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= 001272
(1110 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1JTH|A Chain A, Crystal Structure And Biophysical Properties Of A Complex
Between The N-Terminal Region Of Snap25 And The Snare
Region Of Syntaxin 1a
pdb|1JTH|C Chain C, Crystal Structure And Biophysical Properties Of A Complex
Between The N-Terminal Region Of Snap25 And The Snare
Region Of Syntaxin 1a
Length = 82
Score = 37.0 bits (84), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 34/60 (56%), Gaps = 7/60 (11%)
Query: 920 DHSAYQTPESGPHVVEVVESSRSKAQKMVDVAVQALSSLEKEGNGIERIEEAMDYVNNKL 979
D A ++ ES ++++VE S+ D ++ L L+++G +ERIEE MD +N +
Sbjct: 19 DQLADESLESTRRMLQLVEESK-------DAGIRTLVMLDEQGEQLERIEEGMDQINKDM 71
>pdb|3ZV0|C Chain C, Structure Of The Shq1p-Cbf5p Complex
pdb|3ZV0|D Chain D, Structure Of The Shq1p-Cbf5p Complex
Length = 195
Score = 34.7 bits (78), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 26/115 (22%), Positives = 48/115 (41%), Gaps = 16/115 (13%)
Query: 792 NFTELQMNGQPRERDIEGYMKFTPCENLETAY--------APSHISPSTNYPINNLLQQH 843
++T + P +RD++ Y+ P E L Y A + + I LL+
Sbjct: 44 HYTPIPAGSSPLKRDLKSYISSGPLETLLVGYKRIVVKDSAVNAVCYGAKLMIPGLLRYE 103
Query: 844 KGVSYTDSEVHVGSTGQA-----KEEDVLALSHLRHALDKKVASALFCLRQRNTY 893
+G+ D V + + G+A + + L+ H + VAS C+ +R+ Y
Sbjct: 104 EGIELYDEIVLITTKGEAIAVAIAQMSTVDLASCDHGV---VASVKRCIMERDLY 155
>pdb|1KIL|C Chain C, Three-Dimensional Structure Of The ComplexinSNARE COMPLEX
Length = 74
Score = 33.9 bits (76), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 35/60 (58%), Gaps = 7/60 (11%)
Query: 920 DHSAYQTPESGPHVVEVVESSRSKAQKMVDVAVQALSSLEKEGNGIERIEEAMDYVNNKL 979
D A ++ ES ++++VE S+ D ++ L L+++G ++R+EE M+++N +
Sbjct: 11 DQLADESLESTRRMLQLVEESK-------DAGIRTLVMLDEQGEQLDRVEEGMNHINQDM 63
>pdb|1N7S|C Chain C, High Resolution Structure Of A Truncated Neuronal Snare
Complex
Length = 79
Score = 33.5 bits (75), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 35/60 (58%), Gaps = 7/60 (11%)
Query: 920 DHSAYQTPESGPHVVEVVESSRSKAQKMVDVAVQALSSLEKEGNGIERIEEAMDYVNNKL 979
D A ++ ES ++++VE S+ D ++ L L+++G ++R+EE M+++N +
Sbjct: 15 DQLADESLESTRRMLQLVEESK-------DAGIRTLVMLDEQGEQLDRVEEGMNHINQDM 67
>pdb|3RK2|C Chain C, Truncated Snare Complex
pdb|3RK2|G Chain G, Truncated Snare Complex
pdb|3RK3|C Chain C, Truncated Snare Complex With Complexin
pdb|3RL0|C Chain C, Truncated Snare Complex With Complexin (P1)
pdb|3RL0|G Chain G, Truncated Snare Complex With Complexin (P1)
pdb|3RL0|K Chain K, Truncated Snare Complex With Complexin (P1)
pdb|3RL0|O Chain O, Truncated Snare Complex With Complexin (P1)
pdb|3RL0|S Chain S, Truncated Snare Complex With Complexin (P1)
pdb|3RL0|W Chain W, Truncated Snare Complex With Complexin (P1)
pdb|3RL0|AA Chain a, Truncated Snare Complex With Complexin (P1)
pdb|3RL0|EE Chain e, Truncated Snare Complex With Complexin (P1)
Length = 81
Score = 33.5 bits (75), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 35/60 (58%), Gaps = 7/60 (11%)
Query: 920 DHSAYQTPESGPHVVEVVESSRSKAQKMVDVAVQALSSLEKEGNGIERIEEAMDYVNNKL 979
