 (54%), Gaps = 2/61 (3%)
Query: 12 LSRNPIREI-GDSLLNMKAITKLSLSNCQVQIIG-SSLKSCTELKELRLAHNDIKTLPAE 69
+S N EI S + ++ KL + N QV +I ++ L EL LAHN++ +LP +
Sbjct: 225 MSGNHFPEIRPGSFHGLSSLKKLWVMNSQVSLIERNAFDGLASLVELNLAHNNLSSLPHD 284
Query: 70 L 70
L
Sbjct: 285 L 285
>pdb|3A79|B Chain B, Crystal Structure Of Tlr2-Tlr6-Pam2csk4 Complex
Length = 562
Score = 30.0 bits (66), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 23/35 (65%), Gaps = 1/35 (2%)
Query: 51 TELKELRLAHNDIKTLPAE-LAFNKKLQNLDLGKN 84
+EL+ LRL+HN I++L FN+ L+ LD+ N
Sbjct: 76 SELRVLRLSHNRIRSLDFHVFLFNQDLEYLDVSHN 110
>pdb|3ULU|A Chain A, Structure Of Quaternary Complex Of Human Tlr3ecd With
Three Fabs (Form1)
pdb|3ULV|A Chain A, Structure Of Quaternary Complex Of Human Tlr3ecd With
Three Fabs (Form2)
Length = 694
Score = 30.0 bits (66), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 5/72 (6%)
Query: 21 GDSLLNMKAITKLSLSNCQV----QIIGSSLKSCTELKELRLAHNDIKTLPAELAFNK-K 75
G + +K ++ L + N + +I K ELK + L N++ TLPA + N+
Sbjct: 536 GGPIYFLKGLSHLHILNLESNGFDEIPVEVFKDLFELKIIDLGLNNLNTLPASVFNNQVS 595
Query: 76 LQNLDLGKNLIT 87
L++L+L KNLIT
Sbjct: 596 LKSLNLQKNLIT 607
>pdb|3M18|A Chain A, Crystal Structure Of Variable Lymphocyte Receptor
Vlra.R2.1 In Complex With Hen Egg Lysozyme
Length = 251
Score = 28.5 bits (62), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 35/62 (56%), Gaps = 4/62 (6%)
Query: 26 NMKAITKLSLSNCQVQIIGSS-LKSCTELKELRLAHNDIKTLPAELAFNK--KLQNLDLG 82
++ + KL L Q++ + S T+LKELRL N ++++PA AF+K LQ L L
Sbjct: 105 HLTQLDKLYLGGNQLKSLPSGVFDRLTKLKELRLNTNQLQSIPAG-AFDKLTNLQTLSLS 163
Query: 83 KN 84
N
Sbjct: 164 TN 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 = 28.5 bits (62), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 35/62 (56%), Gaps = 4/62 (6%)
Query: 26 NMKAITKLSLSNCQVQIIGSS-LKSCTELKELRLAHNDIKTLPAELAFNK--KLQNLDLG 82
++ + KL L Q++ + S T+LKELRL N ++++PA AF+K LQ L L
Sbjct: 105 HLTQLDKLYLGGNQLKSLPSGVFDRLTKLKELRLNTNQLQSIPAG-AFDKLTNLQTLSLS 163
Query: 83 KN 84
N
Sbjct: 164 TN 165
>pdb|3LXJ|A Chain A, Crystal Structure Of The Bromodomain Of Human Aaa Domain
Containing 2b (Atad2b)
pdb|3LXJ|B Chain B, Crystal Structure Of The Bromodomain Of Human Aaa Domain
Containing 2b (Atad2b)
pdb|3LXJ|C Chain C, Crystal Structure Of The Bromodomain Of Human Aaa Domain
Containing 2b (Atad2b)
pdb|3LXJ|D Chain D, Crystal Structure Of The Bromodomain Of Human Aaa Domain
Containing 2b (Atad2b)
Length = 136
Score = 27.7 bits (60), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 8/56 (14%)
Query: 8 CPAVLSRNPIREIGDSLLNMKAITKLSLSNCQVQIIGSSL-----KSCTELKELRL 58
C L NP ++ GD ++ +A T L + II + L K C E+KE R+
Sbjct: 81 CSNALEYNPDKDPGDKIIRHRACT---LKDTAHAIIAAELDPEFNKLCEEIKEARI 133
>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 = 27.3 bits (59), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 33/58 (56%), Gaps = 2/58 (3%)
Query: 12 LSRNPIREIGDSLLN-MKAITKLSLSNCQVQIIGSS-LKSCTELKELRLAHNDIKTLP 67
L+ N ++ + + + + +T+L LS Q+Q + T+LK+LRL N +K++P
Sbjct: 140 LAHNQLQSLPKGVFDKLTNLTELDLSYNQLQSLPEGVFDKLTQLKDLRLYQNQLKSVP 197
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
0.314 0.131 0.373
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,179,651
Number of Sequences: 62578
Number of extensions: 172046
Number of successful extensions: 397
Number of sequences better than 100.0: 35
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 34
Number of HSP's that attempted gapping in prelim test: 384
Number of HSP's gapped (non-prelim): 45
length of query: 222
length of database: 14,973,337
effective HSP length: 95
effective length of query: 127
effective length of database: 9,028,427
effective search space: 1146610229
effective search space used: 1146610229
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 49 (23.5 bits)