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= 043008
(517 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 = 38.1 bits (87), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 28/88 (31%), Positives = 41/88 (46%), Gaps = 6/88 (6%)
Query: 144 VPSSTECLTNLQYLFLCSCKKLKRVSTSICKFKSLVWLSLN-NDLTAIPQEIGCLSSLEC 202
+P ++ L + S ++ +S +I K+ L L LN N LT +P EI LS+L
Sbjct: 215 MPKDSKYDDQLWHALDLSNLQIFNISANIFKYDFLTRLYLNGNSLTELPAEIKNLSNLRV 274
Query: 203 LNLGGNNFEGLPASIKQISRLECLDLSY 230
L+L N LPA + C L Y
Sbjct: 275 LDLSHNRLTSLPAELG-----SCFQLKY 297
>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 = 35.4 bits (80), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 30/89 (33%), Positives = 43/89 (48%), Gaps = 3/89 (3%)
Query: 143 EVPSSTECLTNLQYLFLCSCKKLKRVSTSICKFKSLVWLSL-NNDLTA-IPQEIGCLSSL 200
E+P + L+ L L + + + +L W+SL NN LT IP+ IG L +L
Sbjct: 454 EIPQELMYVKTLETLILDFNDLTGEIPSGLSNCTNLNWISLSNNRLTGEIPKWIGRLENL 513
Query: 201 ECLNLGGNNFEG-LPASIKQISRLECLDL 228
L L N+F G +PA + L LDL
Sbjct: 514 AILKLSNNSFSGNIPAELGDCRSLIWLDL 542
Score = 32.7 bits (73), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 27/87 (31%), Positives = 46/87 (52%), Gaps = 4/87 (4%)
Query: 143 EVPSSTECLTNLQYLFLCSCKKLKRVSTSICKFKSLVWLSLNNDLTA--IPQEIGCLSSL 200
E+PS TNL ++ L + + + I + ++L L L+N+ + IP E+G SL
Sbjct: 478 EIPSGLSNCTNLNWISLSNNRLTGEIPKWIGRLENLAILKLSNNSFSGNIPAELGDCRSL 537
Query: 201 ECLNLGGNNFEG-LPASI-KQISRLEC 225
L+L N F G +PA++ KQ ++
Sbjct: 538 IWLDLNTNLFNGTIPAAMFKQSGKIAA 564
Score = 32.7 bits (73), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 34/56 (60%), Gaps = 3/56 (5%)
Query: 177 SLVWLSLNNDLTA--IPQEIGCLSSLECLNLGGNNFEG-LPASIKQISRLECLDLS 229
S+++L ++ ++ + IP+EIG + L LNLG N+ G +P + + L LDLS
Sbjct: 630 SMMFLDMSYNMLSGYIPKEIGSMPYLFILNLGHNDISGSIPDEVGDLRGLNILDLS 685
Score = 31.2 bits (69), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 29/50 (58%), Gaps = 2/50 (4%)
Query: 185 NDLTA-IPQEIGCLSSLECLNLGGNNFEG-LPASIKQISRLECLDLSYCN 232
ND++ IP E+G L L L+L N +G +P ++ ++ L +DLS N
Sbjct: 663 NDISGSIPDEVGDLRGLNILDLSSNKLDGRIPQAMSALTMLTEIDLSNNN 712
>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 = 35.0 bits (79), Expect = 0.095, Method: Compositional matrix adjust.
