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= psy11507
(113 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1LO1|A Chain A, Estrogen Related Receptor 2 Dna Binding Domain In
Complex With Dna
Length = 98
Score = 75.9 bits (185), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 31/36 (86%), Positives = 35/36 (97%)
Query: 37 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQA 72
+P+RLCLVCGD+ASG+HYGVASCEACKAFFKRTIQ
Sbjct: 2 IPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQG 37
>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 = 59.7 bits (143), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 24/31 (77%), Positives = 27/31 (87%)
Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
LC VCGDVASGFHYGV +CE CK FF+R+IQ
Sbjct: 9 LCKVCGDVASGFHYGVLACEGCKGFFRRSIQ 39
>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 = 57.4 bits (137), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 22/32 (68%), Positives = 26/32 (81%)
Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
C VCGD ASGFHYGV +CE CK FF+RTI+ +
Sbjct: 53 CRVCGDKASGFHYGVHACEGCKGFFRRTIRLK 84
>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 = 57.0 bits (136), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 24/33 (72%), Positives = 26/33 (78%)
Query: 40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQA 72
R C VC D ASG+HYGV SCE CKAFFKR+IQ
Sbjct: 5 RYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQG 37
>pdb|1HCP|A Chain A, Dna Recognition By The Oestrogen Receptor: From Solution
To The Crystal
Length = 76
Score = 56.6 bits (135), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 24/33 (72%), Positives = 26/33 (78%)
Query: 40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQA 72
R C VC D ASG+HYGV SCE CKAFFKR+IQ
Sbjct: 5 RYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQG 37
>pdb|4AA6|E Chain E, The Oestrogen Receptor Recognizes An Imperfectly
Palindromic Response Element Through An Alternative
Side- Chain Conformation
Length = 71
Score = 56.6 bits (135), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 24/33 (72%), Positives = 26/33 (78%)
Query: 40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQA 72
R C VC D ASG+HYGV SCE CKAFFKR+IQ
Sbjct: 2 RYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQG 34
>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 = 56.6 bits (135), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 24/33 (72%), Positives = 26/33 (78%)
Query: 40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQA 72
R C VC D ASG+HYGV SCE CKAFFKR+IQ
Sbjct: 2 RYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQG 34
>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 = 55.5 bits (132), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 23/50 (46%), Positives = 30/50 (60%)
Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQKKSSQ 90
LC VCGD SG+HYG+ +CE+CK FFKRT+Q + Q +Q
Sbjct: 11 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYTCIENQNCQIDKTQ 60
>pdb|2ENV|A Chain A, Solution Sturcture Of The C4-Type Zinc Finger Domain
From Human Peroxisome Proliferator-Activated Receptor
Delta
Length = 88
Score = 55.1 bits (131), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 27/56 (48%), Positives = 36/56 (64%), Gaps = 6/56 (10%)
Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQKKSSQIPKEKYN 97
C VCGD ASGFHYGV +CE CK FF+RTI+ + +E ++S +I K+ N
Sbjct: 10 CRVCGDKASGFHYGVHACEGCKGFFRRTIRMKLE------YEKCERSCKIQKKNRN 59
>pdb|1LAT|A Chain A, Glucocorticoid Receptor MutantDNA COMPLEX
pdb|1LAT|B Chain B, Glucocorticoid Receptor MutantDNA COMPLEX
Length = 82
Score = 54.7 bits (130), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 23/36 (63%), Positives = 27/36 (75%)
Query: 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
P R CLVC D ASG HYGV +CE CKAFFKR ++ +
Sbjct: 3 PARPCLVCSDEASGCHYGVLTCEGCKAFFKRAVEGQ 38
>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 = 54.7 bits (130), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 21/31 (67%), Positives = 26/31 (83%)
Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
LC VCGD SG+HYG+ +CE+CK FFKRT+Q
Sbjct: 3 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQ 33
>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 = 54.3 bits (129), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 20/33 (60%), Positives = 26/33 (78%)
Query: 39 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
+ +C +CGD +SG HYGV SCE CK FFKRT++
Sbjct: 137 KHICAICGDRSSGKHYGVYSCEGCKGFFKRTVR 169
>pdb|2HAN|A Chain A, Structural Basis Of Heterodimeric Ecdysteroid Receptor
Interaction With Natural Response Element Hsp27 Gene
Promoter
Length = 93