D A ++ ES ++++VE S+ D ++ L L+++G ++R+EE M+++N +
Sbjct: 17 DQLADESLESTRRMLQLVEESK-------DAGIRTLVMLDEQGEQLDRVEEGMNHINQDM 69
>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 = 33.5 bits (75), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 28/51 (54%)
Query: 46 QWSKEELERFYEAYRKYGKDWKKIAAAVRNRTAEMVEALFTMNRAYLSLPE 96
+W+ EE +A RKYG+D++ I+ + N++ V+ F R ++ E
Sbjct: 135 RWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNYRRRFNIDE 185
>pdb|1SFC|C Chain C, Neuronal Synaptic Fusion Complex
pdb|1SFC|G Chain G, Neuronal Synaptic Fusion Complex
pdb|1SFC|K Chain K, Neuronal Synaptic Fusion Complex
Length = 83
Score = 33.5 bits (75), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 35/60 (58%), Gaps = 7/60 (11%)
Query: 920 DHSAYQTPESGPHVVEVVESSRSKAQKMVDVAVQALSSLEKEGNGIERIEEAMDYVNNKL 979
D A ++ ES ++++VE S+ D ++ L L+++G ++R+EE M+++N +
Sbjct: 19 DQLADESLESTRRMLQLVEESK-------DAGIRTLVMLDEQGEQLDRVEEGMNHINQDM 71
>pdb|1URQ|C Chain C, Crystal Structure Of Neuronal Q-Snares In Complex With
R-Snare Motif Of Tomosyn
pdb|3HD7|C Chain C, Helical Extension Of The Neuronal Snare Complex Into The
Membrane, Spacegroup C 1 2 1
pdb|3HD7|G Chain G, Helical Extension Of The Neuronal Snare Complex Into The
Membrane, Spacegroup C 1 2 1
pdb|3IPD|C Chain C, Helical Extension Of The Neuronal Snare Complex Into The
Membrane, Spacegroup I 21 21 21
pdb|3IPD|G Chain G, Helical Extension Of The Neuronal Snare Complex Into The
Membrane, Spacegroup I 21 21 21
Length = 80
Score = 33.5 bits (75), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 35/60 (58%), Gaps = 7/60 (11%)
Query: 920 DHSAYQTPESGPHVVEVVESSRSKAQKMVDVAVQALSSLEKEGNGIERIEEAMDYVNNKL 979
D A ++ ES ++++VE S+ D ++ L L+++G ++R+EE M+++N +
Sbjct: 16 DQLADESLESTRRMLQLVEESK-------DAGIRTLVMLDEQGEQLDRVEEGMNHINQDM 68
>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 = 32.7 bits (73), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 28/51 (54%)
Query: 46 QWSKEELERFYEAYRKYGKDWKKIAAAVRNRTAEMVEALFTMNRAYLSLPE 96
+W+ EE +A RKYG+D++ I+ + N++ V+ F R ++ E
Sbjct: 78 RWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNYRRRFNIDE 128
>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 = 32.7 bits (73), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 28/51 (54%)
Query: 46 QWSKEELERFYEAYRKYGKDWKKIAAAVRNRTAEMVEALFTMNRAYLSLPE 96
+W+ EE +A RKYG+D++ I+ + N++ V+ F R ++ E
Sbjct: 382 RWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNYRRRFNIDE 432
>pdb|2X0L|B Chain B, Crystal Structure Of A Neuro-Specific Splicing Variant Of
Human Histone Lysine Demethylase Lsd1
Length = 133
Score = 32.3 bits (72), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 28/51 (54%)
Query: 46 QWSKEELERFYEAYRKYGKDWKKIAAAVRNRTAEMVEALFTMNRAYLSLPE 96
+W+ EE +A RKYG+D++ I+ + N++ V+ F R ++ E
Sbjct: 75 RWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNYRRRFNIDE 125
>pdb|2CU7|A Chain A, Solution Structure Of The Sant Domain Of Human Kiaa1915
Protein
Length = 72
Score = 31.6 bits (70), Expect = 2.7, Method: Composition-based stats.
