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= psy13208
(120 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 = 45.1 bits (105), Expect = 9e-06, Method: Composition-based stats.
Identities = 16/30 (53%), Positives = 22/30 (73%)
Query: 41 CIVDKAHRNQCQACRLKKCLNMGMNKDDAQ 70
C++DK RN+CQ CR +KCL MGM ++ Q
Sbjct: 182 CLIDKRQRNRCQYCRYQKCLAMGMKREAVQ 211
Score = 43.9 bits (102), Expect = 2e-05, Method: Composition-based stats.
Identities = 15/28 (53%), Positives = 21/28 (75%)
Query: 90 CIVDKAHRNQCQACRLKKCLNMGMNKDG 117
C++DK RN+CQ CR +KCL MGM ++
Sbjct: 182 CLIDKRQRNRCQYCRYQKCLAMGMKREA 209
>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 = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 18/29 (62%), Positives = 22/29 (75%)
Query: 39 GRCIVDKAHRNQCQACRLKKCLNMGMNKD 67
G+CI+DK RNQCQ CR KKC+ +GM D
Sbjct: 48 GKCIIDKVTRNQCQECRFKKCIYVGMATD 76
Score = 43.9 bits (102), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/45 (46%), Positives = 29/45 (64%), Gaps = 2/45 (4%)
Query: 72 LKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKD 116
++ SL ++C E +CI+DK RNQCQ CR KKC+ +GM D
Sbjct: 34 IQKSLHPSYSCK--YEGKCIIDKVTRNQCQECRFKKCIYVGMATD 76
>pdb|2NLL|B Chain B, Retinoid X Receptor-Thyroid Hormone Receptor Dna-Binding
Domain Heterodimer Bound To Thyroid Response Element
Dna
Length = 103
Score = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 17/29 (58%), Positives = 22/29 (75%)
Query: 39 GRCIVDKAHRNQCQACRLKKCLNMGMNKD 67
G+C++DK RNQCQ CR KKC+ +GM D
Sbjct: 46 GKCVIDKVTRNQCQECRFKKCIYVGMATD 74
Score = 42.0 bits (97), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 17/30 (56%), Positives = 22/30 (73%)
Query: 87 ELRCIVDKAHRNQCQACRLKKCLNMGMNKD 116
E +C++DK RNQCQ CR KKC+ +GM D
Sbjct: 45 EGKCVIDKVTRNQCQECRFKKCIYVGMATD 74
>pdb|2EBL|A Chain A, Solution Structure Of The Zinc Finger, C4-type Domain Of
Human Coup Transcription Factor 1
Length = 89
Score = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 18/30 (60%), Positives = 23/30 (76%)
Query: 41 CIVDKAHRNQCQACRLKKCLNMGMNKDDAQ 70
C +D+ HRNQCQ CRLKKCL +GM ++ Q
Sbjct: 52 CPIDQHHRNQCQYCRLKKCLKVGMRREAVQ 81
Score = 42.4 bits (98), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 20/45 (44%), Positives = 26/45 (57%)
Query: 72 LKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKD 116
K S+ T C +D+ HRNQCQ CRLKKCL +GM ++
Sbjct: 34 FKRSVRRNLTYTCRANRNCPIDQHHRNQCQYCRLKKCLKVGMRRE 78
>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 = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 40/73 (54%), Gaps = 5/73 (6%)
Query: 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLN 61
T +H G + C+ G R V K H C+ + +C+VDK RNQC+ CRLKKC
Sbjct: 11 TGKHYGASSCDGCK-GFFRRSVRKNHMYSCRF----SRQCVVDKDKRNQCRYCRLKKCFR 65
Query: 62 MGMNKDDAQHLKN 74
GM K+ Q+ ++
Sbjct: 66 AGMKKEAVQNERD 78
Score = 39.7 bits (91), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 17/28 (60%), Positives = 20/28 (71%)
Query: 90 CIVDKAHRNQCQACRLKKCLNMGMNKDG 117
C+VDK RNQC+ CRLKKC GM K+
Sbjct: 45 CVVDKDKRNQCRYCRLKKCFRAGMKKEA 72
>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 = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/61 (40%), Positives = 32/61 (52%), Gaps = 5/61 (8%)
Query: 5 HDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGM 64
H G+ +C+ +R V+ H C AG RCI+DK R C ACR +KCL GM
Sbjct: 40 HYGVLTCGSCKVFFKR-AVEGQHNYLC----AGDNRCIIDKIRRKNCPACRYRKCLQAGM 94
Query: 65 N 65
N
Sbjct: 95 N 95
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/30 (53%), Positives = 20/30 (66%)
Query: 89 RCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118
