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= psy12688
(222 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 142 bits (357), Expect = 2e-34, Method: Compositional matrix adjust.
Identities = 66/91 (72%), Positives = 73/91 (80%), Gaps = 1/91 (1%)
Query: 124 EGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCP 183
E +EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQN K YTC+ ++C IDKTQRKRCP
Sbjct: 6 EDLEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYTCIENQNCQIDKTQRKRCP 65
Query: 184 FCRFQKCLEVGMKLE-VSSQSTHGVVVIWSP 213
+CRFQKCL VGMKLE V + G + P
Sbjct: 66 YCRFQKCLSVGMKLEAVRADRMRGGRNKFGP 96
>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 = 137 bits (344), Expect = 5e-33, Method: Compositional matrix adjust.
Identities = 65/88 (73%), Positives = 70/88 (79%), Gaps = 1/88 (1%)
Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
+ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQN K YTC +SC IDKTQRKRCPFCR
Sbjct: 1 DELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKHYTCTESQSCKIDKTQRKRCPFCR 60
Query: 187 FQKCLEVGMKLE-VSSQSTHGVVVIWSP 213
FQKCL VGM+LE V + G + P
Sbjct: 61 FQKCLTVGMRLEAVRADRMRGGRNKFGP 88
>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 = 104 bits (260), Expect = 3e-23, Method: Compositional matrix adjust.
Identities = 45/95 (47%), Positives = 59/95 (62%), Gaps = 2/95 (2%)
Query: 107 PFHTSTIAATPEHP--DTKEGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVY 164
P + + P HP + + +C +CGD+ SG HYG+ +CE CKGFFKRTV+ Y
Sbjct: 115 PLGLNGVLKVPAHPSGNMASFTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTY 174
Query: 165 TCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEV 199
TC + C IDK QR RC +CR+QKCL +GMK E
Sbjct: 175 TCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREA 209
>pdb|2HAN|A Chain A, Structural Basis Of Heterodimeric Ecdysteroid Receptor
Interaction With Natural Response Element Hsp27 Gene
Promoter
Length = 93
Score = 102 bits (254), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 44/83 (53%), Positives = 55/83 (66%)
Query: 125 GIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPF 184
G + LC +CGD+ SG HYG+ +CE CKGFFKRTV+ Y C R+C IDK QR RC +
Sbjct: 8 GSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYACRENRNCIIDKRQRNRCQY 67
Query: 185 CRFQKCLEVGMKLEVSSQSTHGV 207
CR+QKCL GMK E + G+
Sbjct: 68 CRYQKCLTCGMKREAVQEERQGI 90
>pdb|1R0O|A Chain A, Crystal Structure Of The Heterodimeric Ecdysone Receptor
Dna-Binding Complex
Length = 86
Score = 99.0 bits (245), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 43/75 (57%), Positives = 52/75 (69%)
Query: 125 GIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPF 184
G + LC +CGD+ SG HYG+ +CE CKGFFKRTV+ Y C R+C IDK QR RC +
Sbjct: 6 GSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYACRENRNCIIDKRQRNRCQY 65
Query: 185 CRFQKCLEVGMKLEV 199
CR+QKCL GMK E
Sbjct: 66 CRYQKCLTCGMKREA 80
>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 = 98.6 bits (244), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 41/71 (57%), Positives = 51/71 (71%)
Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQ 188
+C +CGD+ SG HYG+ +CE CKGFFKRTV+ YTC + C IDK QR RC +CR+Q
Sbjct: 5 ICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQ 64
Query: 189 KCLEVGMKLEV 199
KCL +GMK E
Sbjct: 65 KCLAMGMKREA 75
>pdb|1R0N|A Chain A, Crystal Structure Of Heterodimeric Ecdsyone Receptor Dna
Binding Complex
Length = 81
Score = 97.4 bits (241), Expect = 6e-21, Method: Compositional matrix adjust.
Identities = 41/73 (56%), Positives = 52/73 (71%)
Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
+ +C +CGD+ SG HYG+ +CE CKGFFKRTV+ YTC + C IDK QR RC +CR
Sbjct: 3 KHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCR 62
Query: 187 FQKCLEVGMKLEV 199
+QKCL +GMK E
Sbjct: 63 YQKCLAMGMKREA 75
>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 = 96.7 bits (239), Expect = 9e-21, Method: Compositional matrix adjust.
