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= psy4160
(160 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1QGV|A Chain A, Human Spliceosomal Protein U5-15kd
pdb|1SYX|A Chain A, The Crystal Structure Of A Binary U5 Snrnp Complex
pdb|1SYX|C Chain C, The Crystal Structure Of A Binary U5 Snrnp Complex
pdb|1SYX|E Chain E, The Crystal Structure Of A Binary U5 Snrnp Complex
Length = 142
Score = 239 bits (609), Expect = 6e-64, Method: Compositional matrix adjust.
Identities = 111/116 (95%), Positives = 115/116 (99%)
Query: 45 VIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYLVDITKVPDFNKMYELYDPCTCMFFFR 104
VIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYLVDIT+VPDFNKMYELYDPCT MFFFR
Sbjct: 27 VIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYLVDITEVPDFNKMYELYDPCTVMFFFR 86
Query: 105 NKHIMIDLGTGNNNKINWALEDKQEMIDIVETVYRGARKGRGLVVSPKDYSTKYRY 160
NKHIMIDLGTGNNNKINWA+EDKQEM+DI+ETVYRGARKGRGLVVSPKDYSTKYRY
Sbjct: 87 NKHIMIDLGTGNNNKINWAMEDKQEMVDIIETVYRGARKGRGLVVSPKDYSTKYRY 142
>pdb|1PQN|A Chain A, Dominant Negative Human Hdim1 (Hdim1 1-128)
Length = 127
Score = 210 bits (535), Expect = 2e-55, Method: Compositional matrix adjust.
Identities = 97/102 (95%), Positives = 101/102 (99%)
Query: 45 VIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYLVDITKVPDFNKMYELYDPCTCMFFFR 104
VIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYLVDIT+VPDFNKMYELYDPCT MFFFR
Sbjct: 26 VIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYLVDITEVPDFNKMYELYDPCTVMFFFR 85
Query: 105 NKHIMIDLGTGNNNKINWALEDKQEMIDIVETVYRGARKGRG 146
NKHIMIDLGTGNNNKINWA+EDKQEM+DI+ETVYRGARKGRG
Sbjct: 86 NKHIMIDLGTGNNNKINWAMEDKQEMVDIIETVYRGARKGRG 127
>pdb|2AV4|A Chain A, Crystal Structure Of Plasmodium Yoelii Thioredoxin-like
Protein 4a (dim1)
Length = 160
Score = 202 bits (514), Expect = 6e-53, Method: Compositional matrix adjust.
Identities = 92/122 (75%), Positives = 108/122 (88%)
Query: 39 EDQCEDVIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYLVDITKVPDFNKMYELYDPCT 98
ED+ IRFGHD+DP CMKMDE+LY +A+ +KNF VIYLVDIT+VPDFN MYELYDP +
Sbjct: 39 EDERLVCIRFGHDYDPDCMKMDELLYKVADDIKNFCVIYLVDITEVPDFNTMYELYDPVS 98
Query: 99 CMFFFRNKHIMIDLGTGNNNKINWALEDKQEMIDIVETVYRGARKGRGLVVSPKDYSTKY 158
MFF+RNKH+MIDLGTGNNNKINW + +KQE IDIVET++RGARKGRGLV+SPKDYSTKY
Sbjct: 99 VMFFYRNKHMMIDLGTGNNNKINWPMNNKQEFIDIVETIFRGARKGRGLVISPKDYSTKY 158
Query: 159 RY 160
+Y
Sbjct: 159 KY 160
>pdb|1XBS|A Chain A, Crystal Structure Of Human Dim2: A Dim1-Like Protein
Length = 149
Score = 90.9 bits (224), Expect = 3e-19, Method: Compositional matrix adjust.