RCI+DK R C ACR +KCL GMN + +
Sbjct: 70 RCIIDKIRRKNCPACRYRKCLQAGMNLEAR 99
>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 = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 31/61 (50%), Gaps = 4/61 (6%)
Query: 5 HDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGM 64
H G+ +C+ +R + + H C AG CI+DK R C ACR +KCL GM
Sbjct: 16 HYGVLTCGSCKVFFKRAVEGRQHNYLC----AGRNDCIIDKIRRKNCPACRYRKCLQAGM 71
Query: 65 N 65
N
Sbjct: 72 N 72
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 15/29 (51%), Positives = 19/29 (65%)
Query: 90 CIVDKAHRNQCQACRLKKCLNMGMNKDGK 118
CI+DK R C ACR +KCL GMN + +
Sbjct: 48 CIIDKIRRKNCPACRYRKCLQAGMNLEAR 76
>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 = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 16/34 (47%), Positives = 26/34 (76%)
Query: 41 CIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKN 74
CI++K RN+CQ CRL+KC +GM+K+ ++ +N
Sbjct: 49 CIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRN 82
Score = 38.9 bits (89), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 15/28 (53%), Positives = 22/28 (78%)
Query: 90 CIVDKAHRNQCQACRLKKCLNMGMNKDG 117
CI++K RN+CQ CRL+KC +GM+K+
Sbjct: 49 CIINKVTRNRCQYCRLQKCFEVGMSKES 76
>pdb|1LAT|A Chain A, Glucocorticoid Receptor MutantDNA COMPLEX
pdb|1LAT|B Chain B, Glucocorticoid Receptor MutantDNA COMPLEX
Length = 82
Score = 40.4 bits (93), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 32/61 (52%), Gaps = 5/61 (8%)
Query: 5 HDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGM 64
H G+ C+A +R V+ H C+ G+CI+DK R C ACR +KCL GM
Sbjct: 18 HYGVLTCEGCKAFFKR-AVEGQHNYLCKY----EGKCIIDKIRRKNCPACRYRKCLQAGM 72
Query: 65 N 65
N
Sbjct: 73 N 73
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/33 (48%), Positives = 21/33 (63%)
Query: 86 VELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118
E +CI+DK R C ACR +KCL GMN + +
Sbjct: 45 YEGKCIIDKIRRKNCPACRYRKCLQAGMNLEAR 77
>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 = 40.0 bits (92), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 16/31 (51%), Positives = 22/31 (70%)
Query: 41 CIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
C++DK RN+CQ CR +KCL MGM ++ Q
Sbjct: 50 CLIDKRQRNRCQYCRYQKCLAMGMKREAVQE 80
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 15/27 (55%), Positives = 21/27 (77%)
Query: 90 CIVDKAHRNQCQACRLKKCLNMGMNKD 116
C++DK RN+CQ CR +KCL MGM ++
Sbjct: 50 CLIDKRQRNRCQYCRYQKCLAMGMKRE 76
>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 = 40.0 bits (92), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 16/31 (51%), Positives = 22/31 (70%)
Query: 41 CIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
C++DK RN+CQ CR +KCL MGM ++ Q
Sbjct: 50 CLIDKRQRNRCQYCRYQKCLAMGMKREAVQE 80
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 15/27 (55%), Positives = 21/27 (77%)
Query: 90 CIVDKAHRNQCQACRLKKCLNMGMNKD 116
C++DK RN+CQ CR +KCL MGM ++
Sbjct: 50 CLIDKRQRNRCQYCRYQKCLAMGMKRE 76
>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 = 40.0 bits (92), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 16/31 (51%), Positives = 22/31 (70%)
Query: 41 CIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
C++DK RN+CQ CR +KCL MGM ++ Q
Sbjct: 48 CLIDKRQRNRCQYCRYQKCLAMGMKREAVQE 78
Score = 38.5 bits (88), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 15/28 (53%), Positives = 21/28 (75%)
Query: 90 CIVDKAHRNQCQACRLKKCLNMGMNKDG 117
C++DK RN+CQ CR +KCL MGM ++
Sbjct: 48 CLIDKRQRNRCQYCRYQKCLAMGMKREA 75
>pdb|1R0N|A Chain A, Crystal Structure Of Heterodimeric Ecdsyone Receptor Dna
Binding Complex
Length = 81