Identities = 41/71 (57%), Positives = 51/71 (71%)
Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQ 188
+C +CGD+ SG HYG+ +CE CKGFFKRTV+ YTC + C IDK QR RC +CR+Q
Sbjct: 7 ICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQ 66
Query: 189 KCLEVGMKLEV 199
KCL +GMK E
Sbjct: 67 KCLAMGMKREA 77
>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 = 96.7 bits (239), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 41/71 (57%), Positives = 51/71 (71%)
Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQ 188
+C +CGD+ SG HYG+ +CE CKGFFKRTV+ YTC + C IDK QR RC +CR+Q
Sbjct: 7 ICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQ 66
Query: 189 KCLEVGMKLEV 199
KCL +GMK E
Sbjct: 67 KCLAMGMKREA 77
>pdb|1CIT|A Chain A, Dna-Binding Mechanism Of The Monomeric Orphan Nuclear
Receptor Ngfi-B
Length = 89
Score = 95.9 bits (237), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 44/70 (62%), Positives = 49/70 (70%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
C VCGD S HYG+ TCE CKGFFKRTVQ Y C+A + C +DK +R RC FCRFQK
Sbjct: 3 CAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYICLANKDCPVDKRRRNRCQFCRFQK 62
Query: 190 CLEVGMKLEV 199
CL VGM EV
Sbjct: 63 CLAVGMVKEV 72
>pdb|1RXR|A Chain A, High Resolution Solution Structure Of The Retinoid X
Receptor Dna Binding Domain, Nmr, 20 Structure
Length = 83
Score = 93.6 bits (231), Expect = 8e-20, Method: Compositional matrix adjust.
Identities = 40/71 (56%), Positives = 50/71 (70%)
Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQ 188
+C +CGD+ SG HYG+ +CE CKGFFKRTV+ YTC + C IDK QR RC +CR+Q
Sbjct: 5 ICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQ 64
Query: 189 KCLEVGMKLEV 199
K L +GMK E
Sbjct: 65 KALAMGMKREA 75
>pdb|2NLL|A Chain A, Retinoid X Receptor-Thyroid Hormone Receptor Dna-Binding
Domain Heterodimer Bound To Thyroid Response Element Dna
Length = 66
Score = 93.6 bits (231), Expect = 8e-20, Method: Composition-based stats.
Identities = 39/66 (59%), Positives = 48/66 (72%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
C +CGD+ SG HYG+ +CE CKGFFKRTV+ YTC + C IDK QR RC +CR+QK
Sbjct: 1 CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQK 60
Query: 190 CLEVGM 195
CL +GM
Sbjct: 61 CLAMGM 66
>pdb|2HAN|B Chain B, Structural Basis Of Heterodimeric Ecdysteroid Receptor
Interaction With Natural Response Element Hsp27 Gene
Promoter
Length = 119
Score = 92.8 bits (229), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 41/72 (56%), Positives = 50/72 (69%)
Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
EELC VCGD+ SGYHY LTCE CKGFF+R+V VY C R+C +D R++C CR
Sbjct: 8 EELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCCKFGRACEMDMYMRRKCQECR 67
Query: 187 FQKCLEVGMKLE 198
+KCL VGM+ E
Sbjct: 68 LKKCLAVGMRPE 79
>pdb|1R0N|B Chain B, Crystal Structure Of Heterodimeric Ecdsyone Receptor Dna
Binding Complex
pdb|1R0O|B Chain B, Crystal Structure Of The Heterodimeric Ecdysone Receptor
Dna-Binding Complex
Length = 109
Score = 92.0 bits (227), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 41/72 (56%), Positives = 50/72 (69%)
Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
EELC VCGD+ SGYHY LTCE CKGFF+R+V VY C R+C +D R++C CR
Sbjct: 6 EELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCCKFGRACEMDMYMRRKCQECR 65
Query: 187 FQKCLEVGMKLE 198
+KCL VGM+ E
Sbjct: 66 LKKCLAVGMRPE 77
>pdb|2EBL|A Chain A, Solution Structure Of The Zinc Finger, C4-type Domain Of
Human Coup Transcription Factor 1
Length = 89
Score = 91.3 bits (225), Expect = 3e-19, Method: Compositional matrix adjust.
