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= 020795
(321 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 37.4 bits (85), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 22/42 (52%)
Query: 57 LPDELLFEVFARMSPYDLGKASCVCRKWKYTIRNPVFWRNAC 98
LP EL V + + P DL +A+ CR W+ + + WR C
Sbjct: 22 LPKELALYVLSFLEPKDLLQAAQTCRYWRILAEDNLLWREKC 63
>pdb|3L2O|B Chain B, Structure-Based Mechanism Of Dimerization-Dependent
Ubiquitination By The Scffbx4 Ubiquitin Ligase
Length = 312
Score = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 24/44 (54%)
Query: 57 LPDELLFEVFARMSPYDLGKASCVCRKWKYTIRNPVFWRNACLK 100
LP ++ + + +SP+DL + W T+R+P+ WR L+
Sbjct: 8 LPIDVQLYILSFLSPHDLCQLGSTNHYWNETVRDPILWRYFLLR 51
>pdb|1FS2|A Chain A, Insights Into Scf Ubiquitin Ligases From The Structure
Of The Skp1-Skp2 Complex
pdb|1FS2|C Chain C, Insights Into Scf Ubiquitin Ligases From The Structure
Of The Skp1-Skp2 Complex
Length = 272
Score = 32.7 bits (73), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 22/39 (56%)
Query: 57 LPDELLFEVFARMSPYDLGKASCVCRKWKYTIRNPVFWR 95
LPDELL +F+ + +L K S VC++W + W+
Sbjct: 12 LPDELLLGIFSCLCLPELLKVSGVCKRWYRLASDESLWQ 50
>pdb|1FQV|A Chain A, Insights Into Scf Ubiquitin Ligases From The Structure
Of The Skp1-Skp2 Complex
pdb|1FQV|C Chain C, Insights Into Scf Ubiquitin Ligases From The Structure
Of The Skp1-Skp2 Complex
pdb|1FQV|E Chain E, Insights Into Scf Ubiquitin Ligases From The Structure
Of The Skp1-Skp2 Complex
pdb|1FQV|G Chain G, Insights Into Scf Ubiquitin Ligases From The Structure
Of The Skp1-Skp2 Complex
pdb|1FQV|I Chain I, Insights Into Scf Ubiquitin Ligases From The Structure
Of The Skp1-Skp2 Complex
pdb|1FQV|K Chain K, Insights Into Scf Ubiquitin Ligases From The Structure
Of The Skp1-Skp2 Complex
pdb|1FQV|M Chain M, Insights Into Scf Ubiquitin Ligases From The Structure
Of The Skp1-Skp2 Complex
pdb|1FQV|O Chain O, Insights Into Scf Ubiquitin Ligases From The Structure
Of The Skp1-Skp2 Complex
pdb|2ASS|B Chain B, Crystal Structure Of The Skp1-Skp2-Cks1 Complex
pdb|2AST|B Chain B, Crystal Structure Of Skp1-Skp2-Cks1 In Complex With A
P27 Peptide
Length = 336
Score = 32.7 bits (73), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 22/39 (56%)
Query: 57 LPDELLFEVFARMSPYDLGKASCVCRKWKYTIRNPVFWR 95
LPDELL +F+ + +L K S VC++W + W+
Sbjct: 12 LPDELLLGIFSCLCLPELLKVSGVCKRWYRLASDESLWQ 50
>pdb|1FS1|A Chain A, Insights Into Scf Ubiquitin Ligases From The Structure
Of The Skp1-Skp2 Complex
pdb|1FS1|C Chain C, Insights Into Scf Ubiquitin Ligases From The Structure
Of The Skp1-Skp2 Complex
Length = 53
Score = 32.0 bits (71), Expect = 0.42, Method: Composition-based stats.
Identities = 14/39 (35%), Positives = 22/39 (56%)
Query: 57 LPDELLFEVFARMSPYDLGKASCVCRKWKYTIRNPVFWR 95
LPDELL +F+ + +L K S VC++W + W+
Sbjct: 12 LPDELLLGIFSCLCLPELLKVSGVCKRWYRLASDESLWQ 50
>pdb|1LDK|E Chain E, Structure Of The Cul1-Rbx1-Skp1-F Boxskp2 Scf Ubiquitin
Ligase Complex
Length = 41
Score = 31.6 bits (70), Expect = 0.64, Method: Composition-based stats.
