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= psy9232
(119 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3DZU|A Chain A, Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex On
Dna Bound With Bvt.13, 9-Cis Retinoic Acid And Ncoa2
Peptide
pdb|3DZY|A Chain A, Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex On
Dna Bound With Rosiglitazone, 9-Cis Retinoic Acid And
Ncoa2 Peptide
pdb|3E00|A Chain A, Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex On
Dna Bound With Gw9662, 9-Cis Retinoic Acid And Ncoa2
Peptide
Length = 467
Score = 49.7 bits (117), Expect = 4e-07, Method: Composition-based stats.
Identities = 16/42 (38%), Positives = 28/42 (66%)
Query: 20 RNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTR 61
++L Y C++ C++D +RN+CQ CR+ KCL + M R+ +
Sbjct: 170 KDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQ 211
>pdb|2EBL|A Chain A, Solution Structure Of The Zinc Finger, C4-type Domain Of
Human Coup Transcription Factor 1
Length = 89
Score = 47.4 bits (111), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 21/44 (47%), Positives = 27/44 (61%)
Query: 20 RNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLG 63
RNL Y C+ +C +D RNQCQ CR KCL+V M R+ + G
Sbjct: 40 RNLTYTCRANRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQRG 83
>pdb|1LAT|A Chain A, Glucocorticoid Receptor MutantDNA COMPLEX
pdb|1LAT|B Chain B, Glucocorticoid Receptor MutantDNA COMPLEX
Length = 82
Score = 47.4 bits (111), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/53 (43%), Positives = 30/53 (56%), Gaps = 4/53 (7%)
Query: 13 SCQFVFVRNLE----YVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTR 61
C+ F R +E Y+CK G CI+D RR C ACR+ KCLQ MN + +
Sbjct: 26 GCKAFFKRAVEGQHNYLCKYEGKCIIDKIRRKNCPACRYRKCLQAGMNLEARK 78
>pdb|4HN5|A Chain A, Gr Dna Binding Domain - Tslp Ngre Complex
pdb|4HN5|B Chain B, Gr Dna Binding Domain - Tslp Ngre Complex
Length = 117
Score = 47.4 bits (111), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/53 (43%), Positives = 30/53 (56%), Gaps = 4/53 (7%)
Query: 13 SCQFVFVRNLE----YVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTR 61
SC+ F R +E Y+C R CI+D RR C ACR+ KCLQ MN + +
Sbjct: 51 SCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEARK 103
>pdb|3G6T|A Chain A, Gr Gamma Dna-Binding Domain:fkbp5 16bp Complex-34
pdb|3G6T|B Chain B, Gr Gamma Dna-Binding Domain:fkbp5 16bp Complex-34
Length = 91
Score = 47.0 bits (110), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 24/58 (41%), Positives = 30/58 (51%)
Query: 4 LDCPDCGVVSCQFVFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTR 61
L C C V + V R Y+C R CI+D RR C ACR+ KCLQ MN + +
Sbjct: 20 LTCGSCKVFFKRAVEGRQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEARK 77
>pdb|1R4O|A Chain A, Crystallographic Analysis Of The Interaction Of The
Glucocorticoid Receptor With Dna
pdb|1R4O|B Chain B, Crystallographic Analysis Of The Interaction Of The
Glucocorticoid Receptor With Dna
pdb|1R4R|A Chain A, Crystallographic Analysis Of The Interaction Of The
Glucocorticoid Receptor With Dna
Length = 92
Score = 46.6 bits (109), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 23/53 (43%), Positives = 30/53 (56%), Gaps = 4/53 (7%)
Query: 13 SCQFVFVRNLE----YVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTR 61
