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  Home > SCOP hierarchy > "Winged helix" DNA-binding domain > Hidden Markov models

"Winged helix" DNA-binding domain superfamily models

A superfamily is represented by one or more models; usually there is more than one model representing the superfamily. Since each model is built to capture the whole superfamily, they are likely to be overlapping and sometimes are mostly overlapping or even redundant to each other. Also models often do not score their own seed sequence more highly than other sequences in the superfamily, so it is a mistake to think that the model represents the seed sequence.

All models are available for immediate download after obtaining a license by filling in a short online registration form. Licenses are free for academic and commercial purposes.

Plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be viewed for each model by following the model ID link.

All 208 SUPERFAMILY models representing the "Winged helix" DNA-binding domain superfamily
Model ID No. of seqs Build date Seed sequence Family of seed
0037340 4 2005-09-08 d1f1za1 TnsA endonuclease, C-terminal domain
0045968 3498 2008-09-10 d1biaa1 Biotin repressor-like
0039384 1320 2005-09-08 d1j5ya1 Biotin repressor-like
0047587 692 2008-09-10 d1jhfa1 LexA repressor, N-terminal DNA-binding domain
0037456 611 2005-09-08 d1f9na1 Arginine repressor (ArgR), N-terminal DNA-binding domain
0035347 613 2005-09-08 d1b4aa1 Arginine repressor (ArgR), N-terminal DNA-binding domain
0045802 402 2008-09-10 d1aoya_ Arginine repressor (ArgR), N-terminal DNA-binding domain
0048601 292 2008-09-10 d1omia2 CAP C-terminal domain-like
0054016 1352 2010-05-31 d2h6ca1 CAP C-terminal domain-like
0054945 1680 2010-05-31 d3e5ua1 CAP C-terminal domain-like
0051665 770 2008-09-10 d1zyba1 CAP C-terminal domain-like
0052860 810 2008-09-10 d2gaua1 CAP C-terminal domain-like
0037767 847 2005-09-08 d1ft9a1 CAP C-terminal domain-like
0054434 2195 2010-05-31 d2oz6a1 CAP C-terminal domain-like
0038753 648 2005-09-08 d1hw5a1 CAP C-terminal domain-like
0052198 1116 2008-09-10 d2coha1 CAP C-terminal domain-like
0043669 1980 2005-09-08 d1smta_ ArsR-like transcriptional regulators
0051170 1478 2008-09-10 d1y0ua_ ArsR-like transcriptional regulators
0049777 2981 2008-09-10 d1u2wa1 ArsR-like transcriptional regulators
0043095 1323 2005-09-08 d1r1ua_ ArsR-like transcriptional regulators
0050048 4804 2008-09-10 d1v4ra1 GntR-like transcriptional regulators
0054059 8784 2010-05-31 d2hs5a1 GntR-like transcriptional regulators
0047247 4248 2008-09-10 d1hw1a1 GntR-like transcriptional regulators
0054845 7601 2010-05-31 d3bwga1 GntR-like transcriptional regulators
0045981 193 2008-09-10 d1bm9a_ Replication terminator protein (RTP)
0045910 1334 2008-09-10 d1b9ma1 N-terminal domain of molybdate-dependent transcriptional regulator ModE
0045974 33 2008-09-10 d1bjaa_ Transcription factor MotA, activation domain
0054291 356 2010-05-31 d2nrac2 Replication initiation protein
0049152 434 2008-09-10 d1repc2 Replication initiation protein
0054290 107 2010-05-31 d2nrac1 Replication initiation protein
0047195 247 2008-09-10 d1hkqa_ Replication initiation protein
0049151 151 2008-09-10 d1repc1 Replication initiation protein
0046825 191 2008-09-10 d1fnna1 Helicase DNA-binding domain
0039091 248 2005-09-08 d1in4a1 Helicase DNA-binding domain
0038673 667 2005-09-08 d1hqca1 Helicase DNA-binding domain
0050373 52 2008-09-10 d1w5sa1 Helicase DNA-binding domain