Identities = 43/75 (57%), Positives = 52/75 (69%), Gaps = 2/75 (2%)
Query: 125 GIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPF 184
GIE C VCGDK SG HYG TCE CK FFKR+V+ YTC A R+C ID+ R +C +
Sbjct: 7 GIE--CVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRANRNCPIDQHHRNQCQY 64
Query: 185 CRFQKCLEVGMKLEV 199
CR +KCL+VGM+ E
Sbjct: 65 CRLKKCLKVGMRREA 79
>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 = 90.9 bits (224), Expect = 4e-19, Method: Compositional matrix adjust.
Identities = 40/72 (55%), Positives = 49/72 (68%)
Query: 128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRF 187
+LC VC D+ SG HYG+LTC SCK FFKR V+ + Y C C IDK +RK CP CR+
Sbjct: 30 KLCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRY 89
Query: 188 QKCLEVGMKLEV 199
+KCL+ GM LE
Sbjct: 90 RKCLQAGMNLEA 101
>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 = 90.9 bits (224), Expect = 5e-19, Method: Compositional matrix adjust.
Identities = 40/72 (55%), Positives = 50/72 (69%)
Query: 128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRF 187
+LC VC D+ SG HYG+LTC SCK FFKR V+ + Y C + C IDK +RK CP CR+
Sbjct: 27 KLCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGDNRCIIDKIRRKNCPACRY 86
Query: 188 QKCLEVGMKLEV 199
+KCL+ GM LE
Sbjct: 87 RKCLQAGMNLEA 98
>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 = 90.5 bits (223), Expect = 6e-19, Method: Compositional matrix adjust.
Identities = 41/73 (56%), Positives = 51/73 (69%)
Query: 126 IEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFC 185
I + C VC DK SGYHYG+ CE CKGFF+R++Q VYTC +++C I+K R RC +C
Sbjct: 3 IYKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYC 62
Query: 186 RFQKCLEVGMKLE 198
R QKC EVGM E
Sbjct: 63 RLQKCFEVGMSKE 75
>pdb|2GDA|A Chain A, Refined Solution Structure Of The Glucocorticoid Receptor
Dna-Binding Domain
Length = 72
Score = 90.5 bits (223), Expect = 7e-19, Method: Composition-based stats.
Identities = 40/70 (57%), Positives = 48/70 (68%)
Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQ 188
LC VC D+ SG HYG+LTC SCK FFKR V+ + Y C C IDK +RK CP CR++
Sbjct: 1 LCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYR 60
Query: 189 KCLEVGMKLE 198
KCL+ GM LE
Sbjct: 61 KCLQAGMNLE 70
>pdb|1GDC|A Chain A, Refined Solution Structure Of The Glucocorticoid Receptor
Dna-Binding Domain
Length = 72
Score = 90.1 bits (222), Expect = 1e-18, Method: Composition-based stats.
Identities = 40/70 (57%), Positives = 48/70 (68%)
Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQ 188
LC VC D+ SG HYG+LTC SCK FFKR V+ + Y C C IDK +RK CP CR++
Sbjct: 1 LCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYR 60
Query: 189 KCLEVGMKLE 198
KCL+ GM LE
Sbjct: 61 KCLQAGMNLE 70
>pdb|1HRA|A Chain A, The Solution Structure Of The Human Retinoic Acid
Receptor- Beta Dna-Binding Domain
Length = 80
Score = 89.7 bits (221), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 39/69 (56%), Positives = 49/69 (71%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
C VC DK SGYHYG+ CE CKGFF+R++Q +YTC +++C I+K R RC +CR QK
Sbjct: 8 CFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMIYTCHRDKNCVINKVTRNRCQYCRLQK 67
Query: 190 CLEVGMKLE 198
C EVGM E
Sbjct: 68 CFEVGMSKE 76
>pdb|1RGD|A Chain A, Structure Refinement Of The Glucocorticoid Receptor-Dna
Binding Domain From Nmr Data By Relaxation Matrix
Calculations
Length = 71
Score = 88.6 bits (218), Expect = 3e-18, Method: Composition-based stats.