SC+ F R +E Y+C R CI+D RR C ACR+ KCLQ MN + +
Sbjct: 26 SCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEARK 78
>pdb|1R4R|B Chain B, Crystallographic Analysis Of The Interaction Of The
Glucocorticoid Receptor With Dna
Length = 92
Score = 46.6 bits (109), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 23/53 (43%), Positives = 30/53 (56%), Gaps = 4/53 (7%)
Query: 13 SCQFVFVRNLE----YVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTR 61
SC+ F R +E Y+C R CI+D RR C ACR+ KCLQ MN + +
Sbjct: 26 SCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEARK 78
>pdb|3G9P|B Chain B, Gr Dna Binding Domain:sgk 16bp Complex-7
pdb|3G9P|A Chain A, Gr Dna Binding Domain:sgk 16bp Complex-7
pdb|3FYL|A Chain A, Gr Dna Binding Domain:cgt Complex
pdb|3FYL|B Chain B, Gr Dna Binding Domain:cgt Complex
pdb|3G6P|A Chain A, Gr Dna Binding Domain:fkbp5 Complex, 18bp
pdb|3G6P|B Chain B, Gr Dna Binding Domain:fkbp5 Complex, 18bp
pdb|3G6Q|B Chain B, Gr Dna Binding Domain:fkbp5 Binding Site Complex-9
pdb|3G6Q|A Chain A, Gr Dna Binding Domain:fkbp5 Binding Site Complex-9
pdb|3G6R|B Chain B, Gr Dna Binding Domain:fkbp5 Complex-52, 18bp
pdb|3G6R|A Chain A, Gr Dna Binding Domain:fkbp5 Complex-52, 18bp
pdb|3G6U|A Chain A, Gr Dna-Binding Domain:fkbp5 16bp Complex-49
pdb|3G6U|B Chain B, Gr Dna-Binding Domain:fkbp5 16bp Complex-49
pdb|3G8U|A Chain A, Dna Binding Domain:gilz 16bp Complex-5
pdb|3G8U|B Chain B, Dna Binding Domain:gilz 16bp Complex-5
pdb|3G8X|A Chain A, Gr Dna Binding Domain:gilz 16bp Complex-65
pdb|3G8X|B Chain B, Gr Dna Binding Domain:gilz 16bp Complex-65
pdb|3G97|B Chain B, Gr Dna-Binding Domain:gilz 16bp Complex-9
pdb|3G97|A Chain A, Gr Dna-Binding Domain:gilz 16bp Complex-9
pdb|3G99|A Chain A, Gr Dna Binding Domain:pal Complex-9
pdb|3G99|B Chain B, Gr Dna Binding Domain:pal Complex-9
pdb|3G9I|A Chain A, Gr Dna Binding Domain: Pal Complex-35
pdb|3G9I|B Chain B, Gr Dna Binding Domain: Pal Complex-35
pdb|3G9J|A Chain A, Gr Dna Binding Domain:pal, 18bp Complex-36
pdb|3G9J|B Chain B, Gr Dna Binding Domain:pal, 18bp Complex-36
pdb|3G9M|A Chain A, Gr Dna-Binding Domain:sgk 16bp Complex-44
pdb|3G9M|B Chain B, Gr Dna-Binding Domain:sgk 16bp Complex-44
pdb|3G9O|B Chain B, Gr Dna-Binding Domain:sgk 16bp Complex-9
pdb|3G9O|A Chain A, Gr Dna-Binding Domain:sgk 16bp Complex-9
Length = 90
Score = 46.6 bits (109), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 23/53 (43%), Positives = 30/53 (56%), Gaps = 4/53 (7%)
Query: 13 SCQFVFVRNLE----YVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTR 61
SC+ F R +E Y+C R CI+D RR C ACR+ KCLQ MN + +
Sbjct: 24 SCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEARK 76
>pdb|1GLU|A Chain A, Crystallographic Analysis Of The Interaction Of The
Glucocorticoid Receptor With Dna
pdb|1GLU|B Chain B, Crystallographic Analysis Of The Interaction Of The
Glucocorticoid Receptor With Dna
Length = 81
Score = 46.2 bits (108), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 23/53 (43%), Positives = 30/53 (56%), Gaps = 4/53 (7%)
Query: 13 SCQFVFVRNLE----YVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTR 61
SC+ F R +E Y+C R CI+D RR C ACR+ KCLQ MN + +
Sbjct: 26 SCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEARK 78