Identities = 30/89 (33%), Positives = 43/89 (48%), Gaps = 3/89 (3%)
Query: 143 EVPSSTECLTNLQYLFLCSCKKLKRVSTSICKFKSLVWLSL-NNDLTA-IPQEIGCLSSL 200
E+P + L+ L L + + + +L W+SL NN LT IP+ IG L +L
Sbjct: 457 EIPQELMYVKTLETLILDFNDLTGEIPSGLSNCTNLNWISLSNNRLTGEIPKWIGRLENL 516
Query: 201 ECLNLGGNNFEG-LPASIKQISRLECLDL 228
L L N+F G +PA + L LDL
Sbjct: 517 AILKLSNNSFSGNIPAELGDCRSLIWLDL 545
Score = 32.7 bits (73), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 34/56 (60%), Gaps = 3/56 (5%)
Query: 177 SLVWLSLNNDLTA--IPQEIGCLSSLECLNLGGNNFEG-LPASIKQISRLECLDLS 229
S+++L ++ ++ + IP+EIG + L LNLG N+ G +P + + L LDLS
Sbjct: 633 SMMFLDMSYNMLSGYIPKEIGSMPYLFILNLGHNDISGSIPDEVGDLRGLNILDLS 688
Score = 32.3 bits (72), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 27/87 (31%), Positives = 46/87 (52%), Gaps = 4/87 (4%)
Query: 143 EVPSSTECLTNLQYLFLCSCKKLKRVSTSICKFKSLVWLSLNNDLTA--IPQEIGCLSSL 200
E+PS TNL ++ L + + + I + ++L L L+N+ + IP E+G SL
Sbjct: 481 EIPSGLSNCTNLNWISLSNNRLTGEIPKWIGRLENLAILKLSNNSFSGNIPAELGDCRSL 540
Query: 201 ECLNLGGNNFEG-LPASI-KQISRLEC 225
L+L N F G +PA++ KQ ++
Sbjct: 541 IWLDLNTNLFNGTIPAAMFKQSGKIAA 567
Score = 31.2 bits (69), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 29/50 (58%), Gaps = 2/50 (4%)
Query: 185 NDLTA-IPQEIGCLSSLECLNLGGNNFEG-LPASIKQISRLECLDLSYCN 232
ND++ IP E+G L L L+L N +G +P ++ ++ L +DLS N
Sbjct: 666 NDISGSIPDEVGDLRGLNILDLSSNKLDGRIPQAMSALTMLTEIDLSNNN 715
>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 = 35.0 bits (79), Expect = 0.098, Method: Compositional matrix adjust.
Identities = 33/94 (35%), Positives = 48/94 (51%), Gaps = 4/94 (4%)
Query: 146 SSTECLTNLQYLFLCSCKKLKRVSTSICKFKSLVWLSL-NNDLTAIPQEI-GCLSSLECL 203
S+ + LTNL YL L + + K +L L L N L ++P + L++L L
Sbjct: 79 SALKELTNLTYLILTGNQLQSLPNGVFDKLTNLKELVLVENQLQSLPDGVFDKLTNLTYL 138
Query: 204 NLGGNNFEGLPASI-KQISRLECLDLSYCNSLQS 236
NL N + LP + +++ L LDLSY N LQS
Sbjct: 139 NLAHNQLQSLPKGVFDKLTNLTELDLSY-NQLQS 171
>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 = 33.5 bits (75), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 35/124 (28%), Positives = 59/124 (47%), Gaps = 7/124 (5%)
Query: 113 IDFSYCVNLTEFPQISGNIIDLILTETAIEEVPSSTECLTNLQYL-FLCSCKKLKRVSTS 171
+ F C + ++F IS +DL + + + S+ L L++L F S K +
Sbjct: 383 LSFKGCCSQSDFGTISLKYLDL--SFNGVITMSSNFLGLEQLEHLDFQHSNLKQMSEFSV 440
Query: 172 ICKFKSLVWLSLNNDLT--AIPQEIGCLSSLECLNLGGNNFEG--LPASIKQISRLECLD 227
++L++L +++ T A LSSLE L + GN+F+ LP ++ L LD
Sbjct: 441 FLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFLD 500
Query: 228 LSYC 231
LS C
Sbjct: 501 LSQC 504
>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type
Iii Effector Xcv3220 (Xopl)
Length = 328
Score = 33.1 bits (74), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 27/101 (26%), Positives = 41/101 (40%), Gaps = 5/101 (4%)
Query: 40 LKFINLSHSQCHIKIPDPSETPNLERIDILNCTNPACVLSSITNFNHLSMLCFRHCKNLR 99
LK + + +S P P LE +D+ CT L L + C NL
