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= psy7682
(383 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4F3L|A Chain A, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 361
Score = 77.4 bits (189), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 43/145 (29%), Positives = 81/145 (55%), Gaps = 11/145 (7%)
Query: 50 VNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQ 109
V++ +EK+RR+Q N I+EL ++ A K DK +LQ++++ +R K+
Sbjct: 14 VSRNKSEKKRRDQFNVLIKELGSMLPGN---------ARKMDKSTVLQKSIDFLRKHKET 64
Query: 110 ETSSDAVQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYS 169
SDA + + KPT ++NE L+LEAL+GF + DG + + +E++ S + +
Sbjct: 65 TAQSDASEIRQ--DWKPTFLSNEEFTQLMLEALDGFFLAIMTDGSIIYVSESVTSLLEHL 122
Query: 170 RQEVLGKSVYNLIHHGDHARFHNCL 194
+++ +S++N I G+H+ + L
Sbjct: 123 PSDLVDQSIFNFIPEGEHSEVYKIL 147
>pdb|4F3L|B Chain B, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 387
Score = 74.3 bits (181), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 41/135 (30%), Positives = 80/135 (59%), Gaps = 13/135 (9%)
Query: 56 EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQETSSDA 115
EKRRR++ N++I+ELA L+ + +++ K DK +L+ V ++ ++ A
Sbjct: 21 EKRRRDKMNSFIDELASLVPTCN------AMSRKLDKLTVLRMAVQHMKTLR------GA 68
Query: 116 VQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPD-GYVNFCTENIKSFIRYSRQEVL 174
++ KPT ++++ L L+L A +GFLFVV D G + F +E++ + YS+ +++
Sbjct: 69 TNPYTEANYKPTFLSDDELKHLILRAADGFLFVVGCDRGKILFVSESVFKILNYSQNDLI 128
Query: 175 GKSVYNLIHHGDHAR 189
G+S+++ +H D A+
Sbjct: 129 GQSLFDYLHPKDIAK 143
>pdb|4H10|A Chain A, Intermolecular Recognition Revealed By The Complex
Structure Of Human Clock-bmal1 Basic Helix-loop-helix
Domains With E-box Dna
Length = 73
Score = 33.9 bits (76), Expect = 0.17, Method: Composition-based stats.
Identities = 16/52 (30%), Positives = 33/52 (63%), Gaps = 6/52 (11%)
Query: 56 EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIK 107
EKRRR++ N++I+ELA L+ + ++++ K DK +L+ V ++ ++
Sbjct: 17 EKRRRDKMNSFIDELASLVP------TCNAMSRKLDKLTVLRMAVQHMKTLR 62
Score = 31.2 bits (69), Expect = 1.1, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 29/47 (61%), Gaps = 6/47 (12%)
Query: 6 EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQ 52
EKRRR++ N++I+ELA L+ + ++++ K DK +L+ V
Sbjct: 17 EKRRRDKMNSFIDELASLVP------TCNAMSRKLDKLTVLRMAVQH 57
>pdb|3RTY|A Chain A, Structure Of An Enclosed Dimer Formed By The Drosophila
Period Protein
pdb|3RTY|B Chain B, Structure Of An Enclosed Dimer Formed By The Drosophila
Period Protein
pdb|3RTY|C Chain C, Structure Of An Enclosed Dimer Formed By The Drosophila
Period Protein
pdb|3RTY|D Chain D, Structure Of An Enclosed Dimer Formed By The Drosophila
Period Protein
pdb|3RTY|E Chain E, Structure Of An Enclosed Dimer Formed By The Drosophila
Period Protein
pdb|3RTY|F Chain F, Structure Of An Enclosed Dimer Formed By The Drosophila
Period Protein
pdb|3RTY|G Chain G, Structure Of An Enclosed Dimer Formed By The Drosophila
Period Protein
pdb|3RTY|H Chain H, Structure Of An Enclosed Dimer Formed By The Drosophila
Period Protein
Length = 339
Score = 31.2 bits (69), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 20/39 (51%)
Query: 152 DGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARF 190
DG V + T +I + Y R LG+S + +H D A F
Sbjct: 13 DGIVLYTTPSITDVLGYPRDMWLGRSFIDFVHLKDRATF 51
>pdb|1WA9|A Chain A, Crystal Structure Of The Pas Repeat Region Of The
Drosophila Clock Protein Period
pdb|1WA9|B Chain B, Crystal Structure Of The Pas Repeat Region Of The
Drosophila Clock Protein Period
Length = 368
Score = 31.2 bits (69), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 20/39 (51%)
Query: 152 DGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARF 190
DG V + T +I + Y R LG+S + +H D A F
Sbjct: 17 DGIVLYTTPSITDVLGYPRDMWLGRSFIDFVHLKDRATF 55
>pdb|3GEC|A Chain A, Crystal Structure Of A Tandem Pas Domain Fragment Of
Drosophila Period
Length = 312
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 20/39 (51%)
Query: 152 DGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARF 190
DG V + T +I + Y R LG+S + +H D A F
Sbjct: 22 DGIVLYTTPSITDVLGYPRDMWLGRSFIDFVHLKDRATF 60
>pdb|4H10|B Chain B, Intermolecular Recognition Revealed By The Complex
Structure Of Human Clock-bmal1 Basic Helix-loop-helix
Domains With E-box Dna
Length = 71
Score = 29.6 bits (65), Expect = 2.6, Method: Composition-based stats.