>pdb|2GDA|A Chain A, Refined Solution Structure Of The Glucocorticoid
Receptor Dna-Binding Domain
Length = 72
Score = 45.8 bits (107), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 23/48 (47%), Positives = 28/48 (58%), Gaps = 4/48 (8%)
Query: 13 SCQFVFVRNLE----YVCKERGHCIVDVTRRNQCQACRFSKCLQVKMN 56
SC+ F R +E Y+C R CI+D RR C ACR+ KCLQ MN
Sbjct: 21 SCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMN 68
>pdb|1GDC|A Chain A, Refined Solution Structure Of The Glucocorticoid
Receptor Dna-Binding Domain
Length = 72
Score = 45.8 bits (107), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 23/48 (47%), Positives = 28/48 (58%), Gaps = 4/48 (8%)
Query: 13 SCQFVFVRNLE----YVCKERGHCIVDVTRRNQCQACRFSKCLQVKMN 56
SC+ F R +E Y+C R CI+D RR C ACR+ KCLQ MN
Sbjct: 21 SCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMN 68
>pdb|1RGD|A Chain A, Structure Refinement Of The Glucocorticoid Receptor-Dna
Binding Domain From Nmr Data By Relaxation Matrix
Calculations
Length = 71
Score = 45.8 bits (107), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 23/48 (47%), Positives = 28/48 (58%), Gaps = 4/48 (8%)
Query: 13 SCQFVFVRNLE----YVCKERGHCIVDVTRRNQCQACRFSKCLQVKMN 56
SC+ F R +E Y+C R CI+D RR C ACR+ KCLQ MN
Sbjct: 20 SCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMN 67
>pdb|3M9E|A Chain A, Thyroid Hormone Beta Dna Binding Domain Homodimer With
Inverted Palindrome Tre
pdb|3M9E|B Chain B, Thyroid Hormone Beta Dna Binding Domain Homodimer With
Inverted Palindrome Tre
pdb|3M9E|E Chain E, Thyroid Hormone Beta Dna Binding Domain Homodimer With
Inverted Palindrome Tre
pdb|3M9E|F Chain F, Thyroid Hormone Beta Dna Binding Domain Homodimer With
Inverted Palindrome Tre
Length = 105
Score = 45.8 bits (107), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 23/53 (43%), Positives = 29/53 (54%), Gaps = 6/53 (11%)
Query: 13 SCQFVFVRNLE------YVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDV 59
C+ F R ++ Y CK G CI+D RNQCQ CRF KC+ V M D+
Sbjct: 25 GCKGFFRRTIQKSLHPSYSCKYEGKCIIDKVTRNQCQECRFKKCIYVGMATDL 77
>pdb|4HN6|A Chain A, Gr Dna Binding Domain R460d/d462r - Tslp Ngre Complex
pdb|4HN6|B Chain B, Gr Dna Binding Domain R460d/d462r - Tslp Ngre Complex
Length = 114
Score = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 22/53 (41%), Positives = 29/53 (54%), Gaps = 4/53 (7%)
Query: 13 SCQFVFVRNLE----YVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTR 61
SC+ F R +E Y+C CI+D RR C ACR+ KCLQ MN + +
Sbjct: 48 SCKVFFKRAVEGQHNYLCAGDNRCIIDKIRRKNCPACRYRKCLQAGMNLEARK 100
>pdb|2NLL|B Chain B, Retinoid X Receptor-Thyroid Hormone Receptor Dna-Binding
Domain Heterodimer Bound To Thyroid Response Element
Dna
Length = 103
Score = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 22/53 (41%), Positives = 29/53 (54%), Gaps = 6/53 (11%)
Query: 13 SCQFVFVRNLE------YVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDV 59
C+ F R ++ Y CK G C++D RNQCQ CRF KC+ V M D+
Sbjct: 23 GCKGFFRRTIQKNLHPSYSCKYEGKCVIDKVTRNQCQECRFKKCIYVGMATDL 75
>pdb|2HAN|A Chain A, Structural Basis Of Heterodimeric Ecdysteroid Receptor
Interaction With Natural Response Element Hsp27 Gene
Promoter
Length = 93
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 32/57 (56%), Gaps = 7/57 (12%)
Query: 10 GVVSCQF-------VFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDV 59
