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= psy16683
(139 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 70.5 bits (171), Expect = 3e-13, Method: Composition-based stats.
Identities = 32/80 (40%), Positives = 42/80 (52%), Gaps = 2/80 (2%)
Query: 1 MNQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKS 60
M C+VCG+ A+GFH+G CEGCK FF R+ + R C+
Sbjct: 49 MAIECRVCGDKASGFHYGVHACEGCKGFFRRTIR--LKLIYDRCDLNCRIHKKSRNKCQY 106
Query: 61 CRLRKCLMVGMSKSGSRYGR 80
CR +KCL VGMS + R+GR
Sbjct: 107 CRFQKCLAVGMSHNAIRFGR 126
>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 = 69.7 bits (169), Expect = 5e-13, Method: Compositional matrix adjust.
Identities = 33/76 (43%), Positives = 40/76 (52%)
Query: 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKSCRLR 64
CKVCG+ A+GFH+G CEGCK FF RS R C+ CR +
Sbjct: 10 CKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKRCLKNENCSIVRINRNRCQQCRFK 69
Query: 65 KCLMVGMSKSGSRYGR 80
KCL VGMS+ R+GR
Sbjct: 70 KCLSVGMSRDAVRFGR 85
>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 = 61.2 bits (147), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 33/77 (42%), Positives = 42/77 (54%), Gaps = 1/77 (1%)
Query: 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKSCRLR 64
C VC + A+G+H+G ++CEGCK+FF RS R SC++CRLR
Sbjct: 7 CAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDY-MCPATNQCTIDKNRRKSCQACRLR 65
Query: 65 KCLMVGMSKSGSRYGRR 81
KC VGM K G R RR
Sbjct: 66 KCYEVGMMKGGIRKDRR 82
>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 = 58.2 bits (139), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 29/72 (40%), Positives = 40/72 (55%), Gaps = 1/72 (1%)
Query: 3 QTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKSCR 62
+ C VCG+ A GFHF A TCEGCK FF RS ++ R +C++CR
Sbjct: 7 RICGVCGDRATGFHFNAMTCEGCKGFFRRSMKR-KALFTCAANGDCRITKDNRRACQACR 65
Query: 63 LRKCLMVGMSKS 74
L++C+ +GM K
Sbjct: 66 LKRCVDIGMMKE 77
>pdb|1HCP|A Chain A, Dna Recognition By The Oestrogen Receptor: From Solution
To The Crystal
Length = 76
Score = 57.8 bits (138), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 30/71 (42%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKSCRLR 64
C VC + A+G+H+G ++CEGCK+FF RS R SC++CRLR
Sbjct: 7 CAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDY-MCPATNQCTIDKNRRKSCQACRLR 65
Query: 65 KCLMVGMSKSG 75
KC VGM K G
Sbjct: 66 KCYEVGMMKGG 76
>pdb|2ENV|A Chain A, Solution Sturcture Of The C4-Type Zinc Finger Domain
From Human Peroxisome Proliferator-Activated Receptor
Delta
Length = 88
Score = 56.6 bits (135), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 29/76 (38%), Positives = 40/76 (52%), Gaps = 2/76 (2%)
Query: 4 TCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKSCRL 63
C+VCG+ A+GFH+G CEGCK FF R+ + R C+ CR
Sbjct: 9 ECRVCGDKASGFHYGVHACEGCKGFFRRTIR--MKLEYEKCERSCKIQKKNRNKCQYCRF 66
Query: 64 RKCLMVGMSKSGSRYG 79
+KCL +GMS + R+G
Sbjct: 67 QKCLALGMSHNAIRFG 82
>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 = 56.6 bits (135), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 29/70 (41%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 2 NQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKSC 61
+ C VCG+ A+G+H+ A TCEGCK FF RS ++ R C+ C
Sbjct: 6 EELCLVCGDRASGYHYNALTCEGCKGFFRRSVTK-SAVYCCKFGRACEMDMYMRRKCQEC 64
Query: 62 RLRKCLMVGM 71
RL+KCL VGM
Sbjct: 65 RLKKCLAVGM 74
>pdb|2HAN|B Chain B, Structural Basis Of Heterodimeric Ecdysteroid Receptor
