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8515  structures 10198  species 384  interactions 2182984  sequences 15155  architectures

Clan: HTH (CL0123)

Summary

Helix-turn-helix clan Add an annotation

This family contains a diverse range of mostly DNA-binding domains that contain a helix-turn-helix motif.

This clan contains 341 families and the total number of domains in the clan is 2182984. The clan was built by A Bateman.

Literature references

  1. Brennan RG, Matthews BW; , J Biol Chem 1989;264:1903-1906.: The helix-turn-helix DNA binding motif. PUBMED:2644244 EPMC:2644244
  2. Brennan RG; , Cell 1993;74:773-776.: The winged-helix DNA-binding motif: another helix-turn-helix takeoff. PUBMED:8374950 EPMC:8374950
  3. Wintjens R, Rooman M; , J Mol Biol 1996;262:294-313.: Structural classification of HTH DNA-binding domains and protein-DNA interaction modes. PUBMED:8831795 EPMC:8831795

Members

This clan contains the following 341 member families:

AbiEi_3_N AbiEi_4 ANAPC2 AphA_like Arg_repressor ARID ArsR B-block_TFIIIC B5 Bac_DnaA_C Baculo_PEP_N BetR BHD_3 BLACT_WH Bot1p BrkDBD BsuBI_PstI_RE_N C_LFY_FLO CaiF_GrlA CarD_CdnL_TRCF CDC27 Cdc6_C Cdh1_DBD_1 CDT1 CDT1_C CENP-B_N Costars CPSase_L_D3 Cro Crp CSN4_RPN5_eIF3a CSN8_PSD8_EIF3K CtsR Cullin_Nedd8 CUT CUTL CvfB_WH DBD_HTH DDRGK DEP Dimerisation Dimerisation2 DNA_meth_N DpnI_C DprA_WH DsrC DsrD DUF1016_N DUF1133 DUF1153 DUF1323 DUF134 DUF1441 DUF1492 DUF1495 DUF1670 DUF1804 DUF1819 DUF1836 DUF1870 DUF2089 DUF2250 DUF2316 DUF2513 DUF2582 DUF3116 DUF3253 DUF3853 DUF3860 DUF3908 DUF433 DUF4364 DUF4423 DUF4447 DUF480 DUF4817 DUF5635 DUF573 DUF722 DUF739 DUF742 DUF977 E2F_TDP EAP30 eIF-5_eIF-2B ELL ESCRT-II Ets EutK_C Exc F-112 FaeA Fe_dep_repr_C Fe_dep_repress FeoC FokI_C FokI_N Forkhead FtsK_gamma FUR GcrA GerE GntR GP3_package HARE-HTH HemN_C HNF-1_N Homeobox_KN Homeodomain Homez HPD HrcA_DNA-bdg HSF_DNA-bind HTH_1 HTH_10 HTH_11 HTH_12 HTH_13 HTH_15 HTH_16 HTH_17 HTH_18 HTH_19 