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= psy16764
(113 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3CJW|A Chain A, Crystal Structure Of The Human Coup-Tfii Ligand Binding
Domain
Length = 244
Score = 53.5 bits (127), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 27/65 (41%), Positives = 43/65 (66%), Gaps = 1/65 (1%)
Query: 44 AIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIGHNTTIKK 103
++Q +Q L +Y+ + YP+QPTRF K+ L LP L+++ S V+E+LFF ++G T I+
Sbjct: 166 SLQEKSQCALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFFVRLVG-KTPIET 224
Query: 104 TIWHM 108
I M
Sbjct: 225 LIRDM 229
>pdb|2Q60|A Chain A, Crystal Structure Of The Ligand Binding Domain Of
Polyandrocarpa Misakiensis Rxr In Tetramer In Absence Of
Ligand
pdb|2Q60|B Chain B, Crystal Structure Of The Ligand Binding Domain Of
Polyandrocarpa Misakiensis Rxr In Tetramer In Absence Of
Ligand
pdb|2Q60|C Chain C, Crystal Structure Of The Ligand Binding Domain Of
Polyandrocarpa Misakiensis Rxr In Tetramer In Absence Of
Ligand
pdb|2Q60|D Chain D, Crystal Structure Of The Ligand Binding Domain Of
Polyandrocarpa Misakiensis Rxr In Tetramer In Absence Of
Ligand
Length = 258
Score = 50.4 bits (119), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 38/110 (34%), Positives = 52/110 (47%), Gaps = 15/110 (13%)
Query: 1 MFQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTV 60
M +TEL LR V N + ++N S +R K + A Y +
Sbjct: 157 MDKTELGCLRAVVLFNPD--VKNPSDSAHIESLREKVYASLEA------------YCRSK 202
Query: 61 YPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIGHNTTIKKTIWHMYK 110
YP QP RF K+ L LP L+SI LE LFF +IG +T I K + +M +
Sbjct: 203 YPDQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIG-DTPIDKFLMNMLE 251
>pdb|1XIU|A Chain A, Crystal Structure Of The Agonist-Bound Ligand-Binding
Domain Of Biomphalaria Glabrata Rxr
pdb|1XIU|B Chain B, Crystal Structure Of The Agonist-Bound Ligand-Binding
Domain Of Biomphalaria Glabrata Rxr
Length = 230
Score = 45.4 bits (106), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 30/85 (35%), Positives = 42/85 (49%), Gaps = 7/85 (8%)
Query: 33 VRFKTGSKFTAAIQGHTQI------FLNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVL 86
V F +K A+Q Q+ L +Y + YP +P RF K+ L LP L+SI L
Sbjct: 142 VLFNPDAKGLTAVQEVEQLREKVYASLEEYTKSRYPEEPGRFAKLLLRLPALRSIGLKCL 201
Query: 87 EELFFRNIIGHNTTIKKTIWHMYKN 111
E LFF +IG + I + M +N
Sbjct: 202 EHLFFFKLIG-DQPIDTFLMEMLEN 225
>pdb|1Z5X|U Chain U, Hemipteran Ecdysone Receptor Ligand-Binding Domain
Complexed With Ponasterone A
Length = 262
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/60 (40%), Positives = 33/60 (55%), Gaps = 1/60 (1%)
Query: 52 FLNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIGHNTTIKKTIWHMYKN 111
L +Y YP Q RF K+ L LP L+SI LE LFF ++G NT+I + M ++
Sbjct: 200 ILEEYCRQTYPDQSGRFAKLLLRLPALRSIGLKCLEHLFFFKLVG-NTSIDSFLLSMLES 258
>pdb|3EYB|A Chain A, Structural And Functional Insights Into The Ligand Binding
Domain Of A Non-Duplicated Rxr From The Invertebrate
Chordate Amphioxus
pdb|3EYB|B Chain B, Structural And Functional Insights Into The Ligand Binding
Domain Of A Non-Duplicated Rxr From The Invertebrate
Chordate Amphioxus
pdb|3EYB|C Chain C, Structural And Functional Insights Into The Ligand Binding
Domain Of A Non-Duplicated Rxr From The Invertebrate
Chordate Amphioxus
pdb|3EYB|D Chain D, Structural And Functional Insights Into The Ligand Binding
Domain Of A Non-Duplicated Rxr From The Invertebrate
Chordate Amphioxus
Length = 219
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/56 (44%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 53 LNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIGHNTTIKKTIWHM 108
L +Y YP QP RF K+ L LP L+SI LE LFF +IG +T I + M
