RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6818
(162 letters)
>4av1_A Poly [ADP-ribose] polymerase 1; transferase, PARP1, DNA-binding
domain, DBD, DNA repair, CAN poly- ADP(ribosyl)ation;
3.10A {Homo sapiens} PDB: 2l30_A
Length = 223
Score = 112 bits (280), Expect = 1e-31
Identities = 56/163 (34%), Positives = 77/163 (47%), Gaps = 27/163 (16%)
Query: 1 SPFFDGKTPKWFHEECFWKKNRPK--ALLDIHNVTSLRHQDQEMIKSKILG--------- 49
SP FDGK P W+H CFWK +++ + LR DQ+ +K
Sbjct: 62 SPMFDGKVPHWYHFSCFWKVGHSIRHPDVEVDGFSELRWDDQQKVKKTAEAGGVTGKGQD 121
Query: 50 -------------NIEYAKSNRSTCRGCEAKIAKGEIRVSKMNYDSDQGKMIGGIPEWYH 96
EYAKSNRSTC+GC KI KG++R+SK D + +G I WYH
Sbjct: 122 GIGSKAEKTLGDFAAEYAKSNRSTCKGCMEKIEKGQVRLSKKMVDP-EKPQLGMIDRWYH 180
Query: 97 LSCFNAVRLDLEF--SASGKQIPGFGSLEKKDQKIVEATLPSL 137
CF R +L F S Q+ GF L +D++ ++ LP +
Sbjct: 181 PGCFVKNREELGFRPEYSASQLKGFSLLATEDKEALKKQLPGV 223
Score = 77.6 bits (190), Expect = 2e-18
Identities = 28/84 (33%), Positives = 41/84 (48%), Gaps = 5/84 (5%)
Query: 51 IEYAKSNRSTCRGCEAKIAKGEIRVSKMNYDSDQGKMIGGIPEWYHLSCFNAVRLDLEFS 110
+EYAKS R++C+ C I K +R++ M G +P WYH SCF V +
Sbjct: 32 VEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFD---GKVPHWYHFSCFWKVGHSIRHP 88
Query: 111 ASGKQIPGFGSLEKKDQKIVEATL 134
++ GF L DQ+ V+ T
Sbjct: 89 D--VEVDGFSELRWDDQQKVKKTA 110
>3odc_A Poly [ADP-ribose] polymerase 1; protein-DNA complex, PARP zinc
finger, DNA binding protein-D complex; 2.80A {Homo
sapiens} PDB: 3ode_A 2l31_A
Length = 111
Score = 95.1 bits (236), Expect = 3e-26
Identities = 40/98 (40%), Positives = 56/98 (57%), Gaps = 4/98 (4%)
Query: 51 IEYAKSNRSTCRGCEAKIAKGEIRVSKMNYDSDQGKMIGGIPEWYHLSCFNAVRLDLEF- 109
EYAKSNRSTC+GC KI KG++R+SK D + +G I WYH CF R +L F
Sbjct: 12 AEYAKSNRSTCKGCMEKIEKGQVRLSKKMVDP-EKPQLGMIDRWYHPGCFVKNREELGFR 70
Query: 110 -SASGKQIPGFGSLEKKDQKIVEATLPSL-SDGVSKTD 145
S Q+ GF L +D++ ++ LP + S+G+
Sbjct: 71 PEYSASQLKGFSLLATEDKEALKKQLPGVKSEGLEHHH 108
Score = 41.1 bits (96), Expect = 1e-05
Identities = 10/51 (19%), Positives = 19/51 (37%), Gaps = 6/51 (11%)
Query: 3 FFDGKTPKWFHEECFWKKNRPKALL------DIHNVTSLRHQDQEMIKSKI 47
G +W+H CF K + + L +D+E +K ++
Sbjct: 46 PQLGMIDRWYHPGCFVKNREELGFRPEYSASQLKGFSLLATEDKEALKKQL 96
>2cs2_A Poly [ADP-ribose] polymerase-1; DNA BIND, DNA repair, necrosis,
apoptosis, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 134
Score = 92.9 bits (230), Expect = 4e-25
Identities = 38/95 (40%), Positives = 53/95 (55%), Gaps = 3/95 (3%)
Query: 51 IEYAKSNRSTCRGCEAKIAKGEIRVSKMNYDSDQGKMIGGIPEWYHLSCFNAVRLDLEF- 109
EYAKSNRSTC+GC KI KG++R+SK D + +G I WYH CF R +L F
Sbjct: 20 AEYAKSNRSTCKGCMEKIEKGQVRLSKKMVDP-EKPQLGMIDRWYHPGCFVKNREELGFR 78
Query: 110 -SASGKQIPGFGSLEKKDQKIVEATLPSLSDGVSK 143
S Q+ GF L +D++ ++ LP + +
Sbjct: 79 PEYSASQLKGFSLLATEDKEALKKQLPGVKSEGKR 113
Score = 41.6 bits (97), Expect = 1e-05
Identities = 15/80 (18%), Positives = 25/80 (31%), Gaps = 6/80 (7%)
Query: 3 FFDGKTPKWFHEECFWKKNRPKALL------DIHNVTSLRHQDQEMIKSKILGNIEYAKS 56
G +W+H CF K + + L +D+E +K ++ G K
Sbjct: 54 PQLGMIDRWYHPGCFVKNREELGFRPEYSASQLKGFSLLATEDKEALKKQLPGVKSEGKR 113
Query: 57 NRSTCRGCEAKIAKGEIRVS 76
G + K S
Sbjct: 114 KGDEVDGVDEVAKKKSGPSS 133
>2dmj_A Poly (ADP-ribose) polymerase family, member 1; zinc finger, PARP-1,
ADPRT, NAD(+) ADP-ribosyltransferase 1, poly(ADP-ribose)
synthetase 1; NMR {Homo sapiens}
Length = 106
Score = 83.8 bits (207), Expect = 6e-22
Identities = 30/93 (32%), Positives = 44/93 (47%), Gaps = 5/93 (5%)
Query: 51 IEYAKSNRSTCRGCEAKIAKGEIRVSKMNYDSDQGKMIGGIPEWYHLSCFNAVRLDLEFS 110
+EYAKS R++C+ C I K +R++ M G +P WYH SCF V +
