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= 041391
(704 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 = 39.7 bits (91), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 27/65 (41%), Positives = 36/65 (55%), Gaps = 2/65 (3%)
Query: 428 IREIPSSIANLSNLRVLDLRCCYYLTKLPKGLDSLKKLTYLDISECYLIEYMPKELSSLS 487
+ E+P+ I NLSNLRVLDL LT LP L S +L Y + ++ +P E +L
Sbjct: 259 LTELPAEIKNLSNLRVLDLSHN-RLTSLPAELGSCFQLKYFYFFDN-MVTTLPWEFGNLC 316
Query: 488 ELQVL 492
LQ L
Sbjct: 317 NLQFL 321
>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 = 39.3 bits (90), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 35/69 (50%), Gaps = 4/69 (5%)
Query: 455 LPKGLDSLKKLTYLDISECYLIEYMPKELSSLSELQVL----KGFLVTDAKPNDKICTLE 510
LP L+ LT+LD+S+C L + P +SLS LQVL F D P + +L+
Sbjct: 462 LPDIFTELRNLTFLDLSQCQLEQLSPTAFNSLSSLQVLNMSHNNFFSLDTFPYKCLNSLQ 521
Query: 511 DLGNSLKEL 519
L SL +
Sbjct: 522 VLDYSLNHI 530
>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 = 39.3 bits (90), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 35/69 (50%), Gaps = 4/69 (5%)
Query: 455 LPKGLDSLKKLTYLDISECYLIEYMPKELSSLSELQVL----KGFLVTDAKPNDKICTLE 510
LP L+ LT+LD+S+C L + P +SLS LQVL F D P + +L+
Sbjct: 486 LPDIFTELRNLTFLDLSQCQLEQLSPTAFNSLSSLQVLNMSHNNFFSLDTFPYKCLNSLQ 545
Query: 511 DLGNSLKEL 519
L SL +
Sbjct: 546 VLDYSLNHI 554
>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 = 38.9 bits (89), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 35/69 (50%), Gaps = 4/69 (5%)
Query: 455 LPKGLDSLKKLTYLDISECYLIEYMPKELSSLSELQVL----KGFLVTDAKPNDKICTLE 510
LP L+ LT+LD+S+C L + P +SLS LQVL F D P + +L+
Sbjct: 167 LPDIFTELRNLTFLDLSQCQLEQLSPTAFNSLSSLQVLNMSHNNFFSLDTFPYKCLNSLQ 226
Query: 511 DLGNSLKEL 519
L SL +
Sbjct: 227 VLDYSLNHI 235
>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type
Iii Effector Xcv3220 (Xopl)
Length = 328
Score = 38.5 bits (88), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 29/82 (35%), Positives = 41/82 (50%), Gaps = 5/82 (6%)
Query: 411 LKNMSALRLLSLQGVYGIREIPSSIANLSNLRVLDLRCCYYLTKLPKGLDSLKKLTYLDI 470
L N+ +LRL GIR +P+SIANL NL+ L +R L+ L + L KL LD+
Sbjct: 182 LVNLQSLRL----EWTGIRSLPASIANLQNLKSLKIRNS-PLSALGPAIHHLPKLEELDL 236
Query: 471 SECYLIEYMPKELSSLSELQVL 492
C + P + L+ L
Sbjct: 237 RGCTALRNYPPIFGGRAPLKRL 258
Score = 37.0 bits (84), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 41/75 (54%), Gaps = 10/75 (13%)
Query: 428 IREIPSSIANLSNLRVLDLRCCYYLTKLPKGLDS---------LKKLTYLDISECYLIEY 478
+R +P+SIA+L+ LR L +R C LT+LP+ L S L L L + E I
Sbjct: 139 LRALPASIASLNRLRELSIRACPELTELPEPLASTDASGEHQGLVNLQSLRL-EWTGIRS 197
Query: 479 MPKELSSLSELQVLK 493
+P +++L L+ LK
Sbjct: 198 LPASIANLQNLKSLK 212
>pdb|2Z63|A Chain A, Crystal Structure Of The Tv8 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
Length = 570
Score = 37.0 bits (84), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 24/38 (63%)
Query: 455 LPKGLDSLKKLTYLDISECYLIEYMPKELSSLSELQVL 492
LP L+ LT+LD+S+C L + P +SLS LQVL
Sbjct: 462 LPDIFTELRNLTFLDLSQCQLEQLSPTAFNSLSSLQVL 499
>pdb|3E6J|A Chain A, Crystal Structure Of Variable Lymphocyte Receptor (Vlr)
Rbc36 In Complex With H-Trisaccharide
Length = 229
Score = 32.7 bits (73), Expect = 0.74, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 38/61 (62%), Gaps = 3/61 (4%)