Sbjct: 164 LEEYCKQQYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIG-DTPIDTFLMEM 218
>pdb|2GL8|A Chain A, Human Retinoic Acid Receptor Rxr-Gamma Ligand-Binding
Domain
pdb|2GL8|B Chain B, Human Retinoic Acid Receptor Rxr-Gamma Ligand-Binding
Domain
pdb|2GL8|C Chain C, Human Retinoic Acid Receptor Rxr-Gamma Ligand-Binding
Domain
pdb|2GL8|D Chain D, Human Retinoic Acid Receptor Rxr-Gamma Ligand-Binding
Domain
Length = 241
Score = 43.9 bits (102), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/58 (43%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 53 LNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIGHNTTIKKTIWHMYK 110
L Y YP QP RF K+ L LP L+SI LE LFF +IG +T I + M +
Sbjct: 179 LEAYTKQKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIG-DTPIDTFLMEMLE 235
>pdb|1LBD|A Chain A, Ligand-Binding Domain Of The Human Nuclear Receptor
Rxr-Alpha
Length = 282
Score = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/58 (43%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 53 LNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIGHNTTIKKTIWHMYK 110
L Y YP QP RF K+ L LP L+SI LE LFF +IG +T I + M +
Sbjct: 220 LEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIG-DTPIDTFLMEMLE 276
>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 = 43.5 bits (101), Expect = 3e-05, Method: Composition-based stats.
Identities = 22/44 (50%), Positives = 25/44 (56%)
Query: 53 LNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIG 96
L Y YP QP RF K+ L LP L+SI LE LFF +IG
Sbjct: 405 LEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIG 448
>pdb|3E94|A Chain A, Crystal Structure Of Rxralpha Ligand Binding Domain In
Complex With Tributyltin And A Coactivator Fragment
pdb|3KWY|A Chain A, Crystal Structure Of Rxralpha Ligand Binding Domain In
Complex With Triphenyltin And A Coactivator Fragment
Length = 244
Score = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/58 (43%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 53 LNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIGHNTTIKKTIWHMYK 110
L Y YP QP RF K+ L LP L+SI LE LFF +IG +T I + M +
Sbjct: 182 LEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIG-DTPIDTFLMEMLE 238
>pdb|1DKF|A Chain A, Crystal Structure Of A Heterodimeric Complex Of Rar And
Rxr Ligand-Binding Domains
Length = 233
Score = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/58 (43%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 53 LNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIGHNTTIKKTIWHMYK 110
L Y YP QP RF K+ L LP L+SI LE LFF +IG +T I + M +
Sbjct: 176 LEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIG-DTPIDTFLMEMLE 232
>pdb|1RDT|A Chain A, Crystal Structure Of A New Rexinoid Bound To The Rxralpha
Ligand Binding Doamin In The RxralphaPPARGAMMA
HETERODIMER
pdb|3FC6|A Chain A, Hrxralpha & Mlxralpha With An Indole Pharmacophore,
Sb786875
pdb|3FC6|C Chain C, Hrxralpha & Mlxralpha With An Indole Pharmacophore,
Sb786875
pdb|3FAL|A Chain A, Humanrxr Alpha & Mouse Lxr Alpha Complexed With Retenoic
Acid And Gsk2186
pdb|3FAL|C Chain C, Humanrxr Alpha & Mouse Lxr Alpha Complexed With Retenoic
Acid And Gsk2186
Length = 242
Score = 43.1 bits (100), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/58 (43%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 53 LNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIGHNTTIKKTIWHMYK 110
L Y YP QP RF K+ L LP L+SI LE LFF +IG +T I + M +
Sbjct: 180 LEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIG-DTPIDTFLMEMLE 236
>pdb|1FM6|A Chain A, The 2.1 Angstrom Resolution Crystal Structure Of The
Heterodimer Of The Human Rxralpha And Ppargamma Ligand
Binding Domains Respectively Bound With 9-Cis Retinoic
Acid And Rosiglitazone And Co-Activator Peptides.