Identities = 14/38 (36%), Positives = 21/38 (55%)
Query: 57 LPDELLFEVFARMSPYDLGKASCVCRKWKYTIRNPVFW 94
LPDELL +F+ + +L K S VC++W + W
Sbjct: 4 LPDELLLGIFSCLCLPELLKVSGVCKRWYRLASDESLW 41
>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 = 3.8, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 36/85 (42%), Gaps = 9/85 (10%)
Query: 241 NNRMDLLS---LVTSGMNDNEVNGHDEDILGVVEGWQDDETHNPDVPAVSHK-----RGL 292
R DL+ +T D ++ H +L VV W+ D+T DVP + K +
Sbjct: 424 GERCDLIQEGGRITDPTIDKRMDFHFNALLDVVSEWRKDKTQLQDVP-LGEKIEEIYKAF 482
Query: 293 TPFVFVPFEEVETSVLNLPVEKMDY 317
+ F E+E VL + ++Y
Sbjct: 483 IKESGIQFSELEGQVLQFHLSNLEY 507
>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 = 4.3, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 36/85 (42%), Gaps = 9/85 (10%)
Query: 241 NNRMDLLS---LVTSGMNDNEVNGHDEDILGVVEGWQDDETHNPDVPAVSHK-----RGL 292
R DL+ +T D ++ H +L VV W+ D+T DVP + K +
Sbjct: 416 GERCDLIQEGGRITDPTIDKRMDFHFNALLDVVSEWRKDKTQLQDVP-LGEKIEEIYKAF 474
Query: 293 TPFVFVPFEEVETSVLNLPVEKMDY 317
+ F E+E VL + ++Y
Sbjct: 475 IKESGIQFSELEGQVLQFHLSNLEY 499
>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 = 28.5 bits (62), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 36/85 (42%), Gaps = 9/85 (10%)
Query: 241 NNRMDLLS---LVTSGMNDNEVNGHDEDILGVVEGWQDDETHNPDVPAVSHK-----RGL 292
R DL+ +T D ++ H +L VV W+ D+T DVP + K +
Sbjct: 436 GERCDLIQEGGRITDPTIDKRMDFHFNALLDVVSEWRKDKTQLQDVP-LGEKIEEIYKAF 494
Query: 293 TPFVFVPFEEVETSVLNLPVEKMDY 317
+ F E+E VL + ++Y
Sbjct: 495 IKESGIQFSELEGQVLQFHLSNLEY 519
>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 = 5.2, Method: Compositional matrix adjust.
Identities = 29/133 (21%), Positives = 52/133 (39%), Gaps = 10/133 (7%)
Query: 193 FRAAKADCVFTGHYTLSEEKVEAAVLYPGLRPTVLRIRLRLRGTTAGAN---NRMDLLSL 249
+ + A TG+Y E +++ A +PG+ P R T + + +D++ L
Sbjct: 84 YTSGVAKSRATGNYGYYEARIKGASTFPGVSPAFWXYSTIDRSLTKEGDVQYSEIDVVEL 143
Query: 250 VTSGMNDNEVNGHDEDILG-VVEGWQDDETHNPDVPAVSHKRGLTPFVFVPFEEVETSVL 308
V D D+ VV+ + P +H P F P + T +
Sbjct: 144 TQKSA----VRESDHDLHNIVVKNGKPTWXRPGSFPQTNHNGYHLP--FDPRNDFHTYGV 197
Query: 309 NLPVEKMDYYVPG 321
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
0.323 0.139 0.440
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,224,441
Number of Sequences: 62578
Number of extensions: 428065
Number of successful extensions: 770
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 764
Number of HSP's gapped (non-prelim): 10
length of query: 321
length of database: 14,973,337
effective HSP length: 99
effective length of query: 222
effective length of database: 8,778,115
effective search space: 1948741530
effective search space used: 1948741530
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: 51 (24.3 bits)