RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9232
(119 letters)
>2ebl_A COUP transcription factor 1; DNA-binding, metal-binding, nuclear
protein, receptor, transcription regulation, zinc,
EAR3, erbal3 tfcoup1; NMR {Homo sapiens}
Length = 89
Score = 64.3 bits (157), Expect = 4e-15
Identities = 21/44 (47%), Positives = 27/44 (61%)
Query: 20 RNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLG 63
RNL Y C+ +C +D RNQCQ CR KCL+V M R+ + G
Sbjct: 40 RNLTYTCRANRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQRG 83
>2han_A Protein ultraspiracle; transcription regulation, transcription
factor, DNA-binding, nuclear protein, nuclear receptor,
zinc finger; 1.95A {Drosophila melanogaster} SCOP:
g.39.1.2
Length = 93
Score = 63.6 bits (155), Expect = 8e-15
Identities = 18/44 (40%), Positives = 28/44 (63%)
Query: 20 RNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLG 63
++L Y C+E +CI+D +RN+CQ CR+ KCL M R+ +
Sbjct: 43 KDLTYACRENRNCIIDKRQRNRCQYCRYQKCLTCGMKREAVQEE 86
>1dsz_A RAR-alpha, retinoic acid receptor alpha; RAR, nuclear receptor,
protein-DNA, transcription/DNA complex; HET: DNA; 1.70A
{Homo sapiens} SCOP: g.39.1.2 PDB: 1hra_A
Length = 86
Score = 63.1 bits (154), Expect = 1e-14
Identities = 16/44 (36%), Positives = 26/44 (59%)
Query: 20 RNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLG 63
+N+ Y C +CI++ RN+CQ CR KC +V M+++ R
Sbjct: 37 KNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRND 80
>1dsz_B RXR-alpha, retinoic acid receptor RXR-alpha; RAR, nuclear
receptor, protein-DNA, transcription/DNA complex; HET:
DNA; 1.70A {Homo sapiens} SCOP: g.39.1.2 PDB: 1by4_A*
1rxr_A 1r0n_A 1r0o_A 2nll_A*
Length = 85
Score = 62.7 bits (153), Expect = 2e-14
Identities = 16/44 (36%), Positives = 28/44 (63%)
Query: 20 RNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLG 63
++L Y C++ C++D +RN+CQ CR+ KCL + M R+ +
Sbjct: 38 KDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEE 81
>1hcq_A Protein (estrogen receptor); protein-DNA complex, complexed with
drug, transcription/DNA complex; HET: DNA; 2.40A {Homo
sapiens} SCOP: g.39.1.2 PDB: 1hcp_A 4aa6_A
Length = 84
Score = 62.4 bits (152), Expect = 2e-14
Identities = 16/44 (36%), Positives = 22/44 (50%)
Query: 20 RNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLG 63
+ +Y+C C +D RR CQACR KC +V M + R
Sbjct: 37 GHNDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRKD 80
>1ynw_B Retinoic acid receptor RXR-alpha, retinoid X receptor; VDR,
nuclear receptor, protein-DNA complex, transcripti
complex; 3.00A {Homo sapiens} SCOP: g.39.1.2
Length = 99
Score = 62.4 bits (152), Expect = 3e-14
Identities = 16/44 (36%), Positives = 28/44 (63%)
Query: 20 RNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLG 63
++L Y C++ C++D +RN+CQ CR+ KCL + M R+ +
Sbjct: 36 KDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEE 79
>3cbb_A HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DNA binding
domain, nuclear; zinc finger; 2.00A {Homo sapiens}
Length = 78
Score = 61.5 bits (150), Expect = 3e-14
Identities = 15/42 (35%), Positives = 24/42 (57%)
Query: 20 RNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTR 61
+N Y C+ C+VD +RNQC+ CR KC + M ++ +
Sbjct: 33 KNHMYSCRFSRQCVVDKDKRNQCRYCRLKKCFRAGMKKEAVQ 74
>3g9m_A Glucocorticoid receptor; glucocorticoid, DNA-binding, allostery,
lever ARM, transcription, hormone; HET: DNA; 1.61A
{Rattus norvegicus} PDB: 3g6p_A* 3g6q_B* 3g6r_B*
3g6u_A* 3g8u_A* 3g8x_A* 3g97_B* 3g99_A* 3g9i_A* 3g9j_A*
3fyl_A* 3g9o_B* 3g9p_B* 3g6t_A* 1r4o_A 1r4r_A 1glu_A*
1gdc_A 2gda_A 1rgd_A ...