Identities = 18/59 (30%), Positives = 33/59 (55%), Gaps = 9/59 (15%)
Query: 50 VNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQ 108
V++ +EK+RR+Q N I+EL ++ A K DK +LQ++++ +R K+
Sbjct: 10 VSRNKSEKKRRDQFNVLIKELGSMLPGN---------ARKMDKSTVLQKSIDFLRKHKE 59
>pdb|4H6J|A Chain A, Identification Of Cys 255 In Hif-1 As A Novel Site For
Development Of Covalent Inhibitors Of Hif-1 ARNT PASB
DOMAIN PROTEIN-Protein Interaction
Length = 113
Score = 29.6 bits (65), Expect = 3.3, Method: Composition-based stats.
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 152 DGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGD 186
D ++C E I + Y +E+LG+S+Y H D
Sbjct: 14 DMKFSYCDERITELMGYEPEELLGRSIYEYYHALD 48
>pdb|1P97|A Chain A, Nmr Structure Of The C-Terminal Pas Domain Of Hif2a
Length = 114
Score = 28.5 bits (62), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 19/39 (48%)
Query: 145 FLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIH 183
FL + D +C + I I Y +E+LG+S Y H
Sbjct: 8 FLSRHSMDMKFTYCDDRITELIGYHPEELLGRSAYEFYH 46
>pdb|4AP2|A Chain A, Crystal Structure Of The Human Klhl11-cul3 Complex At 2.8a
Resolution
pdb|4APF|A Chain A, Crystal Structure Of The Human Klhl11-cul3 Complex At 3.1a
Resolution
Length = 297
Score = 28.5 bits (62), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 2/60 (3%)
Query: 33 MSSLAVKPDKCAILQETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDK 92
+S L + D +L ETV + + +R E+ Y EEL +L+ + + + VKP++
Sbjct: 210 LSDLEITVDSEEVLFETVLKWV--QRNAEERERYFEELFKLLRLSQMKPTYLTRHVKPER 267
>pdb|2YJY|A Chain A, A Specific And Modular Binding Code For Cytosine
Recognition In Puf Domains
pdb|2YJY|B Chain B, A Specific And Modular Binding Code For Cytosine
Recognition In Puf Domains
Length = 350
Score = 28.5 bits (62), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 27/143 (18%), Positives = 60/143 (41%), Gaps = 14/143 (9%)
Query: 28 SFAESMSSLAVKPDKCAILQETVNQCLNEKRR--REQENNYIEELAELISAASFAESMSS 85
+F + +L+ P C ++Q + CL ++ E+ + + E+L + + +
Sbjct: 166 AFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPILEELHQHTEQLVQDQYGSYVIRHVLE 225
Query: 86 LAVKPDKCAILQETVNQIRNIKQQETSSDAVQQ--GEVSSSKPTVITNEVL----GPLLL 139
DK I+ E + + Q + +S+ V++ S ++ V+ +EV GP
Sbjct: 226 HGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGP--- 282
Query: 140 EALEGFLFVVNPDGYVNFCTENI 162
L+ + D Y N+ + +
Sbjct: 283 ---HSALYTMMKDQYANYVVQKM 302
>pdb|2A24|A Chain A, Haddock Structure Of Hif-2aARNT PAS-B Heterodimer
Length = 107
Score = 28.1 bits (61), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 20/42 (47%)
Query: 145 FLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGD 186
FL + D +C + I I Y +E+LG+S Y H D
Sbjct: 3 FLSRHSMDMKFTYCDDRITELIGYHPEELLGRSAYEFYHALD 44
>pdb|3F1N|A Chain A, Crystal Structure Of A High Affinity Heterodimer Of Hif2
Alpha And Arnt C-Terminal Pas Domains, With Internally
Bound Ethylene Glycol.
