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= 003908
(787 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 36.2 bits (82), Expect = 0.080, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 30/49 (61%)
Query: 52 AAWTREEEESFFTALRQVGKNFEKITHRVRSKNKDQVRHYYYRLVRRMN 100
A WT EE+ A+R+ G++F+ I+ + +K+ QV++++ RR N
Sbjct: 134 ARWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNYRRRFN 182
>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 = 35.8 bits (81), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 30/49 (61%)
Query: 52 AAWTREEEESFFTALRQVGKNFEKITHRVRSKNKDQVRHYYYRLVRRMN 100
A WT EE+ A+R+ G++F+ I+ + +K+ QV++++ RR N
Sbjct: 77 ARWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNYRRRFN 125
>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 = 35.8 bits (81), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 30/49 (61%)
Query: 52 AAWTREEEESFFTALRQVGKNFEKITHRVRSKNKDQVRHYYYRLVRRMN 100
A WT EE+ A+R+ G++F+ I+ + +K+ QV++++ RR N
Sbjct: 381 ARWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNYRRRFN 429
>pdb|2X0L|B Chain B, Crystal Structure Of A Neuro-Specific Splicing Variant Of
Human Histone Lysine Demethylase Lsd1
Length = 133
Score = 35.8 bits (81), Expect = 0.10, Method: Composition-based stats.
Identities = 16/49 (32%), Positives = 30/49 (61%)
Query: 52 AAWTREEEESFFTALRQVGKNFEKITHRVRSKNKDQVRHYYYRLVRRMN 100
A WT EE+ A+R+ G++F+ I+ + +K+ QV++++ RR N
Sbjct: 74 ARWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNYRRRFN 122
>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 = 33.9 bits (76), Expect = 0.32, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 28/58 (48%)
Query: 43 SAKRPTRQWAAWTREEEESFFTALRQVGKNFEKITHRVRSKNKDQVRHYYYRLVRRMN 100
S+ R + WT EE + L + G+N+ I V SK Q +++Y+ +R N
Sbjct: 8 SSGRENLYFQGWTEEEMGTAKKGLLEHGRNWSAIARMVGSKTVSQCKNFYFNYKKRQN 65
>pdb|2YQK|A Chain A, Solution Structure Of The Sant Domain In
Arginine-Glutamic Acid Dipeptide (Re) Repeats
Length = 63
Score = 32.0 bits (71), Expect = 1.2, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 54 WTREEEESFFTALRQVGKNFEKITHRV--RSKNKDQVRHYYY 93
WT +E + F LRQ GKNF +I + + + + YYY
Sbjct: 12 WTEDEVKRFVKGLRQYGKNFFRIRKELLPNKETGELITFYYY 53
>pdb|2BS7|1 Chain 1, Crystal Structure Of F17b-G In Complex With Chitobiose
Length = 176
Score = 31.2 bits (69), Expect = 2.1, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 21/42 (50%)
Query: 540 MGDERLSSGTALSAGEWADSLTNISVGDLLAEVPHDLDAAPV 581
MGD S GTA+S W + + SVG+ L+ + PV
Sbjct: 86 MGDTNYSRGTAMSGNSWENVFSGWSVGNYLSTQGLSVHVRPV 127
>pdb|2CU7|A Chain A, Solution Structure Of The Sant Domain Of Human Kiaa1915
Protein
Length = 72
Score = 30.0 bits (66), Expect = 5.0, Method: Composition-based stats.
Identities = 14/38 (36%), Positives = 22/38 (57%)
Query: 54 WTREEEESFFTALRQVGKNFEKITHRVRSKNKDQVRHY 91
WT EE+E F L + G+ + KI+ + S+ QV+ Y
Sbjct: 12 WTIEEKELFEQGLAKFGRRWTKISKLIGSRTVLQVKSY 49
>pdb|3L95|B Chain B, Crystal Structure Of The Human Notch1 Negative Regulatory
Region (Nrr) Bound To The Fab Fragment Of An Antagonist
Antibody
pdb|3L95|H Chain H, Crystal Structure Of The Human Notch1 Negative Regulatory
Region (Nrr) Bound To The Fab Fragment Of An Antagonist
Antibody
Length = 227
Score = 29.6 bits (65), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 24/43 (55%), Gaps = 2/43 (4%)
Query: 446 INVENKKEQIVDSVPGRVPSTSDQSENFVDPYKKLTSVKENDT 488
IN N+ Q DSV GR ++D S+N Y ++ S++ DT
Sbjct: 51 INPPNRSNQYADSVKGRFTISADTSKN--TAYLQMNSLRAEDT 91
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
0.314 0.129 0.380
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,804,272
Number of Sequences: 62578
Number of extensions: 925951
Number of successful extensions: 1618
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1609
Number of HSP's gapped (non-prelim): 10
length of query: 787
length of database: 14,973,337
effective HSP length: 107
effective length of query: 680
effective length of database: 8,277,491
effective search space: 5628693880
effective search space used: 5628693880
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 55 (25.8 bits)