GV SC+ ++L Y C+E +CI+D +RN+CQ CR+ KCL M R+
Sbjct: 26 GVYSCEGCKGFFKRTVRKDLTYACRENRNCIIDKRQRNRCQYCRYQKCLTCGMKREA 82
>pdb|1R0O|A Chain A, Crystal Structure Of The Heterodimeric Ecdysone Receptor
Dna-Binding Complex
Length = 86
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 32/57 (56%), Gaps = 7/57 (12%)
Query: 10 GVVSCQF-------VFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDV 59
GV SC+ ++L Y C+E +CI+D +RN+CQ CR+ KCL M R+
Sbjct: 24 GVYSCEGCKGFFKRTVRKDLTYACRENRNCIIDKRQRNRCQYCRYQKCLTCGMKREA 80
>pdb|1YNW|B Chain B, Crystal Structure Of Vitamin D Receptor And 9-Cis
Retinoic Acid Receptor Dna-Binding Domains Bound To A
Dr3 Response Element
Length = 99
Score = 42.7 bits (99), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 7/57 (12%)
Query: 10 GVVSCQF-------VFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDV 59
GV SC+ ++L Y C++ C++D +RN+CQ CR+ KCL + M R+
Sbjct: 19 GVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREA 75
>pdb|1R0N|A Chain A, Crystal Structure Of Heterodimeric Ecdsyone Receptor Dna
Binding Complex
Length = 81
Score = 42.7 bits (99), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 27/40 (67%)
Query: 20 RNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDV 59
++L Y C++ C++D +RN+CQ CR+ KCL + M R+
Sbjct: 36 KDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREA 75
>pdb|1DSZ|B Chain B, Structure Of The RxrRAR DNA-Binding Domain Heterodimer
In Complex With The Retinoic Acid Response Element Dr1
Length = 85
Score = 42.7 bits (99), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 7/57 (12%)
Query: 10 GVVSCQF-------VFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDV 59
GV SC+ ++L Y C++ C++D +RN+CQ CR+ KCL + M R+
Sbjct: 21 GVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREA 77
>pdb|1BY4|A Chain A, Structure And Mechanism Of The Homodimeric Assembly Of
The Rxr On Dna
pdb|1BY4|B Chain B, Structure And Mechanism Of The Homodimeric Assembly Of
The Rxr On Dna
pdb|1BY4|C Chain C, Structure And Mechanism Of The Homodimeric Assembly Of
The Rxr On Dna
pdb|1BY4|D Chain D, Structure And Mechanism Of The Homodimeric Assembly Of
The Rxr On Dna
Length = 82
Score = 42.4 bits (98), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 7/57 (12%)
Query: 10 GVVSCQF-------VFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDV 59
GV SC+ ++L Y C++ C++D +RN+CQ CR+ KCL + M R+
Sbjct: 21 GVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREA 77
>pdb|1CIT|A Chain A, Dna-Binding Mechanism Of The Monomeric Orphan Nuclear
Receptor Ngfi-B
Length = 89
Score = 42.0 bits (97), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 23/53 (43%), Positives = 30/53 (56%), Gaps = 4/53 (7%)
Query: 13 SCQFVFVRNLE----YVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTR 61
C+ F R ++ Y+C C VD RRN+CQ CRF KCL V M ++V R
Sbjct: 22 GCKGFFKRTVQKSAKYICLANKDCPVDKRRRNRCQFCRFQKCLAVGMVKEVVR 74
>pdb|2C7A|A Chain A, Structure Of The Progesterone Receptor-Dna Complex
pdb|2C7A|B Chain B, Structure Of The Progesterone Receptor-Dna Complex
Length = 78
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/47 (46%), Positives = 25/47 (53%), Gaps = 4/47 (8%)
Query: 13 SCQFVFVRNLE----YVCKERGHCIVDVTRRNQCQACRFSKCLQVKM 55
SC+ F R +E Y+C R CIVD RR C ACR KC Q M
