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= 025286
(255 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2WBK|A Chain A, Structure Of The Michaelis Complex Of Beta-Mannosidase,
Man2a, Provides Insight Into The Conformational
Itinerary Of Mannoside Hydrolysis
pdb|2WBK|B Chain B, Structure Of The Michaelis Complex Of Beta-Mannosidase,
Man2a, Provides Insight Into The Conformational
Itinerary Of Mannoside Hydrolysis
Length = 847
Score = 28.9 bits (63), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 33/68 (48%), Gaps = 12/68 (17%)
Query: 151 DLAAEFRYHIFTKEM-PLVLKAVLHGDSMLFRENPELMNALV------RVYFHSSSKIYN 203
++ +Y F K+ P V + ++HG LFR EL+ + V R Y HSS + N
Sbjct: 437 EILEALKYWGFEKKFTPEVYQGLMHGYDKLFR---ELLPSTVKEFDSDRFYVHSSPYLAN 493
Query: 204 --RMECWG 209
R E WG
Sbjct: 494 WGRPESWG 501
>pdb|2VQU|A Chain A, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VQU|B Chain B, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
Length = 846
Score = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 33/68 (48%), Gaps = 12/68 (17%)
Query: 151 DLAAEFRYHIFTKEM-PLVLKAVLHGDSMLFRENPELMNALV------RVYFHSSSKIYN 203
++ +Y F K+ P V + ++HG LFR EL+ + V R Y HSS + N
Sbjct: 437 EILEALKYWGFEKKFTPEVYQGLMHGYDKLFR---ELLPSTVKEFDSDRFYVHSSPYLAN 493
Query: 204 --RMECWG 209
R E WG
Sbjct: 494 WGRPESWG 501
>pdb|2VJX|A Chain A, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VJX|B Chain B, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VL4|A Chain A, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VL4|B Chain B, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VMF|A Chain A, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VMF|B Chain B, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VO5|A Chain A, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VO5|B Chain B, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VOT|A Chain A, Structural And Biochemical Evidence For A Boat-like
Transition State In Beta-mannosidases
pdb|2VOT|B Chain B, Structural And Biochemical Evidence For A Boat-like
Transition State In Beta-mannosidases
pdb|2VQT|A Chain A, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VQT|B Chain B, Structural And Biochemical Evidence For A Boat-Like
Transition State In Beta-Mannosidases
pdb|2VR4|A Chain A, Transition-state Mimicry In Mannoside Hydrolysis:
Characterisation Of Twenty Six Inhibitors And Insight
Into Binding From Linear Free Energy Relationships And
3-d Structure
pdb|2VR4|B Chain B, Transition-state Mimicry In Mannoside Hydrolysis:
Characterisation Of Twenty Six Inhibitors And Insight
Into Binding From Linear Free Energy Relationships And
3-d Structure
Length = 846
Score = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 33/68 (48%), Gaps = 12/68 (17%)
Query: 151 DLAAEFRYHIFTKEM-PLVLKAVLHGDSMLFRENPELMNALV------RVYFHSSSKIYN 203
++ +Y F K+ P V + ++HG LFR EL+ + V R Y HSS + N
Sbjct: 437 EILEALKYWGFEKKFTPEVYQGLMHGYDKLFR---ELLPSTVKEFDSDRFYVHSSPYLAN 493
Query: 204 --RMECWG 209
R E WG
Sbjct: 494 WGRPESWG 501
>pdb|2JE8|A Chain A, Structure Of A Beta-Mannosidase From Bacteroides
Thetaiotaomicron
pdb|2JE8|B Chain B, Structure Of A Beta-Mannosidase From Bacteroides
Thetaiotaomicron
Length = 848
Score = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 33/68 (48%), Gaps = 12/68 (17%)
Query: 151 DLAAEFRYHIFTKEM-PLVLKAVLHGDSMLFRENPELMNALV------RVYFHSSSKIYN 203
++ +Y F K+ P V + ++HG LFR EL+ + V R Y HSS + N
Sbjct: 439 EILEALKYWGFEKKFTPEVYQGLMHGYDKLFR---ELLPSTVKEFDSDRFYVHSSPYLAN 495
Query: 204 --RMECWG 209
R E WG
Sbjct: 496 WGRPESWG 503
>pdb|3MEX|A Chain A, Crystal Structure Of Mexr In Oxidized State
pdb|3MEX|B Chain B, Crystal Structure Of Mexr In Oxidized State
Length = 142
Score = 28.5 bits (62), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 10/26 (38%), Positives = 18/26 (69%)
Query: 183 NPELMNALVRVYFHSSSKIYNRMECW 208
NP+LM AL+ V+ H ++I + ++C
Sbjct: 6 NPDLMPALMAVFQHVRTRIQSELDCQ 31
>pdb|3ECH|A Chain A, The Marr-Family Repressor Mexr In Complex With Its
Antirepressor Armr
pdb|3ECH|B Chain B, The Marr-Family Repressor Mexr In Complex With Its
Antirepressor Armr
Length = 142
Score = 28.5 bits (62), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 10/26 (38%), Positives = 18/26 (69%)
Query: 183 NPELMNALVRVYFHSSSKIYNRMECW 208
NP+LM AL+ V+ H ++I + ++C
Sbjct: 6 NPDLMPALMAVFQHVRTRIQSELDCQ 31
