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= 029436
(193 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1XG2|B Chain B, Crystal Structure Of The Complex Between Pectin
Methylesterase And Its Inhibitor Protein
Length = 153
Score = 33.5 bits (75), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 27/131 (20%), Positives = 51/131 (38%), Gaps = 11/131 (8%)
Query: 27 DTRFIRSSCKSTTYPALCVQSLSAYAPSIQQSPRQLAVTALSVSLSRAQSAKSFVTKLRK 86
+ I C T P+LC+Q+L + S + + L ++ ++ + A+ + L
Sbjct: 2 ENHLISEICPKTRNPSLCLQALESDPRSASKDLKGLGQFSIDIAQASAKQTSKIIASLTN 61
Query: 87 FRNLKHREYGAIADCLDEMGDTVDRLSKSVQELNHMGRAKGQDFLWHMSNVETWVSAALT 146
+ + G C + D +D L ++ Q L +++ + SAA
Sbjct: 62 -QATDPKLKGRYETCSENYADAIDSLGQAKQFLTS----------GDYNSLNIYASAAFD 110
Query: 147 DENTCTDGFGG 157
TC D F G
Sbjct: 111 GAGTCEDSFEG 121
>pdb|2X0L|A Chain A, Crystal Structure Of A Neuro-Specific Splicing Variant Of
Human Histone Lysine Demethylase Lsd1
Length = 734
Score = 31.6 bits (70), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 7/55 (12%)
Query: 91 KHREYGAIADCLDEMGDTVDRLSKSVQELN-------HMGRAKGQDFLWHMSNVE 138
KHR+ A+ DE+ +T +L + +QEL ++ Q WH +N+E
Sbjct: 365 KHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLE 419
>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 = 31.6 bits (70), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 7/55 (12%)
Query: 91 KHREYGAIADCLDEMGDTVDRLSKSVQELN-------HMGRAKGQDFLWHMSNVE 138
KHR+ A+ DE+ +T +L + +QEL ++ Q WH +N+E
Sbjct: 361 KHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLE 415
>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 = 31.6 bits (70), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 7/55 (12%)
Query: 91 KHREYGAIADCLDEMGDTVDRLSKSVQELN-------HMGRAKGQDFLWHMSNVE 138
KHR+ A+ DE+ +T +L + +QEL ++ Q WH +N+E
Sbjct: 483 KHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLE 537
>pdb|2HKO|A Chain A, Crystal Structure Of Lsd1
Length = 664
Score = 31.6 bits (70), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 7/55 (12%)
Query: 91 KHREYGAIADCLDEMGDTVDRLSKSVQELN-------HMGRAKGQDFLWHMSNVE 138
KHR+ A+ DE+ +T +L + +QEL ++ Q WH +N+E
Sbjct: 312 KHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLE 366
>pdb|2H94|A Chain A, Crystal Structure And Mechanism Of Human Lysine-Specific
Demethylase-1
Length = 664
Score = 31.6 bits (70), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 7/55 (12%)
Query: 91 KHREYGAIADCLDEMGDTVDRLSKSVQELN-------HMGRAKGQDFLWHMSNVE 138
KHR+ A+ DE+ +T +L + +QEL ++ Q WH +N+E
Sbjct: 312 KHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLE 366
>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 = 31.6 bits (70), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 7/55 (12%)
Query: 91 KHREYGAIADCLDEMGDTVDRLSKSVQELN-------HMGRAKGQDFLWHMSNVE 138
KHR+ A+ DE+ +T +L + +QEL ++ Q WH +N+E
Sbjct: 312 KHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLE 366
>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 = 31.6 bits (70), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 7/55 (12%)
Query: 91 KHREYGAIADCLDEMGDTVDRLSKSVQELN-------HMGRAKGQDFLWHMSNVE 138
KHR+ A+ DE+ +T +L + +QEL ++ Q WH +N+E
Sbjct: 313 KHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLE 367
>pdb|2DW4|A Chain A, Crystal Structure Of Human Lsd1 At 2.3 A Resolution
Length = 660
Score = 31.6 bits (70), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 7/55 (12%)
Query: 91 KHREYGAIADCLDEMGDTVDRLSKSVQELN-------HMGRAKGQDFLWHMSNVE 138
KHR+ A+ DE+ +T +L + +QEL ++ Q WH +N+E
Sbjct: 312 KHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLE 366
>pdb|2ZXE|B Chain B, Crystal Structure Of The Sodium - Potassium Pump In The
E2.2k+.Pi State
Length = 305
Score = 28.5 bits (62), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 5/64 (7%)
Query: 52 APSIQQSPRQLAVTALSVSLSRAQSAKSFVTKLRKFRNLKHREYGA----IADCLDEMGD 107
P + +P + T +S S+S +S +SFV + K +L + A DC D D
Sbjct: 75 PPGLSHAPYAIK-TEISFSISNPKSYESFVKSMHKLMDLYNESSQAGNSPFEDCSDTPAD 133
Query: 108 TVDR 111
+ R
Sbjct: 134 YIKR 137
>pdb|3A3Y|B Chain B, Crystal Structure Of The Sodium-potassium Pump With Bound
Potassium And Ouabain
Length = 305
Score = 28.5 bits (62), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 5/64 (7%)
Query: 52 APSIQQSPRQLAVTALSVSLSRAQSAKSFVTKLRKFRNLKHREYGA----IADCLDEMGD 107
P + +P + T +S S+S +S +SFV + K +L + A DC D D
Sbjct: 75 PPGLSHAPYAIK-TEISFSISNPKSYESFVKSMHKLMDLYNESSQAGNSPFEDCSDTPAD 133
Query: 108 TVDR 111
+ R
Sbjct: 134 YIKR 137
>pdb|1LLW|A Chain A, Structural Studies On The Synchronization Of Catalytic
Centers In Glutamate Synthase: Complex With
2-Oxoglutarate
pdb|1LLZ|A Chain A, Structural Studies On The Synchronization Of Catalytic
Centers In Glutamate Synthase: Reduced Enzyme
pdb|1LM1|A Chain A, Structural Studies On The Synchronization Of Catalytic
Centers In Glutamate Synthase: Native Enzyme
pdb|1OFD|A Chain A, Glutamate Synthase From Synechocystis Sp In Complex With
2-Oxoglutarate At 2.0 Angstrom Resolution
pdb|1OFD|B Chain B, Glutamate Synthase From Synechocystis Sp In Complex With
2-Oxoglutarate At 2.0 Angstrom Resolution
pdb|1OFE|A Chain A, Glutamate Synthase From Synechocystis Sp In Complex With
2-Oxoglutarate And L-Don At 2.45 Angstrom Resolution
pdb|1OFE|B Chain B, Glutamate Synthase From Synechocystis Sp In Complex With
2-Oxoglutarate And L-Don At 2.45 Angstrom Resolution
Length = 1520
Score = 27.3 bits (59), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 25/44 (56%)
Query: 88 RNLKHREYGAIADCLDEMGDTVDRLSKSVQELNHMGRAKGQDFL 131
RN+ G +A LDE+GD ++++ + L + +KG++ L
Sbjct: 1418 RNVGAGMTGGLAYFLDEVGDLPEKINPEIITLQRITASKGEEQL 1461
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 0.126 0.360
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,290,509
Number of Sequences: 62578
Number of extensions: 135593
Number of successful extensions: 385
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 373
Number of HSP's gapped (non-prelim): 13
length of query: 193
length of database: 14,973,337
effective HSP length: 93
effective length of query: 100
effective length of database: 9,153,583
effective search space: 915358300
effective search space used: 915358300
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)