Sbjct: 24 SCKVFFKRAMEGQHNYLCAGRNDCIVDKIRRKNCPACRLRKCCQAGM 70
>pdb|1LO1|A Chain A, Estrogen Related Receptor 2 Dna Binding Domain In
Complex With Dna
Length = 98
Score = 40.4 bits (93), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/54 (40%), Positives = 29/54 (53%), Gaps = 4/54 (7%)
Query: 13 SCQFVFVR----NLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRL 62
+C+ F R N+EY C C + RR CQACRF K L+V M ++ RL
Sbjct: 26 ACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFMKALKVGMLKEGVRL 79
>pdb|2A66|A Chain A, Human Liver Receptor Homologue Dna-Binding Domain
(Hlrh-1 Dbd) In Complex With Dsdna From The Hcyp7a1
Promoter
Length = 113
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/53 (41%), Positives = 28/53 (52%), Gaps = 4/53 (7%)
Query: 13 SCQFVFVR----NLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTR 61
SC+ F R N Y C E +C +D T+R +C CRF KCL V M + R
Sbjct: 31 SCKGFFKRTVQNNKRYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVR 83
>pdb|3DZU|D Chain D, Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex On
Dna Bound With Bvt.13, 9-Cis Retinoic Acid And Ncoa2
Peptide
pdb|3DZY|D Chain D, Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex On
Dna Bound With Rosiglitazone, 9-Cis Retinoic Acid And
Ncoa2 Peptide
pdb|3E00|D Chain D, Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex On
Dna Bound With Gw9662, 9-Cis Retinoic Acid And Ncoa2
Peptide
Length = 419
Score = 40.0 bits (92), Expect = 4e-04, Method: Composition-based stats.
Identities = 15/33 (45%), Positives = 20/33 (60%)
Query: 31 HCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLG 63
+C + RN+CQ CRF KCL V M+ + R G
Sbjct: 93 NCRIHKKSRNKCQYCRFQKCLAVGMSHNAIRFG 125
>pdb|1HLZ|A Chain A, Crystal Structure Of The Orphan Nuclear Receptor Rev-
Erb(Alpha) Dna-Binding Domain Bound To Its Cognate
Response Element
pdb|1HLZ|B Chain B, Crystal Structure Of The Orphan Nuclear Receptor Rev-
Erb(Alpha) Dna-Binding Domain Bound To Its Cognate
Response Element
pdb|1GA5|A Chain A, Crystal Structure Of The Orphan Nuclear Receptor Rev-
Erb(Alpha) Dna-Binding Domain Bound To Its Cognate
Response Element
pdb|1GA5|B Chain B, Crystal Structure Of The Orphan Nuclear Receptor Rev-
Erb(Alpha) Dna-Binding Domain Bound To Its Cognate
Response Element
pdb|1GA5|E Chain E, Crystal Structure Of The Orphan Nuclear Receptor Rev-
Erb(Alpha) Dna-Binding Domain Bound To Its Cognate
Response Element
pdb|1GA5|F Chain F, Crystal Structure Of The Orphan Nuclear Receptor Rev-
Erb(Alpha) Dna-Binding Domain Bound To Its Cognate
Response Element
pdb|1A6Y|A Chain A, Reverba Orphan Nuclear ReceptorDNA COMPLEX
pdb|1A6Y|B Chain B, Reverba Orphan Nuclear ReceptorDNA COMPLEX
Length = 94
Score = 40.0 bits (92), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/44 (45%), Positives = 27/44 (61%), Gaps = 1/44 (2%)
Query: 21 NLEYV-CKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLG 63
N++Y C + +C + RN+CQ CRF KCL V M+RD R G
Sbjct: 41 NIQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFG 84
>pdb|2FF0|A Chain A, Solution Structure Of Steroidogenic Factor 1 Dna Binding
Domain Bound To Its Target Sequence In The Inhibin
Alpha- Subunit Promoter
Length = 102
Score = 39.7 bits (91), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/53 (41%), Positives = 27/53 (50%), Gaps = 4/53 (7%)