Identities = 39/69 (56%), Positives = 47/69 (68%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
C VC D+ SG HYG+LTC SCK FFKR V+ + Y C C IDK +RK CP CR++K
Sbjct: 1 CLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRK 60
Query: 190 CLEVGMKLE 198
CL+ GM LE
Sbjct: 61 CLQAGMNLE 69
>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 = 88.2 bits (217), Expect = 3e-18, Method: Compositional matrix adjust.
Identities = 39/71 (54%), Positives = 48/71 (67%)
Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQ 188
+C VC D+ SG HYG+LTC SCK FFKR V+ + Y C C IDK +RK CP CR++
Sbjct: 4 MCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYR 63
Query: 189 KCLEVGMKLEV 199
KCL+ GM LE
Sbjct: 64 KCLQAGMNLEA 74
>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 = 87.8 bits (216), Expect = 4e-18, Method: Compositional matrix adjust.
Identities = 37/66 (56%), Positives = 47/66 (71%), Gaps = 1/66 (1%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
C VCGDK SG+HYG+ CE CKGFF+RT++ K +Y + +C I K R +C +CRFQK
Sbjct: 53 CRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLIYD-RCDLNCRIHKKSRNKCQYCRFQK 111
Query: 190 CLEVGM 195
CL VGM
Sbjct: 112 CLAVGM 117
>pdb|1LAT|A Chain A, Glucocorticoid Receptor MutantDNA COMPLEX
pdb|1LAT|B Chain B, Glucocorticoid Receptor MutantDNA COMPLEX
Length = 82
Score = 87.4 bits (215), Expect = 5e-18, Method: Compositional matrix adjust.
Identities = 40/72 (55%), Positives = 48/72 (66%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
C VC D+ SG HYG+LTCE CK FFKR V+ + Y C E C IDK +RK CP CR++K
Sbjct: 7 CLVCSDEASGCHYGVLTCEGCKAFFKRAVEGQHNYLCKYEGKCIIDKIRRKNCPACRYRK 66
Query: 190 CLEVGMKLEVSS 201
CL+ GM LE
Sbjct: 67 CLQAGMNLEARK 78
>pdb|2ENV|A Chain A, Solution Sturcture Of The C4-Type Zinc Finger Domain From
Human Peroxisome Proliferator-Activated Receptor Delta
Length = 88
Score = 87.0 bits (214), Expect = 7e-18, Method: Compositional matrix adjust.
Identities = 39/66 (59%), Positives = 47/66 (71%), Gaps = 1/66 (1%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
C VCGDK SG+HYG+ CE CKGFF+RT++ K Y ERSC I K R +C +CRFQK
Sbjct: 10 CRVCGDKASGFHYGVHACEGCKGFFRRTIRMKLEYE-KCERSCKIQKKNRNKCQYCRFQK 68
Query: 190 CLEVGM 195
CL +GM
Sbjct: 69 CLALGM 74
>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 = 87.0 bits (214), Expect = 7e-18, Method: Compositional matrix adjust.
Identities = 38/71 (53%), Positives = 47/71 (66%)
Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
++ C +CGD+ SG HYG LTC SCK FFKR + K+ Y C + C IDK +RK CP CR
Sbjct: 7 QKTCLICGDEASGAHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCR 66
Query: 187 FQKCLEVGMKL 197
+KC E GM L
Sbjct: 67 LRKCYEAGMTL 77
>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 = 87.0 bits (214), Expect = 8e-18, Method: Compositional matrix adjust.
Identities = 39/70 (55%), Positives = 47/70 (67%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
C VC D+ SG HYG+LTC SCK FFKR V+ + Y C C IDK +RK CP CR++K
Sbjct: 7 CLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRK 66
Query: 190 CLEVGMKLEV 199
CL+ GM LE
Sbjct: 67 CLQAGMNLEA 76
>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 = 86.7 bits (213), Expect = 9e-18, Method: Compositional matrix adjust.