Identities = 13/38 (34%), Positives = 23/38 (60%)
Query: 46 QWSKEELERFYEAYRKYGKDWKKIAAAVRNRTAEMVEA 83
+W+ EE E F + K+G+ W KI+ + +RT V++
Sbjct: 11 KWTIEEKELFEQGLAKFGRRWTKISKLIGSRTVLQVKS 48
>pdb|3A04|A Chain A, Crystal Structure Of Tryptophanyl-Trna Synthetase From
Hyperthermophilic Archaeon, Aeropyrum Pernix K1
pdb|3A05|A Chain A, Crystal Structure Of Tryptophanyl-Trna Synthetase From
Hyperthermophilic Archaeon, Aeropyrum Pernix K1 Complex
With Tryptophan
Length = 372
Score = 31.2 bits (69), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 29/105 (27%), Positives = 54/105 (51%), Gaps = 12/105 (11%)
Query: 428 PEAVNESKLKGNRSSTGVKDTAIKTSKLG---KDCT----DDVSVIPESEEGNHLTNSGN 480
P V +KL R+ TG + TA + +LG + C+ D ++P+ E H+ S
Sbjct: 271 PPEVARNKL--FRALTGGRATAEEQRRLGGVPEVCSVYHMDLYHLMPDDGEVKHIYTS-- 326
Query: 481 RTKRQKFLPIKLRMDATEELKKFISKGKRSLSASQSKHGKLVKPP 525
+ K L + + A E+L++F+++ + L +++ KLV+PP
Sbjct: 327 -CRLGKILCGECKQIAWEKLERFLAEHQSRLEKAKTIAWKLVEPP 370
>pdb|2R8U|A Chain A, Structure Of Fragment Of Human End-Binding Protein 1 (Eb1)
Containing The N-Terminal Domain At 1.35 A Resolution
pdb|2R8U|B Chain B, Structure Of Fragment Of Human End-Binding Protein 1 (Eb1)
Containing The N-Terminal Domain At 1.35 A Resolution
Length = 268
Score = 30.8 bits (68), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 2/51 (3%)
Query: 787 GKFMDNFTELQMNGQPRERDIEG--YMKFTPCENLETAYAPSHISPSTNYP 835
GKF DNF +Q + + + +G Y + ETA APS ++P+ N P
Sbjct: 99 GKFQDNFEFVQWFKKFFDANYDGKDYDPVAARQGQETAVAPSLVAPALNKP 149
>pdb|3OSF|A Chain A, The Structure Of Protozoan Parasite Trichomonas
Vaginalis Myb2 In Complex With Mre-2f-13 Dna
pdb|3OSF|D Chain D, The Structure Of Protozoan Parasite Trichomonas
Vaginalis Myb2 In Complex With Mre-2f-13 Dna
pdb|3OSG|A Chain A, The Structure Of Protozoan Parasite Trichomonas
Vaginalis Myb2 In Complex With Mre-1-12 Dna
pdb|3OSG|D Chain D, The Structure Of Protozoan Parasite Trichomonas
Vaginalis Myb2 In Complex With Mre-1-12 Dna
Length = 126
Score = 30.0 bits (66), Expect = 7.9, Method: Composition-based stats.
Identities = 14/33 (42%), Positives = 19/33 (57%)
Query: 46 QWSKEELERFYEAYRKYGKDWKKIAAAVRNRTA 78
+++ EE E A ++G DWK IAA NR A
Sbjct: 13 KFTPEEDEMLKRAVAQHGSDWKMIAATFPNRNA 45
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
0.312 0.127 0.359
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 30,388,805
Number of Sequences: 62578
Number of extensions: 1229437
Number of successful extensions: 2579
Number of sequences better than 100.0: 32
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 2554
Number of HSP's gapped (non-prelim): 43
length of query: 1110
length of database: 14,973,337
effective HSP length: 109
effective length of query: 1001
effective length of database: 8,152,335
effective search space: 8160487335
effective search space used: 8160487335
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 57 (26.6 bits)