HTH_20 HTH_21 HTH_22 HTH_23 HTH_24 HTH_25 HTH_26 HTH_27 HTH_28 HTH_29 HTH_3 HTH_30 HTH_31 HTH_32 HTH_33 HTH_34 HTH_35 HTH_36 HTH_37 HTH_38 HTH_39 HTH_40 HTH_41 HTH_42 HTH_43 HTH_45 HTH_46 HTH_47 HTH_48 HTH_49 HTH_5 HTH_50 HTH_51 HTH_52 HTH_53 HTH_54 HTH_55 HTH_56 HTH_57 HTH_6 HTH_7 HTH_8 HTH_9 HTH_ABP1_N HTH_AraC HTH_AsnC-type HTH_CodY HTH_Crp_2 HTH_DeoR HTH_IclR HTH_Mga HTH_micro HTH_OrfB_IS605 HTH_PafC HTH_ParB HTH_psq HTH_SUN2 HTH_Tnp_1 HTH_Tnp_1_2 HTH_Tnp_4 HTH_Tnp_IS1 HTH_Tnp_IS630 HTH_Tnp_ISL3 HTH_Tnp_Mu_1 HTH_Tnp_Mu_2 HTH_Tnp_Tc3_1 HTH_Tnp_Tc3_2 HTH_Tnp_Tc5 HTH_WhiA HxlR IBD IF2_N IRF KicB KilA-N Kin17_mid KORA KorB La LacI LexA_DNA_bind Linker_histone LZ_Tnp_IS481 MADF_DNA_bdg MAGE MarR MarR_2 MerR MerR-DNA-bind MerR_1 MerR_2 Mga Mnd1 MogR_DNAbind Mor MotA_activ MqsA_antitoxin MRP-L20 MukE Myb_DNA-bind_2 Myb_DNA-bind_3 Myb_DNA-bind_4 Myb_DNA-bind_5 Myb_DNA-bind_6 Myb_DNA-bind_7 Myb_DNA-binding Neugrin NFRKB_winged NOD2_WH NUMOD1 ORC_WH_C OST-HTH P22_Cro PaaX PadR PapB PAX PCI Penicillinase_R Phage_AlpA Phage_antitermQ Phage_CI_repr Phage_CII Phage_NinH Phage_Nu1 Phage_rep_O Phage_rep_org_N Phage_terminase PheRS_DBD1 PheRS_DBD2 PheRS_DBD3 Pou Pox_D5 PqqD PRC2_HTH_1 PUFD PuR_N Put_DNA-bind_N Raf1_HTH Rap1-DNA-bind Rep_3 RepA_C RepA_N RepC RepL Replic_Relax RFX_DNA_binding Ribosomal_S18 Ribosomal_S19e Ribosomal_S25 Rio2_N RNA_pol_Rpc34 RNA_pol_Rpc82 RNase_H2-Ydr279 ROQ_II RP-C RPA RPA_C RQC Rrf2 RTP RuvB_C S10_plectin SAC3_GANP SANT_DAMP1_like SatD SelB-wing_1 SelB-wing_2 SelB-wing_3 SgrR_N Sigma54_CBD Sigma54_DBD Sigma70_ECF Sigma70_ner Sigma70_r2 Sigma70_r3 Sigma70_r4 Sigma70_r4_2 Ski_Sno SLIDE Slx4 SMC_Nse1 SMC_ScpB SoPB_HTH SpoIIID SRP19 SRP_SPB STN1_2 Sulfolobus_pRN Suv3_N Swi6_N SWIRM Tau95 TBPIP TEA Terminase_5 TetR_N TFA2_Winged_2 TFIIE_alpha TFIIE_beta TFIIF_alpha TFIIF_beta Tn7_Tnp_TnsA_C Tn916-Xis TraI_2_C Trans_reg_C TrfA TrmB tRNA_bind_2 tRNA_bind_3 Trp_repressor UPF0122 UPF0175 Vir_act_alpha_C YdaS_antitoxin YjcQ YokU z-alpha