Identities = 41/77 (53%), Positives = 52/77 (67%), Gaps = 2/77 (2%)
Query: 125 GIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKK--VYTCVAERSCHIDKTQRKRC 182
G +ELC VCGDK +GYHY +TCE CKGFF+RT+Q Y+C E C IDK R +C
Sbjct: 1 GSDELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKSLHPSYSCKYEGKCIIDKVTRNQC 60
Query: 183 PFCRFQKCLEVGMKLEV 199
CRF+KC+ VGM ++
Sbjct: 61 QECRFKKCIYVGMATDL 77
>pdb|1R4R|B Chain B, Crystallographic Analysis Of The Interaction Of The
Glucocorticoid Receptor With Dna
Length = 92
Score = 86.7 bits (213), Expect = 9e-18, Method: Compositional matrix adjust.
Identities = 39/70 (55%), Positives = 47/70 (67%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
C VC D+ SG HYG+LTC SCK FFKR V+ + Y C C IDK +RK CP CR++K
Sbjct: 7 CLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRK 66
Query: 190 CLEVGMKLEV 199
CL+ GM LE
Sbjct: 67 CLQAGMNLEA 76
>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 = 85.9 bits (211), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 39/70 (55%), Positives = 47/70 (67%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
C VC D+ SG HYG+LTC SCK FFKR V+ + Y C C IDK +RK CP CR++K
Sbjct: 7 CLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRK 66
Query: 190 CLEVGMKLEV 199
CL+ GM LE
Sbjct: 67 CLQAGMNLEA 76
>pdb|1LO1|A Chain A, Estrogen Related Receptor 2 Dna Binding Domain In Complex
With Dna
Length = 98
Score = 85.9 bits (211), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 39/69 (56%), Positives = 47/69 (68%)
Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
+ LC VCGD SGYHYG+ +CE+CK FFKRT+Q Y+C A C I K +RK C CR
Sbjct: 4 KRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACR 63
Query: 187 FQKCLEVGM 195
F K L+VGM
Sbjct: 64 FMKALKVGM 72
>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 = 85.1 bits (209), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 39/72 (54%), Positives = 49/72 (68%), Gaps = 1/72 (1%)
Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKK-VYTCVAERSCHIDKTQRKRCPFCRF 187
+C VC D+ SG HYG+LTC SCK FFKR V+ ++ Y C C IDK +RK CP CR+
Sbjct: 4 MCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGRQHNYLCAGRNDCIIDKIRRKNCPACRY 63
Query: 188 QKCLEVGMKLEV 199
+KCL+ GM LE
Sbjct: 64 RKCLQAGMNLEA 75
>pdb|2NLL|B Chain B, Retinoid X Receptor-Thyroid Hormone Receptor Dna-Binding
Domain Heterodimer Bound To Thyroid Response Element Dna
Length = 103
Score = 85.1 bits (209), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 40/71 (56%), Positives = 49/71 (69%), Gaps = 2/71 (2%)
Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKK--VYTCVAERSCHIDKTQRKRCPF 184
+ELC VCGDK +GYHY +TCE CKGFF+RT+Q Y+C E C IDK R +C
Sbjct: 1 DELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYSCKYEGKCVIDKVTRNQCQE 60
Query: 185 CRFQKCLEVGM 195
CRF+KC+ VGM
Sbjct: 61 CRFKKCIYVGM 71
>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 = 84.7 bits (208), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 33/71 (46%), Positives = 48/71 (67%)
Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQ 188
LC +CGD+ +G HYG +C+ CKGFF+R+V+ +Y+C R C +DK +R +C +CR +
Sbjct: 2 LCAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCRFSRQCVVDKDKRNQCRYCRLK 61
Query: 189 KCLEVGMKLEV 199
KC GMK E
Sbjct: 62 KCFRAGMKKEA 72
>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 = 83.6 bits (205), Expect = 8e-17, Method: Compositional matrix adjust.