Length = 90
Score = 61.3 bits (149), Expect = 5e-14
Identities = 18/42 (42%), Positives = 23/42 (54%)
Query: 20 RNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTR 61
Y+C R CI+D RR C ACR+ KCLQ MN + +
Sbjct: 35 GQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEARK 76
>2a66_A Orphan nuclear receptor NR5A2; protein-DNA complex, zinc finger,
DNA- binding domain, transcription factor, FTZ-F1,
C-terminal extension; 2.20A {Homo sapiens} PDB: 2ff0_A
Length = 113
Score = 61.3 bits (149), Expect = 1e-13
Identities = 18/44 (40%), Positives = 23/44 (52%)
Query: 20 RNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLG 63
N Y C E +C +D T+R +C CRF KCL V M + R
Sbjct: 42 NNKRYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRAD 85
>1cit_A NGFI-B, protein (orphan nuclear receptor NGFI-B); early immediate
response gene product, transcription factor, monomeric
protein-DNA complex; HET: DNA; 2.70A {Rattus
norvegicus} SCOP: g.39.1.2
Length = 89
Score = 60.4 bits (147), Expect = 1e-13
Identities = 20/44 (45%), Positives = 27/44 (61%)
Query: 20 RNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLG 63
++ +Y+C C VD RRN+CQ CRF KCL V M ++V R
Sbjct: 33 KSAKYICLANKDCPVDKRRRNRCQFCRFQKCLAVGMVKEVVRTD 76
>1lo1_A Steroid hormone receptor ERR2; estrogen related receptor 2, DNA
binding domain, HERR2, hormone nuclear receptor; NMR
{Homo sapiens} SCOP: g.39.1.2
Length = 98
Score = 60.1 bits (146), Expect = 2e-13
Identities = 19/44 (43%), Positives = 24/44 (54%)
Query: 20 RNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLG 63
N+EY C C + RR CQACRF K L+V M ++ RL
Sbjct: 37 GNIEYSCPATNECEITKRRRKSCQACRFMKALKVGMLKEGVRLD 80
>1a6y_A Orphan nuclear receptor NR1D1; orphan receptor, DNA-binding,
reverb, REV- ERB, transcription regulation,
transcription/DNA complex; HET: DNA 5IU; 2.30A {Homo
sapiens} SCOP: g.39.1.2 PDB: 1ga5_A* 1hlz_A
Length = 94
Score = 59.7 bits (145), Expect = 3e-13
Identities = 20/45 (44%), Positives = 28/45 (62%), Gaps = 1/45 (2%)
Query: 20 RNLEYV-CKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLG 63
+N++Y C + +C + RN+CQ CRF KCL V M+RD R G
Sbjct: 40 QNIQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFG 84
>1r4i_A Androgen receptor; AR, steroid receptor, protein-DNA complex,
transcription/DNA complex; 3.10A {Rattus norvegicus}
SCOP: g.39.1.2
Length = 105
Score = 59.4 bits (144), Expect = 5e-13
Identities = 14/44 (31%), Positives = 20/44 (45%)
Query: 20 RNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLG 63
+Y+C R C +D RR C +CR KC + M +L
Sbjct: 40 GKQKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMTLGARKLK 83
>2han_B Ecdysone receptor; transcription regulation, transcription
factor, DNA-binding, nuclear protein, nuclear receptor,
zinc finger; 1.95A {Drosophila melanogaster} SCOP:
g.39.1.2 PDB: 1r0o_B 1r0n_B
Length = 119
Score = 58.4 bits (141), Expect = 2e-12
Identities = 15/42 (35%), Positives = 21/42 (50%)
Query: 20 RNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTR 61
++ Y CK C +D+ R +CQ CR KCL V M +