Sbjct: 18 VEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFD---GKVPHWYHFSCFWKVGHSIRHP 74
Query: 111 ASGKQIPGFGSLEKKDQKIVEATLPSLSDGVSK 143
++ GF L DQ+ V+ T + G S
Sbjct: 75 D--VEVDGFSELRWDDQQKVKKTAEAGGSGPSS 105
Score = 53.7 bits (129), Expect = 3e-10
Identities = 18/49 (36%), Positives = 25/49 (51%), Gaps = 2/49 (4%)
Query: 1 SPFFDGKTPKWFHEECFWKKNRPK--ALLDIHNVTSLRHQDQEMIKSKI 47
SP FDGK P W+H CFWK +++ + LR DQ+ +K
Sbjct: 48 SPMFDGKVPHWYHFSCFWKVGHSIRHPDVEVDGFSELRWDDQQKVKKTA 96
>3od8_A Poly [ADP-ribose] polymerase 1; protein-DNA complex, PARP zinc
finger, DNA binding protein-D complex; 2.40A {Homo
sapiens} PDB: 3oda_A
Length = 116
Score = 82.3 bits (203), Expect = 4e-21
Identities = 28/86 (32%), Positives = 42/86 (48%), Gaps = 5/86 (5%)
Query: 51 IEYAKSNRSTCRGCEAKIAKGEIRVSKMNYDSDQGKMIGGIPEWYHLSCFNAVRLDLEFS 110
+EYAKS R++C+ C I K +R++ M G +P WYH SCF V +
Sbjct: 31 VEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFD---GKVPHWYHFSCFWKVGHSIRHP 87
Query: 111 ASGKQIPGFGSLEKKDQKIVEATLPS 136
++ GF L DQ+ V+ T +
Sbjct: 88 D--VEVDGFSELRWDDQQKVKKTAEA 111
Score = 52.3 bits (125), Expect = 9e-10
Identities = 18/49 (36%), Positives = 25/49 (51%), Gaps = 2/49 (4%)
Query: 1 SPFFDGKTPKWFHEECFWKKNRPK--ALLDIHNVTSLRHQDQEMIKSKI 47
SP FDGK P W+H CFWK +++ + LR DQ+ +K
Sbjct: 61 SPMFDGKVPHWYHFSCFWKVGHSIRHPDVEVDGFSELRWDDQQKVKKTA 109
>1uw0_A DNA ligase III; DNA repair, zinc finger, PARP-like finger, cell
division, DNA replication, nuclear protein; HET: DNA;
NMR {Homo sapiens} SCOP: g.39.1.12
Length = 117
Score = 82.0 bits (202), Expect = 4e-21
Identities = 24/98 (24%), Positives = 45/98 (45%), Gaps = 5/98 (5%)
Query: 51 IEYAKSNRSTCRGCEAKIAKGEIRVSKMNYDSDQGKMIGGIPEWYHLSCF----NAVRLD 106
++YAK + C+ C+ KI KG R+ K+ + + G + EWYH+ C R
Sbjct: 8 VDYAKRGTAGCKKCKEKIVKGVCRIGKV-VPNPFSESGGDMKEWYHIKCMFEKLERARAT 66
Query: 107 LEFSASGKQIPGFGSLEKKDQKIVEATLPSLSDGVSKT 144
+ ++ G+ LE +++ + + LS + T
Sbjct: 67 TKKIEDLTELEGWEELEDNEKEQITQHIADLSSKAAGT 104
Score = 44.3 bits (104), Expect = 1e-06
Identities = 12/57 (21%), Positives = 25/57 (43%), Gaps = 10/57 (17%)
Query: 1 SPFFD--GKTPKWFHEECFWKK--------NRPKALLDIHNVTSLRHQDQEMIKSKI 47
+PF + G +W+H +C ++K + + L ++ L ++E I I
Sbjct: 38 NPFSESGGDMKEWYHIKCMFEKLERARATTKKIEDLTELEGWEELEDNEKEQITQHI 94
>1v9x_A Poly (ADP-ribose) polymerase; PARP, DNA repair, inflammation, cell
death, structural genomics; NMR {Arabidopsis thaliana}
Length = 114
Score = 80.4 bits (198), Expect = 1e-20
Identities = 27/96 (28%), Positives = 45/96 (46%), Gaps = 6/96 (6%)
Query: 51 IEYAKSNRSTCRGCEAKIAKGEIRVSKMNYDSDQGKMIGGIPEWYHLSCFNAVRLDLEFS 110
EYAKS+RS+C+ C++ I K R+ K+ + G +P W H SC ++
Sbjct: 13 AEYAKSSRSSCKTCKSVINKENFRLGKLVQSTHFD---GIMPMWNHASCILKKTKQIK-- 67
Query: 111 ASGKQIPGFGSLEKKDQKIVEATLPSLSDGVSKTDA 146
S + G SL +DQ+ + + S + + T
Sbjct: 68 -SVDDVEGIESLRWEDQQKIRKYVESGAGSNTSTST 102
Score = 53.0 bits (127), Expect = 5e-10
Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 1/72 (1%)
Query: 1 SPFFDGKTPKWFHEECFWKKNRP-KALLDIHNVTSLRHQDQEMIKSKILGNIEYAKSNRS 59
S FDG P W H C KK + K++ D+ + SLR +DQ+ I+ + S +
Sbjct: 43 STHFDGIMPMWNHASCILKKTKQIKSVDDVEGIESLRWEDQQKIRKYVESGAGSNTSTST 102
Query: 60 TCRGCEAKIAKG 71
+ + G
Sbjct: 103 GTSTSSSGPSSG 114
>2p54_A PPAR-alpha, peroxisome proliferator-activated receptor alpha; PPAR
alpha GW735 SRC1 agonist HDLC, transcription; HET: 735;
1.79A {Homo sapiens} SCOP: a.123.1.1 PDB: 3fei_A*
1i7g_A* 3kdu_A* 3kdt_A* 2rew_A* 1kkq_A* 3g8i_A* 3et1_A*
2znn_A* 3sp6_A* 1k7l_A* 2npa_A* 2xyj_A* 2xyw_A* 2xyx_A*
2q5g_A* 3gwx_A* 3dy6_A* 1gwx_A* 3peq_A* ...