Identities = 40/110 (36%), Positives = 71/110 (64%), Gaps = 2/110 (1%)
Query: 45 VIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYLVDITKVPDFNKMYEL-YDPCTCMFFF 103
V+RFG D DP C+++D++L + + A IYLVD+ + + + +++ Y P T +FFF
Sbjct: 27 VLRFGRDEDPVCLQLDDILSKTSSDLSKMAAIYLVDVDQTAVYTQYFDISYIPST-VFFF 85
Query: 104 RNKHIMIDLGTGNNNKINWALEDKQEMIDIVETVYRGARKGRGLVVSPKD 153
+H+ +D G+ ++ K + + KQ+ ID++E +YRGA +G+ +V SP D
Sbjct: 86 NGQHMKVDYGSPDHTKFVGSFKTKQDFIDLIEVIYRGAMRGKLIVQSPID 135
>pdb|3GIX|A Chain A, Crystal Structure Of Human Splicing Factor Dim2
pdb|3GIX|B Chain B, Crystal Structure Of Human Splicing Factor Dim2
Length = 149
Score = 90.9 bits (224), Expect = 3e-19, Method: Compositional matrix adjust.
Identities = 40/110 (36%), Positives = 71/110 (64%), Gaps = 2/110 (1%)
Query: 45 VIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYLVDITKVPDFNKMYEL-YDPCTCMFFF 103
V+RFG D DP C+++D++L + + A IYLVD+ + + + +++ Y P T +FFF
Sbjct: 27 VLRFGRDEDPVCLQLDDILSKTSSDLSKMAAIYLVDVDQTAVYTQYFDISYIPST-VFFF 85
Query: 104 RNKHIMIDLGTGNNNKINWALEDKQEMIDIVETVYRGARKGRGLVVSPKD 153
+H+ +D G+ ++ K + + KQ+ ID++E +YRGA +G+ +V SP D
Sbjct: 86 NGQHMKVDYGSPDHTKFVGSFKTKQDFIDLIEVIYRGAMRGKLIVQSPID 135
>pdb|2DIY|A Chain A, The Solution Structure Of The Thioredoxin Domain Of Human
Thioredoxin-Like Protein 2
Length = 130
Score = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 36/64 (56%), Gaps = 1/64 (1%)
Query: 45 VIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYLVDITKVPDFNKMYELYDPCTCMFFFR 104
V+ F W P C +M+EV+ +A+++ + + L + VP+ ++ YE+ T +FF
Sbjct: 42 VVHFWAPWAPQCAQMNEVMAELAKELPQVSFVKL-EAEGVPEVSEKYEISSVPTFLFFKN 100
Query: 105 NKHI 108
++ I
Sbjct: 101 SQKI 104
>pdb|2WZ9|A Chain A, Crystal Structure Of The Thioredoxin Domain Of Human Txnl2
Length = 153
Score = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 36/64 (56%), Gaps = 1/64 (1%)
Query: 45 VIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYLVDITKVPDFNKMYELYDPCTCMFFFR 104
V+ F W P C +M+EV+ +A+++ + + L + VP+ ++ YE+ T +FF
Sbjct: 36 VVHFWAPWAPQCAQMNEVMAELAKELPQVSFVKL-EAEGVPEVSEKYEISSVPTFLFFKN 94
Query: 105 NKHI 108
++ I
Sbjct: 95 SQKI 98
>pdb|1SRA|A Chain A, Structure Of A Novel Extracellular Ca2+-Binding Module In
Bm-40(Slash)sparc(Slash)osteonectin
Length = 151
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 22/39 (56%)
Query: 1 MALEHCIAPFLNKCDADDDHLITLKEWARCLELNEDEIE 39
+ +EHC F CD D+D I L EWA C + + +I+
Sbjct: 108 IPMEHCTTRFFETCDLDNDKYIALDEWAGCFGIKQKDID 146
>pdb|1BMO|A Chain A, Bm-40, FsEC DOMAIN PAIR
pdb|1BMO|B Chain B, Bm-40, FsEC DOMAIN PAIR
Length = 233
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 22/39 (56%)
Query: 1 MALEHCIAPFLNKCDADDDHLITLKEWARCLELNEDEIE 39
+ +EHC F CD D+D I L EWA C + + +I+
Sbjct: 190 IPMEHCTTRFFETCDLDNDKYIALDEWAGCFGIKQKDID 228
>pdb|1NUB|A Chain A, Helix C Deletion Mutant Of Bm-40 Fs-Ec Domain Pair
pdb|1NUB|B Chain B, Helix C Deletion Mutant Of Bm-40 Fs-Ec Domain Pair
Length = 229
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 22/39 (56%)
Query: 1 MALEHCIAPFLNKCDADDDHLITLKEWARCLELNEDEIE 39
+ +EHC F CD D+D I L EWA C + + +I+
Sbjct: 186 IPMEHCTTRFFETCDLDNDKYIALDEWAGCFGIKQKDID 224
>pdb|2V53|A Chain A, Crystal Structure Of A Sparc-Collagen Complex
Length = 230