Score = 39.7 bits (91), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 16/30 (53%), Positives = 22/30 (73%)
Query: 41 CIVDKAHRNQCQACRLKKCLNMGMNKDDAQ 70
C++DK RN+CQ CR +KCL MGM ++ Q
Sbjct: 48 CLIDKRQRNRCQYCRYQKCLAMGMKREAVQ 77
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 15/28 (53%), Positives = 21/28 (75%)
Query: 90 CIVDKAHRNQCQACRLKKCLNMGMNKDG 117
C++DK RN+CQ CR +KCL MGM ++
Sbjct: 48 CLIDKRQRNRCQYCRYQKCLAMGMKREA 75
>pdb|1HRA|A Chain A, The Solution Structure Of The Human Retinoic Acid
Receptor- Beta Dna-Binding Domain
Length = 80
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 24/31 (77%)
Query: 41 CIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
C+++K RN+CQ CRL+KC +GM+K+ ++
Sbjct: 50 CVINKVTRNRCQYCRLQKCFEVGMSKESVRN 80
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 22/28 (78%)
Query: 90 CIVDKAHRNQCQACRLKKCLNMGMNKDG 117
C+++K RN+CQ CRL+KC +GM+K+
Sbjct: 50 CVINKVTRNRCQYCRLQKCFEVGMSKES 77
>pdb|1GDC|A Chain A, Refined Solution Structure Of The Glucocorticoid
Receptor Dna-Binding Domain
Length = 72
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 32/63 (50%), Gaps = 5/63 (7%)
Query: 5 HDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGM 64
H G+ +C+ +R V+ H C AG CI+DK R C ACR +KCL GM
Sbjct: 13 HYGVLTCGSCKVFFKR-AVEGQHNYLC----AGRNDCIIDKIRRKNCPACRYRKCLQAGM 67
Query: 65 NKD 67
N +
Sbjct: 68 NLE 70
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 15/28 (53%), Positives = 18/28 (64%)
Query: 90 CIVDKAHRNQCQACRLKKCLNMGMNKDG 117
CI+DK R C ACR +KCL GMN +
Sbjct: 44 CIIDKIRRKNCPACRYRKCLQAGMNLEA 71
>pdb|2GDA|A Chain A, Refined Solution Structure Of The Glucocorticoid
Receptor Dna-Binding Domain
Length = 72
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 5 HDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGM 64
H G+ +C+ +R V+ H C AG CI+DK R C ACR +KCL GM
Sbjct: 13 HYGVLTCGSCKVFFKR-AVEGQHNYLC----AGRNDCIIDKIRRKNCPACRYRKCLQAGM 67
Query: 65 N 65
N
Sbjct: 68 N 68
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 15/29 (51%), Positives = 19/29 (65%)
Query: 90 CIVDKAHRNQCQACRLKKCLNMGMNKDGK 118
CI+DK R C ACR +KCL GMN + +
Sbjct: 44 CIIDKIRRKNCPACRYRKCLQAGMNLEAR 72
>pdb|2HAN|A Chain A, Structural Basis Of Heterodimeric Ecdysteroid Receptor
Interaction With Natural Response Element Hsp27 Gene
Promoter
Length = 93
Score = 38.9 bits (89), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 23/36 (63%)
Query: 41 CIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSL 76
CI+DK RN+CQ CR +KCL GM ++ Q + +
Sbjct: 55 CIIDKRQRNRCQYCRYQKCLTCGMKREAVQEERQGI 90
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 15/27 (55%), Positives = 20/27 (74%)
Query: 90 CIVDKAHRNQCQACRLKKCLNMGMNKD 116
CI+DK RN+CQ CR +KCL GM ++
Sbjct: 55 CIIDKRQRNRCQYCRYQKCLTCGMKRE 81
>pdb|1RGD|A Chain A, Structure Refinement Of The Glucocorticoid Receptor-Dna
Binding Domain From Nmr Data By Relaxation Matrix
Calculations
Length = 71
Score = 38.9 bits (89), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 5 HDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGM 64
H G+ +C+ +R V+ H C AG CI+DK R C ACR +KCL GM
Sbjct: 12 HYGVLTCGSCKVFFKR-AVEGQHNYLC----AGRNDCIIDKIRRKNCPACRYRKCLQAGM 66
Query: 65 N 65
N
Sbjct: 67 N 67
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 15/29 (51%), Positives = 19/29 (65%)
Query: 90 CIVDKAHRNQCQACRLKKCLNMGMNKDGK 118
CI+DK R C ACR +KCL GMN + +
Sbjct: 43 CIIDKIRRKNCPACRYRKCLQAGMNLEAR 71
>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 = 38.9 bits (89), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 5 HDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGM 64