Length = 267
Score = 30.3 bits (68), Expect = 0.25
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 6/55 (10%)
Query: 75 VSKMNYDSDQGKMIGGIPEWYHLSCFN--AVRLDLEFSASGKQIPGFGSLEKKDQ 127
V+K+ + Q K + ++ C + V EF+ K IPGF +L+ DQ
Sbjct: 54 VAKLVANGIQNKEAE-VRIFHCCQCTSVETVTELTEFA---KAIPGFANLDLNDQ 104
>3ipq_A Oxysterols receptor LXR-alpha; LXR homodimer, LXR signaling,
alternative DNA-binding, metal-binding, nucleus,
polymorphism, receptor transcription; HET: 965; 2.00A
{Homo sapiens} PDB: 3ips_A* 3ipu_A* 3fc6_B* 3fal_B*
1uhl_B* 2acl_B* 1upv_A* 1upw_A* 1p8d_A* 1pq9_A* 1pq6_A*
1pqc_A* 3kfc_A* 4dk7_A* 4dk8_A* 3l0e_A*
Length = 283
Score = 29.7 bits (67), Expect = 0.40
Identities = 15/68 (22%), Positives = 27/68 (39%), Gaps = 5/68 (7%)
Query: 62 RGCEAKIAKGEIRVSKMNYDSDQGKMIGGIPEWYHLSCFNAVRLDL--EFSASGKQIPGF 119
+ C + +RV+ D + H + V + +F+ KQ+PGF
Sbjct: 58 QQCNRRSFSDRLRVTPWPMAPDPHSREARQQRFAHFTELAIVSVQEIVDFA---KQLPGF 114
Query: 120 GSLEKKDQ 127
L ++DQ
Sbjct: 115 LQLSREDQ 122
>3l0l_A Nuclear receptor ROR-gamma; nuclear receptor, rorgamma, alternative
splicing, DNA-bindin binding, nucleus, receptor,
zinc-finger, acetylation, activator; HET: HC3; 1.74A
{Homo sapiens} PDB: 3b0w_A* 3kyt_A* 3l0j_A*
Length = 248
Score = 29.1 bits (65), Expect = 0.56
Identities = 16/98 (16%), Positives = 36/98 (36%), Gaps = 13/98 (13%)
Query: 32 VTSLRHQDQEMIKSKILGNIEYAKSNRSTCRGCEAKIAKGEIRVSKMNYDSDQGKMIGGI 91
+ + + +++S KS R TC+ + + + + +
Sbjct: 4 PYASLTEIEHLVQS-------VCKSYRETCQLRLEDLLRQRSNIFSREEVTGYQRK-SMW 55
Query: 92 PEWYHLSC--FNAVRLDLEFSASGKQIPGFGSLEKKDQ 127
W + A++ +EF+ K++ GF L + DQ
Sbjct: 56 EMWERCAHHLTEAIQYVVEFA---KRLSGFMELCQNDQ 90
>3cqv_A Nuclear receptor subfamily 1 group D member 2; reverb beta, heme,
NR1D2, DNA-binding, metal-binding, nucleus, repressor,
transcription; HET: HEM; 1.90A {Homo sapiens} PDB:
2v7c_A 2v0v_A
Length = 199
Score = 28.9 bits (65), Expect = 0.57
Identities = 17/55 (30%), Positives = 23/55 (41%), Gaps = 5/55 (9%)
Query: 75 VSKMNYDSDQGKMIGGIPEWYHLS--CFNAVRLDLEFSASGKQIPGFGSLEKKDQ 127
V M+ G W S AV+ +EF+ K+IPGF L + DQ
Sbjct: 3 VCPMSKSPYVDPHKSGHEIWEEFSMSFTPAVKEVVEFA---KRIPGFRDLSQHDQ 54
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 28.8 bits (63), Expect = 0.62
Identities = 7/24 (29%), Positives = 13/24 (54%), Gaps = 8/24 (33%)
Query: 123 EKKDQKIVEATL--------PSLS 138
EK+ K ++A+L P+L+
Sbjct: 18 EKQALKKLQASLKLYADDSAPALA 41
>1nq7_A Nuclear receptor ROR-beta; ligand-binding domain, retinoids,
retinoic acid, synthetic ligand, antagonist,
transcription; HET: ARL; 1.50A {Rattus norvegicus} SCOP:
a.123.1.1 PDB: 1k4w_A* 1n4h_A*
Length = 244
Score = 27.9 bits (62), Expect = 1.2
Identities = 16/76 (21%), Positives = 32/76 (42%), Gaps = 8/76 (10%)
Query: 55 KSNRSTCRGCEAKIAKGEIRVSKMNYDSDQGKMIGGIPE-WYHLS--CFNAVRLDLEFSA 111
KS+ TC+ ++ + + Y+ + W + +A++ +EF+
Sbjct: 14 KSHLETCQYTMEELHQ--LAWQTHTYEEIKAYQSKSREALWQQCAIQITHAIQYVVEFA- 70
Query: 112 SGKQIPGFGSLEKKDQ 127
K+I GF L + DQ
Sbjct: 71 --KRITGFMELCQNDQ 84
>3f6q_B LIM and senescent cell antigen-like-containing domain protein 1;
ILK, integrin-linked kinase, pinch, ankyrin repeat, ANK,
IPP; 1.60A {Homo sapiens} PDB: 2kbx_B 3ixe_B
Length = 72
Score = 26.6 bits (59), Expect = 1.2
Identities = 12/51 (23%), Positives = 17/51 (33%), Gaps = 13/51 (25%)
