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= 014788
(418 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 = 92.0 bits (227), Expect = 5e-19, Method: Composition-based stats.
Identities = 41/85 (48%), Positives = 54/85 (63%)
Query: 44 SYSRWFSFDSISECEVKFLPEFFDSRSPSKNPRVYRYYRDSIVKHYRENPSRKITFTDVR 103
SYS+WF+ + I EV+ LPEFF +R PSK P VY YR+ +V YR NP+ + T R
Sbjct: 15 SYSKWFNLEKIHSIEVQSLPEFFTNRIPSKTPEVYMRYRNFMVNSYRLNPNEYFSVTTAR 74
Query: 104 RTLVGDVGSIRRVFDFLETWGLINY 128
R + GD ++ R+ FL WGLINY
Sbjct: 75 RNVSGDAAALFRLHKFLTKWGLINY 99
>pdb|2YUS|A Chain A, Solution Structure Of The Sant Domain Of Human SwiSNF-
Related Matrix-Associated Actin-Dependent Regulator Of
Chromatin Subfamily C Member 1
Length = 79
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 27/59 (45%), Positives = 42/59 (71%), Gaps = 1/59 (1%)
Query: 212 ARSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIKLPFGQEFICKESDS 270
A +WTE+ETL LLEA+ + DDW KV++HV +++ +CI HF++LP ++ + SDS
Sbjct: 17 AGREWTEQETLLLLEALEMYKDDWNKVSEHVGSRTQDECILHFLRLPIEDPYL-ENSDS 74
>pdb|2DCE|A Chain A, Solution Structure Of The Swirm Domain Of Human Kiaa1915
Protein
Length = 111
Score = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 27/77 (35%), Positives = 39/77 (50%), Gaps = 3/77 (3%)
Query: 54 ISECEVKFLPEFFDSRSPSKNPRVYRYYRDSIVKHYRENPSRKITFTDVRRTL--VGDVG 111
I E E + +PEFF+ R +K P Y R+ I+ + + + T VR L GDV
Sbjct: 27 IQEEEKQAIPEFFEGRQ-AKTPERYLKIRNYILDQWEICKPKYLNKTSVRPGLKNCGDVN 85
Query: 112 SIRRVFDFLETWGLINY 128
I R+ +LE G IN+
Sbjct: 86 CIGRIHTYLELIGAINF 102
>pdb|1X41|A Chain A, Solution Structure Of The Myb-Like Dna Binding Domain Of
Human Transcriptional Adaptor 2-Like, Isoform B
Length = 60
Score = 38.1 bits (87), Expect = 0.009, Method: Composition-based stats.
Identities = 16/42 (38%), Positives = 28/42 (66%), Gaps = 1/42 (2%)
Query: 216 WTEKETLQLLEAIMHFG-DDWRKVAQHVSGKSEKDCITHFIK 256
WT +E + LLEA+M G +W+ VA + K++++C H++K
Sbjct: 11 WTAQEEMALLEAVMDCGFGNWQDVANQMCTKTKEECEKHYMK 52
>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 = 35.4 bits (80), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 20/89 (22%), Positives = 40/89 (44%), Gaps = 6/89 (6%)
Query: 44 SYSRWFSFDSISECEVKFLPEFFDSRSPSKNPRVYRYYRDSIVKHYRENPSRKITFTDVR 103
++ D ++ E P+ P + +V+ + R+ ++ + +NP ++TF
Sbjct: 178 AFQSRLPHDRMTSQEAACFPDIISG--PQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATL 235
Query: 104 RTLVGDVGS----IRRVFDFLETWGLINY 128
+ L S + RV +LE GLIN+
Sbjct: 236 QQLEAPYNSDTVLVHRVHSYLERHGLINF 264
>pdb|2X0L|A Chain A, Crystal Structure Of A Neuro-Specific Splicing Variant Of
Human Histone Lysine Demethylase Lsd1
Length = 734
Score = 35.4 bits (80), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 38/81 (46%), Gaps = 6/81 (7%)
Query: 52 DSISECEVKFLPEFFDSRSPSKNPRVYRYYRDSIVKHYRENPSRKITFTDVRRTLVGDVG 111
D ++ E P+ P + +V+ + R+ ++ + +NP ++TF + L
Sbjct: 64 DRMTSQEAACFPDIISG--PQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYN 121
Query: 112 S----IRRVFDFLETWGLINY 128
S + RV +LE GLIN+
Sbjct: 122 SDTVLVHRVHSYLERHGLINF 142
>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 = 35.4 bits (80), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 38/81 (46%), Gaps = 6/81 (7%)
Query: 52 DSISECEVKFLPEFFDSRSPSKNPRVYRYYRDSIVKHYRENPSRKITFTDVRRTLVGDVG 111