H G+ +C+ +R V+ H C AG CI+DK R C ACR +KCL GM
Sbjct: 18 HYGVLTCGSCKVFFKR-AVEGQHNYLC----AGRNDCIIDKIRRKNCPACRYRKCLQAGM 72
Query: 65 N 65
N
Sbjct: 73 N 73
Score = 36.2 bits (82), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 15/29 (51%), Positives = 19/29 (65%)
Query: 90 CIVDKAHRNQCQACRLKKCLNMGMNKDGK 118
CI+DK R C ACR +KCL GMN + +
Sbjct: 49 CIIDKIRRKNCPACRYRKCLQAGMNLEAR 77
>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 = 38.9 bits (89), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 5 HDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGM 64
H G+ +C+ +R V+ H C AG CI+DK R C ACR +KCL GM
Sbjct: 43 HYGVLTCGSCKVFFKR-AVEGQHNYLC----AGRNDCIIDKIRRKNCPACRYRKCLQAGM 97
Query: 65 N 65
N
Sbjct: 98 N 98
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 15/29 (51%), Positives = 19/29 (65%)
Query: 90 CIVDKAHRNQCQACRLKKCLNMGMNKDGK 118
CI+DK R C ACR +KCL GMN + +
Sbjct: 74 CIIDKIRRKNCPACRYRKCLQAGMNLEAR 102
>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 = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 5 HDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGM 64
H G+ +C+ +R V+ H C AG CI+DK R C ACR +KCL GM
Sbjct: 18 HYGVLTCGSCKVFFKR-AVEGQHNYLC----AGRNDCIIDKIRRKNCPACRYRKCLQAGM 72
Query: 65 N 65
N
Sbjct: 73 N 73
Score = 36.2 bits (82), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 15/29 (51%), Positives = 19/29 (65%)
Query: 90 CIVDKAHRNQCQACRLKKCLNMGMNKDGK 118
CI+DK R C ACR +KCL GMN + +
Sbjct: 49 CIIDKIRRKNCPACRYRKCLQAGMNLEAR 77
>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 = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 5 HDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGM 64
H G+ +C+ +R V+ H C AG CI+DK R C ACR +KCL GM
Sbjct: 16 HYGVLTCGSCKVFFKR-AVEGQHNYLC----AGRNDCIIDKIRRKNCPACRYRKCLQAGM 70
Query: 65 N 65
N
Sbjct: 71 N 71
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 15/29 (51%), Positives = 19/29 (65%)
Query: 90 CIVDKAHRNQCQACRLKKCLNMGMNKDGK 118
CI+DK R C ACR +KCL GMN + +
Sbjct: 47 CIIDKIRRKNCPACRYRKCLQAGMNLEAR 75
>pdb|1R4R|B Chain B, Crystallographic Analysis Of The Interaction Of The
Glucocorticoid Receptor With Dna
Length = 92
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 5 HDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGM 64
H G+ +C+ +R V+ H C AG CI+DK R C ACR +KCL GM
Sbjct: 18 HYGVLTCGSCKVFFKR-AVEGQHNYLC----AGRNDCIIDKIRRKNCPACRYRKCLQAGM 72
Query: 65 N 65
N
Sbjct: 73 N 73
Score = 36.2 bits (82), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 15/29 (51%), Positives = 19/29 (65%)
Query: 90 CIVDKAHRNQCQACRLKKCLNMGMNKDGK 118
CI+DK R C ACR +KCL GMN + +
Sbjct: 49 CIIDKIRRKNCPACRYRKCLQAGMNLEAR 77
>pdb|1R0O|A Chain A, Crystal Structure Of The Heterodimeric Ecdysone Receptor
Dna-Binding Complex
Length = 86
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/30 (53%), Positives = 21/30 (70%)
Query: 41 CIVDKAHRNQCQACRLKKCLNMGMNKDDAQ 70
CI+DK RN+CQ CR +KCL GM ++ Q
Sbjct: 53 CIIDKRQRNRCQYCRYQKCLTCGMKREAVQ 82
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 15/27 (55%), Positives = 20/27 (74%)
Query: 90 CIVDKAHRNQCQACRLKKCLNMGMNKD 116
CI+DK RN+CQ CR +KCL GM ++
Sbjct: 53 CIIDKRQRNRCQYCRYQKCLTCGMKRE 79
>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 = 38.5 bits (88), Expect = 0.001, Method: Composition-based stats.
Identities = 14/31 (45%), Positives = 21/31 (67%)
Query: 87 ELRCIVDKAHRNQCQACRLKKCLNMGMNKDG 117
+L C + K RN+CQ CR +KCL +GM+ +
Sbjct: 91 DLNCRIHKKSRNKCQYCRFQKCLAVGMSHNA 121
Score = 36.2 bits (82), Expect = 0.004, Method: Composition-based stats.
