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= 000305
(1696 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4A69|C Chain C, Structure Of Hdac3 Bound To Corepressor And Inositol
Tetraphosphate
pdb|4A69|D Chain D, Structure Of Hdac3 Bound To Corepressor And Inositol
Tetraphosphate
Length = 94
Score = 71.2 bits (173), Expect = 4e-12, Method: Composition-based stats.
Identities = 33/87 (37%), Positives = 55/87 (63%), Gaps = 1/87 (1%)
Query: 686 MPALILDKKEKMSSRFISSNGLVEDPCAVEKERAMINPWTSEEREIFVDKLATFGKDFRK 745
+P ++ D ++ +FI+ NGL+ DP V K+R ++N W+ +E+E F +K K+F
Sbjct: 9 IPPMLYDADQQ-RIKFINMNGLMADPMKVYKDRQVMNMWSEQEKETFREKFMQHPKNFGL 67
Query: 746 IASFLNYKTTADCVEFYYKNHKSDCFE 772
IASFL KT A+CV +YY K++ ++
Sbjct: 68 IASFLERKTVAECVLYYYLTKKNENYK 94
>pdb|1XC5|A Chain A, Solution Structure Of The Smrt Deacetylase Activation
Domain
Length = 71
Score = 65.1 bits (157), Expect = 4e-10, Method: Composition-based stats.
Identities = 30/70 (42%), Positives = 45/70 (64%)
Query: 703 SSNGLVEDPCAVEKERAMINPWTSEEREIFVDKLATFGKDFRKIASFLNYKTTADCVEFY 762
S NGL+ DP V K+R ++N W+ +E+E F +K K+F IASFL KT A+CV +Y
Sbjct: 2 SMNGLMADPMKVYKDRQVMNMWSEQEKETFREKFMQHPKNFGLIASFLERKTVAECVLYY 61
Query: 763 YKNHKSDCFE 772
Y K++ ++
Sbjct: 62 YLTKKNENYK 71
>pdb|2EQR|A Chain A, Solution Structure Of The First Sant Domain From Human
Nuclear Receptor Corepressor 1
Length = 61
Score = 50.4 bits (119), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 23/53 (43%), Positives = 32/53 (60%)
Query: 717 ERAMINPWTSEEREIFVDKLATFGKDFRKIASFLNYKTTADCVEFYYKNHKSD 769
+R +N WT E+EIF DK K+F IAS+L K+ DCV +YY K++
Sbjct: 8 DRQFMNVWTDHEKEIFKDKFIQHPKNFGLIASYLERKSVPDCVLYYYLTKKNE 60
Score = 34.3 bits (77), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 23/44 (52%)
Query: 940 WTDEEKSIFIQAVTSYGKDFSMIARCIRTRSRDQCKVFFSKARK 983
WTD EK IF + K+F +IA + +S C +++ +K
Sbjct: 15 WTDHEKEIFKDKFIQHPKNFGLIASYLERKSVPDCVLYYYLTKK 58
>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 = 45.4 bits (106), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 29/51 (56%)
Query: 940 WTDEEKSIFIQAVTSYGKDFSMIARCIRTRSRDQCKVFFSKARKCLGLDLI 990
WT EE+ + +QA+ YG+DF I+ I +S Q K FF R+ +D +
Sbjct: 383 WTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNYRRRFNIDEV 433
Score = 36.6 bits (83), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 27/55 (49%)
Query: 724 WTSEEREIFVDKLATFGKDFRKIASFLNYKTTADCVEFYYKNHKSDCFEKLKKKH 778
WT E++ +F + GK F +I L K+ A V+FYY K+ + +H
Sbjct: 192 WTVEDKVLFEQAFSFHGKTFHRIQQMLPDKSIASLVKFYYSWKKTRTKTSVMDRH 246
Score = 32.7 bits (73), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 25/48 (52%)
Query: 937 PSDWTDEEKSIFIQAVTSYGKDFSMIARCIRTRSRDQCKVFFSKARKC 984
P +WT E+K +F QA + +GK F I + + +S F+ +K
Sbjct: 189 PDEWTVEDKVLFEQAFSFHGKTFHRIQQMLPDKSIASLVKFYYSWKKT 236