pdb|3F1O|A Chain A, Crystal Structure Of The High Affinity Heterodimer Of Hif2
Alpha And Arnt C-Terminal Pas Domains, With An
Internally- Bound Artificial Ligand
pdb|3F1P|A Chain A, Crystal Structure Of A High Affinity Heterodimer Of Hif2
Alpha And Arnt C-Terminal Pas Domains
pdb|3H7W|A Chain A, Crystal Structure Of The High Affinity Heterodimer Of Hif2
Alpha And Arnt C-Terminal Pas Domains With The
Artificial Ligand Ths017
pdb|3H82|A Chain A, Crystal Structure Of The High Affinity Heterodimer Of Hif2
Alpha And Arnt C-Terminal Pas Domains With The
Artificial Ligand Ths020
pdb|4GHI|A Chain A, Crystal Structure Of The High Affinity Heterodimer Of Hif2
Alpha And Arnt C-terminal Pas Domains In Complex With A
Benzoxadiazole Antagonist
Length = 117
Score = 28.1 bits (61), Expect = 8.0, Method: Composition-based stats.
Identities = 14/42 (33%), Positives = 20/42 (47%)
Query: 145 FLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGD 186
FL + D +C + I I Y +E+LG+S Y H D
Sbjct: 11 FLSEHSMDMKFTYCDDRITELIGYHPEELLGRSAYEFYHALD 52
>pdb|1IB2|A Chain A, Crystal Structure Of A Pumilio-Homology Domain
pdb|1M8Z|A Chain A, Crystal Structure Of A Pumilio-Homology Domain
pdb|1M8W|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Nre1-19 Rna
pdb|1M8W|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Nre1-19 Rna
pdb|1M8X|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Nre1-14 Rna
pdb|1M8X|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Nre1-14 Rna
pdb|1M8Y|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Nre2-10 Rna
pdb|1M8Y|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Nre2-10 Rna
pdb|3Q0L|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With P38alpha Nrea
pdb|3Q0L|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With P38alpha Nrea
pdb|3Q0M|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With P38alpha Nreb
pdb|3Q0M|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With P38alpha Nreb
pdb|3Q0N|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Erk2 Nre
pdb|3Q0N|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Erk2 Nre
pdb|3Q0O|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Erk2 Nre
pdb|3Q0O|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Erk2 Nre
pdb|3Q0P|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Hunchback Nre
pdb|3Q0P|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Hunchback Nre
Length = 349
Score = 27.7 bits (60), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 27/143 (18%), Positives = 60/143 (41%), Gaps = 14/143 (9%)
Query: 28 SFAESMSSLAVKPDKCAILQETVNQCLNEKRR--REQENNYIEELAELISAASFAESMSS 85
+F + +L+ P C ++Q + CL ++ E+ + + E+L + + +
Sbjct: 165 AFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPILEELHQHTEQLVQDQYGNYVIQHVLE 224
Query: 86 LAVKPDKCAILQETVNQIRNIKQQETSSDAVQQ--GEVSSSKPTVITNEVL----GPLLL 139
DK I+ E + + Q + +S+ V++ S ++ V+ +EV GP
Sbjct: 225 HGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGP--- 281
Query: 140 EALEGFLFVVNPDGYVNFCTENI 162
L+ + D Y N+ + +
Sbjct: 282 ---HSALYTMMKDQYANYVVQKM 301
>pdb|1AN4|A Chain A, Structure And Function Of The BHLHZ DOMAIN OF USF
pdb|1AN4|B Chain B, Structure And Function Of The BHLHZ DOMAIN OF USF
Length = 65
Score = 27.7 bits (60), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 31/53 (58%), Gaps = 4/53 (7%)
Query: 56 EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQ 108
E+RRR++ NN+I +L+++I + SM S K IL + + I+ ++Q
Sbjct: 13 ERRRRDKINNWIVQLSKIIPDS----SMESTKSGQSKGGILSKASDYIQELRQ 61
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
0.315 0.128 0.371
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,365,898
Number of Sequences: 62578
Number of extensions: 381975
Number of successful extensions: 891
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 869
Number of HSP's gapped (non-prelim): 28
length of query: 383
length of database: 14,973,337
effective HSP length: 101
effective length of query: 282
effective length of database: 8,652,959
effective search space: 2440134438
effective search space used: 2440134438
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)