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= 008612
(559 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2FQ3|A Chain A, Structure And Function Of The Swirm Domain, A Conserved
Protein Module Found In Chromatin Regulatory Complexes
Length = 104
Score = 83.2 bits (204), Expect = 3e-16, Method: Composition-based stats.
Identities = 34/85 (40%), Positives = 53/85 (62%)
Query: 21 SHSSWFRWDDIHETERTALKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVR 80
S+S WF + IH E +L EFF S+TP++Y YR+FM+N YR P+ + T R
Sbjct: 15 SYSKWFNLEKIHSIEVQSLPEFFTNRIPSKTPEVYMRYRNFMVNSYRLNPNEYFSVTTAR 74
Query: 81 KSLVGDVSLLHKVFRLLDEWGLINF 105
+++ GD + L ++ + L +WGLIN+
Sbjct: 75 RNVSGDAAALFRLHKFLTKWGLINY 99
>pdb|2DCE|A Chain A, Solution Structure Of The Swirm Domain Of Human Kiaa1915
Protein
Length = 111
Score = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 46/79 (58%), Gaps = 3/79 (3%)
Query: 31 IHETERTALKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSL--VGDVS 88
I E E+ A+ EFF+G ++TP+ Y + R+++++++ + L T VR L GDV+
Sbjct: 27 IQEEEKQAIPEFFEGRQ-AKTPERYLKIRNYILDQWEICKPKYLNKTSVRPGLKNCGDVN 85
Query: 89 LLHKVFRLLDEWGLINFGA 107
+ ++ L+ G INFG
Sbjct: 86 CIGRIHTYLELIGAINFGC 104
>pdb|2XAF|A Chain A, Crystal Structure Of Lsd1-Corest In Complex With
Para-Bromo- (+)-Cis-2-Phenylcyclopropyl-1-Amine
pdb|2XAG|A Chain A, Crystal Structure Of Lsd1-Corest In Complex With
Para-Bromo- (-)-Trans-2-Phenylcyclopropyl-1-Amine
pdb|2XAH|A Chain A, Crystal Structure Of Lsd1-Corest In Complex With (+)-
Trans-2-Phenylcyclopropyl-1-Amine
pdb|2XAJ|A Chain A, Crystal Structure Of Lsd1-Corest In Complex With
(-)-Trans- 2-Phenylcyclopropyl-1-Amine
pdb|2XAQ|A Chain A, Crystal Structure Of Lsd1-Corest In Complex With A
Tranylcypromine Derivative (Mc2584, 13b)
pdb|2XAS|A Chain A, Crystal Structure Of Lsd1-Corest In Complex With A
Tranylcypromine Derivative (Mc2580, 14e)
Length = 852
Score = 34.7 bits (78), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 4/65 (6%)
Query: 46 SSISRTPKIYKEYRDFMINKYREEPSRRLTF----TQVRKSLVGDVSLLHKVFRLLDEWG 101
S +T K++ R+ + + + P +LTF Q+ D L+H+V L+ G
Sbjct: 201 SGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHG 260
Query: 102 LINFG 106
LINFG
Sbjct: 261 LINFG 265
>pdb|2V1D|A Chain A, Structural Basis Of Lsd1-Corest Selectivity In Histone H3
Recognition
pdb|2Y48|A Chain A, Crystal Structure Of Lsd1-Corest In Complex With A N-
Terminal Snail Peptide
Length = 730
Score = 34.3 bits (77), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 4/65 (6%)
Query: 46 SSISRTPKIYKEYRDFMINKYREEPSRRLTF----TQVRKSLVGDVSLLHKVFRLLDEWG 101
S +T K++ R+ + + + P +LTF Q+ D L+H+V L+ G
Sbjct: 79 SGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHG 138
Query: 102 LINFG 106
LINFG
Sbjct: 139 LINFG 143
>pdb|2X0L|A Chain A, Crystal Structure Of A Neuro-Specific Splicing Variant Of
Human Histone Lysine Demethylase Lsd1
Length = 734
Score = 34.3 bits (77), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 4/65 (6%)
Query: 46 SSISRTPKIYKEYRDFMINKYREEPSRRLTF----TQVRKSLVGDVSLLHKVFRLLDEWG 101
S +T K++ R+ + + + P +LTF Q+ D L+H+V L+ G
Sbjct: 79 SGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHG 138
Query: 102 LINFG 106
LINFG
Sbjct: 139 LINFG 143
>pdb|2HKO|A Chain A, Crystal Structure Of Lsd1
Length = 664
Score = 34.3 bits (77), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 4/65 (6%)
Query: 46 SSISRTPKIYKEYRDFMINKYREEPSRRLTF----TQVRKSLVGDVSLLHKVFRLLDEWG 101
S +T K++ R+ + + + P +LTF Q+ D L+H+V L+ G
Sbjct: 30 SGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHG 89
Query: 102 LINFG 106
LINFG
Sbjct: 90 LINFG 94
>pdb|2EJR|A Chain A, Lsd1-Tranylcypromine Complex
pdb|2Z3Y|A Chain A, Crystal Structure Of Lysine-Specific Demethylase1
pdb|2Z5U|A Chain A, Crystal Structure Of Lysine-Specific Histone Demethylase 1
pdb|3ABT|A Chain A, Crystal Structure Of Lsd1 In Complex With Trans-2-
Pentafluorophenylcyclopropylamine
pdb|3ABU|A Chain A, Crystal Structure Of Lsd1 In Complex With A 2-Pcpa
Derivative, S1201
Length = 662
Score = 34.3 bits (77), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 4/65 (6%)
Query: 46 SSISRTPKIYKEYRDFMINKYREEPSRRLTF----TQVRKSLVGDVSLLHKVFRLLDEWG 101
S +T K++ R+ + + + P +LTF Q+ D L+H+V L+ G
Sbjct: 30 SGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHG 89
Query: 102 LINFG 106
LINFG