Query: 413 NMSALRLLSLQGVYGIREIPSSIAN-LSNLRVLDLRCCYYLTKLPKGLDSLKKLTYLDIS 471
+++ L +L L G + +PS++ + L +L+ L CC LT+LP+G++ L LT+L +
Sbjct: 86 SLTQLTVLDL-GTNQLTVLPSAVFDRLVHLKEL-FMCCNKLTELPRGIERLTHLTHLALD 143
Query: 472 E 472
+
Sbjct: 144 Q 144
>pdb|2X0L|B Chain B, Crystal Structure Of A Neuro-Specific Splicing Variant Of
Human Histone Lysine Demethylase Lsd1
Length = 133
Score = 32.0 bits (71), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 30/128 (23%), Positives = 57/128 (44%), Gaps = 20/128 (15%)
Query: 103 EVNAATNSKSNNDLKQKDN---LVKKYLDKIKKDSTENREKLGELIKDHIRRFEGILEKL 159
E +A + + L+Q D VK+ + IK+ ++ +EKL I+ + R +++K
Sbjct: 15 EAVSANATAATTVLRQLDMELVSVKRQIQNIKQTNSALKEKLDGGIEPY--RLPEVIQKC 72
Query: 160 SSGSIQSEQCLDESREEVRNFEDKVPLVNKYS---STESDGLKQSEIVELMEMFINFREK 216
++ EQ L V + KY SD + +V++ F+N+R +
Sbjct: 73 NARWTTEEQLL------------AVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNYRRR 120
Query: 217 FGFDEFME 224
F DE ++
Sbjct: 121 FNIDEVLQ 128
>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 = 1.4, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 37/73 (50%)
Query: 409 KELKNMSALRLLSLQGVYGIREIPSSIANLSNLRVLDLRCCYYLTKLPKGLDSLKKLTYL 468
KE+ +M L +L+L IP + +L L +LDL ++P+ + +L LT +
Sbjct: 647 KEIGSMPYLFILNLGHNDISGSIPDEVGDLRGLNILDLSSNKLDGRIPQAMSALTMLTEI 706
Query: 469 DISECYLIEYMPK 481
D+S L +P+
Sbjct: 707 DLSNNNLSGPIPE 719
>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 = 31.6 bits (70), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 37/73 (50%)
Query: 409 KELKNMSALRLLSLQGVYGIREIPSSIANLSNLRVLDLRCCYYLTKLPKGLDSLKKLTYL 468
KE+ +M L +L+L IP + +L L +LDL ++P+ + +L LT +
Sbjct: 650 KEIGSMPYLFILNLGHNDISGSIPDEVGDLRGLNILDLSSNKLDGRIPQAMSALTMLTEI 709
Query: 469 DISECYLIEYMPK 481
D+S L +P+
Sbjct: 710 DLSNNNLSGPIPE 722
>pdb|2V1D|B Chain B, Structural Basis Of Lsd1-Corest Selectivity In Histone H3
Recognition
pdb|2Y48|B Chain B, Crystal Structure Of Lsd1-Corest In Complex With A N-
Terminal Snail Peptide
Length = 178
Score = 31.2 bits (69), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 25/105 (23%), Positives = 48/105 (45%), Gaps = 17/105 (16%)
Query: 123 VKKYLDKIKKDSTENREKLGELIKDHIRRFEGILEKLSSGSIQSEQCLDESREEVRNFED 182
VK+ + IK+ ++ +EKL I+ + R +++K ++ EQ L
Sbjct: 41 VKRQIQNIKQTNSALKEKLDGGIEPY--RLPEVIQKCNARWTTEEQLL------------ 86
Query: 183 KVPLVNKYS---STESDGLKQSEIVELMEMFINFREKFGFDEFME 224
V + KY SD + +V++ F+N+R +F DE ++
Sbjct: 87 AVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNYRRRFNIDEVLQ 131
>pdb|2O6Q|A Chain A, Structural Diversity Of The Hagfish Variable Lymphocyte
Receptors A29
Length = 270
Score = 31.2 bits (69), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 43/135 (31%), Positives = 65/135 (48%), Gaps = 26/135 (19%)
Query: 367 SEQFPDFQSKWFSNLKKVKVLHLGRWKNSAKHFVEVQGSKFLKELKNMSAL-----RLLS 421
S + SK F L K+++L+L K ++ + KELKN+ L +L +
Sbjct: 46 SNKLSSLPSKAFHRLTKLRLLYLNDNK------LQTLPAGIFKELKNLETLWVTDNKLQA 99
Query: 422 LQ-GVYGIREIPSSIANLSNLRVLDLRCCYYLTKLPKGLDSLKKLTYLDISECYLIEYMP 480
L GV+ + NL+ LR LD L P+ DSL KLTYL + L + +P
Sbjct: 100 LPIGVF------DQLVNLAELR-LDRNQLKSLP--PRVFDSLTKLTYLSLGYNEL-QSLP 149
Query: 481 K----ELSSLSELQV 491
K +L+SL EL++
Sbjct: 150 KGVFDKLTSLKELRL 164
>pdb|2XAF|B Chain B, Crystal Structure Of Lsd1-Corest In Complex With