Query: 13 SCQFVFVR----NLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTR 61
SC+ F R N Y C E C +D T+R +C CRF KCL V M + R
Sbjct: 23 SCKGFFKRTVQNNKHYTCTESQSCKIDKTQRKRCPFCRFQKCLTVGMRLEAVR 75
>pdb|2NLL|A Chain A, Retinoid X Receptor-Thyroid Hormone Receptor Dna-Binding
Domain Heterodimer Bound To Thyroid Response Element
Dna
Length = 66
Score = 39.7 bits (91), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 25/36 (69%)
Query: 20 RNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKM 55
++L Y C++ C++D +RN+CQ CR+ KCL + M
Sbjct: 31 KDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGM 66
>pdb|1RXR|A Chain A, High Resolution Solution Structure Of The Retinoid X
Receptor Dna Binding Domain, Nmr, 20 Structure
Length = 83
Score = 39.7 bits (91), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 7/57 (12%)
Query: 10 GVVSCQF-------VFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDV 59
GV SC+ ++L Y C++ C++D +RN+CQ CR+ K L + M R+
Sbjct: 19 GVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKALAMGMKREA 75
>pdb|1DSZ|A Chain A, Structure Of The RxrRAR DNA-Binding Domain Heterodimer
In Complex With The Retinoic Acid Response Element Dr1
Length = 86
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 26/42 (61%)
Query: 20 RNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTR 61
+N+ Y C +CI++ RN+CQ CR KC +V M+++ R
Sbjct: 37 KNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVR 78
>pdb|1HRA|A Chain A, The Solution Structure Of The Human Retinoic Acid
Receptor- Beta Dna-Binding Domain
Length = 80
Score = 38.9 bits (89), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 26/42 (61%)
Query: 20 RNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTR 61
+N+ Y C +C+++ RN+CQ CR KC +V M+++ R
Sbjct: 38 KNMIYTCHRDKNCVINKVTRNRCQYCRLQKCFEVGMSKESVR 79
>pdb|1HCQ|A Chain A, The Crystal Structure Of The Estrogen Receptor
Dna-Binding Domain Bound To Dna: How Receptors
Discriminate Between Their Response Elements
pdb|1HCQ|B Chain B, The Crystal Structure Of The Estrogen Receptor
Dna-Binding Domain Bound To Dna: How Receptors
Discriminate Between Their Response Elements
pdb|1HCQ|E Chain E, The Crystal Structure Of The Estrogen Receptor
Dna-Binding Domain Bound To Dna: How Receptors
Discriminate Between Their Response Elements
pdb|1HCQ|F Chain F, The Crystal Structure Of The Estrogen Receptor
Dna-Binding Domain Bound To Dna: How Receptors
Discriminate Between Their Response Elements
Length = 84
Score = 38.9 bits (89), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 27/53 (50%), Gaps = 4/53 (7%)
Query: 13 SCQFVFVRNL----EYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTR 61
C+ F R++ +Y+C C +D RR CQACR KC +V M + R
Sbjct: 26 GCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIR 78
>pdb|1HCP|A Chain A, Dna Recognition By The Oestrogen Receptor: From Solution
To The Crystal
Length = 76
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 4/47 (8%)
Query: 13 SCQFVFVRNLE----YVCKERGHCIVDVTRRNQCQACRFSKCLQVKM 55
C+ F R+++ Y+C C +D RR CQACR KC +V M
Sbjct: 26 GCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGM 72
>pdb|4AA6|E Chain E, The Oestrogen Receptor Recognizes An Imperfectly
Palindromic Response Element Through An Alternative
Side- Chain Conformation