Interaction With Natural Response Element Hsp27 Gene
Promoter
Length = 119
Score = 56.6 bits (135), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 29/71 (40%), Positives = 38/71 (53%), Gaps = 1/71 (1%)
Query: 1 MNQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKS 60
+ C VCG+ A+G+H+ A TCEGCK FF RS ++ R C+
Sbjct: 7 QEELCLVCGDRASGYHYNALTCEGCKGFFRRSVTK-SAVYCCKFGRACEMDMYMRRKCQE 65
Query: 61 CRLRKCLMVGM 71
CRL+KCL VGM
Sbjct: 66 CRLKKCLAVGM 76
>pdb|4AA6|E Chain E, The Oestrogen Receptor Recognizes An Imperfectly
Palindromic Response Element Through An Alternative
Side- Chain Conformation
Length = 71
Score = 56.2 bits (134), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 29/69 (42%), Positives = 38/69 (55%), Gaps = 1/69 (1%)
Query: 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKSCRLR 64
C VC + A+G+H+G ++CEGCK+FF RS R SC++CRLR
Sbjct: 4 CAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDY-MCPATNQCTIDKNRRKSCQACRLR 62
Query: 65 KCLMVGMSK 73
KC VGM K
Sbjct: 63 KCYEVGMMK 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 = 56.2 bits (134), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 29/72 (40%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 3 QTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKSCR 62
+ C VCG+ A GFHF A TCEGCK FF RS ++ R C++CR
Sbjct: 7 RICGVCGDRATGFHFNAMTCEGCKGFFRRSMKR-KALFTCPFNGDCRITKDNRRHCQACR 65
Query: 63 LRKCLMVGMSKS 74
L++C+ +GM K
Sbjct: 66 LKRCVDIGMMKE 77
>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 = 56.2 bits (134), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 29/69 (42%), Positives = 38/69 (55%), Gaps = 1/69 (1%)
Query: 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKSCRLR 64
C VC + A+G+H+G ++CEGCK+FF RS R SC++CRLR
Sbjct: 4 CAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDY-MCPATNQCTIDKNRRKSCQACRLR 62
Query: 65 KCLMVGMSK 73
KC VGM K
Sbjct: 63 KCYEVGMMK 71
>pdb|2EBL|A Chain A, Solution Structure Of The Zinc Finger, C4-type Domain Of
Human Coup Transcription Factor 1
Length = 89
Score = 55.8 bits (133), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 31/75 (41%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKSCRLR 64
C VCG+ ++G H+G FTCEGCKSFF RS + + R C+ CRL+
Sbjct: 10 CVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYT-CRANRNCPIDQHHRNQCQYCRLK 68
Query: 65 KCLMVGMSKSGSRYG 79
KCL VGM + + G
Sbjct: 69 KCLKVGMRREAVQRG 83
>pdb|2NLL|B Chain B, Retinoid X Receptor-Thyroid Hormone Receptor Dna-Binding
Domain Heterodimer Bound To Thyroid Response Element
Dna
Length = 103
Score = 55.8 bits (133), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 27/72 (37%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 2 NQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYN-NLPSISXXXXXXXXXXXXXXRTSCKS 60
++ C VCG+ A G+H+ TCEGCK FF R+ NL R C+
Sbjct: 1 DELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYSCKYEGKCVIDKVTRNQCQE 60
Query: 61 CRLRKCLMVGMS 72
CR +KC+ VGM+
Sbjct: 61 CRFKKCIYVGMA 72
>pdb|1LO1|A Chain A, Estrogen Related Receptor 2 Dna Binding Domain In
Complex With Dna
Length = 98
Score = 54.3 bits (129), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 30/76 (39%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKSCRLR 64
C VCG+ A+G+H+G +CE CK+FF R+ S R SC++CR
Sbjct: 7 CLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYS-CPATNECEITKRRRKSCQACRFM 65
Query: 65 KCLMVGMSKSGSRYGR 80