Para-Bromo- (+)-Cis-2-Phenylcyclopropyl-1-Amine
pdb|2XAG|B Chain B, Crystal Structure Of Lsd1-Corest In Complex With
Para-Bromo- (-)-Trans-2-Phenylcyclopropyl-1-Amine
pdb|2XAH|B Chain B, Crystal Structure Of Lsd1-Corest In Complex With (+)-
Trans-2-Phenylcyclopropyl-1-Amine
pdb|2XAJ|B Chain B, Crystal Structure Of Lsd1-Corest In Complex With
(-)-Trans- 2-Phenylcyclopropyl-1-Amine
pdb|2XAQ|B Chain B, Crystal Structure Of Lsd1-Corest In Complex With A
Tranylcypromine Derivative (Mc2584, 13b)
pdb|2XAS|B Chain B, Crystal Structure Of Lsd1-Corest In Complex With A
Tranylcypromine Derivative (Mc2580, 14e)
Length = 482
Score = 31.2 bits (69), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 25/105 (23%), Positives = 48/105 (45%), Gaps = 17/105 (16%)
Query: 123 VKKYLDKIKKDSTENREKLGELIKDHIRRFEGILEKLSSGSIQSEQCLDESREEVRNFED 182
VK+ + IK+ ++ +EKL I+ + R +++K ++ EQ L
Sbjct: 345 VKRQIQNIKQTNSALKEKLDGGIEPY--RLPEVIQKCNARWTTEEQLL------------ 390
Query: 183 KVPLVNKYS---STESDGLKQSEIVELMEMFINFREKFGFDEFME 224
V + KY SD + +V++ F+N+R +F DE ++
Sbjct: 391 AVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNYRRRFNIDEVLQ 435
>pdb|2IW5|B Chain B, Structural Basis For Corest-dependent Demethylation Of
Nucleosomes By The Human Lsd1 Histone Demethylase
pdb|2UXN|B Chain B, Structural Basis Of Histone Demethylation By Lsd1 Revealed
By Suicide Inactivation
pdb|2UXX|B Chain B, Human Lsd1 Histone Demethylase-Corest In Complex With An
Fad-Tranylcypromine Adduct
Length = 235
Score = 30.4 bits (67), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 25/105 (23%), Positives = 48/105 (45%), Gaps = 17/105 (16%)
Query: 123 VKKYLDKIKKDSTENREKLGELIKDHIRRFEGILEKLSSGSIQSEQCLDESREEVRNFED 182
VK+ + IK+ ++ +EKL I+ + R +++K ++ EQ L
Sbjct: 98 VKRQIQNIKQTNSALKEKLDGGIEPY--RLPEVIQKCNARWTTEEQLL------------ 143
Query: 183 KVPLVNKYS---STESDGLKQSEIVELMEMFINFREKFGFDEFME 224
V + KY SD + +V++ F+N+R +F DE ++
Sbjct: 144 AVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNYRRRFNIDEVLQ 188
>pdb|1H6U|A Chain A, Internalin H: Crystal Structure Of Fused N-Terminal
Domains
Length = 308
Score = 29.6 bits (65), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 28/87 (32%), Positives = 45/87 (51%), Gaps = 8/87 (9%)
Query: 408 LKELKNMSALRLLSLQGVYGIREIPSSIANLSNLRVLDLRCCYYLTKLP-KGLDSLKKLT 466
L LKN++ + L L G ++ + S+IA L +++ LDL P GL +L+ L
Sbjct: 78 LAPLKNLTKITELELSG-NPLKNV-SAIAGLQSIKTLDLTSTQITDVTPLAGLSNLQVL- 134
Query: 467 YLDISECYLIEYMPKELSSLSELQVLK 493
YLD+++ I L+ L+ LQ L
Sbjct: 135 YLDLNQITNIS----PLAGLTNLQYLS 157
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
0.316 0.135 0.390
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,045,816
Number of Sequences: 62578
Number of extensions: 776670
Number of successful extensions: 2597
Number of sequences better than 100.0: 35
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 26
Number of HSP's that attempted gapping in prelim test: 2559
Number of HSP's gapped (non-prelim): 63
length of query: 704
length of database: 14,973,337
effective HSP length: 106
effective length of query: 598
effective length of database: 8,340,069
effective search space: 4987361262
effective search space used: 4987361262
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)