Length = 71
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 4/47 (8%)
Query: 13 SCQFVFVRNLE----YVCKERGHCIVDVTRRNQCQACRFSKCLQVKM 55
C+ F R+++ Y+C C +D RR CQACR KC +V M
Sbjct: 23 GCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGM 69
>pdb|4AA6|A Chain A, The Oestrogen Receptor Recognizes An Imperfectly
Palindromic Response Element Through An Alternative
Side- Chain Conformation
pdb|4AA6|B Chain B, The Oestrogen Receptor Recognizes An Imperfectly
Palindromic Response Element Through An Alternative
Side- Chain Conformation
pdb|4AA6|F Chain F, The Oestrogen Receptor Recognizes An Imperfectly
Palindromic Response Element Through An Alternative
Side- Chain Conformation
Length = 71
Score = 37.7 bits (86), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 4/47 (8%)
Query: 13 SCQFVFVRNLE----YVCKERGHCIVDVTRRNQCQACRFSKCLQVKM 55
C+ F R+++ Y+C C +D RR CQACR KC +V M
Sbjct: 23 GCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGM 69
>pdb|1R4I|A Chain A, Crystal Structure Of Androgen Receptor Dna-Binding
Domain Bound To A Direct Repeat Response Element
pdb|1R4I|B Chain B, Crystal Structure Of Androgen Receptor Dna-Binding
Domain Bound To A Direct Repeat Response Element
Length = 105
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 23/47 (48%), Gaps = 4/47 (8%)
Query: 13 SCQFVFVRNLE----YVCKERGHCIVDVTRRNQCQACRFSKCLQVKM 55
SC+ F R E Y+C R C +D RR C +CR KC + M
Sbjct: 29 SCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGM 75
>pdb|2ENV|A Chain A, Solution Sturcture Of The C4-Type Zinc Finger Domain
From Human Peroxisome Proliferator-Activated Receptor
Delta
Length = 88
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 28/55 (50%), Gaps = 5/55 (9%)
Query: 13 SCQFVFVR----NLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLG 63
C+ F R LEY ER C + RN+CQ CRF KCL + M+ + R G
Sbjct: 29 GCKGFFRRTIRMKLEYEKCER-SCKIQKKNRNKCQYCRFQKCLALGMSHNAIRFG 82
>pdb|3CBB|A Chain A, Crystal Structure Of Hepatocyte Nuclear Factor 4alpha In
Complex With Dna: Diabetes Gene Product
pdb|3CBB|B Chain B, Crystal Structure Of Hepatocyte Nuclear Factor 4alpha In
Complex With Dna: Diabetes Gene Product
Length = 78
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 23/40 (57%)
Query: 20 RNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDV 59
+N Y C+ C+VD +RNQC+ CR KC + M ++
Sbjct: 33 KNHMYSCRFSRQCVVDKDKRNQCRYCRLKKCFRAGMKKEA 72
>pdb|1YNW|A Chain A, Crystal Structure Of Vitamin D Receptor And 9-Cis
Retinoic Acid Receptor Dna-Binding Domains Bound To A
Dr3 Response Element
Length = 110
Score = 30.8 bits (68), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 25/50 (50%), Gaps = 4/50 (8%)
Query: 13 SCQFVFVRNLE----YVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRD 58
C+ F R+++ + C G C + R CQACR +C+ + M ++
Sbjct: 28 GCKGFFRRSMKRKALFTCAANGDCRITKDNRRACQACRLKRCVDIGMMKE 77
>pdb|1KB2|A Chain A, Crystal Structure Of Vdr Dna-Binding Domain Bound To
Mouse Osteopontin (Spp) Response Element
pdb|1KB2|B Chain B, Crystal Structure Of Vdr Dna-Binding Domain Bound To
Mouse Osteopontin (Spp) Response Element
pdb|1KB4|A Chain A, Crystal Structure Of Vdr Dna-Binding Domain Bound To A
Canonical Direct Repeat With Three Base Pair Spacer
(Dr3) Response Element
pdb|1KB4|B Chain B, Crystal Structure Of Vdr Dna-Binding Domain Bound To A