Query: 50 NIEYAKSNRSTCRGCEAKIAKGEIRVSKMNYDSDQGKMIGGIPEWYHLSCF 100
N+ + S +TC C+ A E V+ YH CF
Sbjct: 3 NLYFQGSASATCERCKGGFAPAEKIVNSNGEL-------------YHEQCF 40
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 28.3 bits (62), Expect = 1.3
Identities = 8/32 (25%), Positives = 13/32 (40%)
Query: 17 FWKKNRPKALLDIHNVTSLRHQDQEMIKSKIL 48
K LL + NV + + + + KIL
Sbjct: 238 LKSKPYENCLLVLLNVQNAKAWNAFNLSCKIL 269
Score = 27.1 bits (59), Expect = 3.8
Identities = 23/165 (13%), Positives = 43/165 (26%), Gaps = 46/165 (27%)
Query: 12 FHEECFWKKNRPKALLDIHNVT--SLRHQDQEMIKSKILGNIE-YAKSNRSTCRGCEAKI 68
H+ +K ++ + I ++ + E + + ++ Y
Sbjct: 411 LHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSI--VDHYNIPKTFDSDDLIPPY 468
Query: 69 AKGEIRVSKMNYDSDQGKMIGGIPEWYHLSCFN---------AVRLDLEF---------- 109
++ IG +HL V LD F
Sbjct: 469 LDQYF----YSH-------IG-----HHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDST 512
Query: 110 --SASGKQIPGFGSLEKKDQKIVEATLPSLSDGVSKTDAISHFLL 152
+ASG + L+ I + P +AI FL
Sbjct: 513 AWNASGSILNTLQQLKFYKPYICDND-PKYE---RLVNAILDFLP 553
>1n83_A Nuclear receptor ROR-alpha; three-layered alpha helical sandwich,
transcription regulation, nuclear protein, DNA binding,
lipid binding protein; HET: CLR; 1.63A {Homo sapiens}
SCOP: a.123.1.1 PDB: 1s0x_A*
Length = 270
Score = 27.9 bits (62), Expect = 1.4
Identities = 16/74 (21%), Positives = 34/74 (45%), Gaps = 4/74 (5%)
Query: 55 KSNRSTCRGCEAKIAKGEIR-VSKMNYDSDQGKMIGGIPEWYHLSCFNAVRLDLEFSASG 113
KS+ TC+ ++ + + + ++ Q K + + + A++ +EF+
Sbjct: 29 KSHLETCQYLREELQQITWQTFLQEEIENYQNKQREVMWQLCAIKITEAIQYVVEFA--- 85
Query: 114 KQIPGFGSLEKKDQ 127
K+I GF L + DQ
Sbjct: 86 KRIDGFMELCQNDQ 99
>3u9q_A Peroxisome proliferator-activated receptor gamma; nuclear receptor,
adipogenesis, RXRA, nucleus, transcription; HET: DKA;
1.52A {Homo sapiens} PDB: 1i7i_A* 3ty0_A* 1zeo_A*
2p4y_A* 3et3_A* 3et0_A* 2hwq_A* 2ath_A* 2f4b_A* 2g0g_A*
2g0h_A* 2gtk_A* 2fvj_A* 2hwr_A* 2prg_A* 2q8s_A* 3fej_A*
3g9e_A* 3gbk_A* 3ia6_A* ...
Length = 269
Score = 27.4 bits (61), Expect = 2.1
Identities = 13/58 (22%), Positives = 25/58 (43%), Gaps = 6/58 (10%)
Query: 72 EIRVSKMNYDSDQGKMIGGIPEWYHLSCFNAVRLDL--EFSASGKQIPGFGSLEKKDQ 127
+I+ + +Q K + I + + + E++ K IPGF +L+ DQ
Sbjct: 54 KIKFKHITPLQEQSKEVA-IRIFQGCQFRSVEAVQEITEYA---KSIPGFVNLDLNDQ 107
>1x61_A Thyroid receptor interacting protein 6; LIM domain, OPA-interacting
protein 1, zyxin related protein 1 (ZRP-1), structural
genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3
g.39.1.3
Length = 72
Score = 25.9 bits (57), Expect = 2.5
Identities = 9/47 (19%), Positives = 14/47 (29%), Gaps = 13/47 (27%)
Query: 54 AKSNRSTCRGCEAKIAKGEIRVSKMNYDSDQGKMIGGIPEWYHLSCF 100
S S C GC + V ++ +H+ CF
Sbjct: 1 GSSGSSGCGGCGEDVVGDGAGVVALDRV-------------FHVGCF 34
>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 = 27.3 bits (60), Expect = 2.7
Identities = 14/60 (23%), Positives = 26/60 (43%), Gaps = 19/60 (31%)
Query: 12 FHEECFWKKNRPKALLDIHNVT-SLRHQD-------QEMIKS----KILGNIEYAKSNRS 59
F E C+ + N DIH + L ++ +E+IK+ +I+ + K + S
Sbjct: 91 F-ENCYLEGN------DIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNS 143
Score = 26.9 bits (59), Expect = 4.2
Identities = 25/134 (18%), Positives = 40/134 (29%), Gaps = 48/134 (35%)