Sbjct: 90 LINFG 94
>pdb|2DW4|A Chain A, Crystal Structure Of Human Lsd1 At 2.3 A Resolution
Length = 660
Score = 33.9 bits (76), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 4/65 (6%)
Query: 46 SSISRTPKIYKEYRDFMINKYREEPSRRLTF----TQVRKSLVGDVSLLHKVFRLLDEWG 101
S +T K++ R+ + + + P +LTF Q+ D L+H+V L+ G
Sbjct: 30 SGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHG 89
Query: 102 LINFG 106
LINFG
Sbjct: 90 LINFG 94
>pdb|2IW5|A Chain A, Structural Basis For Corest-dependent Demethylation Of
Nucleosomes By The Human Lsd1 Histone Demethylase
pdb|2UXN|A Chain A, Structural Basis Of Histone Demethylation By Lsd1 Revealed
By Suicide Inactivation
pdb|2UXX|A Chain A, Human Lsd1 Histone Demethylase-Corest In Complex With An
Fad-Tranylcypromine Adduct
Length = 666
Score = 33.9 bits (76), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 4/65 (6%)
Query: 46 SSISRTPKIYKEYRDFMINKYREEPSRRLTF----TQVRKSLVGDVSLLHKVFRLLDEWG 101
S +T K++ R+ + + + P +LTF Q+ D L+H+V L+ G
Sbjct: 31 SGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHG 90
Query: 102 LINFG 106
LINFG
Sbjct: 91 LINFG 95
>pdb|2H94|A Chain A, Crystal Structure And Mechanism Of Human Lysine-Specific
Demethylase-1
Length = 664
Score = 33.9 bits (76), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 4/65 (6%)
Query: 46 SSISRTPKIYKEYRDFMINKYREEPSRRLTF----TQVRKSLVGDVSLLHKVFRLLDEWG 101
S +T K++ R+ + + + P +LTF Q+ D L+H+V L+ G
Sbjct: 30 SGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHG 89
Query: 102 LINFG 106
LINFG
Sbjct: 90 LINFG 94
>pdb|2L3D|A Chain A, The Solution Structure Of The Short Form Swirm Domain Of
Lsd1
Length = 102
Score = 33.5 bits (75), Expect = 0.30, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 4/65 (6%)
Query: 46 SSISRTPKIYKEYRDFMINKYREEPSRRLTF----TQVRKSLVGDVSLLHKVFRLLDEWG 101
S +T K++ R+ + + + P +LTF Q+ D L+H+V L+ G
Sbjct: 30 SGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHG 89
Query: 102 LINFG 106
LINFG
Sbjct: 90 LINFG 94
>pdb|2COM|A Chain A, The Solution Structure Of The Swirm Domain Of Human Lsd1
Length = 124
Score = 33.1 bits (74), Expect = 0.38, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 4/65 (6%)
Query: 46 SSISRTPKIYKEYRDFMINKYREEPSRRLTF----TQVRKSLVGDVSLLHKVFRLLDEWG 101
S +T K++ R+ + + + P +LTF Q+ D L+H+V L+ G
Sbjct: 40 SGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHG 99
Query: 102 LINFG 106
LINFG
Sbjct: 100 LINFG 104
>pdb|1QB7|A Chain A, Crystal Structures Of Adenine Phosphoribosyltransferase
From Leishmania Donovani.
pdb|1QB8|A Chain A, Crystal Structures Of Adenine Phosphoribosyltransferase
From Leishmania Donovani
pdb|1QCC|A Chain A, Crystal Structures Of Adenine Phosphoribosyltransferase
From Leishmania Donovani
pdb|1QCD|A Chain A, Crystal Structures Of Adenine Phosphoribosyltransferase
From Leishmania Donovani
Length = 236
Score = 32.7 bits (73), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 26 FRWDDIHETERTALKEFFDGSSISRTPKIYKEYRDFMINKYR 67
+RW + R + F D SSI+ +P+ K RDF++ +YR
Sbjct: 26 YRWYSPVFSPRN-VPRFADVSSITESPETLKAIRDFLVQRYR 66
>pdb|1MZV|A Chain A, Crystal Structure Of Adenine Phosphoribosyltransferase
(Aprt) From Leishmania Tarentolae
Length = 235
Score = 32.7 bits (73), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 26 FRWDDIHETERTALKEFFDGSSISRTPKIYKEYRDFMINKYR 67
+RW + R + F D SSI+ +P+ K RDF++ +YR
Sbjct: 27 YRWYSPIFSPRN-VPRFADVSSITESPETLKAIRDFLVERYR 67
>pdb|2CQR|A Chain A, Solution Structure Of Rsgi Ruh-043, A Myb Dna-Binding
Domain In Human Cdna
Length = 73
Score = 29.6 bits (65), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 11/21 (52%), Positives = 17/21 (80%)
Query: 272 DNWELVAQNVPTKSKLDCISK 292
D W+ +A+ VP+KSK DCI++
Sbjct: 42 DCWDKIARCVPSKSKEDCIAR 62
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
0.313 0.131 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,558,591
Number of Sequences: 62578
Number of extensions: 602153
Number of successful extensions: 1007
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 1002
Number of HSP's gapped (non-prelim): 16
length of query: 559
length of database: 14,973,337
effective HSP length: 104
effective length of query: 455
effective length of database: 8,465,225
effective search space: 3851677375
effective search space used: 3851677375
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 54 (25.4 bits)