pdb|1FM6|U Chain U, The 2.1 Angstrom Resolution Crystal Structure Of The
Heterodimer Of The Human Rxralpha And Ppargamma Ligand
Binding Domains Respectively Bound With 9-Cis Retinoic
Acid And Rosiglitazone And Co-Activator Peptides.
pdb|1FM9|A Chain A, The 2.1 Angstrom Resolution Crystal Structure Of The
Heterodimer Of The Human Rxralpha And Ppargamma Ligand
Binding Domains Respectively Bound With 9-Cis Retinoic
Acid And Gi262570 And Co-Activator Peptides.
pdb|1G5Y|A Chain A, The 2.0 Angstrom Resolution Crystal Structure Of The
Rxralpha Ligand Binding Domain Tetramer In The Presence
Of A Non-Activating Retinoic Acid Isomer.
pdb|1G5Y|B Chain B, The 2.0 Angstrom Resolution Crystal Structure Of The
Rxralpha Ligand Binding Domain Tetramer In The Presence
Of A Non-Activating Retinoic Acid Isomer.
pdb|1G5Y|C Chain C, The 2.0 Angstrom Resolution Crystal Structure Of The
Rxralpha Ligand Binding Domain Tetramer In The Presence
Of A Non-Activating Retinoic Acid Isomer.
pdb|1G5Y|D Chain D, The 2.0 Angstrom Resolution Crystal Structure Of The
Rxralpha Ligand Binding Domain Tetramer In The Presence
Of A Non-Activating Retinoic Acid Isomer.
pdb|1G1U|A Chain A, The 2.5 Angstrom Resolution Crystal Structure Of The
Rxralpha Ligand Binding Domain In Tetramer In The
Absence Of Ligand
pdb|1G1U|B Chain B, The 2.5 Angstrom Resolution Crystal Structure Of The
Rxralpha Ligand Binding Domain In Tetramer In The
Absence Of Ligand
pdb|1G1U|C Chain C, The 2.5 Angstrom Resolution Crystal Structure Of The
Rxralpha Ligand Binding Domain In Tetramer In The
Absence Of Ligand
pdb|1G1U|D Chain D, The 2.5 Angstrom Resolution Crystal Structure Of The
Rxralpha Ligand Binding Domain In Tetramer In The
Absence Of Ligand
pdb|1K74|A Chain A, The 2.3 Angstrom Resolution Crystal Structure Of The
Heterodimer Of The Human Ppargamma And Rxralpha Ligand
Binding Domains Respectively Bound With Gw409544 And
9-Cis Retinoic Acid And Co-Activator Peptides.
pdb|2ACL|A Chain A, Liver X-Receptor Alpha Ligand Binding Domain With Sb313987
pdb|2ACL|C Chain C, Liver X-Receptor Alpha Ligand Binding Domain With Sb313987
pdb|2ACL|E Chain E, Liver X-Receptor Alpha Ligand Binding Domain With Sb313987
pdb|2ACL|G Chain G, Liver X-Receptor Alpha Ligand Binding Domain With Sb313987
pdb|3OZJ|A Chain A, Crystal Structure Of Human Retinoic X Receptor Alpha
Complexed With Bigelovin And Coactivator Src-1
pdb|3OZJ|C Chain C, Crystal Structure Of Human Retinoic X Receptor Alpha
Complexed With Bigelovin And Coactivator Src-1
Length = 238
Score = 43.1 bits (100), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/58 (43%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 53 LNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIGHNTTIKKTIWHMYK 110
L Y YP QP RF K+ L LP L+SI LE LFF +IG +T I + M +
Sbjct: 176 LEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIG-DTPIDTFLMEMLE 232
>pdb|3UVV|B Chain B, Crystal Structure Of The Ligand Binding Domains Of The
Thyroid Receptor:retinoid X Receptor Complexed With
3,3',5 Triiodo-L- Thyronine And 9-Cis Retinoic Acid
Length = 244
Score = 43.1 bits (100), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/58 (43%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 53 LNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIGHNTTIKKTIWHMYK 110
L Y YP QP RF K+ L LP L+SI LE LFF +IG +T I + M +
Sbjct: 180 LEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIG-DTPIDTFLMEMLE 236