>pdb|1AXN|A Chain A, The High Resolution Structure Of Annexin Iii Shows
Differences With Annexin V
Length = 323
Score = 28.1 bits (61), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 20/37 (54%)
Query: 50 GTFVSEAVRLLGPPASFEASKLKVVFLGEGMNDYSRI 86
G F V L+ PPA F+A +LK G G N+ + I
Sbjct: 78 GHFEHLMVALVTPPAVFDAKQLKKSMKGAGTNEDALI 114
>pdb|1AII|A Chain A, Annexin Iii
Length = 323
Score = 28.1 bits (61), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 20/37 (54%)
Query: 50 GTFVSEAVRLLGPPASFEASKLKVVFLGEGMNDYSRI 86
G F V L+ PPA F+A +LK G G N+ + I
Sbjct: 78 GHFEHLMVALVTPPAVFDAKQLKKSMKGAGTNEDALI 114
>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 = 28.1 bits (61), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 31/55 (56%), Gaps = 4/55 (7%)
Query: 81 NDYSRILPRTYILSH-CDFTA--NLTLTISNVINLE-QLRGWYIKDDVVAEWKKV 131
+++R+L T LSH DF N +++ + + QL+ ++KD+ + WKK+
Sbjct: 380 QEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKHVKDEQIEHWKKI 434
>pdb|2X0L|A Chain A, Crystal Structure Of A Neuro-Specific Splicing Variant Of
Human Histone Lysine Demethylase Lsd1
Length = 734
Score = 27.7 bits (60), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 40/74 (54%), Gaps = 6/74 (8%)
Query: 64 ASFEASKLKVVFLGEGM--NDYSRILPRTYILSH-CDFTA--NLTLTISNVINLE-QLRG 117
A+ +A +KV + M +++R+L T LSH DF N +++ + + QL+
Sbjct: 243 ANGQADTVKVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQE 302
Query: 118 WYIKDDVVAEWKKV 131
++KD+ + WKK+
Sbjct: 303 KHVKDEQIEHWKKI 316
>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 = 27.3 bits (59), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 31/55 (56%), Gaps = 4/55 (7%)
Query: 81 NDYSRILPRTYILSH-CDFTA--NLTLTISNVINLE-QLRGWYIKDDVVAEWKKV 131
+++R+L T LSH DF N +++ + + QL+ ++KD+ + WKK+
Sbjct: 258 QEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKHVKDEQIEHWKKI 312
>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 = 27.3 bits (59), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 31/55 (56%), Gaps = 4/55 (7%)
Query: 81 NDYSRILPRTYILSH-CDFTA--NLTLTISNVINLE-QLRGWYIKDDVVAEWKKV 131
+++R+L T LSH DF N +++ + + QL+ ++KD+ + WKK+
Sbjct: 209 QEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKHVKDEQIEHWKKI 263
>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 = 27.3 bits (59), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 31/55 (56%), Gaps = 4/55 (7%)
Query: 81 NDYSRILPRTYILSH-CDFTA--NLTLTISNVINLE-QLRGWYIKDDVVAEWKKV 131
+++R+L T LSH DF N +++ + + QL+ ++KD+ + WKK+
Sbjct: 210 QEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKHVKDEQIEHWKKI 264
>pdb|2DW4|A Chain A, Crystal Structure Of Human Lsd1 At 2.3 A Resolution
Length = 660
Score = 27.3 bits (59), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 31/55 (56%), Gaps = 4/55 (7%)
Query: 81 NDYSRILPRTYILSH-CDFTA--NLTLTISNVINLE-QLRGWYIKDDVVAEWKKV 131
+++R+L T LSH DF N +++ + + QL+ ++KD+ + WKK+
Sbjct: 209 QEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKHVKDEQIEHWKKI 263
>pdb|2H94|A Chain A, Crystal Structure And Mechanism Of Human Lysine-Specific
Demethylase-1
Length = 664
Score = 27.3 bits (59), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 31/55 (56%), Gaps = 4/55 (7%)
Query: 81 NDYSRILPRTYILSH-CDFTA--NLTLTISNVINLE-QLRGWYIKDDVVAEWKKV 131
+++R+L T LSH DF N +++ + + QL+ ++KD+ + WKK+
Sbjct: 209 QEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKHVKDEQIEHWKKI 263
>pdb|2HKO|A Chain A, Crystal Structure Of Lsd1
Length = 664
Score = 27.3 bits (59), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 31/55 (56%), Gaps = 4/55 (7%)
Query: 81 NDYSRILPRTYILSH-CDFTA--NLTLTISNVINLE-QLRGWYIKDDVVAEWKKV 131
+++R+L T LSH DF N +++ + + QL+ ++KD+ + WKK+
Sbjct: 209 QEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKHVKDEQIEHWKKI 263
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
0.323 0.136 0.416
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,280,155
Number of Sequences: 62578
Number of extensions: 275462
Number of successful extensions: 625
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 621
Number of HSP's gapped (non-prelim): 17
length of query: 255
length of database: 14,973,337
effective HSP length: 97
effective length of query: 158
effective length of database: 8,903,271
effective search space: 1406716818
effective search space used: 1406716818
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 50 (23.9 bits)