Sbjct: 41 KSAVYCCKFGRACEMDMYMRRKCQECRLKKCLAVGMRPECVV 82
>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus
interaction, metal-binding, nucleus, receptor,
transcription, transcription regulation, zinc-FIN
activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB:
3dzu_A* 3e00_A*
Length = 467
Score = 59.7 bits (144), Expect = 6e-12
Identities = 16/44 (36%), Positives = 28/44 (63%)
Query: 20 RNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLG 63
++L Y C++ C++D +RN+CQ CR+ KCL + M R+ +
Sbjct: 170 KDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEE 213
>1kb2_A Vitamin D3 receptor; VDR, nuclear receptor, protein-DNA complex,
transcription/DNA complex; 2.70A {Homo sapiens} SCOP:
g.39.1.2 PDB: 1kb4_A 1kb6_A 1ynw_A
Length = 110
Score = 55.2 bits (133), Expect = 2e-11
Identities = 12/44 (27%), Positives = 19/44 (43%)
Query: 20 RNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLG 63
R + C G C + R CQACR +C+ + M ++
Sbjct: 39 RKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTD 82
>2nll_B Protein (thyroid hormone receptor); complex (transcription
regulation/DNA), DNA-binding, nuclear protein, zinc-
finger, multigene family; HET: DNA 5IU; 1.90A {Homo
sapiens} SCOP: g.39.1.2 PDB: 3m9e_A*
Length = 103
Score = 52.1 bits (125), Expect = 3e-10
Identities = 19/39 (48%), Positives = 23/39 (58%)
Query: 23 EYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTR 61
Y CK G C++D RNQCQ CRF KC+ V M D+
Sbjct: 39 SYSCKYEGKCVIDKVTRNQCQECRFKKCIYVGMATDLVL 77
>3dzy_D Peroxisome proliferator-activated receptor gamma; DNA-binding,
HOST-virus interaction, metal-binding, nucleus,
receptor, transcription, transcription regulation,
zinc-FIN activator; HET: DNA REA BRL; 3.10A {Homo
sapiens} PDB: 3dzu_D* 3e00_D* 2env_A
Length = 419
Score = 54.7 bits (131), Expect = 4e-10
Identities = 20/62 (32%), Positives = 28/62 (45%), Gaps = 8/62 (12%)
Query: 9 CGVVSCQFVFV-------RNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTR 61
GV +C+ L Y + +C + RN+CQ CRF KCL V M+ + R
Sbjct: 65 YGVHACEGCKGFFRRTIRLKLIYDRCD-LNCRIHKKSRNKCQYCRFQKCLAVGMSHNAIR 123
Query: 62 LG 63
G
Sbjct: 124 FG 125
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 31.9 bits (72), Expect = 0.027
Identities = 9/31 (29%), Positives = 13/31 (41%), Gaps = 1/31 (3%)
Query: 6 CPDCGVVSCQFVF-VRNLEYVCKERGHCIVD 35
CP+C V + V + VC G + D
Sbjct: 24 CPECKVYPPKIVERFSEGDVVCALCGLVLSD 54
>1z5x_E Ecdysone receptor ligand binding domain; ponasterone A, nuclear
receptor, ECR, USP, hormone/growth factor receptor
complex; HET: P1A; 3.07A {Bemisia tabaci}
Length = 310
Score = 29.8 bits (67), Expect = 0.17
Identities = 5/37 (13%), Positives = 11/37 (29%)
Query: 25 VCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTR 61
V ++ D + N +C Q + +
Sbjct: 25 VKRKEKKAQKDKDKPNSTTSCSPDGIKQEIDPQRLDT 61
Score = 25.5 bits (56), Expect = 5.0
Identities = 6/18 (33%), Positives = 6/18 (33%)
Query: 36 VTRRNQCQACRFSKCLQV 53
V QC R K Q
Sbjct: 17 VVPEFQCAVKRKEKKAQK 34
>1lbd_A RXR_LBD, retinoid X receptor; transcription factor, nuclear