External database links

Domain organisation

Below is a listing of the unique domain organisations or architectures from this clan. More...

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Alignments

The table below shows the number of occurrences of each domain throughout the sequence database. More...

Pfam family Num. domains Alignment
TetR_N (PF00440) 149328 (6.8%) View
HTH_1 (PF00126) 127571 (5.8%) View
HTH_18 (PF12833) 110635 (5.1%) View
Sigma70_r2 (PF04542) 105709 (4.8%) View
GntR (PF00392) 89733 (4.1%) View
Trans_reg_C (PF00486) 89163 (4.1%) View
Sigma70_r4_2 (PF08281) 85376 (3.9%) View
HTH_3 (PF01381) 71626 (3.3%) View
Homeodomain (PF00046) 69869 (3.2%) View
Myb_DNA-binding (PF00249) 61767 (2.8%) View
LacI (PF00356) 49099 (2.2%) View
MarR_2 (PF12802) 38704 (1.8%) View
HTH_31 (PF13560) 35499 (1.6%) View
Sigma70_r4 (PF04545) 34096 (1.6%) View
MerR_1 (PF13411) 33728 (1.5%) View
HTH_8 (PF02954) 32175 (1.5%) View
MarR (PF01047) 29768 (1.4%) View
HTH_IclR (PF09339) 26205 (1.2%) View
HTH_20 (PF12840) 24618 (1.1%) View
HTH_24 (PF13412) 24055 (1.1%) View
GerE (PF00196) 23757 (1.1%) View
HTH_5 (PF01022) 20980 (1.0%) View
HxlR (PF01638) 20911 (1.0%) View
HTH_Crp_2 (PF13545) 20854 (1.0%) View
Sigma70_r3 (PF04539) 19848 (0.9%) View
PadR (PF03551) 19552 (0.9%) View
HTH_17 (PF12728) 19457 (0.9%) View
PCI (PF01399) 19173 (0.9%) View
HTH_11 (PF08279) 17383 (0.8%) View
FUR (PF01475) 16262 (0.7%) View
HTH_DeoR (PF08220) 15907 (0.7%) View
Forkhead (PF00250) 14580 (0.7%) View
HTH_Tnp_1 (PF01527) 14429 (0.7%) View
HTH_30 (PF13556) 14208 (0.7%) View
Rrf2 (PF02082) 13786 (0.6%) View
HTH_AsnC-type (PF13404) 13598 (0.6%) View
HTH_6 (PF01418) 10966 (0.5%) View
Myb_DNA-bind_6 (PF13921) 10866 (0.5%) View
IF2_N (PF04760) 10386 (0.5%) View
Myb_DNA-bind_4 (PF13837) 10275 (0.5%) View
DEP (PF00610) 10171 (0.5%) View
Homeobox_KN (PF05920) 10084 (0.5%) View
CarD_CdnL_TRCF (PF02559) 9965 (0.5%) View
HTH_21 (PF13276) 9741 (0.4%) View
CPSase_L_D3 (PF02787) 9341 (0.4%) View
HTH_26 (PF13443) 8972 (0.4%) View
Ribosomal_S18 (PF01084) 8944 (0.4%) View
ARID (PF01388) 8771 (0.4%) View
SRP_SPB (PF02978) 8590 (0.4%) View
HSF_DNA-bind (PF00447) 8363 (0.4%) View
Ets (PF00178) 8351 (0.4%) View
B5 (PF03484) 8196 (0.4%) View
OST-HTH (PF12872) 7255 (0.3%) View
HTH_ParB (PF17762) 7163 (0.3%) View
Bac_DnaA_C (PF08299) 7132 (0.3%) View
RQC (PF09382) 7109 (0.3%) View
FtsK_gamma (PF09397) 7080 (0.3%) View
Penicillinase_R (PF03965) 7041 (0.3%) View
MerR (PF00376) 7040 (0.3%) View