D ++ E P+ P + +V+ + R+ ++ + +NP ++TF + L
Sbjct: 15 DRMTSQEAACFPDIISG--PQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYN 72
Query: 112 S----IRRVFDFLETWGLINY 128
S + RV +LE GLIN+
Sbjct: 73 SDTVLVHRVHSYLERHGLINF 93
>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 = 35.4 bits (80), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 38/81 (46%), Gaps = 6/81 (7%)
Query: 52 DSISECEVKFLPEFFDSRSPSKNPRVYRYYRDSIVKHYRENPSRKITFTDVRRTLVGDVG 111
D ++ E P+ P + +V+ + R+ ++ + +NP ++TF + L
Sbjct: 64 DRMTSQEAACFPDIISG--PQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYN 121
Query: 112 S----IRRVFDFLETWGLINY 128
S + RV +LE GLIN+
Sbjct: 122 SDTVLVHRVHSYLERHGLINF 142
>pdb|2HKO|A Chain A, Crystal Structure Of Lsd1
Length = 664
Score = 35.4 bits (80), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 38/81 (46%), Gaps = 6/81 (7%)
Query: 52 DSISECEVKFLPEFFDSRSPSKNPRVYRYYRDSIVKHYRENPSRKITFTDVRRTLVGDVG 111
D ++ E P+ P + +V+ + R+ ++ + +NP ++TF + L
Sbjct: 15 DRMTSQEAACFPDIISG--PQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYN 72
Query: 112 S----IRRVFDFLETWGLINY 128
S + RV +LE GLIN+
Sbjct: 73 SDTVLVHRVHSYLERHGLINF 93
>pdb|2DW4|A Chain A, Crystal Structure Of Human Lsd1 At 2.3 A Resolution
Length = 660
Score = 35.4 bits (80), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 38/81 (46%), Gaps = 6/81 (7%)
Query: 52 DSISECEVKFLPEFFDSRSPSKNPRVYRYYRDSIVKHYRENPSRKITFTDVRRTLVGDVG 111
D ++ E P+ P + +V+ + R+ ++ + +NP ++TF + L
Sbjct: 15 DRMTSQEAACFPDIISG--PQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYN 72
Query: 112 S----IRRVFDFLETWGLINY 128
S + RV +LE GLIN+
Sbjct: 73 SDTVLVHRVHSYLERHGLINF 93
>pdb|2H94|A Chain A, Crystal Structure And Mechanism Of Human Lysine-Specific
Demethylase-1
Length = 664
Score = 35.0 bits (79), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 38/81 (46%), Gaps = 6/81 (7%)
Query: 52 DSISECEVKFLPEFFDSRSPSKNPRVYRYYRDSIVKHYRENPSRKITFTDVRRTLVGDVG 111
D ++ E P+ P + +V+ + R+ ++ + +NP ++TF + L
Sbjct: 15 DRMTSQEAACFPDIISG--PQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYN 72
Query: 112 S----IRRVFDFLETWGLINY 128
S + RV +LE GLIN+
Sbjct: 73 SDTVLVHRVHSYLERHGLINF 93
>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 = 35.0 bits (79), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 38/81 (46%), Gaps = 6/81 (7%)
Query: 52 DSISECEVKFLPEFFDSRSPSKNPRVYRYYRDSIVKHYRENPSRKITFTDVRRTLVGDVG 111
D ++ E P+ P + +V+ + R+ ++ + +NP ++TF + L
Sbjct: 16 DRMTSQEAACFPDIISG--PQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYN 73
Query: 112 S----IRRVFDFLETWGLINY 128
S + RV +LE GLIN+
Sbjct: 74 SDTVLVHRVHSYLERHGLINF 94
>pdb|2L3D|A Chain A, The Solution Structure Of The Short Form Swirm Domain Of
Lsd1
Length = 102
Score = 34.7 bits (78), Expect = 0.10, Method: Composition-based stats.
Identities = 20/81 (24%), Positives = 38/81 (46%), Gaps = 6/81 (7%)
Query: 52 DSISECEVKFLPEFFDSRSPSKNPRVYRYYRDSIVKHYRENPSRKITFTDVRRTLVGDVG 111
D ++ E P+ P + +V+ + R+ ++ + +NP ++TF + L
Sbjct: 15 DRMTSQEAACFPDIISG--PQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYN 72
Query: 112 S----IRRVFDFLETWGLINY 128
S + RV +LE GLIN+
Sbjct: 73 SDTVLVHRVHSYLERHGLINF 93
>pdb|2COM|A Chain A, The Solution Structure Of The Swirm Domain Of Human Lsd1
Length = 124
Score = 34.3 bits (77), Expect = 0.12, Method: Composition-based stats.