K L VGM K G R R
Sbjct: 66 KALKVGMLKEGVRLDR 81
>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 = 54.3 bits (129), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 28/80 (35%), Positives = 37/80 (46%), Gaps = 1/80 (1%)
Query: 1 MNQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKS 60
+ + C VCG+ +G+H+G TCE CK FF R+ N + R C
Sbjct: 8 LEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYT-CIENQNCQIDKTQRKRCPY 66
Query: 61 CRLRKCLMVGMSKSGSRYGR 80
CR +KCL VGM R R
Sbjct: 67 CRFQKCLSVGMKLEAVRADR 86
>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 = 54.3 bits (129), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 38/73 (52%), Gaps = 3/73 (4%)
Query: 2 NQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNL--PSISXXXXXXXXXXXXXXRTSCK 59
++ C VCG+ A G+H+ TCEGCK FF R+ PS S R C+
Sbjct: 3 DELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKSLHPSYS-CKYEGKCIIDKVTRNQCQ 61
Query: 60 SCRLRKCLMVGMS 72
CR +KC+ VGM+
Sbjct: 62 ECRFKKCIYVGMA 74
>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 = 53.9 bits (128), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 28/79 (35%), Positives = 37/79 (46%), Gaps = 1/79 (1%)
Query: 2 NQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKSC 61
++ C VCG+ +G+H+G TCE CK FF R+ N + R C C
Sbjct: 1 DELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKHYT-CTESQSCKIDKTQRKRCPFC 59
Query: 62 RLRKCLMVGMSKSGSRYGR 80
R +KCL VGM R R
Sbjct: 60 RFQKCLTVGMRLEAVRADR 78
>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 = 53.1 bits (126), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 29/76 (38%), Positives = 37/76 (48%), Gaps = 1/76 (1%)
Query: 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKSCRLR 64
C VC + ++G+H+G CEGCK FF RS + R C+ CRL+
Sbjct: 7 CFVCQDKSSGYHYGVSACEGCKGFFRRSIQK-NMVYTCHRDKNCIINKVTRNRCQYCRLQ 65
Query: 65 KCLMVGMSKSGSRYGR 80
KC VGMSK R R
Sbjct: 66 KCFEVGMSKESVRNDR 81
>pdb|1HRA|A Chain A, The Solution Structure Of The Human Retinoic Acid
Receptor- Beta Dna-Binding Domain
Length = 80
Score = 52.4 bits (124), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 29/73 (39%), Positives = 36/73 (49%), Gaps = 1/73 (1%)
Query: 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKSCRLR 64
C VC + ++G+H+G CEGCK FF RS I R C+ CRL+
Sbjct: 8 CFVCQDKSSGYHYGVSACEGCKGFFRRSIQK-NMIYTCHRDKNCVINKVTRNRCQYCRLQ 66
Query: 65 KCLMVGMSKSGSR 77
KC VGMSK R
Sbjct: 67 KCFEVGMSKESVR 79
>pdb|1R0O|A Chain A, Crystal Structure Of The Heterodimeric Ecdysone Receptor
Dna-Binding Complex
Length = 86
Score = 50.1 bits (118), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKSCRLR 64
C +CG+ A+G H+G ++CEGCK FF R+ + + R C+ CR +
Sbjct: 11 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYA-CRENRNCIIDKRQRNRCQYCRYQ 69
Query: 65 KCLMVGMSKSGSRYGRR 81
KCL GM + + R+
Sbjct: 70 KCLTCGMKREAVQEERQ 86
>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 = 49.7 bits (117), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 1/77 (1%)
Query: 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKSCRLR 64
C +CG+ ++G H+G ++CEGCK FF R+ + + R C+ CR +
Sbjct: 6 CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYT-CRDNKDCLIDKRQRNRCQYCRYQ 64
Query: 65 KCLMVGMSKSGSRYGRR 81
KCL +GM + + R+
Sbjct: 65 KCLAMGMKREAVQEERQ 81
>pdb|2HAN|A Chain A, Structural Basis Of Heterodimeric Ecdysteroid Receptor
Interaction With Natural Response Element Hsp27 Gene
Promoter
Length = 93