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 22/39 (56%)
Query: 1 MALEHCIAPFLNKCDADDDHLITLKEWARCLELNEDEIE 39
+ +EHC F CD D+D I L EWA C + + +I+
Sbjct: 187 IPMEHCTTRFFETCDLDNDKYIALDEWAGCFGIKQKDID 225
>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 = 30.4 bits (67), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 19/46 (41%), Positives = 21/46 (45%), Gaps = 4/46 (8%)
Query: 9 PFLNKCDADDDHLITLKEWA-RCLELNEDEIEDQCEDVIRFGHDWD 53
P N C A D L TL EWA R E +EDQ VI W+
Sbjct: 32 PVTNICQAADKQLFTLVEWAKRIPHFTELPLEDQ---VILLRAGWN 74
>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 = 30.0 bits (66), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 22/46 (47%), Gaps = 4/46 (8%)
Query: 9 PFLNKCDADDDHLITLKEWA-RCLELNEDEIEDQCEDVIRFGHDWD 53
P N C A D L TL EWA R +E ++DQ VI W+
Sbjct: 269 PVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQ---VILLRAGWN 311
>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 = 29.6 bits (65), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 22/46 (47%), Gaps = 4/46 (8%)
Query: 9 PFLNKCDADDDHLITLKEWA-RCLELNEDEIEDQCEDVIRFGHDWD 53
P N C A D L TL EWA R +E ++DQ VI W+
Sbjct: 44 PVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQ---VILLRAGWN 86
>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 = 29.6 bits (65), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 23/46 (50%), Gaps = 4/46 (8%)
Query: 9 PFLNKCDADDDHLITLKEWA-RCLELNEDEIEDQCEDVIRFGHDWD 53
P N C A D L+TL EWA R ++ I+DQ VI W+
Sbjct: 28 PVTNICQAADKQLVTLVEWAKRIPHFSDLPIDDQ---VILLRAGWN 70
>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 = 29.6 bits (65), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 22/46 (47%), Gaps = 4/46 (8%)
Query: 9 PFLNKCDADDDHLITLKEWA-RCLELNEDEIEDQCEDVIRFGHDWD 53
P N C A D L TL EWA R +E ++DQ VI W+
Sbjct: 46 PVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQ---VILLRAGWN 88
>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 = 29.6 bits (65), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 22/46 (47%), Gaps = 4/46 (8%)
Query: 9 PFLNKCDADDDHLITLKEWA-RCLELNEDEIEDQCEDVIRFGHDWD 53
P N C A D L TL EWA R +E ++DQ VI W+
Sbjct: 44 PVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQ---VILLRAGWN 86
>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 = 29.6 bits (65), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 22/46 (47%), Gaps = 4/46 (8%)
Query: 9 PFLNKCDADDDHLITLKEWA-RCLELNEDEIEDQCEDVIRFGHDWD 53
P N C A D L TL EWA R +E ++DQ VI W+
Sbjct: 42 PVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQ---VILLRAGWN 84
>pdb|1DKF|A Chain A, Crystal Structure Of A Heterodimeric Complex Of Rar And
Rxr Ligand-Binding Domains
Length = 233
Score = 29.6 bits (65), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 22/46 (47%), Gaps = 4/46 (8%)
Query: 9 PFLNKCDADDDHLITLKEWA-RCLELNEDEIEDQCEDVIRFGHDWD 53
P N C A D L TL EWA R +E ++DQ VI W+
Sbjct: 40 PVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQ---VILLRAGWN 82
>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 = 29.6 bits (65), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 22/46 (47%), Gaps = 4/46 (8%)
Query: 9 PFLNKCDADDDHLITLKEWA-RCLELNEDEIEDQCEDVIRFGHDWD 53
P N C A D L TL EWA R +E ++DQ VI W+
Sbjct: 37 PVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQ---VILLRAGWN 79