Query: 61 CRGCEAKIAKGEIRVSKMNYDSDQGKMIGGIPEWYHLSCFNAVRLDLEFSASG--KQIPG 118
+ + V+K N GK + +S N + SG + + G
Sbjct: 341 ISNL--TQEQVQDYVNKTNSHLPAGKQV-------EISLVNGAK---NLVVSGPPQSLYG 388
Query: 119 FG-SLEK------KDQ--------KIVEAT--LP------S--LSDGVSK--TDAISH-- 149
+L K DQ K+ + LP S L D + +
Sbjct: 389 LNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNV 448
Query: 150 -F----LLIPLYLT 158
F + IP+Y T
Sbjct: 449 SFNAKDIQIPVYDT 462
Score = 25.8 bits (56), Expect = 9.2
Identities = 11/61 (18%), Positives = 27/61 (44%), Gaps = 12/61 (19%)
Query: 102 AVRLDLEFSASGKQIPGFGSLEKKDQKIVEATL-PSLSD----------GVSKTDAISHF 150
V+ ++ F+A QIP + + + D +++ ++ + D ++ A +H
Sbjct: 443 LVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKA-THI 501
Query: 151 L 151
L
Sbjct: 502 L 502
>1g47_A Pinch protein; LIM domain, Zn finger, cell adhesion; NMR {Homo
sapiens} SCOP: g.39.1.3 g.39.1.3
Length = 77
Score = 25.8 bits (57), Expect = 2.8
Identities = 11/48 (22%), Positives = 16/48 (33%), Gaps = 13/48 (27%)
Query: 53 YAKSNRSTCRGCEAKIAKGEIRVSKMNYDSDQGKMIGGIPEWYHLSCF 100
+TC C+ A E V+ G++ YH CF
Sbjct: 6 ANALASATCERCKGGFAPAEKIVNSN------GEL-------YHEQCF 40
>2k16_A Transcription initiation factor TFIID subunit 3; protein,
alternative splicing, metal-binding, nucleus,
phosphoprotein, transcription regulation; NMR {Mus
musculus} PDB: 2k17_A*
Length = 75
Score = 25.6 bits (56), Expect = 3.5
Identities = 9/38 (23%), Positives = 12/38 (31%), Gaps = 5/38 (13%)
Query: 81 DSDQGKMIG--GIPEWYHLSCFNAVRLDLEFSASGKQI 116
D MIG +WYH C V + +
Sbjct: 27 PDDGSPMIGCDDCDDWYHWPC---VGIMAAPPEEMQWF 61
>3kmr_A Retinoic acid receptor alpha; nuclear receptor transcription factor
ligand binding domain, binding, metal-binding, nucleus,
phosphoprotein; HET: EQN; 1.80A {Homo sapiens} PDB:
3kmz_B* 3a9e_B* 4dm6_A* 1xap_A* 4dm8_A* 2lbd_A* 3lbd_A*
4lbd_A*
Length = 266
Score = 26.6 bits (59), Expect = 3.5
Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 5/49 (10%)
Query: 81 DSDQGKMIGGIPEWYHLSCFNAVRLDL--EFSASGKQIPGFGSLEKKDQ 127
+S + ++ I W S + + EF+ KQ+PGF +L DQ
Sbjct: 57 NSSEQRVSLDIDLWDKFSELSTKCIIKTVEFA---KQLPGFTTLTIADQ 102
>1ovl_A Orphan nuclear receptor NURR1 (MSe 414, 496, 511); NUUR1, LBD,
transcription; 2.20A {Homo sapiens} SCOP: a.123.1.1
Length = 271
Score = 26.6 bits (59), Expect = 3.6
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 114 KQIPGFGSLEKKDQKI 129
++IPGF L K DQ +
Sbjct: 95 EKIPGFADLPKADQDL 110
>1ibr_B P95, importin beta-1 subunit, nuclear factor; small GTPase, nuclear
transport receptor, cell cycle, translation; HET: GNP;
2.30A {Homo sapiens} SCOP: a.118.1.1 PDB: 1m5n_S 1gcj_A
1f59_A 1o6o_A 1o6p_A
Length = 462
Score = 26.7 bits (58), Expect = 4.0
Identities = 10/58 (17%), Positives = 19/58 (32%)
Query: 16 CFWKKNRPKALLDIHNVTSLRHQDQEMIKSKILGNIEYAKSNRSTCRGCEAKIAKGEI 73
K+ ++ + +K+ +L + S+ C A IA EI
Sbjct: 64 SLTSKDPDIKAQYQQRWLAIDANARREVKNYVLQTLGTETYRPSSASQCVAGIACAEI 121
>1xpc_A Estrogen receptor; nuclear receptor, transcription factor,
ER-alpha, antagonist hormone-growth factor receptor
complex; HET: AIT; 1.60A {Homo sapiens} SCOP: a.123.1.1
PDB: 1sj0_A* 1xp1_A* 1xp9_A* 1xp6_A* 1yim_A* 1yin_A*
3ert_A* 1r5k_A* 3erd_A* 1l2i_A* 2iok_A* 1a52_A* 2ouz_A*
1ere_A* 1err_A* 2qxs_A* 3q95_A* 3q97_A* 2b1z_A* 1zky_A*
...