Score = 49.7 bits (117), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKSCRLR 64
C +CG+ A+G H+G ++CEGCK FF R+ + + R C+ CR +
Sbjct: 13 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYA-CRENRNCIIDKRQRNRCQYCRYQ 71
Query: 65 KCLMVGMSKSGSRYGRR 81
KCL GM + + R+
Sbjct: 72 KCLTCGMKREAVQEERQ 88
>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 = 49.7 bits (117), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 39/78 (50%), Gaps = 5/78 (6%)
Query: 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSY--NNLPSISXXXXXXXXXXXXXXRTSCKSCR 62
C +CG+ A G H+GA +C+GCK FF RS N++ S R C+ CR
Sbjct: 3 CAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCR---FSRQCVVDKDKRNQCRYCR 59
Query: 63 LRKCLMVGMSKSGSRYGR 80
L+KC GM K + R
Sbjct: 60 LKKCFRAGMKKEAVQNER 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 = 49.3 bits (116), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 1/77 (1%)
Query: 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKSCRLR 64
C +CG+ ++G H+G ++CEGCK FF R+ + + R C+ CR +
Sbjct: 8 CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYT-CRDNKDCLIDKRQRNRCQYCRYQ 66
Query: 65 KCLMVGMSKSGSRYGRR 81
KCL +GM + + R+
Sbjct: 67 KCLAMGMKREAVQEERQ 83
>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 = 49.3 bits (116), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKSCRLR 64
C +CG+ ++G H+G ++CEGCK FF R+ + + R C+ CR +
Sbjct: 8 CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYT-CRDNKDCLIDKRQRNRCQYCRYQ 66
Query: 65 KCLMVGMSKSGSRYGR 80
KCL +GM + + R
Sbjct: 67 KCLAMGMKREAVQEER 82
>pdb|1LAT|A Chain A, Glucocorticoid Receptor MutantDNA COMPLEX
pdb|1LAT|B Chain B, Glucocorticoid Receptor MutantDNA COMPLEX
Length = 82
Score = 49.3 bits (116), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 26/68 (38%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKSCRLR 64
C VC + A+G H+G TCEGCK+FF R+ + R +C +CR R
Sbjct: 7 CLVCSDEASGCHYGVLTCEGCKAFFKRAVEGQHNY-LCKYEGKCIIDKIRRKNCPACRYR 65
Query: 65 KCLMVGMS 72
KCL GM+
Sbjct: 66 KCLQAGMN 73
>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 = 48.9 bits (115), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 35/71 (49%), Gaps = 1/71 (1%)
Query: 2 NQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKSC 61
+TC +CG+ A+G H+GA TC CK FF R+ R +C SC
Sbjct: 7 QKTCLICGDEASGAHYGALTCGSCKVFFKRAAEGKQKY-LCASRNDCTIDKFRRKNCPSC 65
Query: 62 RLRKCLMVGMS 72
RLRKC GM+
Sbjct: 66 RLRKCYEAGMT 76
>pdb|1R0N|A Chain A, Crystal Structure Of Heterodimeric Ecdsyone Receptor Dna
Binding Complex
Length = 81
Score = 48.9 bits (115), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 37/71 (52%), Gaps = 1/71 (1%)
Query: 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKSCRLR 64
C +CG+ ++G H+G ++CEGCK FF R+ + + R C+ CR +
Sbjct: 6 CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYT-CRDNKDCLIDKRQRNRCQYCRYQ 64
Query: 65 KCLMVGMSKSG 75
KCL +GM +
Sbjct: 65 KCLAMGMKREA 75
>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 = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 1/77 (1%)
Query: 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKSCRLR 64
C +CG+ ++G H+G ++CEGCK FF R+ + + R C+ CR +
Sbjct: 140 CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYT-CRDNKDCLIDKRQRNRCQYCRYQ 198
Query: 65 KCLMVGMSKSGSRYGRR 81
KCL +GM + + R+
Sbjct: 199 KCLAMGMKREAVQEERQ 215
>pdb|2NLL|A Chain A, Retinoid X Receptor-Thyroid Hormone Receptor Dna-Binding