>pdb|1MV9|A Chain A, Crystal Structure Of The Human Rxr Alpha Ligand Binding
Domain Bound To The Eicosanoid Dha (Docosa Hexaenoic
Acid) And A Coactivator Peptide
pdb|1MVC|A Chain A, Crystal Structure Of The Human Rxr Alpha Ligand Binding
Domain Bound To The Synthetic Agonist Compound Bms 649
And A Coactivator Peptide
pdb|1MZN|A Chain A, Crystal Structure At 1.9 Angstroems Resolution Of The
Homodimer Of Human Rxr Alpha Ligand Binding Domain Bound
To The Synthetic Agonist Compound Bms 649 And A
Coactivator Peptide
pdb|1MZN|C Chain C, Crystal Structure At 1.9 Angstroems Resolution Of The
Homodimer Of Human Rxr Alpha Ligand Binding Domain Bound
To The Synthetic Agonist Compound Bms 649 And A
Coactivator Peptide
pdb|1MZN|E Chain E, Crystal Structure At 1.9 Angstroems Resolution Of The
Homodimer Of Human Rxr Alpha Ligand Binding Domain Bound
To The Synthetic Agonist Compound Bms 649 And A
Coactivator Peptide
pdb|1MZN|G Chain G, Crystal Structure At 1.9 Angstroems Resolution Of The
Homodimer Of Human Rxr Alpha Ligand Binding Domain Bound
To The Synthetic Agonist Compound Bms 649 And A
Coactivator Peptide
pdb|2P1T|A Chain A, Crystal Structure Of The Ligand Binding Domain Of The
Retinoid X Receptor Alpha In Complex With
3-(2'-Methoxy)- Tetrahydronaphtyl Cinnamic Acid And A
Fragment Of The Coactivator Tif-2
pdb|2P1U|A Chain A, Crystal Structure Of The Ligand Binding Domain Of The
Retinoid X Receptor Alpha In Complex With 3-(2'-Ethoxy)-
Tetrahydronaphtyl Cinnamic Acid And A Fragment Of The
Coactivator Tif-2
pdb|2P1V|A Chain A, Crystal Structure Of The Ligand Binding Domain Of The
Retinoid X Receptor Alpha In Complex With
3-(2'-Propoxy)- Tetrahydronaphtyl Cinnamic Acid And A
Fragment Of The Coactivator Tif-2
pdb|3FUG|A Chain A, Crystal Structure Of The Retinoid X Receptor Ligand
Binding Domain Bound To The Synthetic Agonist
3-[4-Hydroxy-3-(3,5,
5,8,8-Pentamethyl-5,6,7,8-Tetrahydronaphthalen-2-Yl)-
Phenyl]acrylic Acid
pdb|2ZXZ|A Chain A, Crystal Structure Of The Human Rxr Alpha Ligand Binding
Domain Bound To A Synthetic Agonist Compound And A
Coactivator Peptide
pdb|2ZY0|A Chain A, Crystal Structure Of The Human Rxr Alpha Ligand Binding
Domain Bound To A Synthetic Agonist Compound And A
Coactivator Peptide
pdb|2ZY0|C Chain C, Crystal Structure Of The Human Rxr Alpha Ligand Binding
Domain Bound To A Synthetic Agonist Compound And A
Coactivator Peptide
pdb|3NSP|A Chain A, Crystal Structure Of Tetrameric Rxralpha-Lbd
pdb|3NSP|B Chain B, Crystal Structure Of Tetrameric Rxralpha-Lbd
pdb|3NSQ|A Chain A, Crystal Structure Of Tetrameric Rxralpha-Lbd Complexed
With Antagonist Danthron
pdb|3NSQ|B Chain B, Crystal Structure Of Tetrameric Rxralpha-Lbd Complexed
With Antagonist Danthron
pdb|3R29|A Chain A, Crystal Structure Of Rxralpha Ligand-Binding Domain
Complexed With Corepressor Smrt2
pdb|3R29|B Chain B, Crystal Structure Of Rxralpha Ligand-Binding Domain
Complexed With Corepressor Smrt2
pdb|3R2A|A Chain A, Crystal Structure Of Rxralpha Ligand-Binding Domain
Complexed With Corepressor Smrt2 And Antagonist Rhein
pdb|3R2A|B Chain B, Crystal Structure Of Rxralpha Ligand-Binding Domain
Complexed With Corepressor Smrt2 And Antagonist Rhein
pdb|3R2A|C Chain C, Crystal Structure Of Rxralpha Ligand-Binding Domain
Complexed With Corepressor Smrt2 And Antagonist Rhein
pdb|3R2A|D Chain D, Crystal Structure Of Rxralpha Ligand-Binding Domain
Complexed With Corepressor Smrt2 And Antagonist Rhein