Identities = 13/27 (48%), Positives = 19/27 (70%)
Query: 41 CIVDKAHRNQCQACRLKKCLNMGMNKD 67
C + K RN+CQ CR +KCL +GM+ +
Sbjct: 94 CRIHKKSRNKCQYCRFQKCLAVGMSHN 120
>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 = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/62 (40%), Positives = 34/62 (54%), Gaps = 5/62 (8%)
Query: 5 HDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGM 64
H G+ C+A +R I + H + C A T +C +DK R CQACRL+KC +GM
Sbjct: 15 HYGVWSCEGCKAFFKRSI--QGHNDY--MCPA-TNQCTIDKNRRKSCQACRLRKCYEVGM 69
Query: 65 NK 66
K
Sbjct: 70 MK 71
Score = 35.0 bits (79), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 15/27 (55%), Positives = 19/27 (70%)
Query: 89 RCIVDKAHRNQCQACRLKKCLNMGMNK 115
+C +DK R CQACRL+KC +GM K
Sbjct: 45 QCTIDKNRRKSCQACRLRKCYEVGMMK 71
>pdb|4AA6|E Chain E, The Oestrogen Receptor Recognizes An Imperfectly
Palindromic Response Element Through An Alternative
Side- Chain Conformation
Length = 71
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/62 (40%), Positives = 34/62 (54%), Gaps = 5/62 (8%)
Query: 5 HDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGM 64
H G+ C+A +R I + H + C A T +C +DK R CQACRL+KC +GM
Sbjct: 15 HYGVWSCEGCKAFFKRSI--QGHNDY--MCPA-TNQCTIDKNRRKSCQACRLRKCYEVGM 69
Query: 65 NK 66
K
Sbjct: 70 MK 71
Score = 35.0 bits (79), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 15/27 (55%), Positives = 19/27 (70%)
Query: 89 RCIVDKAHRNQCQACRLKKCLNMGMNK 115
+C +DK R CQACRL+KC +GM K
Sbjct: 45 QCTIDKNRRKSCQACRLRKCYEVGMMK 71
>pdb|1HCP|A Chain A, Dna Recognition By The Oestrogen Receptor: From Solution
To The Crystal
Length = 76
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/62 (40%), Positives = 34/62 (54%), Gaps = 5/62 (8%)
Query: 5 HDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGM 64
H G+ C+A +R I + H + C A T +C +DK R CQACRL+KC +GM
Sbjct: 18 HYGVWSCEGCKAFFKRSI--QGHNDY--MCPA-TNQCTIDKNRRKSCQACRLRKCYEVGM 72
Query: 65 NK 66
K
Sbjct: 73 MK 74
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/29 (55%), Positives = 20/29 (68%)
Query: 89 RCIVDKAHRNQCQACRLKKCLNMGMNKDG 117
+C +DK R CQACRL+KC +GM K G
Sbjct: 48 QCTIDKNRRKSCQACRLRKCYEVGMMKGG 76
>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 = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/28 (57%), Positives = 19/28 (67%)
Query: 90 CIVDKAHRNQCQACRLKKCLNMGMNKDG 117
C +DK R CQACRL+KC +GM K G
Sbjct: 49 CTIDKNRRKSCQACRLRKCYEVGMMKGG 76
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/62 (40%), Positives = 34/62 (54%), Gaps = 5/62 (8%)
Query: 5 HDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGM 64
H G+ C+A +R I + H + C A T +C +DK R CQACRL+KC +GM
Sbjct: 18 HYGVWSCEGCKAFFKRSI--QGHNDY--MCPA-TNQCTIDKNRRKSCQACRLRKCYEVGM 72
Query: 65 NK 66
K
Sbjct: 73 MK 74
>pdb|1RXR|A Chain A, High Resolution Solution Structure Of The Retinoid X
Receptor Dna Binding Domain, Nmr, 20 Structure
Length = 83
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 15/31 (48%), Positives = 21/31 (67%)
Query: 41 CIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
C++DK RN+CQ CR +K L MGM ++ Q
Sbjct: 48 CLIDKRQRNRCQYCRYQKALAMGMKREAVQE 78
Score = 35.8 bits (81), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 14/27 (51%), Positives = 20/27 (74%)
Query: 90 CIVDKAHRNQCQACRLKKCLNMGMNKD 116
C++DK RN+CQ CR +K L MGM ++
Sbjct: 48 CLIDKRQRNRCQYCRYQKALAMGMKRE 74
>pdb|2NLL|A Chain A, Retinoid X Receptor-Thyroid Hormone Receptor Dna-Binding
Domain Heterodimer Bound To Thyroid Response Element
Dna
Length = 66
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 15/24 (62%), Positives = 19/24 (79%)
Query: 41 CIVDKAHRNQCQACRLKKCLNMGM 64
C++DK RN+CQ CR +KCL MGM
Sbjct: 43 CLIDKRQRNRCQYCRYQKCLAMGM 66
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 15/24 (62%), Positives = 19/24 (79%)
Query: 90 CIVDKAHRNQCQACRLKKCLNMGM 113
C++DK RN+CQ CR +KCL MGM
Sbjct: 43 CLIDKRQRNRCQYCRYQKCLAMGM 66
>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 = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 16/32 (50%), Positives = 23/32 (71%)