Identities = 20/81 (24%), Positives = 38/81 (46%), Gaps = 6/81 (7%)
Query: 52 DSISECEVKFLPEFFDSRSPSKNPRVYRYYRDSIVKHYRENPSRKITFTDVRRTLVGDVG 111
D ++ E P+ P + +V+ + R+ ++ + +NP ++TF + L
Sbjct: 25 DRMTSQEAACFPDIISG--PQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYN 82
Query: 112 S----IRRVFDFLETWGLINY 128
S + RV +LE GLIN+
Sbjct: 83 SDTVLVHRVHSYLERHGLINF 103
>pdb|2CQR|A Chain A, Solution Structure Of Rsgi Ruh-043, A Myb Dna-Binding
Domain In Human Cdna
Length = 73
Score = 32.0 bits (71), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 RVEISEEARSDWTEKETLQLLEAIMHF----GDDWRKVAQHVSGKSEKDCITHFIKLPFG 260
R E + A WT+ + L A+ + D W K+A+ V KS++DCI + L G
Sbjct: 10 RKERARSAEEPWTQNQQKLLELALQQYPRGSSDCWDKIARCVPSKSKEDCIARYKLLVSG 69
>pdb|2M2E|A Chain A, Solution Nmr Structure Of The Sant Domain Of Human Dnajc2,
Northeast Structural Genomics Consortium Target Hr8254a
Length = 73
Score = 31.2 bits (69), Expect = 1.0, Method: Composition-based stats.
Identities = 14/46 (30%), Positives = 28/46 (60%), Gaps = 4/46 (8%)
Query: 216 WTEKETLQLLEAIMHFG----DDWRKVAQHVSGKSEKDCITHFIKL 257
WT +E L +A+ + + W+K+A+ V G+++KDC+ + +L
Sbjct: 6 WTTEEQKLLEQALKTYPVNTPERWKKIAEAVPGRTKKDCMKRYKEL 51
>pdb|1A5J|A Chain A, Chicken B-Myb Dna Binding Domain, Repeat 2 And Repeat3,
Nmr, 32 Structures
Length = 110
Score = 30.8 bits (68), Expect = 1.4, Method: Composition-based stats.
Identities = 13/45 (28%), Positives = 25/45 (55%)
Query: 210 EEARSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHF 254
E +S WTE+E + EA G+ W ++A+ + G+++ H+
Sbjct: 56 EVKKSSWTEEEDRIIFEAHKVLGNRWAEIAKLLPGRTDNAVKNHW 100
Score = 30.4 bits (67), Expect = 2.1, Method: Composition-based stats.
Identities = 12/44 (27%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 208 ISEEARSDWTEKETLQLLEAIMHFG-DDWRKVAQHVSGKSEKDC 250
I + + WT++E +++E + +G W +A+H+ G+ K C
Sbjct: 2 IPDLVKGPWTKEEDQKVIELVKKYGTKQWTLIAKHLKGRLGKQC 45
>pdb|1H8A|C Chain C, Crystal Structure Of Ternary Protein-Dna Complex3
Length = 128
Score = 30.4 bits (67), Expect = 1.8, Method: Composition-based stats.
Identities = 13/49 (26%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 203 FRRVEISEEARSDWTEKETLQLLEAIMHFGDD-WRKVAQHVSGKSEKDC 250
+++V E + WT++E +++E + +G W +A+H+ G+ K C
Sbjct: 17 WQKVLNPELNKGPWTKEEDQRVIEHVQKYGPKRWSDIAKHLKGRIGKQC 65
Score = 28.9 bits (63), Expect = 5.4, Method: Composition-based stats.
Identities = 11/45 (24%), Positives = 25/45 (55%)
Query: 210 EEARSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHF 254
E ++ WTE+E + +A G+ W ++A+ + G+++ H+
Sbjct: 76 EVKKTSWTEEEDRIIYQAHKRLGNRWAEIAKLLPGRTDNAVKNHW 120
>pdb|1MBG|A Chain A, Mouse C-Myb Dna-Binding Domain Repeat 2
pdb|1MBH|A Chain A, Mouse C-Myb Dna-Binding Domain Repeat 2
Length = 53
Score = 30.0 bits (66), Expect = 2.3, Method: Composition-based stats.