Sbjct: 208 LKSLKIRNSPLSALGPAIHHLPKLEELDLRGCTALRNYPPIFGGRAPLKRLILKDCSNLL 267
Query: 100 HFPNNLHFVCPI-IIDFSYCVNLTEFP----QISGNIIDLI 135
P ++H + + +D CVNL+ P Q+ N I L+
Sbjct: 268 TLPLDIHRLTQLEKLDLRGCVNLSRLPSLIAQLPANCIILV 308
Score = 31.2 bits (69), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 22/48 (45%)
Query: 187 LTAIPQEIGCLSSLECLNLGGNNFEGLPASIKQISRLECLDLSYCNSL 234
L +P + LE L L N LPASI ++RL L + C L
Sbjct: 116 LXELPDTXQQFAGLETLTLARNPLRALPASIASLNRLRELSIRACPEL 163
>pdb|2Z63|A Chain A, Crystal Structure Of The Tv8 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
Length = 570
Score = 31.6 bits (70), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 34/124 (27%), Positives = 58/124 (46%), Gaps = 7/124 (5%)
Query: 113 IDFSYCVNLTEFPQISGNIIDLILTETAIEEVPSSTECLTNLQYL-FLCSCKKLKRVSTS 171
+ F C + ++F S +DL + + + S+ L L++L F S K +
Sbjct: 359 LSFKGCCSQSDFGTTSLKYLDL--SFNGVITMSSNFLGLEQLEHLDFQHSNLKQMSEFSV 416
Query: 172 ICKFKSLVWLSLNNDLT--AIPQEIGCLSSLECLNLGGNNFEG--LPASIKQISRLECLD 227
++L++L +++ T A LSSLE L + GN+F+ LP ++ L LD
Sbjct: 417 FLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFLD 476
Query: 228 LSYC 231
LS C
Sbjct: 477 LSQC 480
>pdb|2Z66|A Chain A, Crystal Structure Of The Vt3 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
pdb|2Z66|B Chain B, Crystal Structure Of The Vt3 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
pdb|2Z66|C Chain C, Crystal Structure Of The Vt3 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
pdb|2Z66|D Chain D, Crystal Structure Of The Vt3 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
Length = 306
Score = 30.4 bits (67), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 34/125 (27%), Positives = 59/125 (47%), Gaps = 9/125 (7%)
Query: 113 IDFSYCVNLTEFPQISGNIIDLILTETAIEEVPSSTECLTNLQYLFLCSCKKLKRVS--T 170
+ F C + ++F S +DL + + S+ L L++L LK++S +
Sbjct: 64 LSFKGCCSQSDFGTTSLKYLDLSFN--GVITMSSNFLGLEQLEHLDF-QHSNLKQMSEFS 120
Query: 171 SICKFKSLVWLSLNNDLT--AIPQEIGCLSSLECLNLGGNNFEG--LPASIKQISRLECL 226
++L++L +++ T A LSSLE L + GN+F+ LP ++ L L
Sbjct: 121 VFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFL 180
Query: 227 DLSYC 231
DLS C
Sbjct: 181 DLSQC 185
>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 = 29.6 bits (65), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 28/81 (34%), Positives = 40/81 (49%), Gaps = 6/81 (7%)
Query: 185 NDLTAIPQEI-GCLSSLECLNLGGNNFEGLPASI-KQISRLECLDLSYCNSLQS---XXX 239
N L ++P + L+SL L LGGN + LP + +++ L L+LS N LQS
Sbjct: 38 NSLKSLPNGVFDELTSLTQLYLGGNKLQSLPNGVFNKLTSLTYLNLS-TNQLQSLPNGVF 96
Query: 240 XXXXXXXXXATNCKRLQSLPE 260
A N +LQSLP+
Sbjct: 97 DKLTQLKELALNTNQLQSLPD 117
>pdb|3OJA|A Chain A, Crystal Structure Of Lrim1APL1C COMPLEX
Length = 487
Score = 29.3 bits (64), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 33/101 (32%), Positives = 47/101 (46%), Gaps = 22/101 (21%)
Query: 132 IDLILTE---TAIEEVPSSTECLT--NLQYLFLCSCK------KLKRVSTSICK------ 174