Score = 53.1 bits (126), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 22/33 (66%), Positives = 26/33 (78%)
Query: 39 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
+ LC +CGD ASG HYGV SCE CK FFKRT++
Sbjct: 10 KHLCSICGDRASGKHYGVYSCEGCKGFFKRTVR 42
>pdb|1R0O|A Chain A, Crystal Structure Of The Heterodimeric Ecdysone Receptor
Dna-Binding Complex
Length = 86
Score = 53.1 bits (126), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 22/33 (66%), Positives = 26/33 (78%)
Query: 39 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
+ LC +CGD ASG HYGV SCE CK FFKRT++
Sbjct: 8 KHLCSICGDRASGKHYGVYSCEGCKGFFKRTVR 40
>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 = 53.1 bits (126), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 20/35 (57%), Positives = 26/35 (74%)
Query: 37 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
+ +C +CGD +SG HYGV SCE CK FFKRT++
Sbjct: 1 FTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVR 35
>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 = 52.8 bits (125), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 21/40 (52%), Positives = 28/40 (70%)
Query: 34 EEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
+ P +LCLVC D ASG HYGV +C +CK FFKR ++ +
Sbjct: 21 QSNAPPKLCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQ 60
>pdb|2HAN|B Chain B, Structural Basis Of Heterodimeric Ecdysteroid Receptor
Interaction With Natural Response Element Hsp27 Gene
Promoter
Length = 119
Score = 52.8 bits (125), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 24/48 (50%), Positives = 31/48 (64%), Gaps = 5/48 (10%)
Query: 27 GSTDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARA 74
GS ++EE LCLVCGD ASG+HY +CE CK FF+R++ A
Sbjct: 1 GSAPRVQEE-----LCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSA 43
>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 = 52.8 bits (125), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 20/36 (55%), Positives = 29/36 (80%)
Query: 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
P+++CL+CGD ASG HYGV +C +CK FFKR ++ +
Sbjct: 1 PQKICLICGDEASGCHYGVLTCGSCKVFFKRAMEGQ 36
>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 = 52.8 bits (125), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 21/36 (58%), Positives = 27/36 (75%)
Query: 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
P +LCLVC D ASG HYGV +C +CK FFKR ++ +
Sbjct: 28 PPKLCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQ 63
>pdb|1CIT|A Chain A, Dna-Binding Mechanism Of The Monomeric Orphan Nuclear
Receptor Ngfi-B
Length = 89
Score = 52.4 bits (124), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 23/38 (60%), Positives = 26/38 (68%)
Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSL 79
C VCGD AS HYGV +CE CK FFKRT+Q A + L
Sbjct: 3 CAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYICL 40
>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 = 52.0 bits (123), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 20/35 (57%), Positives = 26/35 (74%)
Query: 37 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
+ +C +CGD +SG HYGV SCE CK FFKRT++
Sbjct: 3 FTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVR 37
>pdb|1RXR|A Chain A, High Resolution Solution Structure Of The Retinoid X
Receptor Dna Binding Domain, Nmr, 20 Structure
Length = 83
Score = 52.0 bits (123), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 20/31 (64%), Positives = 25/31 (80%)
Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
+C +CGD +SG HYGV SCE CK FFKRT++
Sbjct: 5 ICAICGDRSSGKHYGVYSCEGCKGFFKRTVR 35
>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 = 52.0 bits (123), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 20/35 (57%), Positives = 26/35 (74%)
Query: 37 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
+ +C +CGD +SG HYGV SCE CK FFKRT++
Sbjct: 3 FTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVR 37
>pdb|1HRA|A Chain A, The Solution Structure Of The Human Retinoic Acid
Receptor- Beta Dna-Binding Domain
Length = 80
Score = 52.0 bits (123), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 21/37 (56%), Positives = 29/37 (78%), Gaps = 2/37 (5%)
Query: 37 LPR--RLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
+PR + C VC D +SG+HYGV++CE CK FF+R+IQ
Sbjct: 1 MPRVYKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQ 37
>pdb|2NLL|B Chain B, Retinoid X Receptor-Thyroid Hormone Receptor Dna-Binding
Domain Heterodimer Bound To Thyroid Response Element
Dna
Length = 103
Score = 51.6 bits (122), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 20/31 (64%), Positives = 25/31 (80%)
Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