Length = 248
Score = 26.7 bits (59), Expect = 4.0
Identities = 7/14 (50%), Positives = 9/14 (64%)
Query: 114 KQIPGFGSLEKKDQ 127
K++PGF L DQ
Sbjct: 56 KRVPGFVDLTLHDQ 69
>1fcy_A RAR-gamma-1, retinoic acid receptor gamma-1; isotype selectivity,
retinoid ligand complexes, drug design, antiparallel
alpha-helical sandwich fold; HET: 564 LMU; 1.30A {Homo
sapiens} SCOP: a.123.1.1 PDB: 1fcz_A* 1fcx_A* 1fd0_A*
1exa_A* 1exx_A* 1dkf_B*
Length = 236
Score = 26.5 bits (59), Expect = 4.1
Identities = 11/36 (30%), Positives = 15/36 (41%), Gaps = 5/36 (13%)
Query: 94 WYHLSCFNAVRLDL--EFSASGKQIPGFGSLEKKDQ 127
W S + EF+ K++PGF L DQ
Sbjct: 46 WDKFSELATKCIIKIVEFA---KRLPGFTGLSIADQ 78
>1xdk_B RAR-beta, retinoic acid receptor, beta; nuclear receptor,
coactivator, ligand, hormone/growth factor receptor
complex; HET: REA; 2.90A {Mus musculus} SCOP: a.123.1.1
Length = 303
Score = 26.7 bits (59), Expect = 4.3
Identities = 11/36 (30%), Positives = 15/36 (41%), Gaps = 5/36 (13%)
Query: 94 WYHLSCFNAVRLDL--EFSASGKQIPGFGSLEKKDQ 127
W S + EF+ K++PGF L DQ
Sbjct: 73 WDKFSELATKCIIKIVEFA---KRLPGFTGLTIADQ 105
>3gyt_A Nuclear hormone receptor of the steroid/thyroid hormone receptors
superfamily; nuclear receptor, ligand binding domain,
dafachronic acid, nematode, DNA-binding, metal-binding,
nucleus, receptor; HET: DL4; 2.40A {Strongyloides
stercoralis} PDB: 3gyu_A*
Length = 244
Score = 26.5 bits (58), Expect = 4.6
Identities = 3/26 (11%), Positives = 12/26 (46%), Gaps = 3/26 (11%)
Query: 102 AVRLDLEFSASGKQIPGFGSLEKKDQ 127
+R ++ + K++ F + + +
Sbjct: 53 TMRRLVKMA---KRLGAFNEISEAGK 75
>3n00_A REV-ERBA-alpha; reverba ncorid1, anti-parallel B-sheet,
transcription regula; 2.60A {Homo sapiens}
Length = 245
Score = 26.3 bits (58), Expect = 4.6
Identities = 12/36 (33%), Positives = 15/36 (41%), Gaps = 5/36 (13%)
Query: 94 WYHLSCFNAVRLDL--EFSASGKQIPGFGSLEKKDQ 127
W S + EF+ K IPGF L + DQ
Sbjct: 67 WEDFSMSFTPAVREVVEFA---KHIPGFRDLSQHDQ 99
>1yje_A Orphan nuclear receptor NR4A1; NGFI-B, NUR77, ligand-binding
domain, novel coregulator interface, cell-specific;
2.40A {Rattus norvegicus} PDB: 2qw4_A
Length = 264
Score = 26.3 bits (58), Expect = 4.8
Identities = 7/14 (50%), Positives = 9/14 (64%)
Query: 114 KQIPGFGSLEKKDQ 127
++IPGF L DQ
Sbjct: 88 EKIPGFIELSPGDQ 101
>3oll_A Estrogen receptor beta; steroid binding, phosphorylation, hormone
receptor-activator; HET: PTR EST; 1.50A {Homo sapiens}
PDB: 1u3s_A* 1u3q_A* 1x78_A* 1x7b_A* 1x7j_A* 1x76_A*
2yjd_A* 3ols_A* 3omo_A* 3omp_A* 3omq_A* 1u3r_A* 1u9e_A*
1qkm_A* 2giu_A* 1nde_A* 2jj3_A* 2i0g_A* 2qtu_A* 2z4b_A*
...
Length = 240
Score = 26.3 bits (58), Expect = 5.0
Identities = 8/14 (57%), Positives = 9/14 (64%)
Query: 114 KQIPGFGSLEKKDQ 127
K+IPGF L DQ
Sbjct: 54 KKIPGFVELSLFDQ 67
>2r40_D Ecdysone receptor, 20-hydroxy-ecdysone receptor; nuclear receptor
ligand-binding domain, anti-parallel alpha- sandwich,
ecdysone receptor, ECR, gene regulation; HET: FLC 20E
EPH; 2.40A {Heliothis virescens} SCOP: a.123.1.1 PDB:
1r1k_D* 3ixp_D* 1r20_D*
Length = 266
Score = 26.2 bits (58), Expect = 5.0
Identities = 9/36 (25%), Positives = 18/36 (50%), Gaps = 5/36 (13%)
Query: 94 WYHLSCFNAVRLDL--EFSASGKQIPGFGSLEKKDQ 127
+ ++ + + L EF+ K +PGF + + DQ
Sbjct: 70 FRQITEMTILTVQLIVEFA---KGLPGFAKISQSDQ 102
>3b0t_A Vitamin D3 receptor; nuclear receptor, transcription, gene
regulation; HET: MCZ; 1.30A {Homo sapiens} PDB: 3a40_X*
1s0z_A* 1s19_A* 2ham_A* 2har_A* 2has_A* 1txi_A* 2hb8_A*
2hb7_A* 3a3z_X* 3a78_A* 3auq_A* 3aur_A* 3ax8_A* 3cs4_A*
3cs6_A* 1ie9_A* 1db1_A* 1ie8_A* 3kpz_A* ...
Length = 254
Score = 26.3 bits (58), Expect = 5.1
Identities = 16/92 (17%), Positives = 35/92 (38%), Gaps = 11/92 (11%)
Query: 38 QDQEMIKSKILGNIEYAKSNRSTCRGCEAKIAKGEIRVSKMNYDSDQGKMIGGIPEWYHL 97
++Q+ I + +L ++ T + + V + + + HL
Sbjct: 8 EEQQRIIAILL------DAHHKTYDPTYSDFCQFRPPVRVNDGGGSVTLELSQLSMLPHL 61
Query: 98 S--CFNAVRLDLEFSASGKQIPGFGSLEKKDQ 127
+ +++ + F+ K IPGF L +DQ
Sbjct: 62 ADLVSYSIQKVIGFA---KMIPGFRDLTSEDQ 90
>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 = 26.3 bits (58), Expect = 5.4
Identities = 13/49 (26%), Positives = 20/49 (40%), Gaps = 5/49 (10%)
Query: 81 DSDQGKMIGGIPEWYHLSCFNAVRLDL--EFSASGKQIPGFGSLEKKDQ 127
DS + + HL+ + + F+ K IPGF L +DQ
Sbjct: 91 DSSEEDQQSRLSMLPHLADLVSYSIQKVIGFA---KMIPGFRDLTAEDQ 136
>1x63_A Skeletal muscle LIM-protein 1; LIM domain, four and A half LIM
domains protein 1, structural genomics, NPPSFA; NMR
{Homo sapiens} SCOP: g.39.1.3 g.39.1.3
Length = 82
Score = 25.0 bits (55), Expect = 5.6
Identities = 9/49 (18%), Positives = 14/49 (28%), Gaps = 13/49 (26%)
Query: 53 YAKSNRSTCRGCEAKIAKGEIRVSKMNYDSDQGKMIGGIPEWYHLSCFN 101
+ + C+GC I G+ V +H CF
Sbjct: 10 TTREDSPKCKGCFKAIVAGDQNVEYKGTV-------------WHKDCFT 45
>3ilz_A Thyroid hormone receptor, alpha isoform 1 variant; nuclear
receptor, signaling protein; HET: B72; 1.85A {Homo
sapiens} PDB: 3jzb_A* 3hzf_A* 2h79_A* 2h77_A* 1nav_A*
3uvv_A* 1xzx_X* 1y0x_X* 1nq1_A* 3jzc_A* 1nuo_A* 3imy_A*
1nq0_A* 1bsx_A* 1r6g_A* 1nq2_A* 3gws_X* 1n46_A* 2h6w_X*
2j4a_A* ...