Domain Heterodimer Bound To Thyroid Response Element
Dna
Length = 66
Score = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 36/67 (53%), Gaps = 1/67 (1%)
Query: 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKSCRLR 64
C +CG+ ++G H+G ++CEGCK FF R+ + + R C+ CR +
Sbjct: 1 CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYT-CRDNKDCLIDKRQRNRCQYCRYQ 59
Query: 65 KCLMVGM 71
KCL +GM
Sbjct: 60 KCLAMGM 66
>pdb|1CIT|A Chain A, Dna-Binding Mechanism Of The Monomeric Orphan Nuclear
Receptor Ngfi-B
Length = 89
Score = 47.4 bits (111), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 35/73 (47%), Gaps = 1/73 (1%)
Query: 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKSCRLR 64
C VCG+ A+ H+G TCEGCK FF R+ + R C+ CR +
Sbjct: 3 CAVCGDNASCQHYGVRTCEGCKGFFKRTVQK-SAKYICLANKDCPVDKRRRNRCQFCRFQ 61
Query: 65 KCLMVGMSKSGSR 77
KCL VGM K R
Sbjct: 62 KCLAVGMVKEVVR 74
>pdb|1RXR|A Chain A, High Resolution Solution Structure Of The Retinoid X
Receptor Dna Binding Domain, Nmr, 20 Structure
Length = 83
Score = 46.6 bits (109), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKSCRLR 64
C +CG+ ++G H+G ++CEGCK FF R+ + + R C+ CR +
Sbjct: 6 CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYT-CRDNKDCLIDKRQRNRCQYCRYQ 64
Query: 65 KCLMVGMSKSGSRYGRR 81
K L +GM + + R+
Sbjct: 65 KALAMGMKREAVQEERQ 81
>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 = 46.6 bits (109), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 36/77 (46%), Gaps = 1/77 (1%)
Query: 2 NQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKSC 61
+ C +CG+ A+G H+G TC CK FF R+ + R +C +C
Sbjct: 2 QKICLICGDEASGCHYGVLTCGSCKVFFKRAMEGQHNY-LCAGRNDCIVDKIRRKNCPAC 60
Query: 62 RLRKCLMVGMSKSGSRY 78
RLRKC GM G ++
Sbjct: 61 RLRKCCQAGMVLGGRKF 77
>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 = 46.2 bits (108), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 31/68 (45%)
Query: 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKSCRLR 64
C VC + A+G H+G TC CK FF R+ R +C +CR R
Sbjct: 5 CLVCSDEASGCHYGVLTCGSCKVFFKRAVEGRQHNYLCAGRNDCIIDKIRRKNCPACRYR 64
Query: 65 KCLMVGMS 72
KCL GM+
Sbjct: 65 KCLQAGMN 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 = 43.1 bits (100), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 32/68 (47%), Gaps = 1/68 (1%)
Query: 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKSCRLR 64
C VC + A+G H+G TC CK FF R+ + R +C +CR R
Sbjct: 29 CLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNY-LCAGDNRCIIDKIRRKNCPACRYR 87
Query: 65 KCLMVGMS 72
KCL GM+
Sbjct: 88 KCLQAGMN 95
>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 = 43.1 bits (100), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 32/68 (47%), Gaps = 1/68 (1%)
Query: 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKSCRLR 64
C VC + A+G H+G TC CK FF R+ + R +C +CR R
Sbjct: 32 CLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNY-LCAGRNDCIIDKIRRKNCPACRYR 90
Query: 65 KCLMVGMS 72
KCL GM+
Sbjct: 91 KCLQAGMN 98
>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 = 43.1 bits (100), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 32/68 (47%), Gaps = 1/68 (1%)
Query: 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKSCRLR 64
C VC + A+G H+G TC CK FF R+ + R +C +CR R
Sbjct: 5 CLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNY-LCAGRNDCIIDKIRRKNCPACRYR 63
Query: 65 KCLMVGMS 72
KCL GM+
Sbjct: 64 KCLQAGMN 71