Identities = 31/73 (42%), Positives = 50/73 (68%)
Query: 126 IEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFC 185
+ +C VCGD+ +G+H+ +TCE CKGFF+R+++ K ++TC A C I K R+ C C
Sbjct: 5 VPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCAANGDCRITKDNRRACQAC 64
Query: 186 RFQKCLEVGMKLE 198
R ++C+++GM E
Sbjct: 65 RLKRCVDIGMMKE 77
>pdb|1HLZ|A Chain A, Crystal Structure Of The Orphan Nuclear Receptor Rev-
Erb(Alpha) Dna-Binding Domain Bound To Its Cognate
Response Element
pdb|1HLZ|B Chain B, Crystal Structure Of The Orphan Nuclear Receptor Rev-
Erb(Alpha) Dna-Binding Domain Bound To Its Cognate
Response Element
pdb|1GA5|A Chain A, Crystal Structure Of The Orphan Nuclear Receptor Rev-
Erb(Alpha) Dna-Binding Domain Bound To Its Cognate
Response Element
pdb|1GA5|B Chain B, Crystal Structure Of The Orphan Nuclear Receptor Rev-
Erb(Alpha) Dna-Binding Domain Bound To Its Cognate
Response Element
pdb|1GA5|E Chain E, Crystal Structure Of The Orphan Nuclear Receptor Rev-
Erb(Alpha) Dna-Binding Domain Bound To Its Cognate
Response Element
pdb|1GA5|F Chain F, Crystal Structure Of The Orphan Nuclear Receptor Rev-
Erb(Alpha) Dna-Binding Domain Bound To Its Cognate
Response Element
pdb|1A6Y|A Chain A, Reverba Orphan Nuclear ReceptorDNA COMPLEX
pdb|1A6Y|B Chain B, Reverba Orphan Nuclear ReceptorDNA COMPLEX
Length = 94
Score = 83.6 bits (205), Expect = 8e-17, Method: Compositional matrix adjust.
Identities = 38/72 (52%), Positives = 49/72 (68%), Gaps = 1/72 (1%)
Query: 125 GIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTV-QNKKVYTCVAERSCHIDKTQRKRCP 183
G+ LC VCGD SG+HYG+L CE CKGFF+R++ QN + C+ +C I + R RC
Sbjct: 5 GMVLLCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKRCLKNENCSIVRINRNRCQ 64
Query: 184 FCRFQKCLEVGM 195
CRF+KCL VGM
Sbjct: 65 QCRFKKCLSVGM 76
>pdb|1HCP|A Chain A, Dna Recognition By The Oestrogen Receptor: From Solution
To The Crystal
Length = 76
Score = 83.2 bits (204), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 37/68 (54%), Positives = 43/68 (63%)
Query: 128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRF 187
C VC D SGYHYG+ +CE CK FFKR++Q Y C A C IDK +RK C CR
Sbjct: 5 RYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRL 64
Query: 188 QKCLEVGM 195
+KC EVGM
Sbjct: 65 RKCYEVGM 72
>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 = 83.2 bits (204), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 37/68 (54%), Positives = 43/68 (63%)
Query: 128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRF 187
C VC D SGYHYG+ +CE CK FFKR++Q Y C A C IDK +RK C CR
Sbjct: 5 RYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRL 64
Query: 188 QKCLEVGM 195
+KC EVGM
Sbjct: 65 RKCYEVGM 72
>pdb|4AA6|E Chain E, The Oestrogen Receptor Recognizes An Imperfectly
Palindromic Response Element Through An Alternative
Side- Chain Conformation
Length = 71
Score = 83.2 bits (204), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 37/68 (54%), Positives = 43/68 (63%)
Query: 128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRF 187
C VC D SGYHYG+ +CE CK FFKR++Q Y C A C IDK +RK C CR
Sbjct: 2 RYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRL 61
Query: 188 QKCLEVGM 195
+KC EVGM
Sbjct: 62 RKCYEVGM 69
>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 = 83.2 bits (204), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 37/68 (54%), Positives = 43/68 (63%)
Query: 128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRF 187
C VC D SGYHYG+ +CE CK FFKR++Q Y C A C IDK +RK C CR
Sbjct: 2 RYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRL 61
Query: 188 QKCLEVGM 195
+KC EVGM
Sbjct: 62 RKCYEVGM 69