pdb|3R5M|A Chain A, Crystal Structure Of Rxralphalbd Complexed With The
Agonist Magnolol
pdb|3R5M|C Chain C, Crystal Structure Of Rxralphalbd Complexed With The
Agonist Magnolol
Length = 240
Score = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 25/58 (43%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 53 LNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIGHNTTIKKTIWHMYK 110
L Y YP QP RF K+ L LP L+SI LE LFF +IG +T I + M +
Sbjct: 178 LEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIG-DTPIDTFLMEMLE 234
>pdb|1FBY|A Chain A, Crystal Structure Of The Human Rxr Alpha Ligand Binding
Domain Bound To 9-Cis Retinoic Acid
pdb|1FBY|B Chain B, Crystal Structure Of The Human Rxr Alpha Ligand Binding
Domain Bound To 9-Cis Retinoic Acid
Length = 239
Score = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 25/58 (43%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 53 LNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIGHNTTIKKTIWHMYK 110
L Y YP QP RF K+ L LP L+SI LE LFF +IG +T I + M +
Sbjct: 177 LEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIG-DTPIDTFLMEMLE 233
>pdb|3A9E|A Chain A, Crystal Structure Of A Mixed Agonist-Bound Rar-Alpha And
Antagonist- Bound Rxr-Alpha Heterodimer Ligand Binding
Domains
Length = 240
Score = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 25/58 (43%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 53 LNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIGHNTTIKKTIWHMYK 110
L Y YP QP RF K+ L LP L+SI LE LFF +IG +T I + M +
Sbjct: 178 LEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIG-DTPIDTFLMEMLE 234
>pdb|1XDK|A Chain A, Crystal Structure Of The RarbetaRXRALPHA LIGAND BINDING
Domain Heterodimer In Complex With 9-Cis Retinoic Acid
And A Fragment Of The Trap220 Coactivator
pdb|1XDK|E Chain E, Crystal Structure Of The RarbetaRXRALPHA LIGAND BINDING
Domain Heterodimer In Complex With 9-Cis Retinoic Acid
And A Fragment Of The Trap220 Coactivator
Length = 238
Score = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 25/58 (43%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 53 LNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIGHNTTIKKTIWHMYK 110
L Y YP QP RF K+ L LP L+SI LE LFF +IG +T I + M +
Sbjct: 176 LEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIG-DTPIDTFLMEMLE 232
>pdb|3PCU|A Chain A, Crystal Structure Of Human Retinoic X Receptor Alpha
Ligand-Binding Domain Complexed With Lx0278 And Src1
Peptide
Length = 230
Score = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 25/58 (43%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 53 LNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIGHNTTIKKTIWHMYK 110
L Y YP QP RF K+ L LP L+SI LE LFF +IG +T I + M +
Sbjct: 172 LEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIG-DTPIDTFLMEMLE 228
>pdb|3OAP|A Chain A, Crystal Structure Of Human Retinoid X Receptor
Alpha-Ligand Binding Domain Complex With 9-Cis Retinoic
Acid And The Coactivator Peptide Grip-1
Length = 231
Score = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 25/58 (43%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 53 LNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIGHNTTIKKTIWHMYK 110
L Y YP QP RF K+ L LP L+SI LE LFF +IG +T I + M +
Sbjct: 173 LEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIG-DTPIDTFLMEMLE 229
>pdb|1XV9|A Chain A, Crystal Structure Of CarRXR HETERODIMER BOUND WITH SRC1
Peptide, Fatty Acid, And 5b-Pregnane-3,20-Dione.