>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 = 29.6 bits (65), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 22/46 (47%), Gaps = 4/46 (8%)
Query: 9 PFLNKCDADDDHLITLKEWA-RCLELNEDEIEDQCEDVIRFGHDWD 53
P N C A D L TL EWA R +E ++DQ VI W+
Sbjct: 42 PVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQ---VILLRAGWN 84
>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 = 29.6 bits (65), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 22/46 (47%), Gaps = 4/46 (8%)
Query: 9 PFLNKCDADDDHLITLKEWA-RCLELNEDEIEDQCEDVIRFGHDWD 53
P N C A D L TL EWA R +E ++DQ VI W+
Sbjct: 41 PVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQ---VILLRAGWN 83
>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 = 29.3 bits (64), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 22/46 (47%), Gaps = 4/46 (8%)
Query: 9 PFLNKCDADDDHLITLKEWA-RCLELNEDEIEDQCEDVIRFGHDWD 53
P N C A D L TL EWA R +E ++DQ VI W+
Sbjct: 36 PVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQ---VILLRAGWN 78
>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 = 29.3 bits (64), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 22/46 (47%), Gaps = 4/46 (8%)
Query: 9 PFLNKCDADDDHLITLKEWA-RCLELNEDEIEDQCEDVIRFGHDWD 53
P N C A D L TL EWA R +E ++DQ VI W+
Sbjct: 40 PVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQ---VILLRAGWN 82
>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 = 29.3 bits (64), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 22/46 (47%), Gaps = 4/46 (8%)
Query: 9 PFLNKCDADDDHLITLKEWA-RCLELNEDEIEDQCEDVIRFGHDWD 53
P N C A D L TL EWA R +E ++DQ VI W+
Sbjct: 38 PVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQ---VILLRAGWN 80
>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 = 29.3 bits (64), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 22/46 (47%), Gaps = 4/46 (8%)
Query: 9 PFLNKCDADDDHLITLKEWA-RCLELNEDEIEDQCEDVIRFGHDWD 53
P N C A D L TL EWA R +E ++DQ VI W+
Sbjct: 38 PVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQ---VILLRAGWN 80
>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 = 29.3 bits (64), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 22/46 (47%), Gaps = 4/46 (8%)
Query: 9 PFLNKCDADDDHLITLKEWA-RCLELNEDEIEDQCEDVIRFGHDWD 53
P N C A D L TL EWA R +E ++DQ VI W+
Sbjct: 40 PVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQ---VILLRAGWN 82
>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 = 29.3 bits (64), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 22/46 (47%), Gaps = 4/46 (8%)
Query: 9 PFLNKCDADDDHLITLKEWA-RCLELNEDEIEDQCEDVIRFGHDWD 53
P N C A D L TL EWA R +E ++DQ VI W+
Sbjct: 37 PVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQ---VILLRAGWN 79
>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 = 29.3 bits (64), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 22/46 (47%), Gaps = 4/46 (8%)
Query: 9 PFLNKCDADDDHLITLKEWA-RCLELNEDEIEDQCEDVIRFGHDWD 53
P N C A D L+TL EWA R + +EDQ VI W+
Sbjct: 59 PVSNICKAADRQLVTLVEWAKRIPHFSSLPLEDQ---VILLRAGWN 101
>pdb|1LBD|A Chain A, Ligand-Binding Domain Of The Human Nuclear Receptor
Rxr-Alpha
Length = 282
Score = 29.3 bits (64), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 22/46 (47%), Gaps = 4/46 (8%)
