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= psy11140
(89 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3M7V|A Chain A, Crystal Structure Of Phosphopentomutase From Streptococcus
M
pdb|3M7V|B Chain B, Crystal Structure Of Phosphopentomutase From Streptococcus
M
Length = 413
Score = 27.7 bits (60), Expect = 1.6, Method: Composition-based stats.
Identities = 13/33 (39%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 2 SVGPKNIIYNGGGYVKDLGSSESNMAQGLSQMI 34
+VG N I+NG G D+G ++SN + G+ +I
Sbjct: 248 AVGKINDIFNGSGITNDMGHNKSN-SHGVDTLI 279
>pdb|1FP2|A Chain A, Crystal Structure Analysis Of Isoflavone
O-Methyltransferase
Length = 352
Score = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 4/47 (8%)
Query: 4 GPKNIIYNGGGYVKDLGSSESNMAQGLSQMIIHKWLDERTRVILIEC 50
G N+ Y GG D+ +S N L + I+H W D+ IL +C
Sbjct: 229 GSNNLTYVGG----DMFTSIPNADAVLLKYILHNWTDKDCLRILKKC 271
>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 = 26.6 bits (57), Expect = 4.2, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 25/58 (43%)
Query: 3 VGPKNIIYNGGGYVKDLGSSESNMAQGLSQMIIHKWLDERTRVILIECSLYNPNINAI 60
VG + + G YV DLG+ G ++ K ++ I +C LY N A+
Sbjct: 313 VGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAV 370
>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 = 26.6 bits (57), Expect = 4.2, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 25/58 (43%)
Query: 3 VGPKNIIYNGGGYVKDLGSSESNMAQGLSQMIIHKWLDERTRVILIECSLYNPNINAI 60
VG + + G YV DLG+ G ++ K ++ I +C LY N A+
Sbjct: 142 VGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAV 199
>pdb|2DW4|A Chain A, Crystal Structure Of Human Lsd1 At 2.3 A Resolution
Length = 660
Score = 26.6 bits (57), Expect = 4.2, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 25/58 (43%)
Query: 3 VGPKNIIYNGGGYVKDLGSSESNMAQGLSQMIIHKWLDERTRVILIECSLYNPNINAI 60
VG + + G YV DLG+ G ++ K ++ I +C LY N A+
Sbjct: 142 VGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAV 199
>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 = 26.6 bits (57), Expect = 4.2, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 25/58 (43%)
Query: 3 VGPKNIIYNGGGYVKDLGSSESNMAQGLSQMIIHKWLDERTRVILIECSLYNPNINAI 60
VG + + G YV DLG+ G ++ K ++ I +C LY N A+
Sbjct: 191 VGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAV 248
>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 = 26.6 bits (57), Expect = 4.2, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 25/58 (43%)
Query: 3 VGPKNIIYNGGGYVKDLGSSESNMAQGLSQMIIHKWLDERTRVILIECSLYNPNINAI 60
VG + + G YV DLG+ G ++ K ++ I +C LY N A+
Sbjct: 143 VGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAV 200
>pdb|2HKO|A Chain A, Crystal Structure Of Lsd1
Length = 664
Score = 26.6 bits (57), Expect = 4.2, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 25/58 (43%)
Query: 3 VGPKNIIYNGGGYVKDLGSSESNMAQGLSQMIIHKWLDERTRVILIECSLYNPNINAI 60
VG + + G YV DLG+ G ++ K ++ I +C LY N A+
Sbjct: 142 VGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAV 199
>pdb|2H94|A Chain A, Crystal Structure And Mechanism Of Human Lysine-Specific
Demethylase-1
Length = 664
Score = 26.6 bits (57), Expect = 4.2, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 25/58 (43%)
Query: 3 VGPKNIIYNGGGYVKDLGSSESNMAQGLSQMIIHKWLDERTRVILIECSLYNPNINAI 60
VG + + G YV DLG+ G ++ K ++ I +C LY N A+
Sbjct: 142 VGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAV 199
>pdb|1FPX|A Chain A, Crystal Structure Analysis Of Selenomethionine Substituted
Isoflavone O-Methyltransferase
Length = 352
Score = 25.8 bits (55), Expect = 5.7, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 4/47 (8%)
Query: 4 GPKNIIYNGGGYVKDLGSSESNMAQGLSQMIIHKWLDERTRVILIEC 50
G N+ Y GG D +S N L + I+H W D+ IL +C
Sbjct: 229 GSNNLTYVGG----DXFTSIPNADAVLLKYILHNWTDKDCLRILKKC 271
>pdb|2X0L|A Chain A, Crystal Structure Of A Neuro-Specific Splicing Variant Of
Human Histone Lysine Demethylase Lsd1
Length = 734
Score = 25.4 bits (54), Expect = 8.9, Method: Composition-based stats.
Identities = 16/57 (28%), Positives = 24/57 (42%)
Query: 3 VGPKNIIYNGGGYVKDLGSSESNMAQGLSQMIIHKWLDERTRVILIECSLYNPNINA 59
VG + + G YV DLG+ G ++ K ++ I +C LY N A
Sbjct: 191 VGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQA 247
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 0.385
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,605,267
Number of Sequences: 62578
Number of extensions: 82027
Number of successful extensions: 181
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 172
Number of HSP's gapped (non-prelim): 12
length of query: 89
length of database: 14,973,337
effective HSP length: 56
effective length of query: 33
effective length of database: 11,468,969
effective search space: 378475977
effective search space used: 378475977
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: 45 (21.9 bits)