pdb|1XV9|C Chain C, Crystal Structure Of CarRXR HETERODIMER BOUND WITH SRC1
Peptide, Fatty Acid, And 5b-Pregnane-3,20-Dione.
pdb|1XVP|A Chain A, Crystal Structure Of CarRXR HETERODIMER BOUND WITH SRC1
Peptide, Fatty Acid And Citco
pdb|1XVP|C Chain C, Crystal Structure Of CarRXR HETERODIMER BOUND WITH SRC1
Peptide, Fatty Acid And Citco
Length = 236
Score = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 25/58 (43%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 53 LNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIGHNTTIKKTIWHMYK 110
L Y YP QP RF K+ L LP L+SI LE LFF +IG +T I + M +
Sbjct: 174 LEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIG-DTPIDTFLMEMLE 230
>pdb|1XLS|A Chain A, Crystal Structure Of The Mouse CarRXR LBD HETERODIMER
Bound To Tcpobop And 9cra And A Tif2 Peptide Containg
The Third Lxxll Motifs
pdb|1XLS|B Chain B, Crystal Structure Of The Mouse CarRXR LBD HETERODIMER
Bound To Tcpobop And 9cra And A Tif2 Peptide Containg
The Third Lxxll Motifs
pdb|1XLS|C Chain C, Crystal Structure Of The Mouse CarRXR LBD HETERODIMER
Bound To Tcpobop And 9cra And A Tif2 Peptide Containg
The Third Lxxll Motifs
pdb|1XLS|D Chain D, Crystal Structure Of The Mouse CarRXR LBD HETERODIMER
Bound To Tcpobop And 9cra And A Tif2 Peptide Containg
The Third Lxxll Motifs
Length = 232
Score = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 25/58 (43%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 53 LNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIGHNTTIKKTIWHMYK 110
L Y YP QP RF K+ L LP L+SI LE LFF +IG +T I + M +
Sbjct: 174 LEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIG-DTPIDTFLMEMLE 230
>pdb|2NXX|A Chain A, Crystal Structure Of The Ligand-Binding Domains Of The
T.Castaneum (Coleoptera) Heterodimer Ecrusp Bound To
Ponasterone A
pdb|2NXX|B Chain B, Crystal Structure Of The Ligand-Binding Domains Of The
T.Castaneum (Coleoptera) Heterodimer Ecrusp Bound To
Ponasterone A
pdb|2NXX|C Chain C, Crystal Structure Of The Ligand-Binding Domains Of The
T.Castaneum (Coleoptera) Heterodimer Ecrusp Bound To
Ponasterone A
pdb|2NXX|D Chain D, Crystal Structure Of The Ligand-Binding Domains Of The
T.Castaneum (Coleoptera) Heterodimer Ecrusp Bound To
Ponasterone A
Length = 235
Score = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 21/45 (46%), Positives = 28/45 (62%)
Query: 53 LNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIGH 97
L +Y T +P++P RF K+ L LP L+SI LE LFF +IG
Sbjct: 174 LEEYTRTTHPNEPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGD 218
>pdb|3H0A|A Chain A, Crystal Structure Of Peroxisome Proliferator-Activated
Receptor Gamma (Pparg) And Retinoic Acid Receptor Alpha
(Rxra) In Complex With 9-Cis Retinoic Acid, Co-Activator
Peptide, And A Partial Agonist
Length = 228
Score = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 25/56 (44%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 53 LNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIGHNTTIKKTIWHM 108
L Y YP QP RF K+ L LP L+SI LE LFF +IG +T I + M
Sbjct: 173 LEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIG-DTPIDTFLMEM 227
>pdb|1UHL|A Chain A, Crystal Structure Of The Lxralfa-Rxrbeta Lbd Heterodimer
Length = 236
Score = 39.7 bits (91), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/58 (41%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 53 LNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIGHNTTIKKTIWHMYK 110
L Y YP Q RF K+ L LP L+SI LE LFF +IG +T I + M +
Sbjct: 174 LETYCKQKYPEQQGRFAKLLLRLPALRSIGLKCLEHLFFFKLIG-DTPIDTFLMEMLE 230