>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 = 81.6 bits (200), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 35/71 (49%), Positives = 48/71 (67%)
Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
+++C +CGD+ SG HYG+LTC SCK FFKR ++ + Y C C +DK +RK CP CR
Sbjct: 2 QKICLICGDEASGCHYGVLTCGSCKVFFKRAMEGQHNYLCAGRNDCIVDKIRRKNCPACR 61
Query: 187 FQKCLEVGMKL 197
+KC + GM L
Sbjct: 62 LRKCCQAGMVL 72
>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 = 79.3 bits (194), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 30/73 (41%), Positives = 49/73 (67%)
Query: 126 IEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFC 185
+ +C VCGD+ +G+H+ +TCE CKGFF+R+++ K ++TC C I K R+ C C
Sbjct: 5 VPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQAC 64
Query: 186 RFQKCLEVGMKLE 198
R ++C+++GM E
Sbjct: 65 RLKRCVDIGMMKE 77
>pdb|3LWO|B Chain B, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
5BRU
pdb|3LWP|B Chain B, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
5BRDU
pdb|3LWQ|B Chain B, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
3MU
pdb|3LWR|B Chain B, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
4SU
pdb|3LWV|B Chain B, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
2'- Deoxyuridine
Length = 60
Score = 26.9 bits (58), Expect = 8.0, Method: Composition-based stats.
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 126 IEELCPVCGDKVSGYHYGLLTCESCKGFFKR 156
++E+CPVCG+K H + E G ++R
Sbjct: 16 LKEVCPVCGEKTKVAHPPRFSPEDPYGEYRR 46
>pdb|2HVY|C Chain C, Crystal Structure Of An HACA BOX RNP FROM PYROCOCCUS
FURIOSUS
pdb|3HAX|C Chain C, Crystal Structure Of A Substrate-Bound Gar1-Minus HACA RNP
FROM Pyrococcus Furiosus
pdb|3HAY|C Chain C, Crystal Structure Of A Substrate-Bound Full HACA RNP FROM
Pyrococcus Furiosus
Length = 60
Score = 26.9 bits (58), Expect = 8.3, Method: Composition-based stats.
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 126 IEELCPVCGDKVSGYHYGLLTCESCKGFFKR 156
++E+CPVCG+K H + E G ++R
Sbjct: 16 LKEVCPVCGEKTKVAHPPRFSPEDPYGEYRR 46
>pdb|2EY4|E Chain E, Crystal Structure Of A Cbf5-Nop10-Gar1 Complex
pdb|2EY4|F Chain F, Crystal Structure Of A Cbf5-Nop10-Gar1 Complex
Length = 55
Score = 26.9 bits (58), Expect = 8.8, Method: Composition-based stats.
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 126 IEELCPVCGDKVSGYHYGLLTCESCKGFFKR 156
++E+CPVCG+K H + E G ++R
Sbjct: 16 LKEVCPVCGEKTKVAHPPRFSPEDPYGEYRR 46
>pdb|2RFK|B Chain B, Substrate Rna Positioning In The Archaeal HACA
Ribonucleoprotein Complex
pdb|3HJW|B Chain B, Structure Of A Functional Ribonucleoprotein Pseudouridine
Synthase Bound To A Substrate Rna
pdb|3HJY|B Chain B, Structure Of A Functional Ribonucleoprotein Pseudouridine
Synthase Bound To A Substrate Rna
Length = 53
Score = 26.9 bits (58), Expect = 9.4, Method: Composition-based stats.
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 126 IEELCPVCGDKVSGYHYGLLTCESCKGFFKR 156
++E+CPVCG+K H + E G ++R
Sbjct: 14 LKEVCPVCGEKTKVAHPPRFSPEDPYGEYRR 44
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
0.317 0.130 0.399
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,203,411
Number of Sequences: 62578
Number of extensions: 231808
Number of successful extensions: 534
Number of sequences better than 100.0: 49
Number of HSP's better than 100.0 without gapping: 49
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 479
Number of HSP's gapped (non-prelim): 49
length of query: 222
length of database: 14,973,337
effective HSP length: 95
effective length of query: 127
effective length of database: 9,028,427
effective search space: 1146610229
effective search space used: 1146610229
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)