0052725 42 2008-09-10 d2fnaa1 Helicase DNA-binding domain
0045284 3 2005-09-08 d2foka2 Restriction endonuclease FokI, N-terminal (recognition) domain
0052734 10 2008-09-10 d2foka3 Restriction endonuclease FokI, N-terminal (recognition) domain
0045283 3 2005-09-08 d2foka1 Restriction endonuclease FokI, N-terminal (recognition) domain
0046835 10 2008-09-10 d1foka3 Restriction endonuclease FokI, N-terminal (recognition) domain
0049992 883 2008-09-10 d1ussa_ Linker histone H1/H5
0047234 910 2008-09-10 d1hsta_ Linker histone H1/H5
0046987 826 2008-09-10 d1ghca_ Linker histone H1/H5
0049993 822 2008-09-10 d1usta_ Linker histone H1/H5
0051371 881 2008-09-10 d1yqaa1 Linker histone H1/H5
0051672 1949 2008-09-10 d2a07f1 Forkhead DNA-binding domain
0053005 1952 2008-09-10 d2hdca_ Forkhead DNA-binding domain
0040207 624 2005-09-08 d1kq8a_ Forkhead DNA-binding domain
0039808 629 2005-09-08 d1jxsa_ Forkhead DNA-binding domain
0046435 1948 2008-09-10 d1e17a_ Forkhead DNA-binding domain
0036285 628 2005-09-08 d1d5va_ Forkhead DNA-binding domain
0045923 115 2008-09-10 d1bbya_ DNA-binding domain from rap30
0036548 46 2005-09-08 d1dpua_ C-terminal domain of RPA32
0035958 182 2005-09-08 d1cf7b_ Cell cycle transcription factor e2f-dp
0046129 596 2008-09-10 d1cf7a_ Cell cycle transcription factor e2f-dp
0046283 45 2008-09-10 d1d8ja_ The central core domain of TFIIE beta
0042770 258 2005-09-08 d1qgpa_ Z-DNA binding domain
0043589 136 2005-09-08 d1sfua_ Z-DNA binding domain
0047523 304 2008-09-10 d1j75a_ Z-DNA binding domain
0042079 110 2005-09-08 d1oyia_ Z-DNA binding domain
0051026 105 2008-09-10 d1xmka1 Z-DNA binding domain
0047770 50 2008-09-10 d1ka8a_ P4 origin-binding domain-like
0036540 92 2005-09-08 d1dp7p_ P4 origin-binding domain-like
0051354 1052 2008-09-10 d1yo5c1 ets domain
0048143 437 2008-09-10 d1md0a_ ets domain
0037648 338 2005-09-08 d1flia_ ets domain
0045833 432 2008-09-10 d1awca_ ets domain
0048817 1044 2008-09-10 d1puee_ ets domain
0050732 1053 2008-09-10 d1wwxa1 ets domain
0036614 337 2005-09-08 d1duxc_ ets domain
0047161 1066 2008-09-10 d1hbxg_ ets domain
0037479 712 2005-09-08 d1fbqa_ Heat-shock transcription factor
0038616 726 2005-09-08 d1hksa_ Heat-shock transcription factor
0045339 431 2005-09-08 d2irfg_ Interferon regulatory factor
0047353 369 2008-09-10 d1if1a_ Interferon regulatory factor
0049520 371 2008-09-10 d1t2ka_ Interferon regulatory factor
0046914 741 2008-09-10 d1g3sa1 Iron-dependent repressor protein
0048605 725 2008-09-10 d1on2a1 Iron-dependent repressor protein
0045862 1043 2008-09-10 d1b1ba1 Iron-dependent repressor protein
0045043 106 2005-09-08 d1xgsa1 Methionine aminopeptidase, insert domain
0045885 282 2008-09-10 d1b6aa1 Methionine aminopeptidase, insert domain
0038701 660 2005-09-08 d1hsja1 MarR-like transcriptional regulators
0040586 1587 2005-09-08 d1lnwa_ MarR-like transcriptional regulators
0042156 608 2005-09-08 d1p4xa1 MarR-like transcriptional regulators
0044258 1903 2005-09-08 d1ub9a_ MarR-like transcriptional regulators
0052641 4512 2008-09-10 d2fbia1 MarR-like transcriptional regulators
0037861 401 2005-09-08 d1fzpb_ MarR-like transcriptional regulators
0047585 4082 2008-09-10 d1jgsa_ MarR-like transcriptional regulators
0048695 3652 2008-09-10 d1p4xa2 MarR-like transcriptional regulators
0049308 4157 2008-09-10 d1s3ja_ MarR-like transcriptional regulators
0053037 4286 2008-09-10 d2hr3a1 MarR-like transcriptional regulators
0054842 3960 2010-05-31 d3broa1 MarR-like transcriptional regulators