Query: 36 AGTGRCIVDKAHRNQCQACRLKKCLNMGMNKD 67
A G C + K +R CQACRLK+C+++GM K+
Sbjct: 46 AANGDCRITKDNRRACQACRLKRCVDIGMMKE 77
Score = 33.9 bits (76), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 14/27 (51%), Positives = 21/27 (77%)
Query: 90 CIVDKAHRNQCQACRLKKCLNMGMNKD 116
C + K +R CQACRLK+C+++GM K+
Sbjct: 51 CRITKDNRRACQACRLKRCVDIGMMKE 77
>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 = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 23/31 (74%)
Query: 41 CIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
C + + +RN+CQ CR KKCL++GM++D +
Sbjct: 53 CSIVRINRNRCQQCRFKKCLSVGMSRDAVRF 83
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 14/27 (51%), Positives = 22/27 (81%)
Query: 90 CIVDKAHRNQCQACRLKKCLNMGMNKD 116
C + + +RN+CQ CR KKCL++GM++D
Sbjct: 53 CSIVRINRNRCQQCRFKKCLSVGMSRD 79
>pdb|1CIT|A Chain A, Dna-Binding Mechanism Of The Monomeric Orphan Nuclear
Receptor Ngfi-B
Length = 89
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 16/27 (59%), Positives = 20/27 (74%)
Query: 41 CIVDKAHRNQCQACRLKKCLNMGMNKD 67
C VDK RN+CQ CR +KCL +GM K+
Sbjct: 45 CPVDKRRRNRCQFCRFQKCLAVGMVKE 71
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 16/27 (59%), Positives = 20/27 (74%)
Query: 90 CIVDKAHRNQCQACRLKKCLNMGMNKD 116
C VDK RN+CQ CR +KCL +GM K+
Sbjct: 45 CPVDKRRRNRCQFCRFQKCLAVGMVKE 71
>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 = 35.0 bits (79), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 15/29 (51%), Positives = 22/29 (75%)
Query: 39 GRCIVDKAHRNQCQACRLKKCLNMGMNKD 67
G C + K +R CQACRLK+C+++GM K+
Sbjct: 49 GDCRITKDNRRHCQACRLKRCVDIGMMKE 77
Score = 33.9 bits (76), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 14/27 (51%), Positives = 21/27 (77%)
Query: 90 CIVDKAHRNQCQACRLKKCLNMGMNKD 116
C + K +R CQACRLK+C+++GM K+
Sbjct: 51 CRITKDNRRHCQACRLKRCVDIGMMKE 77
>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 = 34.7 bits (78), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 23/60 (38%), Positives = 30/60 (50%), Gaps = 5/60 (8%)
Query: 5 HDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGM 64
H G+ +C+ +R ++ H C AG CIVDK R C ACRL+KC GM
Sbjct: 16 HYGVLTCGSCKVFFKR-AMEGQHNYLC----AGRNDCIVDKIRRKNCPACRLRKCCQAGM 70
Score = 34.3 bits (77), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 16/31 (51%), Positives = 18/31 (58%)
Query: 90 CIVDKAHRNQCQACRLKKCLNMGMNKDGKSM 120
CIVDK R C ACRL+KC GM G+
Sbjct: 47 CIVDKIRRKNCPACRLRKCCQAGMVLGGRKF 77
>pdb|2ENV|A Chain A, Solution Sturcture Of The C4-Type Zinc Finger Domain From
Human Peroxisome Proliferator-Activated Receptor Delta
Length = 88
Score = 34.3 bits (77), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 20/28 (71%)
Query: 87 ELRCIVDKAHRNQCQACRLKKCLNMGMN 114
E C + K +RN+CQ CR +KCL +GM+
Sbjct: 48 ERSCKIQKKNRNKCQYCRFQKCLALGMS 75
Score = 33.5 bits (75), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 6/61 (9%)
Query: 5 HDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGM 64
H G+ C+ R I K +C+ C + K +RN+CQ CR +KCL +GM
Sbjct: 21 HYGVHACEGCKGFFRRTIRMKLEYEKCER------SCKIQKKNRNKCQYCRFQKCLALGM 74
Query: 65 N 65
+
Sbjct: 75 S 75
>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 = 33.9 bits (76), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 5/60 (8%)
Query: 5 HDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGM 64
H G+ +C+ +R + + H C Q+ C +DK R +C CR +KCL +GM
Sbjct: 15 HYGLLTCESCKGFFKRTVQNNKHYT-CTESQS----CKIDKTQRKRCPFCRFQKCLTVGM 69
Score = 31.6 bits (70), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 90 CIVDKAHRNQCQACRLKKCLNMGM 113
C +DK R +C CR +KCL +GM
Sbjct: 46 CKIDKTQRKRCPFCRFQKCLTVGM 69
>pdb|1LO1|A Chain A, Estrogen Related Receptor 2 Dna Binding Domain In Complex
With Dna
Length = 98
Score = 33.1 bits (74), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 22/39 (56%), Gaps = 2/39 (5%)
Query: 79 EFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDG 117
E++C E C + K R CQACR K L +GM K+G