receptor, structural proteomic europe, spine,
structural genomics; 2.70A {Homo sapiens} SCOP:
a.123.1.1 PDB: 1z5x_U* 2q60_A
Length = 282
Score = 29.0 bits (65), Expect = 0.32
Identities = 1/25 (4%), Positives = 6/25 (24%), Gaps = 3/25 (12%)
Query: 39 RNQCQACRFSKCLQVKMNRDVTRLG 63
+ + + R+ +
Sbjct: 7 HHHHSSGLVPR---GSHKREAVQEE 28
>2hc4_A Vitamin D receptor; alpha helical sandwich, gene regulation; HET:
VDX; 2.20A {Danio rerio} PDB: 2hbh_A* 2hcd_A* 3dr1_A*
3o1d_A* 3o1e_A*
Length = 302
Score = 28.6 bits (64), Expect = 0.43
Identities = 2/23 (8%), Positives = 5/23 (21%)
Query: 39 RNQCQACRFSKCLQVKMNRDVTR 61
+ RF ++
Sbjct: 26 DSYSDFVRFRPPVREGPVTRSAS 48
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 28.9 bits (64), Expect = 0.44
Identities = 17/78 (21%), Positives = 28/78 (35%), Gaps = 13/78 (16%)
Query: 41 QCQACRFSKCLQVKMNRDVTRLGFWYPSFLLRV--VSSRFL------FGQESPAWMCFVR 92
+C + L + D PS +L + ++ + PA +
Sbjct: 309 RCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPA----GK 364
Query: 93 CVEIRLQVNTMEFQVVTG 110
VEI L VN + VV+G
Sbjct: 365 QVEISL-VNGAKNLVVSG 381
>3n5f_A L-carbamoylase, N-carbamoyl-L-amino acid hydrolase; hinge domain,
M20 peptidase family, evolution, residue, dimerization
domain; 2.75A {Bacillus stearothermophilus}
Length = 408
Score = 26.0 bits (58), Expect = 3.9
Identities = 17/82 (20%), Positives = 24/82 (29%), Gaps = 11/82 (13%)
Query: 18 FVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLGFWYPSFLLRVVS-- 75
E + KER V R + S ++ +LG+ + S
Sbjct: 300 IAVRAETIAKERN-VRVTTERLQEMPPVLCSDEVKRAAEAACQKLGYPSF----WLPSGA 354
Query: 76 ---SRFLFGQESPAWMCFVRCV 94
S L P M FVR
Sbjct: 355 AHDSVQL-APICPIGMIFVRSQ 375
>3saj_A Glutamate receptor 1; rossman fold, ION channel, membrane,
transport protein; HET: NAG BMA MAN; 2.50A {Rattus
norvegicus}
Length = 384
Score = 24.7 bits (53), Expect = 9.7
Identities = 4/25 (16%), Positives = 10/25 (40%)
Query: 56 NRDVTRLGFWYPSFLLRVVSSRFLF 80
+ + ++G+W + LF
Sbjct: 359 HDGIRKIGYWNEDDKFVPAALEVLF 383
>2csv_A Tripartite motif protein 29; ZF-B_BOX domain, TRIM29,
ataxia-telangiectasia group D-associated protein, ATDC,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
g.43.1.1
Length = 72
Score = 23.5 bits (51), Expect = 9.8
Identities = 7/31 (22%), Positives = 11/31 (35%), Gaps = 8/31 (25%)
Query: 20 RNLEYVCKERGHCIVDVTRRNQCQACRFSKC 50
+ +E C+ CI C C F +
Sbjct: 26 KTMELFCQTDQTCI--------CYLCMFQEH 48
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.332 0.139 0.466
Gapped
Lambda K H
0.267 0.0507 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,773,090
Number of extensions: 90911
Number of successful extensions: 240
Number of sequences better than 10.0: 1
Number of HSP's gapped: 237
Number of HSP's successfully gapped: 34
Length of query: 119
Length of database: 6,701,793
Length adjustment: 81
Effective length of query: 38
Effective length of database: 4,440,192
Effective search space: 168727296
Effective search space used: 168727296
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (22.0 bits)
S2: 51 (23.9 bits)