0040517 1430 2005-09-08 d1lj9a_ MarR-like transcriptional regulators
0052640 7373 2008-09-10 d2fbha1 MarR-like transcriptional regulators
0054933 7314 2010-05-31 d3deua1 MarR-like transcriptional regulators
0052514 7377 2008-09-10 d2etha1 MarR-like transcriptional regulators
0051708 8103 2008-09-10 d2a61a1 MarR-like transcriptional regulators
0052644 4734 2008-09-10 d2fbka1 MarR-like transcriptional regulators
0053759 6016 2010-05-31 d2bv6a1 MarR-like transcriptional regulators
0051528 7463 2008-09-10 d1z91a1 MarR-like transcriptional regulators
0052801 4219 2008-09-10 d2fxaa1 MarR-like transcriptional regulators
0054905 4277 2010-05-31 d3ctaa1 MarR-like transcriptional regulators
0046839 408 2008-09-10 d1fp2a1 Plant O-methyltransferase, N-terminal domain
0047910 393 2008-09-10 d1kywa1 Plant O-methyltransferase, N-terminal domain
0046837 406 2008-09-10 d1fp1d1 Plant O-methyltransferase, N-terminal domain
0044139 262 2005-09-08 d1tw3a1 Plant O-methyltransferase, N-terminal domain
0043062 198 2005-09-08 d1qzza1 Plant O-methyltransferase, N-terminal domain
0047290 56 2008-09-10 d1i27a_ C-terminal domain of the rap74 subunit of TFIIF
0052282 674 2008-09-10 d2csoa1 DEP domain
0044604 227 2005-09-08 d1v3fa_ DEP domain
0041732 215 2005-09-08 d1o7fa1 DEP domain
0044373 211 2005-09-08 d1uhwa_ DEP domain
0037759 232 2005-09-08 d1fsha_ DEP domain
0049173 48 2008-09-10 d1ri7a1 Lrp/AsnC-like transcriptional regulator N-terminal domain
0052161 750 2008-09-10 d2cg4a1 Lrp/AsnC-like transcriptional regulator N-terminal domain
0047283 56 2008-09-10 d1i1ga1 Lrp/AsnC-like transcriptional regulator N-terminal domain
0052159 15 2008-09-10 d2cfxa1 Lrp/AsnC-like transcriptional regulator N-terminal domain
0048177 916 2008-09-10 d1mkma1 Transcriptional regulator IclR, N-terminal domain
0047445 583 2008-09-10 d1iuya_ SCF ubiquitin ligase complex WHB domain
0047959 579 2008-09-10 d1ldja1 SCF ubiquitin ligase complex WHB domain
0054069 539 2010-05-31 d2hyec1 SCF ubiquitin ligase complex WHB domain
0047958 78 2008-09-10 d1ldda_ SCF ubiquitin ligase complex WHB domain
0040682 169 2005-09-08 d1lvaa4 C-terminal fragment of elongation factor SelB
0048042 119 2008-09-10 d1lvaa3 C-terminal fragment of elongation factor SelB
0040679 2 2005-09-08 d1lvaa1 C-terminal fragment of elongation factor SelB
0048041 152 2008-09-10 d1lvaa2 C-terminal fragment of elongation factor SelB
0040266 1167 2005-09-08 d1ku9a_ DNA-binding protein Mj223
0047461 20606 2008-09-10 d1ixca1 LysR-like transcriptional regulators
0052508 12021 2008-09-10 d2esna1 LysR-like transcriptional regulators
0045030 408 2005-09-08 d1xcba1 Transcriptional repressor Rex, N-terminal domain
0041905 602 2005-09-08 d1okra_ Penicillinase repressor
0049363 1024 2008-09-10 d1sd4a_ Penicillinase repressor
0053941 1188 2010-05-31 d2g9wa1 Penicillinase repressor
0048703 832 2008-09-10 d1p6ra_ Penicillinase repressor
0048491 108 2008-09-10 d1o57a1 N-terminal domain of Bacillus PurR
0048861 204 2008-09-10 d1q1ha_ Transcription factor E/IIe-alpha, N-terminal domain
0041150 458 2005-09-08 d1mzba_ FUR-like
0054468 101 2010-05-31 d2p6ra1 RecQ helicase DNA-binding domain-like
0051849 315 2008-09-10 d2axla1 RecQ helicase DNA-binding domain-like
0042087 176 2005-09-08 d1oywa1 RecQ helicase DNA-binding domain-like
0042414 2 2005-09-08 d1pp7u_ 39 kda initiator binding protein, IBP39, N-terminal domain
0049859 19 2008-09-10 d1ucra_ Dissimilatory sulfite reductase DsvD
0052246 536 2008-09-10 d2cqka1 La domain
0043473 174 2005-09-08 d1s29a_ La domain