+DL L E E+ +S++ L NLQY F+ K KLK + S K
Sbjct: 149 LDLKLNEIDTVNFAELAASSDTLEHLNLQYNFIYDVKGQVVFAKLKTLDLSSNKLAFMGP 208
Query: 175 -FKS---LVWLSL-NNDLTAIPQEIGCLSSLECLNLGGNNF 210
F+S + W+SL NN L I + + +LE +L GN F
Sbjct: 209 EFQSAAGVTWISLRNNKLVLIEKALRFSQNLEHFDLRGNGF 249
>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 = 28.9 bits (63), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 35/117 (29%), Positives = 58/117 (49%), Gaps = 11/117 (9%)
Query: 127 ISGNIIDLILTETAIEEVPSST-ECLTNLQYLFLCSCKKLKRVSTSICKFKSLVWLS--- 182
I + L L T + + +T LT L +L L +L+ +S + F L L
Sbjct: 33 IPADTEKLDLQSTGLATLSDATFRGLTKLTWLNL-DYNQLQTLSAGV--FDDLTELGTLG 89
Query: 183 -LNNDLTAIPQEI-GCLSSLECLNLGGNNFEGLPASI-KQISRLECLDLSYCNSLQS 236
NN L ++P + L+ L+ L LGGN + LP+ + ++++L+ L L+ N LQS
Sbjct: 90 LANNQLASLPLGVFDHLTQLDKLYLGGNQLKSLPSGVFDRLTKLKELRLN-TNQLQS 145
>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 = 8.3, Method: Compositional matrix adjust.
Identities = 35/117 (29%), Positives = 58/117 (49%), Gaps = 11/117 (9%)
Query: 127 ISGNIIDLILTETAIEEVPSST-ECLTNLQYLFLCSCKKLKRVSTSICKFKSLVWLS--- 182
I + L L T + + +T LT L +L L +L+ +S + F L L
Sbjct: 33 IPADTEKLDLQSTGLATLSDATFRGLTKLTWLNL-DYNQLQTLSAGV--FDDLTELGTLG 89
Query: 183 -LNNDLTAIPQEI-GCLSSLECLNLGGNNFEGLPASI-KQISRLECLDLSYCNSLQS 236
NN L ++P + L+ L+ L LGGN + LP+ + ++++L+ L L+ N LQS
Sbjct: 90 LANNQLASLPLGVFDHLTQLDKLYLGGNQLKSLPSGVFDRLTKLKELRLN-TNQLQS 145
>pdb|3G06|A Chain A, The Salmonella Virulence Effector Ssph2 Functions As A
Novel E3 Ligase
Length = 622
Score = 28.5 bits (62), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 41/166 (24%), Positives = 68/166 (40%), Gaps = 15/166 (9%)
Query: 104 NLHFVCPIIIDFSYCVN-LTEFPQISGNIIDLILTETAIEEVPSSTECLTNLQYLFLCSC 162
+L + P +++ S N LT P + + L + + +P L L +
Sbjct: 95 SLPVLPPGLLELSIFSNPLTHLPALPSGLCKLWIFGNQLTSLPVLPPGLQELS-VSDNQL 153
Query: 163 KKLKRVSTSICKFKSLVWLSLNNDLTAIPQEIGCLSSLECLNLGGNNFEGLPASIKQISR 222
L + + +CK W + NN LT++P S L+ L++ N LP ++ +
Sbjct: 154 ASLPALPSELCKL----W-AYNNQLTSLPM---LPSGLQELSVSDNQLASLPTLPSELYK 205
Query: 223 LECLDLSYCNSLQSXXXXXXXXXXXXATNCKRLQSLPEIPSCLEEL 268
L +Y N L S + RL SLP +PS L+EL
Sbjct: 206 L----WAYNNRLTSLPALPSGLKELIVSG-NRLTSLPVLPSELKEL 246
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
0.324 0.138 0.435
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,642,524
Number of Sequences: 62578
Number of extensions: 568943
Number of successful extensions: 1414
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 24
Number of HSP's that attempted gapping in prelim test: 1377
Number of HSP's gapped (non-prelim): 62
length of query: 517
length of database: 14,973,337
effective HSP length: 103
effective length of query: 414
effective length of database: 8,527,803
effective search space: 3530510442
effective search space used: 3530510442
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (25.4 bits)