>pdb|1H9U|A Chain A, The Structure Of The Human Retinoid-X-Receptor Beta Ligand
Binding Domain In Complex With The Specific Synthetic
Agonist Lg100268
pdb|1H9U|B Chain B, The Structure Of The Human Retinoid-X-Receptor Beta Ligand
Binding Domain In Complex With The Specific Synthetic
Agonist Lg100268
pdb|1H9U|C Chain C, The Structure Of The Human Retinoid-X-Receptor Beta Ligand
Binding Domain In Complex With The Specific Synthetic
Agonist Lg100268
pdb|1H9U|D Chain D, The Structure Of The Human Retinoid-X-Receptor Beta Ligand
Binding Domain In Complex With The Specific Synthetic
Agonist Lg100268
Length = 224
Score = 38.9 bits (89), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 21/44 (47%), Positives = 24/44 (54%)
Query: 53 LNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIG 96
L Y YP Q RF K+ L LP L+SI LE LFF +IG
Sbjct: 173 LETYCKQKYPEQQGRFAKLLLRLPALRSIGLKCLEHLFFFKLIG 216
>pdb|3P0U|A Chain A, Crystal Structure Of The Ligand Binding Domain Of Human
Testicular Receptor 4
pdb|3P0U|B Chain B, Crystal Structure Of The Ligand Binding Domain Of Human
Testicular Receptor 4
Length = 249
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 33/65 (50%), Gaps = 1/65 (1%)
Query: 46 QGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIGHNTTIKKTI 105
Q Q+ L Y+ Y R +I + LP L+ + S + EELFF +IG N +I I
Sbjct: 171 QEAAQMELQDYVQATYSEDTYRLARILVRLPALRLMSSNITEELFFTGLIG-NVSIDSII 229
Query: 106 WHMYK 110
++ K
Sbjct: 230 PYILK 234
>pdb|1PK5|A Chain A, Crystal Structure Of The Orphan Nuclear Receptor Lrh-1
pdb|1PK5|B Chain B, Crystal Structure Of The Orphan Nuclear Receptor Lrh-1
pdb|3F5C|A Chain A, Structure Of Dax-1:lrh-1 Complex
Length = 248
Score = 29.6 bits (65), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 16/67 (23%), Positives = 30/67 (44%)
Query: 30 GSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEEL 89
S V+ + +Q L Y YP Q +F ++ L LP L++I + L
Sbjct: 165 SSDVKNLENLQLVEGVQEQVNAALLDYTVCNYPQQTEKFGQLLLRLPELRAISKQAEDYL 224
Query: 90 FFRNIIG 96
+++++ G
Sbjct: 225 YYKHVNG 231
>pdb|3TX7|B Chain B, Crystal Structure Of Lrh-1BETA-Catenin Complex
Length = 352
Score = 28.9 bits (63), Expect = 0.67, Method: Composition-based stats.
Identities = 14/57 (24%), Positives = 27/57 (47%)
Query: 40 KFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIG 96
+ +Q L Y YP Q +F ++ L LP +++I E L+++++ G
Sbjct: 279 QLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNG 335
>pdb|1YUC|A Chain A, Human Nuclear Receptor Liver Receptor Homologue-1, Lrh-1,
Bound To Phospholipid And A Fragment Of Human Shp
pdb|1YUC|B Chain B, Human Nuclear Receptor Liver Receptor Homologue-1, Lrh-1,
Bound To Phospholipid And A Fragment Of Human Shp
pdb|4DOR|A Chain A, Human Nuclear Receptor Liver Receptor Homologue-1, Lrh-1,
In Its Apo State Bound To A Fragment Of Human Shp Box1
pdb|4DOR|B Chain B, Human Nuclear Receptor Liver Receptor Homologue-1, Lrh-1,
In Its Apo State Bound To A Fragment Of Human Shp Box1
Length = 255
Score = 28.9 bits (63), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 27/57 (47%)
Query: 40 KFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIG 96
+ +Q L Y YP Q +F ++ L LP +++I E L+++++ G
Sbjct: 182 QLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNG 238
>pdb|3PLZ|A Chain A, Human Lrh1 Lbd Bound To Gr470
pdb|3PLZ|B Chain B, Human Lrh1 Lbd Bound To Gr470
Length = 257
Score = 28.9 bits (63), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 27/57 (47%)
Query: 40 KFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIG 96
+ +Q L Y YP Q +F ++ L LP +++I E L+++++ G
Sbjct: 184 QLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNG 240