0049335 537 2008-09-10 d1s7aa_ La domain
0049886 662 2008-09-10 d1ufma_ PCI domain (PINT motif)
0050578 38 2008-09-10 d1wi9a_ PCI domain (PINT motif)
0043935 856 2005-09-08 d1tbxa_ F93-like
0053783 729 2010-05-31 d2co5a1 F93-like
0054502 2 2010-05-31 d2pg4a1 F93-like
0043164 513 2005-09-08 d1r7ja_ Archaeal DNA-binding protein
0049384 5104 2008-09-10 d1sfxa_ TrmB-like
0052364 6094 2008-09-10 d2d1ha1 TrmB-like
0043758 480 2005-09-08 d1stza1 Heat-inducible transcription repressor HrcA, N-terminal domain
0050651 92 2008-09-10 d1wlqc_ DNA replication factor Cdt1
0049276 97 2008-09-10 d1rz4a1 Eukaryotic translation initiation factor 3 subunit 12, eIF3k, C-terminal domain
0044207 38 2005-09-08 d1u5ta1 Vacuolar sorting protein domain
0050391 50 2008-09-10 d1w7pd2 Vacuolar sorting protein domain
0044211 31 2005-09-08 d1u5tc1 Vacuolar sorting protein domain
0049797 85 2008-09-10 d1u5tc2 Vacuolar sorting protein domain
0044208 101 2005-09-08 d1u5ta2 Vacuolar sorting protein domain
0049796 96 2008-09-10 d1u5tb1 Vacuolar sorting protein domain
0051337 899 2008-09-10 d1ylfa1 Transcriptional regulator Rrf2
0045032 406 2005-09-08 d1xd7a_ Transcriptional regulator Rrf2
0044089 224 2005-09-08 d1tqia1 Rio2 serine protein kinase N-terminal domain
0050338 152 2008-09-10 d1w1we_ Rad21/Rec8-like
0049944 2320 2008-09-10 d1ulya_ Hypothetical protein PH1932
0050608 22 2008-09-10 d1wj5a_ An Obfc1 domain
0049556 665 2008-09-10 d1t6sa2 ScpB/YpuH-like
0049555 343 2008-09-10 d1t6sa1 ScpB/YpuH-like
0051024 1293 2008-09-10 d1xmaa_ PadR-like
0052506 1402 2008-09-10 d2esha1 PadR-like
0051302 1033 2008-09-10 d1yg2a_ PadR-like
0051033 79 2008-09-10 d1xn7a_ Hypothetical protein YhgG
0051507 1305 2008-09-10 d1z6ra1 ROK associated domain
0053027 87 2008-09-10 d2hoea1 ROK associated domain
0051455 232 2008-09-10 d1z05a1 ROK associated domain
0053261 5470 2008-09-10 d2p4wa1 PF1790-like
0049573 93 2008-09-10 d1t98a1 MukF N-terminal domain-like
0051874 115 2008-09-10 d2b0la1 CodY HTH domain
0053154 1068 2008-09-10 d2j5pa1 FtsK C-terminal domain-like
0053153 1068 2008-09-10 d2j5oa1 FtsK C-terminal domain-like
0052718 9 2008-09-10 d2fmla1 Nudix-associated domain
0052633 264 2008-09-10 d2fb1a1 Nudix-associated domain
0051521 3532 2008-09-10 d1z7ua1 HxlR-like
0052579 1684 2008-09-10 d2f2ea1 HxlR-like
0052755 1428 2008-09-10 d2fswa1 HxlR-like
0054074 3455 2010-05-31 d2hzta1 HxlR-like
0051444 1910 2008-09-10 d1yyva1 HxlR-like
0054362 4 2010-05-31 d2od5a1 Marine metagenome family WH1
0054356 385 2010-05-31 d2obpa1 ReutB4095-like
0054478 1150 2010-05-31 d2p8ta1 PH0730 N-terminal domain-like
0054062 2523 2010-05-31 d2htja1 FaeA-like
0054152 93 2010-05-31 d2ipqx1 STY4665 C-terminal domain-like
0054851 168 2010-05-31 d3bz6a2 PSPTO2686-like
0054850 166 2010-05-31 d3bz6a1 PSPTO2686-like
0054295 80 2010-05-31 d2ns0a1 RHA1 ro06458-like
0054036 23 2010-05-31 d2hgca1 YjcQ-like
0054732 4 2010-05-31 d2vqca1 F112-like
0053603 28 2010-05-31 d1s6la1 MerB N-terminal domain-like
0053684 4 2010-05-31 d2a5yb1 CED-4 C-terminal domain-like
0053835 95 2010-05-31 d2doaa1 ELL N2 domain-like
0053953 56 2010-05-31 d2gmga1 PF0610-like
0053666 3 2010-05-31 d1zela1 Rv2827c N-terminal domain-like
0054702 235 2010-05-31 d2v7fa1 Rps19E-like
0053826 38 2010-05-31 d2dk8a1 RPO3F domain-like
0053825 227 2010-05-31 d2dk5a1 RPO3F domain-like


Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

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© Copyright 2013 The SUPERFAMILY authors and Julian Gough.