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= 025376
(253 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3L2O|B Chain B, Structure-Based Mechanism Of Dimerization-Dependent
Ubiquitination By The Scffbx4 Ubiquitin Ligase
Length = 312
Score = 30.8 bits (68), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 1 MSPYDLGKASCVCRKWKYTIRNPVFWRNACLK 32
+SP+DL + W T+R+P+ WR L+
Sbjct: 20 LSPHDLCQLGSTNHYWNETVRDPILWRYFLLR 51
>pdb|2OVP|B Chain B, Structure Of The Skp1-Fbw7 Complex
pdb|2OVQ|B Chain B, Structure Of The Skp1-Fbw7-Cyclinedegc Complex
pdb|2OVR|B Chain B, Structure Of The Skp1-Fbw7-Cyclinedegn Complex
Length = 445
Score = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 10/30 (33%), Positives = 16/30 (53%)
Query: 1 MSPYDLGKASCVCRKWKYTIRNPVFWRNAC 30
+ P DL +A+ CR W+ + + WR C
Sbjct: 34 LEPKDLLQAAQTCRYWRILAEDNLLWREKC 63
>pdb|4GU1|A Chain A, Crystal Structure Of Lsd2
pdb|4GU1|B Chain B, Crystal Structure Of Lsd2
Length = 784
Score = 28.9 bits (63), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 36/85 (42%), Gaps = 9/85 (10%)
Query: 173 NNRMDLLS---LVTSGMNDNEVNGHDEDILGVVEGWQDDETHNPDVPAVSHK-----RGL 224
R DL+ +T D ++ H +L VV W+ D+T DVP + K +
Sbjct: 424 GERCDLIQEGGRITDPTIDKRMDFHFNALLDVVSEWRKDKTQLQDVP-LGEKIEEIYKAF 482
Query: 225 TPFVFVPFEEVETSVLNLPVEKMDY 249
+ F E+E VL + ++Y
Sbjct: 483 IKESGIQFSELEGQVLQFHLSNLEY 507
>pdb|4FWE|A Chain A, Native Structure Of Lsd2 /aof1/kdm1b In Spacegroup Of
C2221 At 2.13a
pdb|4FWF|A Chain A, Complex Structure Of Lsd2/aof1/kdm1b With H3k4 Mimic
pdb|4FWJ|A Chain A, Native Structure Of Lsd2/aof1/kdm1b In Spacegroup Of I222
At 2.9a
pdb|4FWJ|B Chain B, Native Structure Of Lsd2/aof1/kdm1b In Spacegroup Of I222
At 2.9a
Length = 796
Score = 28.9 bits (63), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 36/85 (42%), Gaps = 9/85 (10%)
Query: 173 NNRMDLLS---LVTSGMNDNEVNGHDEDILGVVEGWQDDETHNPDVPAVSHK-----RGL 224
R DL+ +T D ++ H +L VV W+ D+T DVP + K +
Sbjct: 436 GERCDLIQEGGRITDPTIDKRMDFHFNALLDVVSEWRKDKTQLQDVP-LGEKIEEIYKAF 494
Query: 225 TPFVFVPFEEVETSVLNLPVEKMDY 249
+ F E+E VL + ++Y
Sbjct: 495 IKESGIQFSELEGQVLQFHLSNLEY 519
>pdb|4GUR|A Chain A, Crystal Structure Of Lsd2-npac With H3 In Space Group P21
pdb|4GUS|A Chain A, Crystal Structure Of Lsd2-npac With H3 In Space Group
P3221
pdb|4GUT|A Chain A, Crystal Structure Of Lsd2-npac
pdb|4GUU|A Chain A, Crystal Structure Of Lsd2-npac With Tranylcypromine
pdb|4GU0|A Chain A, Crystal Structure Of Lsd2 With H3
pdb|4GU0|B Chain B, Crystal Structure Of Lsd2 With H3
pdb|4GU0|C Chain C, Crystal Structure Of Lsd2 With H3
pdb|4GU0|D Chain D, Crystal Structure Of Lsd2 With H3
pdb|4HSU|A Chain A, Crystal Structure Of Lsd2-npac With H3(1-26)in Space Group
P21
Length = 776
Score = 28.9 bits (63), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 36/85 (42%), Gaps = 9/85 (10%)
Query: 173 NNRMDLLS---LVTSGMNDNEVNGHDEDILGVVEGWQDDETHNPDVPAVSHK-----RGL 224
R DL+ +T D ++ H +L VV W+ D+T DVP + K +
Sbjct: 416 GERCDLIQEGGRITDPTIDKRMDFHFNALLDVVSEWRKDKTQLQDVP-LGEKIEEIYKAF 474
Query: 225 TPFVFVPFEEVETSVLNLPVEKMDY 249
+ F E+E VL + ++Y
Sbjct: 475 IKESGIQFSELEGQVLQFHLSNLEY 499
>pdb|1DYP|A Chain A, 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate-3,6-Anhydro-D-
Galactose 4 Galactohydrolase
Length = 271
Score = 28.5 bits (62), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 29/133 (21%), Positives = 51/133 (38%), Gaps = 10/133 (7%)
Query: 125 FRAAKADCVFTGHYTLSEEKVEAAVLYPGLRPTVLRIRLRLRGTTAGAN---NRMDLLSL 181
+ + A TG+Y E +++ A +PG+ P R T + + +D++ L
Sbjct: 84 YTSGVAKSRATGNYGYYEARIKGASTFPGVSPAFWXYSTIDRSLTKEGDVQYSEIDVVEL 143
Query: 182 VTSGMNDNEVNGHDEDILGVVEGWQDDETHNP-DVPAVSHKRGLTPFVFVPFEEVETSVL 240
V D D+ +V P P +H P F P + T +
Sbjct: 144 TQKSA----VRESDHDLHNIVVKNGKPTWXRPGSFPQTNHNGYHLP--FDPRNDFHTYGV 197
Query: 241 NLPVEKMDYYVPG 253
N+ +K+ +YV G
Sbjct: 198 NVTKDKITWYVDG 210
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
0.322 0.138 0.439
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,197,896
Number of Sequences: 62578
Number of extensions: 339211
Number of successful extensions: 621
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 619
Number of HSP's gapped (non-prelim): 6
length of query: 253
length of database: 14,973,337
effective HSP length: 97
effective length of query: 156
effective length of database: 8,903,271
effective search space: 1388910276
effective search space used: 1388910276
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 bits)