Sbjct: 40 EYSCPATNE--CEITKRRRKSCQACRFMKALKVGMLKEG 76
Score = 33.1 bits (74), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 31/66 (46%), Gaps = 5/66 (7%)
Query: 5 HDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGM 64
H G+ C+A +R I N +C A T C + K R CQACR K L +GM
Sbjct: 18 HYGVASCEACKAFFKRTI----QGNIEYSCPA-TNECEITKRRRKSCQACRFMKALKVGM 72
Query: 65 NKDDAQ 70
K+ +
Sbjct: 73 LKEGVR 78
>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 = 32.0 bits (71), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 12/25 (48%), Positives = 15/25 (60%)
Query: 41 CIVDKAHRNQCQACRLKKCLNMGMN 65
C +DK R C +CRL+KC GM
Sbjct: 52 CTIDKFRRKNCPSCRLRKCYEAGMT 76
Score = 32.0 bits (71), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 12/25 (48%), Positives = 15/25 (60%)
Query: 90 CIVDKAHRNQCQACRLKKCLNMGMN 114
C +DK R C +CRL+KC GM
Sbjct: 52 CTIDKFRRKNCPSCRLRKCYEAGMT 76
>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 = 32.0 bits (71), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 17/24 (70%)
Query: 41 CIVDKAHRNQCQACRLKKCLNMGM 64
C +DK R +C CR +KCL++GM
Sbjct: 54 CQIDKTQRKRCPYCRFQKCLSVGM 77
Score = 32.0 bits (71), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 17/24 (70%)
Query: 90 CIVDKAHRNQCQACRLKKCLNMGM 113
C +DK R +C CR +KCL++GM
Sbjct: 54 CQIDKTQRKRCPYCRFQKCLSVGM 77
>pdb|2HAN|B Chain B, Structural Basis Of Heterodimeric Ecdysteroid Receptor
Interaction With Natural Response Element Hsp27 Gene
Promoter
Length = 119
Score = 31.6 bits (70), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 14/27 (51%), Positives = 18/27 (66%)
Query: 41 CIVDKAHRNQCQACRLKKCLNMGMNKD 67
C +D R +CQ CRLKKCL +GM +
Sbjct: 53 CEMDMYMRRKCQECRLKKCLAVGMRPE 79
Score = 31.6 bits (70), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 14/27 (51%), Positives = 18/27 (66%)
Query: 90 CIVDKAHRNQCQACRLKKCLNMGMNKD 116
C +D R +CQ CRLKKCL +GM +
Sbjct: 53 CEMDMYMRRKCQECRLKKCLAVGMRPE 79
>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 = 31.6 bits (70), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 14/27 (51%), Positives = 18/27 (66%)
Query: 41 CIVDKAHRNQCQACRLKKCLNMGMNKD 67
C +D R +CQ CRLKKCL +GM +
Sbjct: 51 CEMDMYMRRKCQECRLKKCLAVGMRPE 77
Score = 31.6 bits (70), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 14/27 (51%), Positives = 18/27 (66%)
Query: 90 CIVDKAHRNQCQACRLKKCLNMGMNKD 116
C +D R +CQ CRLKKCL +GM +
Sbjct: 51 CEMDMYMRRKCQECRLKKCLAVGMRPE 77
>pdb|3TLX|A Chain A, Crystal Structure Of Pf10_0086, Adenylate Kinase From
Plasmodium Falciparum
pdb|3TLX|B Chain B, Crystal Structure Of Pf10_0086, Adenylate Kinase From
Plasmodium Falciparum
pdb|3TLX|C Chain C, Crystal Structure Of Pf10_0086, Adenylate Kinase From
Plasmodium Falciparum
pdb|3TLX|D Chain D, Crystal Structure Of Pf10_0086, Adenylate Kinase From
Plasmodium Falciparum
Length = 243
Score = 26.2 bits (56), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 29/98 (29%), Positives = 41/98 (41%), Gaps = 6/98 (6%)
Query: 12 PTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71
P GT+ + K+H C C TG + + A + ++K +N G DD
Sbjct: 38 PGSGKGTQSLNLKKSH---C-YCHLSTGDLLREAAEKKTELGLKIKNIINEGKLVDDQMV 93
Query: 72 LKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCL 109
L SL+ E T + I+D RN QA L K L
Sbjct: 94 L--SLVDEKLKTPQCKKGFILDGYPRNVKQAEDLNKLL 129
>pdb|4HGA|A Chain A, Structure Of The Variant Histone H3.3-H4 Heterodimer In
Complex With Its Chaperone Daxx
Length = 213
Score = 25.8 bits (55), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 2/68 (2%)
Query: 48 RNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKK 107
R Q Q ++G+ + +HL L+Y F C + R VD A + A RL++
Sbjct: 129 RQQLQLMAQDAFRDVGIRLQERRHL--DLIYNFGCHLTDDYRPGVDPALSDPVLARRLRE 186
Query: 108 CLNMGMNK 115
++ M++
Sbjct: 187 NRSLAMSR 194
>pdb|4H9N|C Chain C, Complex Structure 1 Of DaxxH3.3(SUB5)H4
pdb|4H9O|C Chain C, Complex Structure 2 Of DaxxH3.3(SUB5,G90M)H4
pdb|4H9P|C Chain C, Complex Structure 3 Of DaxxH3.3(SUB5,G90A)H4
Length = 212