HTH_Tnp_Tc5 (PF03221) 6846 (0.3%) View
RuvB_C (PF05491) 6572 (0.3%) View
HemN_C (PF06969) 6564 (0.3%) View
NOD2_WH (PF17779) 6497 (0.3%) View
Linker_histone (PF00538) 6318 (0.3%) View
Myb_DNA-bind_3 (PF12776) 6005 (0.3%) View
Cullin_Nedd8 (PF10557) 5959 (0.3%) View
MerR-DNA-bind (PF09278) 5920 (0.3%) View
Fe_dep_repr_C (PF02742) 5842 (0.3%) View
La (PF05383) 5836 (0.3%) View
Fe_dep_repress (PF01325) 5731 (0.3%) View
SMC_ScpB (PF04079) 5698 (0.3%) View
SWIRM (PF04433) 5622 (0.3%) View
LexA_DNA_bind (PF01726) 5612 (0.3%) View
E2F_TDP (PF02319) 5583 (0.3%) View
HTH_Tnp_Tc3_2 (PF01498) 5463 (0.3%) View
HTH_23 (PF13384) 5419 (0.2%) View
HTH_42 (PF06224) 4956 (0.2%) View
HTH_OrfB_IS605 (PF12323) 4808 (0.2%) View
HTH_38 (PF13936) 4784 (0.2%) View
MADF_DNA_bdg (PF10545) 4782 (0.2%) View
PAX (PF00292) 4471 (0.2%) View
Sigma54_DBD (PF04552) 4424 (0.2%) View
Sigma54_CBD (PF04963) 4388 (0.2%) View
DprA_WH (PF17782) 4268 (0.2%) View
CUT (PF02376) 4158 (0.2%) View
HTH_19 (PF12844) 4151 (0.2%) View
Pou (PF00157) 4143 (0.2%) View
DUF742 (PF05331) 3909 (0.2%) View
HTH_25 (PF13413) 3874 (0.2%) View
HTH_28 (PF13518) 3799 (0.2%) View
HTH_psq (PF05225) 3734 (0.2%) View
HTH_7 (PF02796) 3666 (0.2%) View
SAC3_GANP (PF03399) 3626 (0.2%) View
Dimerisation (PF08100) 3531 (0.2%) View
CSN8_PSD8_EIF3K (PF10075) 3471 (0.2%) View
Arg_repressor (PF01316) 3428 (0.2%) View
eIF-5_eIF-2B (PF01873) 3353 (0.2%) View
HTH_48 (PF17906) 3336 (0.2%) View
RFX_DNA_binding (PF02257) 3274 (0.1%) View
MAGE (PF01454) 3133 (0.1%) View
KilA-N (PF04383) 3126 (0.1%) View
TrmB (PF01978) 3126 (0.1%) View
PqqD (PF05402) 3101 (0.1%) View
HTH_32 (PF13565) 3048 (0.1%) View
Mga (PF05043) 2995 (0.1%) View
Vir_act_alpha_C (PF10400) 2978 (0.1%) View
HTH_10 (PF04967) 2977 (0.1%) View
HTH_WhiA (PF02650) 2826 (0.1%) View
DUF433 (PF04255) 2788 (0.1%) View
BLACT_WH (PF17778) 2782 (0.1%) View
EAP30 (PF04157) 2674 (0.1%) View
Put_DNA-bind_N (PF06971) 2637 (0.1%) View
Sigma70_ner (PF04546) 2486 (0.1%) View
IRF (PF00605) 2456 (0.1%) View
Phage_AlpA (PF05930) 2453 (0.1%) View
HTH_27 (PF13463) 2417 (0.1%) View
Dimerisation2 (PF16864) 2350 (0.1%) View
CENP-B_N (PF04218) 2327 (0.1%) View
TEA (PF01285) 2319 (0.1%) View
CvfB_WH (PF17783) 2292 (0.1%) View
Myb_DNA-bind_5 (PF13873) 2266 (0.1%) View
HTH_40 (PF14493) 2242 (0.1%) View
DUF1016_N (PF17761) 2125 (0.1%) View
HTH_29 (PF13551) 2116 (0.1%) View
HTH_Tnp_4 (PF13613) 2089 (0.1%) View
HARE-HTH (PF05066) 2084 (0.1%) View
HTH_34 (PF13601) 2081 (0.1%) View
HTH_36 (PF13730) 2074 (0.1%) View