LC+VCGD A+G+HY +CE CK FF+RTIQ
Sbjct: 3 LCVVCGDKATGYHYRCITCEGCKGFFRRTIQ 33
>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 = 51.6 bits (122), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 20/31 (64%), Positives = 25/31 (80%)
Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
LC+VCGD A+G+HY +CE CK FF+RTIQ
Sbjct: 5 LCVVCGDKATGYHYRCITCEGCKGFFRRTIQ 35
>pdb|1R0N|A Chain A, Crystal Structure Of Heterodimeric Ecdsyone Receptor Dna
Binding Complex
Length = 81
Score = 51.6 bits (122), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 20/35 (57%), Positives = 26/35 (74%)
Query: 37 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
+ +C +CGD +SG HYGV SCE CK FFKRT++
Sbjct: 1 FTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVR 35
>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 = 51.2 bits (121), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 19/30 (63%), Positives = 25/30 (83%)
Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
C VC D +SG+HYGV++CE CK FF+R+IQ
Sbjct: 7 CFVCQDKSSGYHYGVSACEGCKGFFRRSIQ 36
>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 = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 19/30 (63%), Positives = 24/30 (80%)
Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTI 70
LCLVCGD ASG+HY +CE CK FF+R++
Sbjct: 8 LCLVCGDRASGYHYNALTCEGCKGFFRRSV 37
>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 = 50.4 bits (119), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 19/36 (52%), Positives = 26/36 (72%)
Query: 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
P++ CL+CGD ASG HYG +C +CK FFKR + +
Sbjct: 6 PQKTCLICGDEASGAHYGALTCGSCKVFFKRAAEGK 41
>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 = 50.4 bits (119), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 21/36 (58%), Positives = 26/36 (72%)
Query: 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
P R CLVC D ASG HYGV +C +CK FFKR ++ +
Sbjct: 3 PARPCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQ 38
>pdb|1R4R|B Chain B, Crystallographic Analysis Of The Interaction Of The
Glucocorticoid Receptor With Dna
Length = 92
Score = 50.4 bits (119), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 21/36 (58%), Positives = 26/36 (72%)
Query: 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
P R CLVC D ASG HYGV +C +CK FFKR ++ +
Sbjct: 3 PARPCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQ 38
>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 = 50.4 bits (119), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 18/35 (51%), Positives = 27/35 (77%)
Query: 40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQARA 74
R+C VCGD A+GFH+ +CE CK FF+R+++ +A
Sbjct: 7 RICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKA 41
>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 = 50.4 bits (119), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 21/36 (58%), Positives = 26/36 (72%)
Query: 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
P R CLVC D ASG HYGV +C +CK FFKR ++ +
Sbjct: 3 PARPCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQ 38
>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 = 50.1 bits (118), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 18/35 (51%), Positives = 27/35 (77%)
Query: 40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQARA 74
R+C VCGD A+GFH+ +CE CK FF+R+++ +A
Sbjct: 7 RICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKA 41
>pdb|2NLL|A Chain A, Retinoid X Receptor-Thyroid Hormone Receptor Dna-Binding
Domain Heterodimer Bound To Thyroid Response Element
Dna
Length = 66
Score = 50.1 bits (118), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 20/30 (66%), Positives = 24/30 (80%)
Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
C +CGD +SG HYGV SCE CK FFKRT++
Sbjct: 1 CAICGDRSSGKHYGVYSCEGCKGFFKRTVR 30
>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 = 49.7 bits (117), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 20/33 (60%), Positives = 25/33 (75%)
Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
+CLVC D ASG HYGV +C +CK FFKR ++ R
Sbjct: 4 MCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGR 36
>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 = 48.1 bits (113), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 17/31 (54%), Positives = 25/31 (80%)
Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
LC +CGD A+G HYG +SC+ CK FF+R+++
Sbjct: 2 LCAICGDRATGKHYGASSCDGCKGFFRRSVR 32
>pdb|2GDA|A Chain A, Refined Solution Structure Of The Glucocorticoid
Receptor Dna-Binding Domain
Length = 72
Score = 48.1 bits (113), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 20/33 (60%), Positives = 25/33 (75%)
Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
LCLVC D ASG HYGV +C +CK FFKR ++ +
Sbjct: 1 LCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQ 33
>pdb|1GDC|A Chain A, Refined Solution Structure Of The Glucocorticoid
Receptor Dna-Binding Domain
Length = 72
Score = 48.1 bits (113), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 20/33 (60%), Positives = 25/33 (75%)
Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
LCLVC D ASG HYGV +C +CK FFKR ++ +
Sbjct: 1 LCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQ 33
>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 = 47.8 bits (112), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 19/33 (57%), Positives = 25/33 (75%)
Query: 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
+CLVC D ASG HYGV +C +CK FFKR ++ +
Sbjct: 4 MCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQ 36
>pdb|2EBL|A Chain A, Solution Structure Of The Zinc Finger, C4-type Domain Of
Human Coup Transcription Factor 1
Length = 89
Score = 47.0 bits (110), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 18/30 (60%), Positives = 25/30 (83%)
Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQ 71
C+VCGD +SG HYG +CE CK+FFKR+++
Sbjct: 10 CVVCGDKSSGKHYGQFTCEGCKSFFKRSVR 39
>pdb|1RGD|A Chain A, Structure Refinement Of The Glucocorticoid Receptor-Dna
Binding Domain From Nmr Data By Relaxation Matrix
Calculations
Length = 71
Score = 46.2 bits (108), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 19/32 (59%), Positives = 24/32 (75%)
Query: 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQAR 73
CLVC D ASG HYGV +C +CK FFKR ++ +
Sbjct: 1 CLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQ 32
>pdb|4A14|A Chain A, Human Kif7, A Kinesin Involved In Hedgehog Signalling
Length = 344
Score = 27.3 bits (59), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 5/46 (10%)
Query: 66 FKRTIQARASLVSLRG-----HEPQKKSSQIPKEKYNLAYLMSDSL 106
K +IQ +SL++L +PQ++ S IP + ++ DSL
Sbjct: 266 LKESIQINSSLLALGNVISALGDPQRRGSHIPYRDSKITRILKDSL 311
>pdb|1PDJ|D Chain D, Fitting Of Gp27 Into Cryoem Reconstruction Of
Bacteriophage T4 Baseplate
pdb|1PDJ|E Chain E, Fitting Of Gp27 Into Cryoem Reconstruction Of
Bacteriophage T4 Baseplate
pdb|1PDJ|F Chain F, Fitting Of Gp27 Into Cryoem Reconstruction Of
Bacteriophage T4 Baseplate
pdb|1WTH|D Chain D, Crystal Structure Of Gp5-S351l Mutant And Gp27 Complex
pdb|2Z6B|D Chain D, Crystal Structure Analysis Of (Gp27-Gp5)3 Conjugated
With Fe(Iii) Protoporphyrin
Length = 391
Score = 26.9 bits (58), Expect = 2.9, Method: Composition-based stats.
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 4 WSSKRLVELSVYLQTYTVEQKFRGSTDGI 32
WS+ R VEL+ + T T+ G +G+
Sbjct: 23 WSNNRFVELAATITTLTMRDSLYGRNEGM 51
>pdb|2XT3|A Chain A, Human Kif7, A Kinesin Involved In Hedgehog Signalling
Length = 344
Score = 26.6 bits (57), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 24/45 (53%), Gaps = 5/45 (11%)
Query: 67 KRTIQARASLVSLRG-----HEPQKKSSQIPKEKYNLAYLMSDSL 106
K +IQ +SL++L +PQ++ S IP + ++ DSL
Sbjct: 267 KESIQINSSLLALGNVISALGDPQRRGSNIPYRDSKITRILKDSL 311
>pdb|2DLQ|A Chain A, Solution Structure Of The Tandem Four Zf-C2h2 Domain
Repeats Of Murine Gli-Kruppel Family Member Hkr3
Length = 124
Score = 26.6 bits (57), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 19/34 (55%)
Query: 56 VASCEACKAFFKRTIQARASLVSLRGHEPQKKSS 89
V +C C+ F+R ++ R +VS G P K SS
Sbjct: 66 VFTCSVCQETFRRRMELRLHMVSHTGEMPYKCSS 99
>pdb|3L6U|A Chain A, Crystal Structure Of Abc-Type Sugar Transport System,
Periplasmic Component From Exiguobacterium Sibiricum
pdb|3L6U|B Chain B, Crystal Structure Of Abc-Type Sugar Transport System,
Periplasmic Component From Exiguobacterium Sibiricum
Length = 293
Score = 25.4 bits (54), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 5 SSKRLVELSVYLQTYTVEQKFRGSTDGIKEE 35
S+ R+VE++ YT ++ RG GI+ E
Sbjct: 134 STGRIVEITGTANVYTTNERHRGFLKGIENE 164
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
0.320 0.132 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,205,828
Number of Sequences: 62578
Number of extensions: 104208
Number of successful extensions: 251
Number of sequences better than 100.0: 48
Number of HSP's better than 100.0 without gapping: 46
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 205
Number of HSP's gapped (non-prelim): 48
length of query: 113
length of database: 14,973,337
effective HSP length: 77
effective length of query: 36
effective length of database: 10,154,831
effective search space: 365573916
effective search space used: 365573916
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)