Canonical Direct Repeat With Three Base Pair Spacer
(Dr3) Response Element
pdb|1KB6|A Chain A, Crystal Structure Of Vdr Dna-Binding Domain Bound To Rat
Osteocalcin (Oc) Response Element
pdb|1KB6|B Chain B, Crystal Structure Of Vdr Dna-Binding Domain Bound To Rat
Osteocalcin (Oc) Response Element
Length = 110
Score = 30.0 bits (66), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 25/50 (50%), Gaps = 4/50 (8%)
Query: 13 SCQFVFVRNLE----YVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRD 58
C+ F R+++ + C G C + R CQACR +C+ + M ++
Sbjct: 28 GCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKE 77
>pdb|2HAN|B Chain B, Structural Basis Of Heterodimeric Ecdysteroid Receptor
Interaction With Natural Response Element Hsp27 Gene
Promoter
Length = 119
Score = 30.0 bits (66), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 24/47 (51%), Gaps = 4/47 (8%)
Query: 13 SCQFVFVRNLE----YVCKERGHCIVDVTRRNQCQACRFSKCLQVKM 55
C+ F R++ Y CK C +D+ R +CQ CR KCL V M
Sbjct: 30 GCKGFFRRSVTKSAVYCCKFGRACEMDMYMRRKCQECRLKKCLAVGM 76
>pdb|1R0N|B Chain B, Crystal Structure Of Heterodimeric Ecdsyone Receptor Dna
Binding Complex
pdb|1R0O|B Chain B, Crystal Structure Of The Heterodimeric Ecdysone Receptor
Dna-Binding Complex
Length = 109
Score = 29.6 bits (65), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 15/32 (46%), Positives = 18/32 (56%)
Query: 24 YVCKERGHCIVDVTRRNQCQACRFSKCLQVKM 55
Y CK C +D+ R +CQ CR KCL V M
Sbjct: 43 YCCKFGRACEMDMYMRRKCQECRLKKCLAVGM 74
>pdb|1VSY|5 Chain 5, Proteasome Activator Complex
pdb|1VSY|8 Chain 8, Proteasome Activator Complex
pdb|3L5Q|6 Chain 6, Proteasome Activator Complex
pdb|3L5Q|8 Chain 8, Proteasome Activator Complex
Length = 997
Score = 27.7 bits (60), Expect = 1.7, Method: Composition-based stats.
Identities = 17/75 (22%), Positives = 33/75 (44%), Gaps = 13/75 (17%)
Query: 25 VCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDV----TRLGFWYP---------SFLL 71
VC + + D+ +R+ +KCL ++N D + L +W P +F
Sbjct: 536 VCGSKFMSVSDLDKRDTFIENFLAKCLDYELNHDAFEIWSTLAWWLPAVVDLRRSKTFFC 595
Query: 72 RVVSSRFLFGQESPA 86
+++ +F +ES A
Sbjct: 596 HFINADGMFDRESDA 610
>pdb|2CJQ|A Chain A, Bovine Viral Diarrhea Virus Cp7-R12 Rna-Dependent Rna
Polymerase
Length = 720
Score = 25.8 bits (55), Expect = 7.3, Method: Composition-based stats.
Identities = 13/54 (24%), Positives = 22/54 (40%)
Query: 35 DVTRRNQCQACRFSKCLQVKMNRDVTRLGFWYPSFLLRVVSSRFLFGQESPAWM 88
DV +N C+ R +N ++ LG W R++ G+E W+
Sbjct: 594 DVIGKNLCELKRTGFEKLANLNLSLSTLGIWSKHTSKRIIQDCVTIGKEEGNWL 647
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
0.332 0.139 0.466
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,044,025
Number of Sequences: 62578
Number of extensions: 94296
Number of successful extensions: 267
Number of sequences better than 100.0: 48
Number of HSP's better than 100.0 without gapping: 47
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 220
Number of HSP's gapped (non-prelim): 48
length of query: 119
length of database: 14,973,337
effective HSP length: 81
effective length of query: 38
effective length of database: 9,904,519
effective search space: 376371722
effective search space used: 376371722
T: 11
A: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (22.0 bits)
S2: 45 (21.9 bits)