HTH_33 (PF13592) 2040 (0.1%) View
Cdc6_C (PF09079) 2033 (0.1%) View
Ski_Sno (PF02437) 1988 (0.1%) View
Ribosomal_S19e (PF01090) 1977 (0.1%) View
S10_plectin (PF03501) 1913 (0.1%) View
SLIDE (PF09111) 1818 (0.1%) View
PaaX (PF07848) 1804 (0.1%) View
HTH_50 (PF18024) 1788 (0.1%) View
HTH_22 (PF13309) 1773 (0.1%) View
BHD_3 (PF10405) 1766 (0.1%) View
Ribosomal_S25 (PF03297) 1740 (0.1%) View
HTH_37 (PF13744) 1710 (0.1%) View
TFIIE_alpha (PF02002) 1696 (0.1%) View
ORC_WH_C (PF18137) 1668 (0.1%) View
Trp_repressor (PF01371) 1666 (0.1%) View
RNA_pol_Rpc34 (PF05158) 1660 (0.1%) View
UPF0122 (PF04297) 1654 (0.1%) View
Rep_3 (PF01051) 1637 (0.1%) View
SRP19 (PF01922) 1635 (0.1%) View
HrcA_DNA-bdg (PF03444) 1563 (0.1%) View
TFIIF_beta (PF02270) 1529 (0.1%) View
HTH_Tnp_ISL3 (PF13542) 1527 (0.1%) View
Myb_DNA-bind_7 (PF15963) 1516 (0.1%) View
Rio2_N (PF09202) 1488 (0.1%) View
SelB-wing_3 (PF09107) 1465 (0.1%) View
RPA_C (PF08784) 1456 (0.1%) View
Tau95 (PF09734) 1425 (0.1%) View
tRNA_bind_2 (PF13725) 1416 (0.1%) View
B-block_TFIIIC (PF04182) 1370 (0.1%) View
Kin17_mid (PF10357) 1364 (0.1%) View
TFIIF_alpha (PF05793) 1354 (0.1%) View
AbiEi_4 (PF13338) 1348 (0.1%) View
CDC27 (PF09507) 1334 (0.1%) View
PheRS_DBD3 (PF18553) 1320 (0.1%) View
SANT_DAMP1_like (PF16282) 1314 (0.1%) View
ESCRT-II (PF05871) 1309 (0.1%) View
DUF4817 (PF16087) 1308 (0.1%) View
HNF-1_N (PF04814) 1307 (0.1%) View
DsrC (PF04358) 1283 (0.1%) View
RNA_pol_Rpc82 (PF05645) 1264 (0.1%) View
RPA (PF10134) 1245 (0.1%) View
GcrA (PF07750) 1245 (0.1%) View
UPF0175 (PF03683) 1242 (0.1%) View
continued
Pfam family Num. domains Alignment
TFA2_Winged_2 (PF18121) 1234 (0.1%) View
SMC_Nse1 (PF07574) 1234 (0.1%) View
MerR_2 (PF13591) 1229 (0.1%) View
CDT1_C (PF16679) 1223 (0.1%) View
HTH_9 (PF08221) 1218 (0.1%) View
Sigma70_ECF (PF07638) 1191 (0.1%) View
TFIIE_beta (PF02186) 1177 (0.1%) View
RNase_H2-Ydr279 (PF09468) 1173 (0.1%) View
DUF573 (PF04504) 1148 (0.1%) View
CDT1 (PF08839) 1141 (0.1%) View
HTH_PafC (PF19187) 1123 (0.1%) View
Pox_D5 (PF03288) 1075 (0.0%) View
ANAPC2 (PF08672) 1070 (0.0%) View
Mnd1 (PF03962) 1063 (0.0%) View
DUF1836 (PF08876) 1059 (0.0%) View
HTH_CodY (PF08222) 1057 (0.0%) View
HTH_16 (PF12645) 1034 (0.0%) View
LZ_Tnp_IS481 (PF13011) 1024 (0.0%) View
CtsR (PF05848) 1015 (0.0%) View
SpoIIID (PF12116) 996 (0.0%) View
ELL (PF10390) 986 (0.0%) View
DUF1153 (PF06627) 977 (0.0%) View
DUF134 (PF02001) 958 (0.0%) View
PuR_N (PF09182) 946 (0.0%) View
SelB-wing_2 (PF09106) 931 (0.0%) View