Score = 32.3 bits (72), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 15/66 (22%), Positives = 35/66 (53%), Gaps = 1/66 (1%)
Query: 724 WTSEEREIFVDKLATFGKDFRKIASFLNYKTTADCVEFYYKNHKSDCFEKLKKKHDFSKQ 783
WT+EE+ + V + +G+DF+ I+ + K+ F+ + +++ ++ + ++
Sbjct: 383 WTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNYRRRFNIDEVLQEWE-AEH 441
Query: 784 GKTSTN 789
GK TN
Sbjct: 442 GKEETN 447
>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 = 45.1 bits (105), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 29/51 (56%)
Query: 940 WTDEEKSIFIQAVTSYGKDFSMIARCIRTRSRDQCKVFFSKARKCLGLDLI 990
WT EE+ + +QA+ YG+DF I+ I +S Q K FF R+ +D +
Sbjct: 136 WTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNYRRRFNIDEV 186
Score = 33.5 bits (75), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 15/66 (22%), Positives = 35/66 (53%), Gaps = 1/66 (1%)
Query: 724 WTSEEREIFVDKLATFGKDFRKIASFLNYKTTADCVEFYYKNHKSDCFEKLKKKHDFSKQ 783
WT+EE+ + V + +G+DF+ I+ + K+ F+ + +++ ++ + ++
Sbjct: 136 WTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNYRRRFNIDEVLQEWE-AEH 194
Query: 784 GKTSTN 789
GK TN
Sbjct: 195 GKEETN 200
>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 = 44.7 bits (104), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 29/51 (56%)
Query: 940 WTDEEKSIFIQAVTSYGKDFSMIARCIRTRSRDQCKVFFSKARKCLGLDLI 990
WT EE+ + +QA+ YG+DF I+ I +S Q K FF R+ +D +
Sbjct: 79 WTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNYRRRFNIDEV 129
Score = 32.7 bits (73), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 15/66 (22%), Positives = 35/66 (53%), Gaps = 1/66 (1%)
Query: 724 WTSEEREIFVDKLATFGKDFRKIASFLNYKTTADCVEFYYKNHKSDCFEKLKKKHDFSKQ 783
WT+EE+ + V + +G+DF+ I+ + K+ F+ + +++ ++ + ++
Sbjct: 79 WTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNYRRRFNIDEVLQEWE-AEH 137
Query: 784 GKTSTN 789
GK TN
Sbjct: 138 GKEETN 143
>pdb|2X0L|B Chain B, Crystal Structure Of A Neuro-Specific Splicing Variant Of
Human Histone Lysine Demethylase Lsd1
Length = 133
Score = 41.2 bits (95), Expect = 0.005, Method: Composition-based stats.
Identities = 19/49 (38%), Positives = 28/49 (57%)
Query: 940 WTDEEKSIFIQAVTSYGKDFSMIARCIRTRSRDQCKVFFSKARKCLGLD 988
WT EE+ + +QA+ YG+DF I+ I +S Q K FF R+ +D
Sbjct: 76 WTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNYRRRFNID 124
>pdb|2LTP|A Chain A, Solution Structure Of The Sant2 Domain Of The Human
Nuclear Receptor Corepressor 2 (Ncor2), Northeast
Structural Genomics Consortium (Nesg) Target Id Hr4636e
Length = 89
Score = 36.2 bits (82), Expect = 0.16, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 30/51 (58%)
Query: 940 WTDEEKSIFIQAVTSYGKDFSMIARCIRTRSRDQCKVFFSKARKCLGLDLI 990
WT+EE + + +G+++S IAR + +++ QCK F+ +K LD I
Sbjct: 19 WTEEEMGTAKKGLLEHGRNWSAIARMVGSKTVSQCKNFYFNYKKRQNLDEI 69
Score = 32.3 bits (72), Expect = 2.1, Method: Composition-based stats.