Length = 267
Score = 26.0 bits (57), Expect = 5.6
Identities = 11/58 (18%), Positives = 23/58 (39%), Gaps = 7/58 (12%)
Query: 72 EIRVSKMNYDSDQGKMIGGIPEWYHLSCFNAVRLDL--EFSASGKQIPGFGSLEKKDQ 127
+I S + D K+ + + + + +F+ K++P F L +DQ
Sbjct: 52 DIGQSPIVSMPDGDKV--DLEAFSEFTKIITPAITRVVDFA---KKLPMFSELPXEDQ 104
>3k6p_A Steroid hormone receptor ERR1; estrogen related receptor alpha,
DNA-binding, isopeptide BON binding, nucleus,
phosphoprotein, transcription; HET: 5FB; 2.00A {Homo
sapiens} PDB: 1xb7_A 2pjl_A* 3d24_A
Length = 248
Score = 26.2 bits (58), Expect = 5.7
Identities = 9/14 (64%), Positives = 9/14 (64%)
Query: 114 KQIPGFGSLEKKDQ 127
K IPGF SL DQ
Sbjct: 69 KSIPGFSSLSLSDQ 82
>1we9_A PHD finger family protein; structural genomics, PHD domain, riken
structural genomics/proteomics initiative, RSGI, DNA
binding protein; NMR {Arabidopsis thaliana} SCOP:
g.50.1.2
Length = 64
Score = 24.8 bits (54), Expect = 5.7
Identities = 6/25 (24%), Positives = 10/25 (40%), Gaps = 3/25 (12%)
Query: 77 KMNYDSDQGKMIG--GIPEWYHLSC 99
+Y +D+ I W+H C
Sbjct: 13 GESYAADE-FWICCDLCEMWFHGKC 36
>2nxx_E Ecdysone receptor (ECR, NRH1); hormone receptor, APO and holo
ligand binding pocket, hormone/growth factor complex;
HET: P1A; 2.75A {Tribolium castaneum}
Length = 248
Score = 25.8 bits (57), Expect = 6.2
Identities = 11/39 (28%), Positives = 21/39 (53%), Gaps = 5/39 (12%)
Query: 91 IPEWYHLSCFNAVRLDL--EFSASGKQIPGFGSLEKKDQ 127
+ H++ + + L EF+ K++PGF L ++DQ
Sbjct: 51 DVRFRHITEITILTVQLIVEFA---KRLPGFDKLLREDQ 86
>2e2r_A Estrogen-related receptor gamma; ERR gamma, BPA, nuclear receptor,
transcription; HET: 2OH; 1.60A {Homo sapiens} SCOP:
a.123.1.1 PDB: 2zas_A* 2zbs_A 2zkc_A* 2p7g_A* 1vjb_A*
1tfc_A 2p7a_A* 2p7z_A* 2gpu_A* 1kv6_A 2gp7_A 2gpp_A*
2gpo_A* 2gpv_A* 1s9q_A* 1s9p_A* 2ewp_A*
Length = 244
Score = 25.8 bits (57), Expect = 6.3
Identities = 8/14 (57%), Positives = 9/14 (64%)
Query: 114 KQIPGFGSLEKKDQ 127
K IPGF +L DQ
Sbjct: 69 KHIPGFSTLSLADQ 82
>2ocf_A Estrogen receptor; estrogen receptor, LBD, monobody, estradiol,
hormone-growth complex; HET: CME EST; 2.95A {Homo
sapiens}
Length = 298
Score = 26.0 bits (57), Expect = 6.7
Identities = 7/14 (50%), Positives = 9/14 (64%)
Query: 114 KQIPGFGSLEKKDQ 127
K++PGF L DQ
Sbjct: 65 KRVPGFVDLTLHDQ 78
>3ltx_A Estrogen receptor; constitutive, nuclear receptor, DNA-binding,
metal-binding, nucleus, transcription, transcription
regulation, zinc-finger; 2.60A {Crassostrea gigas}
Length = 243
Score = 25.8 bits (57), Expect = 6.9
Identities = 6/14 (42%), Positives = 8/14 (57%)
Query: 114 KQIPGFGSLEKKDQ 127
K +PG+ L DQ
Sbjct: 57 KNVPGYTDLSLSDQ 70
>2o4j_A Vitamin D3 receptor; nuclear receptor-ligand complex,
hormone/growth factor receptor complex; HET: VD4; 1.74A
{Rattus norvegicus} SCOP: a.123.1.1 PDB: 1rk3_A* 1rjk_A*
1rkh_A* 1rkg_A* 2o4r_A*
Length = 292
Score = 25.9 bits (57), Expect = 7.0
Identities = 17/92 (18%), Positives = 30/92 (32%), Gaps = 11/92 (11%)
Query: 38 QDQEMIKSKILGNIEYAKSNRSTCRGCEAKIAKGEIRVSKMNYDSDQGKMIGGIPEWYHL 97
++Q+ I + +L ++ T A V + + HL
Sbjct: 11 EEQQHIIAILL------DAHHKTYDPTYADFRDFRPPVRMDGSTGSVTLDLSPLSMLPHL 64
Query: 98 SCFNAVRLDL--EFSASGKQIPGFGSLEKKDQ 127
+ + + F+ K IPGF L DQ
Sbjct: 65 ADLVSYSIQKVIGFA---KMIPGFRDLTSDDQ 93
>1osh_A BIle acid receptor; nuclear receptor, ligand binding domain,
transcription; HET: FEX; 1.80A {Homo sapiens} SCOP:
a.123.1.1 PDB: 3l1b_A* 3bej_A* 3fli_A* 3hc5_A* 3rvf_A*
3dct_A* 3dcu_A* 3ruu_A* 3rut_A* 3olf_A* 3okh_A* 3fxv_A*
3oki_A* 3omk_A* 3omm_A* 3oof_A* 3ook_A* 3hc6_A* 3p89_A*
3p88_A* ...