RP-C (PF03428) 909 (0.0%) View
Mor (PF08765) 906 (0.0%) View
TBPIP (PF07106) 905 (0.0%) View
RepA_N (PF06970) 888 (0.0%) View
Costars (PF14705) 883 (0.0%) View
Myb_DNA-bind_2 (PF08914) 868 (0.0%) View
DUF480 (PF04337) 867 (0.0%) View
Neugrin (PF06413) 842 (0.0%) View
HTH_12 (PF08461) 835 (0.0%) View
Slx4 (PF09494) 819 (0.0%) View
PRC2_HTH_1 (PF18118) 796 (0.0%) View
HPD (PF05044) 791 (0.0%) View
Replic_Relax (PF13814) 773 (0.0%) View
Bot1p (PF12298) 761 (0.0%) View
DUF3253 (PF11625) 751 (0.0%) View
HTH_Tnp_IS630 (PF01710) 706 (0.0%) View
HTH_35 (PF13693) 686 (0.0%) View
ROQ_II (PF18386) 681 (0.0%) View
DDRGK (PF09756) 675 (0.0%) View
DUF2089 (PF09862) 672 (0.0%) View
MRP-L20 (PF12824) 658 (0.0%) View
HTH_AraC (PF00165) 646 (0.0%) View
Phage_rep_org_N (PF09681) 639 (0.0%) View
Phage_CI_repr (PF07022) 626 (0.0%) View
CUTL (PF16557) 613 (0.0%) View
SgrR_N (PF12793) 608 (0.0%) View
PheRS_DBD1 (PF18552) 594 (0.0%) View
z-alpha (PF02295) 594 (0.0%) View
DUF1492 (PF07374) 585 (0.0%) View
DUF4364 (PF14277) 582 (0.0%) View
HTH_51 (PF18558) 574 (0.0%) View
Terminase_5 (PF06056) 562 (0.0%) View
PUFD (PF16553) 550 (0.0%) View
Homez (PF11569) 532 (0.0%) View
SatD (PF16264) 528 (0.0%) View
Tn916-Xis (PF09035) 478 (0.0%) View
Crp (PF00325) 473 (0.0%) View
FeoC (PF09012) 467 (0.0%) View
AbiEi_3_N (PF17194) 459 (0.0%) View
MqsA_antitoxin (PF15731) 456 (0.0%) View
DUF1819 (PF08849) 454 (0.0%) View
BrkDBD (PF09607) 439 (0.0%) View
Suv3_N (PF18114) 434 (0.0%) View
YdaS_antitoxin (PF15943) 429 (0.0%) View
HTH_SUN2 (PF18580) 426 (0.0%) View
HTH_Tnp_Tc3_1 (PF11427) 413 (0.0%) View
HTH_45 (PF14947) 405 (0.0%) View
PheRS_DBD2 (PF18554) 387 (0.0%) View
HTH_Tnp_Mu_1 (PF02316) 368 (0.0%) View
NUMOD1 (PF07453) 356 (0.0%) View
DUF2582 (PF10771) 339 (0.0%) View
CSN4_RPN5_eIF3a (PF18420) 331 (0.0%) View
HTH_ABP1_N (PF18107) 329 (0.0%) View
DBD_HTH (PF18430) 327 (0.0%) View
NFRKB_winged (PF14465) 325 (0.0%) View
Cdh1_DBD_1 (PF18196) 317 (0.0%) View
Tn7_Tnp_TnsA_C (PF08721) 317 (0.0%) View
HTH_47 (PF16221) 308 (0.0%) View
RepA_C (PF04796) 307 (0.0%) View
DUF2513 (PF10711) 301 (0.0%) View
HTH_52 (PF18576) 299 (0.0%) View
HTH_13 (PF11972) 293 (0.0%) View
Phage_antitermQ (PF06530) 293 (0.0%) View
Phage_rep_O (PF04492) 284 (0.0%) View
HTH_Tnp_Mu_2 (PF09039) 267 (0.0%) View
Raf1_HTH (PF18579) 264 (0.0%) View
STN1_2 (PF09170) 264 (0.0%) View
SoPB_HTH (PF18090) 261 (0.0%) View
HTH_39 (PF14090) 258 (0.0%) View
HTH_Mga (PF08280) 258 (0.0%) View
HTH_Tnp_IS1 (PF12759) 252 (0.0%) View
TraI_2_C (PF07515) 252 (0.0%) View