Identities = 16/63 (25%), Positives = 28/63 (44%)
Query: 716 KERAMINPWTSEEREIFVDKLATFGKDFRKIASFLNYKTTADCVEFYYKNHKSDCFEKLK 775
+E WT EE L G+++ IA + KT + C FY+ K +++
Sbjct: 11 RENLYFQGWTEEEMGTAKKGLLEHGRNWSAIARMVGSKTVSQCKNFYFNYKKRQNLDEIL 70
Query: 776 KKH 778
++H
Sbjct: 71 QQH 73
>pdb|2CRG|A Chain A, Solution Structure Of The Myb-Like Dna-Binding Domain Of
Mouse Mta3 Protein
Length = 70
Score = 35.8 bits (81), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 721 INPWTSEEREIFVDKLATFGKDFRKI-ASFLNYKTTADCVEFYYKNHKSDCFEKLKK 776
+ W++ E +F + L +GKDF I FL +K+ +E+YY +D + + K+
Sbjct: 8 MEEWSASEACLFEEALEKYGKDFNDIRQDFLPWKSLTSIIEYYYMWKTTDRYVQQKR 64
>pdb|2CU7|A Chain A, Solution Structure Of The Sant Domain Of Human Kiaa1915
Protein
Length = 72
Score = 33.9 bits (76), Expect = 0.80, Method: Composition-based stats.
Identities = 16/45 (35%), Positives = 25/45 (55%), Gaps = 3/45 (6%)
Query: 724 WTSEEREIFVDKLATFGKDFRKIASFLNYKTTADCVEF---YYKN 765
WT EE+E+F LA FG+ + KI+ + +T + Y+KN
Sbjct: 12 WTIEEKELFEQGLAKFGRRWTKISKLIGSRTVLQVKSYARQYFKN 56
Score = 33.9 bits (76), Expect = 0.91, Method: Composition-based stats.
Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 5/53 (9%)
Query: 940 WTDEEKSIFIQAVTSYGKDFSMIARCIRTRSRDQCKV----FFSKARKCLGLD 988
WT EEK +F Q + +G+ ++ I++ I +R+ Q K +F KC GLD
Sbjct: 12 WTIEEKELFEQGLAKFGRRWTKISKLIGSRTVLQVKSYARQYFKNKVKC-GLD 63
>pdb|2YQK|A Chain A, Solution Structure Of The Sant Domain In Arginine-Glutamic
Acid Dipeptide (Re) Repeats
Length = 63
Score = 31.2 bits (69), Expect = 4.6, Method: Composition-based stats.
Identities = 16/41 (39%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 724 WTSEEREIFVDKLATFGKDFRKI-ASFLNYKTTADCVEFYY 763
WT +E + FV L +GK+F +I L K T + + FYY
Sbjct: 12 WTEDEVKRFVKGLRQYGKNFFRIRKELLPNKETGELITFYY 52
>pdb|1H88|C Chain C, Crystal Structure Of Ternary Protein-Dna Complex1
pdb|1H89|C Chain C, Crystal Structure Of Ternary Protein-Dna Complex2
Length = 159
Score = 30.8 bits (68), Expect = 6.5, Method: Composition-based stats.
Identities = 27/98 (27%), Positives = 42/98 (42%), Gaps = 24/98 (24%)
Query: 897 GQRDWRRQKADSVMRLPSTSDVTQNVDDD---------TCSDESCG---------EMDPS 938
G+ W R++ + + +L V QN DD +D C E+
Sbjct: 5 GKTRWTREEDEKLKKL-----VEQNGTDDWKVIANYLPNRTDVQCQHRWQKVLNPELIKG 59
Query: 939 DWTDEEKSIFIQAVTSYG-KDFSMIARCIRTRSRDQCK 975
WT EE I+ V YG K +S+IA+ ++ R QC+
Sbjct: 60 PWTKEEDQRVIKLVQKYGPKRWSVIAKHLKGRIGKQCR 97
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
0.311 0.127 0.364
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 46,098,849
Number of Sequences: 62578
Number of extensions: 1832474
Number of successful extensions: 3036
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 3013
Number of HSP's gapped (non-prelim): 32
length of query: 1696
length of database: 14,973,337
effective HSP length: 112
effective length of query: 1584
effective length of database: 7,964,601
effective search space: 12615927984
effective search space used: 12615927984
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 58 (26.9 bits)