Identities = 11/39 (28%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 213 RSDWTEKETLQLLEAIMHFGDD-WRKVAQHVSGKSEKDC 250
+ WT++E +++E + +G W +A+H+ G+ K C
Sbjct: 3 KGPWTKEEDQRVIELVQKYGPKRWSVIAKHLKGRIGKQC 41
>pdb|1GVD|A Chain A, Crystal Structure Of C-Myb R2 V103l Mutant
Length = 52
Score = 29.6 bits (65), Expect = 2.9, Method: Composition-based stats.
Identities = 11/39 (28%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 213 RSDWTEKETLQLLEAIMHFGDD-WRKVAQHVSGKSEKDC 250
+ WT++E +L++ + +G W +A+H+ G+ K C
Sbjct: 3 KGPWTKEEDQRLIKLVQKYGPKRWSVIAKHLKGRIGKQC 41
>pdb|2D9A|A Chain A, Solution Structure Of Rsgi Ruh-050, A Myb Dna-Binding
Domain In Mouse Cdna
Length = 60
Score = 29.6 bits (65), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 13/46 (28%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 216 WTEKETLQLLEAIMHFGD-DWRKVAQHVSGKSEKDCITHFIKLPFG 260
WT +E QL + FG DW+ +A H ++++ C ++++ G
Sbjct: 11 WTHEEDEQLRALVRQFGQQDWKFLASHFPNRTDQQCQYRWLRVLSG 56
>pdb|1IDY|A Chain A, Structure Of Myb Transforming Protein, Nmr, Minimized
Average Structure
pdb|1IDZ|A Chain A, Structure Of Myb Transforming Protein, Nmr, 20 Structures
Length = 54
Score = 29.6 bits (65), Expect = 3.6, Method: Composition-based stats.
Identities = 12/45 (26%), Positives = 25/45 (55%)
Query: 210 EEARSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHF 254
E ++ WTE+E L +A G+ W ++A+ + G+++ H+
Sbjct: 2 EVKKTSWTEEEDRILYQAHKRLGNRWAEIAKLLPGRTDNAIKNHW 46
>pdb|1MSE|C Chain C, Solution Structure Of A Specific Dna Complex Of The Myb
Dna- Binding Domain With Cooperative Recognition Helices
pdb|1MSF|C Chain C, Solution Structure Of A Specific Dna Complex Of The Myb
Dna- Binding Domain With Cooperative Recognition Helices
Length = 105
Score = 28.9 bits (63), Expect = 5.0, Method: Composition-based stats.
Identities = 11/45 (24%), Positives = 25/45 (55%)
Query: 210 EEARSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHF 254
E ++ WTE+E + +A G+ W ++A+ + G+++ H+
Sbjct: 53 EVKKTSWTEEEDRIIYQAHKRLGNRWAEIAKLLPGRTDNAIKNHW 97
>pdb|1GV2|A Chain A, Crystal Structure Of C-Myb R2r3
Length = 105
Score = 28.9 bits (63), Expect = 5.5, Method: Composition-based stats.
Identities = 11/45 (24%), Positives = 25/45 (55%)
Query: 210 EEARSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHF 254
E ++ WTE+E + +A G+ W ++A+ + G+++ H+
Sbjct: 53 EVKKTSWTEEEDRIIYQAHKRLGNRWAEIAKLLPGRTDNAIKNHW 97
Score = 28.1 bits (61), Expect = 9.3, Method: Composition-based stats.
Identities = 11/42 (26%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 210 EEARSDWTEKETLQLLEAIMHFGDD-WRKVAQHVSGKSEKDC 250
E + WT++E ++++ + +G W +A+H+ G+ K C
Sbjct: 1 ELIKGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLKGRIGKQC 42
>pdb|1GV5|A Chain A, Crystal Structure Of C-Myb R2
Length = 52
Score = 28.5 bits (62), Expect = 7.3, Method: Composition-based stats.
Identities = 10/39 (25%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 213 RSDWTEKETLQLLEAIMHFGDD-WRKVAQHVSGKSEKDC 250
+ WT++E ++++ + +G W +A+H+ G+ K C
Sbjct: 3 KGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLKGRIGKQC 41
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
0.319 0.132 0.395
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,274,158
Number of Sequences: 62578
Number of extensions: 364338
Number of successful extensions: 886
Number of sequences better than 100.0: 27
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 860
Number of HSP's gapped (non-prelim): 32
length of query: 418
length of database: 14,973,337
effective HSP length: 101
effective length of query: 317
effective length of database: 8,652,959
effective search space: 2742988003
effective search space used: 2742988003
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)