BetR (PF08667) 251 (0.0%) View
MukE (PF04288) 247 (0.0%) View
DUF4423 (PF14394) 242 (0.0%) View
BsuBI_PstI_RE_N (PF17728) 240 (0.0%) View
KicB (PF03882) 240 (0.0%) View
HTH_43 (PF09904) 240 (0.0%) View
tRNA_bind_3 (PF17176) 221 (0.0%) View
Phage_terminase (PF10668) 220 (0.0%) View
GP3_package (PF16677) 215 (0.0%) View
DUF739 (PF05339) 203 (0.0%) View
HTH_41 (PF14502) 195 (0.0%) View
KorB (PF08535) 191 (0.0%) View
RepL (PF05732) 190 (0.0%) View
FaeA (PF04703) 190 (0.0%) View
Phage_CII (PF05269) 176 (0.0%) View
Phage_Nu1 (PF07471) 169 (0.0%) View
HTH_53 (PF18606) 166 (0.0%) View
DUF1804 (PF08822) 156 (0.0%) View
HTH_46 (PF15977) 150 (0.0%) View
C_LFY_FLO (PF17538) 149 (0.0%) View
HTH_Tnp_1_2 (PF13022) 145 (0.0%) View
DUF3853 (PF12964) 135 (0.0%) View
YokU (PF14122) 133 (0.0%) View
TrfA (PF07042) 131 (0.0%) View
P22_Cro (PF14549) 128 (0.0%) View
DUF1323 (PF07037) 117 (0.0%) View
YjcQ (PF09639) 108 (0.0%) View
IBD (PF10416) 107 (0.0%) View
Baculo_PEP_N (PF04512) 105 (0.0%) View
DUF2316 (PF10078) 105 (0.0%) View
HTH_15 (PF12324) 104 (0.0%) View
DUF2250 (PF10007) 103 (0.0%) View
DsrD (PF08679) 102 (0.0%) View
Phage_NinH (PF06322) 100 (0.0%) View
HTH_49 (PF18010) 98 (0.0%) View
HTH_54 (PF18607) 97 (0.0%) View
DNA_meth_N (PF18284) 97 (0.0%) View
HTH_56 (PF18662) 96 (0.0%) View
DpnI_C (PF17726) 95 (0.0%) View
DUF1441 (PF07278) 93 (0.0%) View
DUF722 (PF05263) 91 (0.0%) View
RTP (PF02334) 91 (0.0%) View
DUF1670 (PF07900) 86 (0.0%) View
KORA (PF16509) 76 (0.0%) View
Cro (PF09048) 75 (0.0%) View
Rap1-DNA-bind (PF09197) 73 (0.0%) View
Exc (PF07825) 71 (0.0%) View
ArsR (PF09824) 61 (0.0%) View
HTH_55 (PF18622) 56 (0.0%) View
RepC (PF06504) 51 (0.0%) View
AphA_like (PF14557) 50 (0.0%) View
DUF977 (PF06163) 50 (0.0%) View
DUF1870 (PF08965) 49 (0.0%) View
CaiF_GrlA (PF07180) 39 (0.0%) View
MotA_activ (PF09114) 38 (0.0%) View
DUF1495 (PF07381) 33 (0.0%) View
FokI_C (PF02980) 30 (0.0%) View
FokI_N (PF02981) 28 (0.0%) View
EutK_C (PF16365) 27 (0.0%) View
DUF5635 (PF18685) 26 (0.0%) View
HTH_57 (PF18679) 25 (0.0%) View
DUF1133 (PF06576) 24 (0.0%) View
HTH_micro (PF17007) 23 (0.0%) View
Swi6_N (PF18530) 21 (0.0%) View
PapB (PF03333) 20 (0.0%) View
DUF3908 (PF13048) 18 (0.0%) View
DUF4447 (PF14590) 17 (0.0%) View
DUF3116 (PF11313) 17 (0.0%) View
Sulfolobus_pRN (PF05584) 13 (0.0%) View
MogR_DNAbind (PF12181) 11 (0.0%) View
SelB-wing_1 (PF09105) 4 (0.0%) View
F-112 (PF09645) 3 (0.0%) View
DUF3860 (PF12976) 2 (0.0%) View
Total: 341 Total: 2182984
No alignment ℹ
 