>pdb|1YOK|A Chain A, Crystal Structure Of Human Lrh-1 Bound With Tif-2 Peptide
And Phosphatidylglycerol
Length = 256
Score = 28.9 bits (63), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 27/57 (47%)
Query: 40 KFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIG 96
+ +Q L Y YP Q +F ++ L LP +++I E L+++++ G
Sbjct: 183 QLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNG 239
>pdb|1ZDU|A Chain A, The Crystal Structure Of Human Liver Receptor Homologue-1
Length = 245
Score = 28.9 bits (63), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 27/57 (47%)
Query: 40 KFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIG 96
+ +Q L Y YP Q +F ++ L LP +++I E L+++++ G
Sbjct: 172 QLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNG 228
>pdb|4DOS|A Chain A, Human Nuclear Receptor Liver Receptor Homologue-1, Lrh-1,
Bound To Dlpc And A Fragment Of Tif-2
Length = 242
Score = 28.5 bits (62), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 27/57 (47%)
Query: 40 KFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIG 96
+ +Q L Y YP Q +F ++ L LP +++I E L+++++ G
Sbjct: 172 QLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNG 228
>pdb|1ZH7|A Chain A, Structural And Biochemical Basis For Selective Repression
Of The Orphan Nuclear Receptor Lrh-1 By Shp
pdb|1ZH7|B Chain B, Structural And Biochemical Basis For Selective Repression
Of The Orphan Nuclear Receptor Lrh-1 By Shp
Length = 243
Score = 28.5 bits (62), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 15/67 (22%), Positives = 30/67 (44%)
Query: 30 GSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEEL 89
S V+ + +Q L Y YP Q +F ++ L LP +++I + L
Sbjct: 160 SSDVKNLENLQLVEGVQEQVNAALLDYTVCNYPQQTEKFGQLLLRLPEIRAISKQAEDYL 219
Query: 90 FFRNIIG 96
+++++ G
Sbjct: 220 YYKHVNG 226
>pdb|3KBR|A Chain A, The Crystal Structure Of Cyclohexadienyl Dehydratase
Precursor From Pseudomonas Aeruginosa Pa01
Length = 239
Score = 27.7 bits (60), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 23/48 (47%)
Query: 33 VRFKTGSKFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKS 80
V K T AI+ Q L+ + V+P QP F + +LPR ++
Sbjct: 163 VDGKADLXXTDAIEARLQSRLHPELCAVHPQQPFDFAEKAYLLPRDEA 210
>pdb|3F5C|B Chain B, Structure Of Dax-1:lrh-1 Complex
pdb|3F5C|C Chain C, Structure Of Dax-1:lrh-1 Complex
Length = 268
Score = 27.7 bits (60), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 29/57 (50%)
Query: 40 KFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFRNIIG 96
K+ +Q TQ L ++I + R ++ L L+ I S V+ ELFFR IIG
Sbjct: 196 KYIEGLQWRTQQILTEHIRMMQREYQIRSAELNSALFLLRFINSDVVTELFFRPIIG 252
>pdb|4DOO|A Chain A, Crystal Structure Of Arabidopsis Thaliana Fatty-Acid
Binding Protein At3g63170 (Atfap1)
pdb|4DOO|B Chain B, Crystal Structure Of Arabidopsis Thaliana Fatty-Acid
Binding Protein At3g63170 (Atfap1)
Length = 205
Score = 25.4 bits (54), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 11/36 (30%), Positives = 20/36 (55%)
Query: 21 IRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKY 56
+RNA+ G+R++ GS +Q T +F ++Y
Sbjct: 103 VRNAFQESVGNRLKKFGGSDNDELLQSFTSLFKDEY 138
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
0.324 0.136 0.400
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,960,648
Number of Sequences: 62578
Number of extensions: 98205
Number of successful extensions: 255
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: 212
Number of HSP's gapped (non-prelim): 43
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: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 45 (21.9 bits)