Score = 25.8 bits (55), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 2/68 (2%)
Query: 48 RNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKK 107
R Q Q ++G+ + +HL L+Y F C + R VD A + A RL++
Sbjct: 129 RQQLQLMAQDAFRDVGIRLQERRHL--DLIYNFGCHLTDDYRPGVDPALSDPVLARRLRE 186
Query: 108 CLNMGMNK 115
++ M++
Sbjct: 187 NRSLAMSR 194
>pdb|4H9Q|C Chain C, Complex Structure 4 Of Daxx(E225a)H3.3(SUB5)H4
pdb|4H9R|C Chain C, Complex Structure 5 Of Daxx(E225a)H3.3(SUB5,G90A)H4
Length = 212
Score = 25.8 bits (55), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 2/68 (2%)
Query: 48 RNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKK 107
R Q Q ++G+ + +HL L+Y F C + R VD A + A RL++
Sbjct: 129 RQQLQLMAQDAFRDVGIRLQERRHL--DLIYNFGCHLTDDYRPGVDPALSDPVLARRLRE 186
Query: 108 CLNMGMNK 115
++ M++
Sbjct: 187 NRSLAMSR 194
>pdb|4H9S|E Chain E, Complex Structure 6 Of DaxxH3.3(SUB7)H4
pdb|4H9S|F Chain F, Complex Structure 6 Of DaxxH3.3(SUB7)H4
Length = 216
Score = 25.8 bits (55), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 2/68 (2%)
Query: 48 RNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKK 107
R Q Q ++G+ + +HL L+Y F C + R VD A + A RL++
Sbjct: 124 RQQLQLMAQDAFRDVGIRLQERRHL--DLIYNFGCHLTDDYRPGVDPALSDPVLARRLRE 181
Query: 108 CLNMGMNK 115
++ M++
Sbjct: 182 NRSLAMSR 189
>pdb|3LY6|A Chain A, Crystal Structure Of Human Transglutaminase 2 Complex With
Adenosine 5' Triphosphate
pdb|3LY6|B Chain B, Crystal Structure Of Human Transglutaminase 2 Complex With
Adenosine 5' Triphosphate
pdb|3LY6|C Chain C, Crystal Structure Of Human Transglutaminase 2 Complex With
Adenosine 5' Triphosphate
Length = 697
Score = 25.0 bits (53), Expect = 9.8, Method: Composition-based stats.
Identities = 12/50 (24%), Positives = 23/50 (46%)
Query: 42 IVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCI 91
+ +K R+ + +NMG + D H+ N+ E+ C L+ R +
Sbjct: 465 LAEKEETGMAMRIRVGQSMNMGSDFDVFAHITNNTAEEYVCRLLLCARTV 514
>pdb|3S3J|A Chain A, Transglutaminase 2 In Complex With A Novel Inhibitor
pdb|3S3P|A Chain A, Transglutaminase 2 In Complex With A Novel Inhibitor
pdb|3S3S|A Chain A, Transglutaminase 2 In Complex With A Novel Inhibitor
Length = 694
Score = 25.0 bits (53), Expect = 9.9, Method: Composition-based stats.
Identities = 12/50 (24%), Positives = 23/50 (46%)
Query: 42 IVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCI 91
+ +K R+ + +NMG + D H+ N+ E+ C L+ R +
Sbjct: 472 LAEKEETGMAMRIRVGQSMNMGSDFDVFAHITNNTAEEYVCRLLLCARTV 521
>pdb|1KV3|A Chain A, Human Tissue Transglutaminase In Gdp Bound Form
pdb|1KV3|B Chain B, Human Tissue Transglutaminase In Gdp Bound Form
pdb|1KV3|C Chain C, Human Tissue Transglutaminase In Gdp Bound Form
pdb|1KV3|D Chain D, Human Tissue Transglutaminase In Gdp Bound Form
pdb|1KV3|E Chain E, Human Tissue Transglutaminase In Gdp Bound Form
pdb|1KV3|F Chain F, Human Tissue Transglutaminase In Gdp Bound Form
pdb|2Q3Z|A Chain A, Transglutaminase 2 Undergoes Large Conformational Change
Upon Activation
Length = 687
Score = 25.0 bits (53), Expect = 9.9, Method: Composition-based stats.
Identities = 12/50 (24%), Positives = 23/50 (46%)
Query: 42 IVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCI 91
+ +K R+ + +NMG + D H+ N+ E+ C L+ R +
Sbjct: 465 LAEKEETGMAMRIRVGQSMNMGSDFDVFAHITNNTAEEYVCRLLLCARTV 514
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
0.326 0.133 0.442
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,686,819
Number of Sequences: 62578
Number of extensions: 132133
Number of successful extensions: 436
Number of sequences better than 100.0: 60
Number of HSP's better than 100.0 without gapping: 49
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 303
Number of HSP's gapped (non-prelim): 118
length of query: 120
length of database: 14,973,337
effective HSP length: 82
effective length of query: 38
effective length of database: 9,841,941
effective search space: 373993758
effective search space used: 373993758
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 45 (21.9 bits)