Length = 232
Score = 25.7 bits (57), Expect = 7.0
Identities = 10/36 (27%), Positives = 20/36 (55%), Gaps = 5/36 (13%)
Query: 94 WYHLSCFNAVRLDL--EFSASGKQIPGFGSLEKKDQ 127
+ L+ + + EF+ K++PGF +L+ +DQ
Sbjct: 44 FLILTEMATNHVQVLVEFT---KKLPGFQTLDHEDQ 76
>1pdu_A DHR38, nuclear hormone receptor HR38; nuclear receptor,
ligand-binding domain, hormone/growth factor receptor
complex; 2.30A {Drosophila melanogaster} SCOP: a.123.1.1
Length = 244
Score = 25.8 bits (57), Expect = 7.1
Identities = 6/14 (42%), Positives = 10/14 (71%)
Query: 114 KQIPGFGSLEKKDQ 127
++IPG+ L +DQ
Sbjct: 68 EKIPGYFDLLPEDQ 81
>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 = 25.9 bits (57), Expect = 7.7
Identities = 7/14 (50%), Positives = 8/14 (57%)
Query: 114 KQIPGFGSLEKKDQ 127
K+IP F L DQ
Sbjct: 104 KRIPHFSELPLDDQ 117
>3up3_A Acedaf-12; ligand binding domain, nematode, steroid binding
protein- transcription complex; HET: XCA; 1.25A
{Ancylostoma ceylanicum} PDB: 3up0_A*
Length = 243
Score = 25.6 bits (56), Expect = 8.6
Identities = 5/26 (19%), Positives = 13/26 (50%), Gaps = 3/26 (11%)
Query: 102 AVRLDLEFSASGKQIPGFGSLEKKDQ 127
+R ++ + K++P F L + +
Sbjct: 53 TMRRFVKMA---KRLPAFNDLSQDGK 75
>2l3k_A Rhombotin-2, linker, LIM domain-binding protein 1;
LMO2(LIM2)-LDB1(LID), chimera, fusion protein,
oncoprotein; NMR {Mus musculus} PDB: 2l6y_B 2l6z_C
Length = 123
Score = 25.0 bits (54), Expect = 9.0
Identities = 9/44 (20%), Positives = 14/44 (31%), Gaps = 13/44 (29%)
Query: 57 NRSTCRGCEAKIAKGEIRVSKMNYDSDQGKMIGGIPEWYHLSCF 100
C C+ +I E+ + + YHL CF
Sbjct: 7 QDGLCASCDKRIRAYEMTMRVKDKV-------------YHLECF 37
>2cup_A Skeletal muscle LIM-protein 1; four and half LIM domains protein 1,
LIM domain, structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: g.39.1.3 g.39.1.3 g.39.1.3
Length = 101
Score = 24.7 bits (54), Expect = 9.2
Identities = 9/48 (18%), Positives = 14/48 (29%), Gaps = 13/48 (27%)
Query: 53 YAKSNRSTCRGCEAKIAKGEIRVSKMNYDSDQGKMIGGIPEWYHLSCF 100
+ + C+GC I G+ V +H CF
Sbjct: 61 TTREDSPKCKGCFKAIVAGDQNVEYKGTV-------------WHKDCF 95
>2nxx_A Ultraspiracle (USP, NR2B4); hormone receptor, APO and holo ligand
binding pocket, hormone/growth factor complex; HET: P1A;
2.75A {Tribolium castaneum}
Length = 235
Score = 25.4 bits (56), Expect = 9.5
Identities = 7/14 (50%), Positives = 8/14 (57%)
Query: 114 KQIPGFGSLEKKDQ 127
K +P F SL DQ
Sbjct: 58 KLVPHFTSLPLTDQ 71
>3cjw_A COUP transcription factor 2; COUP-TFII, nuclear receptor, ligand
binding domain, orphan receptor, three-layered helical
sandwich, DNA-binding; 1.48A {Homo sapiens}
Length = 244
Score = 25.5 bits (56), Expect = 9.6
Identities = 6/14 (42%), Positives = 8/14 (57%)
Query: 114 KQIPGFGSLEKKDQ 127
+ IP F L+ DQ
Sbjct: 58 RNIPFFPDLQITDQ 71
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
0.318 0.135 0.410
Gapped
Lambda K H
0.267 0.0548 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,431,337
Number of extensions: 130096
Number of successful extensions: 398
Number of sequences better than 10.0: 1
Number of HSP's gapped: 369
Number of HSP's successfully gapped: 92
Length of query: 162
Length of database: 6,701,793
Length adjustment: 86
Effective length of query: 76
Effective length of database: 4,300,587
Effective search space: 326844612
Effective search space used: 326844612
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.6 bits)