Query: 9 PFLNKCDADDDHLITLKEWA-RCLELNEDEIEDQCEDVIRFGHDWD 53
P N C A D L TL EWA R +E ++DQ VI W+
Sbjct: 84 PVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQ---VILLRAGWN 126
>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 = 28.9 bits (63), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 22/46 (47%), Gaps = 4/46 (8%)
Query: 9 PFLNKCDADDDHLITLKEWA-RCLELNEDEIEDQCEDVIRFGHDWD 53
P N C A D L TL EWA R ++ +EDQ VI W+
Sbjct: 43 PVTNICHAADKQLFTLVEWAKRIPHFSDLTLEDQ---VILLRAGWN 85
>pdb|1YMT|A Chain A, Mouse Sf-1 Lbd
Length = 246
Score = 28.1 bits (61), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 8 APFLNKCDADDDHLITLKEWA-RCLELNEDEIEDQ 41
APF C D I++ +WA RC+ E E+ DQ
Sbjct: 45 APFSLLCRMADQTFISIVDWARRCMVFKELEVADQ 79
>pdb|1YP0|A Chain A, Structure Of The Steroidogenic Factor-1 Ligand Binding
Domain Bound To Phospholipid And A Shp Peptide Motif
Length = 239
Score = 28.1 bits (61), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 8 APFLNKCDADDDHLITLKEWA-RCLELNEDEIEDQ 41
APF C D I++ +WA RC+ E E+ DQ
Sbjct: 39 APFSLLCRMADQTFISIVDWARRCMVFKELEVADQ 73
>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 = 27.3 bits (59), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 21/46 (45%), Gaps = 4/46 (8%)
Query: 9 PFLNKCDADDDHLITLKEWA-RCLELNEDEIEDQCEDVIRFGHDWD 53
P N C A D L TL EWA R + ++DQ VI W+
Sbjct: 37 PVTNICQAADKQLFTLVEWAKRIPHFSSLPLDDQ---VILLRAGWN 79
>pdb|1UHL|A Chain A, Crystal Structure Of The Lxralfa-Rxrbeta Lbd Heterodimer
Length = 236
Score = 27.3 bits (59), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 11/21 (52%), Positives = 12/21 (57%)
Query: 9 PFLNKCDADDDHLITLKEWAR 29
P N C A D L TL EWA+
Sbjct: 38 PVTNICQAADKQLFTLVEWAK 58
>pdb|3IYG|G Chain G, Ca Model Of Bovine TricCCT DERIVED FROM A 4.0 ANGSTROM
Cryo-Em Map
Length = 515
Score = 26.9 bits (58), Expect = 4.9, Method: Composition-based stats.
Identities = 14/40 (35%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 13 KCDADDDHLITLKE-WARCLELNEDEIEDQCEDVIRFGHD 51
K ++ D IT +E + R L++ E+ I+ CED+I+ D
Sbjct: 237 KGESQTDIEITREEDFTRILQMEEEYIQQLCEDIIQLKPD 276
>pdb|3OJW|A Chain A, Disulfide Crosslinked Cytochrome P450 Reductase Inactive
pdb|3OJX|A Chain A, Disulfide Crosslinked Cytochrome P450 Reductase Inactive
Length = 622
Score = 26.6 bits (57), Expect = 7.0, Method: Composition-based stats.
Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 1/63 (1%)
Query: 74 AVIYLVDITKVPDFNKMYELYDPCTCMFFFRNKHIMI-DLGTGNNNKINWALEDKQEMID 132
A+ Y +DIT P N +YEL + + H M G G ++W +E ++ ++
Sbjct: 314 ALTYYLDITNPPRTNVLYELAQYASEPSEQEHLHKMASSSGEGKELYLSWVVEARRHILA 373
Query: 133 IVE 135
I++
Sbjct: 374 ILQ 376
>pdb|1JA1|A Chain A, Cypor-Triple Mutant
pdb|1JA1|B Chain B, Cypor-Triple Mutant
Length = 622
Score = 26.6 bits (57), Expect = 7.3, Method: Composition-based stats.
Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 1/63 (1%)
Query: 74 AVIYLVDITKVPDFNKMYELYDPCTCMFFFRNKHIMI-DLGTGNNNKINWALEDKQEMID 132
A+ Y +DIT P N +YEL + + H M G G ++W +E ++ ++
Sbjct: 314 ALTYYLDITNPPRTNVLYELAQYASEPSEQEHLHKMASSSGEGKELYLSWVVEARRHILA 373
Query: 133 IVE 135
I++
Sbjct: 374 ILQ 376
>pdb|1J9Z|A Chain A, Cypor-W677g
pdb|1J9Z|B Chain B, Cypor-W677g
Length = 622
Score = 26.2 bits (56), Expect = 7.5, Method: Composition-based stats.
Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 1/63 (1%)
Query: 74 AVIYLVDITKVPDFNKMYELYDPCTCMFFFRNKHIMI-DLGTGNNNKINWALEDKQEMID 132
A+ Y +DIT P N +YEL + + H M G G ++W +E ++ ++
Sbjct: 314 ALTYYLDITNPPRTNVLYELAQYASEPSEQEHLHKMASSSGEGKELYLSWVVEARRHILA 373
Query: 133 IVE 135
I++
Sbjct: 374 ILQ 376
>pdb|3ES9|A Chain A, Nadph-Cytochrome P450 Reductase In An Open Conformation
pdb|3ES9|B Chain B, Nadph-Cytochrome P450 Reductase In An Open Conformation
pdb|3ES9|C Chain C, Nadph-Cytochrome P450 Reductase In An Open Conformation
Length = 618
Score = 26.2 bits (56), Expect = 7.6, Method: Composition-based stats.
Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 1/63 (1%)
Query: 74 AVIYLVDITKVPDFNKMYELYDPCTCMFFFRNKHIMI-DLGTGNNNKINWALEDKQEMID 132
A+ Y +DIT P N +YEL + + H M G G ++W +E ++ ++
Sbjct: 310 ALTYYLDITNPPRTNVLYELAQYASEPSEQEHLHKMASSSGEGKELYLSWVVEARRHILA 369
Query: 133 IVE 135
I++
Sbjct: 370 ILQ 372
>pdb|1JA0|A Chain A, Cypor-W677x
pdb|1JA0|B Chain B, Cypor-W677x
Length = 620
Score = 26.2 bits (56), Expect = 7.7, Method: Composition-based stats.
Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 1/63 (1%)
Query: 74 AVIYLVDITKVPDFNKMYELYDPCTCMFFFRNKHIMI-DLGTGNNNKINWALEDKQEMID 132
A+ Y +DIT P N +YEL + + H M G G ++W +E ++ ++
Sbjct: 314 ALTYYLDITNPPRTNVLYELAQYASEPSEQEHLHKMASSSGEGKELYLSWVVEARRHILA 373
Query: 133 IVE 135
I++
Sbjct: 374 ILQ 376
>pdb|1AMO|A Chain A, Three-Dimensional Structure Of Nadph-Cytochrome P450
Reductase: Prototype For Fmn-And Fad-Containing Enzymes
pdb|1AMO|B Chain B, Three-Dimensional Structure Of Nadph-Cytochrome P450
Reductase: Prototype For Fmn-And Fad-Containing Enzymes
Length = 615
Score = 26.2 bits (56), Expect = 7.8, Method: Composition-based stats.
Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 1/63 (1%)
Query: 74 AVIYLVDITKVPDFNKMYELYDPCTCMFFFRNKHIMI-DLGTGNNNKINWALEDKQEMID 132
A+ Y +DIT P N +YEL + + H M G G ++W +E ++ ++
Sbjct: 307 ALTYYLDITNPPRTNVLYELAQYASEPSEQEHLHKMASSSGEGKELYLSWVVEARRHILA 366
Query: 133 IVE 135
I++
Sbjct: 367 ILQ 369
>pdb|1B35|A Chain A, Cricket Paralysis Virus (Crpv)
Length = 260
Score = 26.2 bits (56), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 10/32 (31%), Positives = 17/32 (53%)
Query: 44 DVIRFGHDWDPTCMKMDEVLYSIAEKVKNFAV 75
D R ++W P M + E + SI + +K F +
Sbjct: 23 DTHRISNNWSPQAMCIGEKVVSIRQLIKRFGI 54
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
0.323 0.140 0.448
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,364,751
Number of Sequences: 62578
Number of extensions: 226295
Number of successful extensions: 466
Number of sequences better than 100.0: 49
Number of HSP's better than 100.0 without gapping: 38
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 428
Number of HSP's gapped (non-prelim): 49
length of query: 160
length of database: 14,973,337
effective HSP length: 91
effective length of query: 69
effective length of database: 9,278,739
effective search space: 640232991
effective search space used: 640232991
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 47 (22.7 bits)