>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 = 43.1 bits (100), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 32/68 (47%), Gaps = 1/68 (1%)
Query: 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKSCRLR 64
C VC + A+G H+G TC CK FF R+ + R +C +CR R
Sbjct: 7 CLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNY-LCAGRNDCIIDKIRRKNCPACRYR 65
Query: 65 KCLMVGMS 72
KCL GM+
Sbjct: 66 KCLQAGMN 73
>pdb|1R4R|B Chain B, Crystallographic Analysis Of The Interaction Of The
Glucocorticoid Receptor With Dna
Length = 92
Score = 43.1 bits (100), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 32/68 (47%), Gaps = 1/68 (1%)
Query: 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKSCRLR 64
C VC + A+G H+G TC CK FF R+ + R +C +CR R
Sbjct: 7 CLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNY-LCAGRNDCIIDKIRRKNCPACRYR 65
Query: 65 KCLMVGMS 72
KCL GM+
Sbjct: 66 KCLQAGMN 73
>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 = 43.1 bits (100), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 32/68 (47%), Gaps = 1/68 (1%)
Query: 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKSCRLR 64
C VC + A+G H+G TC CK FF R+ + R +C +CR R
Sbjct: 7 CLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNY-LCAGRNDCIIDKIRRKNCPACRYR 65
Query: 65 KCLMVGMS 72
KCL GM+
Sbjct: 66 KCLQAGMN 73
>pdb|1GDC|A Chain A, Refined Solution Structure Of The Glucocorticoid
Receptor Dna-Binding Domain
Length = 72
Score = 43.1 bits (100), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 32/68 (47%), Gaps = 1/68 (1%)
Query: 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKSCRLR 64
C VC + A+G H+G TC CK FF R+ + R +C +CR R
Sbjct: 2 CLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNY-LCAGRNDCIIDKIRRKNCPACRYR 60
Query: 65 KCLMVGMS 72
KCL GM+
Sbjct: 61 KCLQAGMN 68
>pdb|2GDA|A Chain A, Refined Solution Structure Of The Glucocorticoid
Receptor Dna-Binding Domain
Length = 72
Score = 42.7 bits (99), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 32/68 (47%), Gaps = 1/68 (1%)
Query: 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKSCRLR 64
C VC + A+G H+G TC CK FF R+ + R +C +CR R
Sbjct: 2 CLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNY-LCAGRNDCIIDKIRRKNCPACRYR 60
Query: 65 KCLMVGMS 72
KCL GM+
Sbjct: 61 KCLQAGMN 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 = 42.7 bits (99), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 32/68 (47%), Gaps = 1/68 (1%)
Query: 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISXXXXXXXXXXXXXXRTSCKSCRLR 64
C VC + A+G H+G TC CK FF R+ + R +C +CR R
Sbjct: 1 CLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNY-LCAGRNDCIIDKIRRKNCPACRYR 59
Query: 65 KCLMVGMS 72
KCL GM+
Sbjct: 60 KCLQAGMN 67
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
0.328 0.140 0.476
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,882,482
Number of Sequences: 62578
Number of extensions: 72881
Number of successful extensions: 199
Number of sequences better than 100.0: 43
Number of HSP's better than 100.0 without gapping: 43
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 112
Number of HSP's gapped (non-prelim): 43
length of query: 139
length of database: 14,973,337
effective HSP length: 89
effective length of query: 50
effective length of database: 9,403,895
effective search space: 470194750
effective search space used: 470194750
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: 46 (22.3 bits)