Please note: Clan alignments can be very large and can cause problems for some browsers. Read the note above before viewing.

Family relationships

This diagram shows the relationships between members of this clan. More...

Species distribution

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This tree shows the occurrence of the domains in this clan across different species. More...

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Interactions

There are 384 interactions for this clan. More...

Interacting families
A B
7tm_1 SRP_SPB
AAA RuvB_C
AAA_22 Cdc6_C
Adap_comp_sub DEP
Amino_oxidase Myb_DNA-binding
ANAPC2 ANAPC2
Arg_repressor Arg_repressor
Arg_repressor_C
Arg_repressor_C Arg_repressor
AsiA Sigma70_r4
AsnC_trans_reg HTH_24
Autoind_bind GerE
B3_4 B5
B5 B5
tRNA-synt_2d
Bac_DnaA Bac_DnaA_C
BHD_2 BHD_3
BTAD Trans_reg_C
CarD_CdnL_TRCF TRCF
CDC27 DNA_pol_E_B
Cdc6_C AAA_22
CDT1 Geminin
CecR_C TetR_N
cNMP_binding Crp
HTH_Crp_2
CoA_binding Put_DNA-bind_N
CodY HTH_CodY
Couple_hipA HTH_3
CPSase_L_D2 CPSase_L_D3
CPSase_L_D3 Biotin_carb_N
CPSase_L_D3
CPSase_sm_chain
GATase
Cro Cro
Crp cNMP_binding
CtsR CtsR
Cullin Cullin_Nedd8
Cullin_binding Cullin_Nedd8
Cullin_Nedd8 Cullin_Nedd8
zf-rbx1
Cupin_2 HTH_3
CUT Homeodomain
DEAD RQC
DEP Adap_comp_sub
RasGEF
WD40
Dimerisation Dimerisation
Methyltransf_2
DNA_pol_E_B CDC27
DsrC DsrC
DsrD DsrD
DUF1819 DUF1819
DUF1870 DUF1870
DUF2582 DUF2582
DUF4447 DUF4447
E2F_TDP E2F_TDP
EAP30 EAP30
ESCRT-II
eIF-5_eIF-2B eIF-5_eIF-2B
EIF_2_alpha eIF-5_eIF-2B
ESCRT-II EAP30
ESCRT-II
Snf7
Ets Ank_2
Ets
PAX
SRF-TF
Exc Exc
FCD GntR
Fe_dep_repr_C Fe_dep_repr_C
Fe_dep_repress
FeoA
Fe_dep_repress Fe_dep_repr_C
Fe_dep_repress
FeoA
FeoA Fe_dep_repr_C
FeoB_N FeoC
FHA Trans_reg_C
FlgM Sigma70_r4
FokI_C Endonuc-FokI_C
FokI_N FokI_C
FokI_N
Forkhead Forkhead
TIG
FtsK_gamma FtsK_gamma
FUR FUR
Geminin CDT1
GerE Autoind_bind
GerE
Prok-TraM
Response_reg
GNAT_acetyltr_2 tRNA_bind_2
GntR FadR_C
FCD
GntR
UTRA
GTP_EFTU eIF-5_eIF-2B
GTP_EFTU_D2 eIF-5_eIF-2B
HATPase_c Sigma70_r3
HipA_C HTH_3
HNF-1_N HNF-1_N
Homeodomain
Homeobox_KN Homeobox_KN
Homeodomain Engrail_1_C_sig
Geminin
HNF-1_N
Homeodomain
PD-C2-AF1
Pou
HSF_DNA-bind HSF_DNA-bind
HTH_1 HTH_1
LysR_substrate
HTH_11 3H
BPL_LplA_LipB
HTH_15 HTH_15
MerB
HTH_18 GyrI-like
HTH_18
RNA_pol_A_CTD
HTH_19 HTH_19
HTH_20 HTH_20
HTH_23 HTH_23
HTH_24 AsnC_trans_reg
HTH_24
HTH_26 HTH_26
HTH_27 HTH_27
HTH_3 Cupin_2
HipA_C
HTH_3
ParBc
SinI
HTH_30 HTH_30
HTH_31 HTH_31
HTH_37 HTH_37
HTH_38 HTH_38
Sugar-bind
HTH_43 HTH_43
HTH_45 HTH_45
HTH_5 HTH_5
HTH_6 HTH_6
SIS
HTH_7 HTH_7
HTH_8 HTH_8
HTH_9 RNA_pol_Rpc82
HTH_AsnC-type HTH_AsnC-type
HTH_CodY HTH_CodY
HTH_Crp_2 cNMP_binding
DUF3539
HTH_Crp_2
HTH_IclR HTH_IclR
IclR
HTH_Mga Mga
HTH_Tnp_1_2 HTH_Tnp_1_2
HTH_Tnp_Mu_1 HTH_Tnp_Mu_2
HTH_Tnp_Tc3_2 HTH_Tnp_Tc3_2
HxlR HxlR
IBD IBD
IclR HTH_IclR
IRF bZIP_1
IRF
RHD_DNA_bind
KH_2 S10_plectin
KicB KicB
MukE
KorB ParBc
La RRM_1
LacI Peripla_BP_1
LexA_DNA_bind LexA_DNA_bind
Linker_histone Linker_histone
LysR_substrate HTH_1
MAGE SMC_Nse1
MarR MarR
ROK
MarR_2 MarR_2
MBF1 HTH_3
MerB HTH_15
MerR MerR
MerR-DNA-bind
MerR-DNA-bind MerR-DNA-bind
TipAS
MerR_2 DnaJ
Methyltransf_2 Dimerisation
MHC_I MAGE
MogR_DNAbind MogR_DNAbind
MotA_activ MotA_activ
MreB_Mbl HTH_25
MukB KicB
MukE
MukE KicB
MukE
Myb_DNA-bind_6 Myb_DNA-bind_6
NFRKB_winged NFRKB_winged
NIR_SIR DsrC
OST-HTH OST-HTH
P22_Cro P22_Cro
PaaX PaaX_C
PadR PadR
Vir_act_alpha_C
PapB PapB
ParBc HTH_3
KorB
PAS_9 GerE
PAX Ets
PCI DSS1_SEM1
MitMem_reg
PCI
Rpn3_C
SAC3_GANP
PCNA_C CDC27
RNase_H2-Ydr279
PCNA_N CDC27
RNase_H2-Ydr279
Penicillinase_R Penicillinase_R
Peripla_BP_1 LacI
Peripla_BP_3 HTH_AraC
Phage_CII Phage_CII
Phage_Nu1 Phage_Nu1
Pou HMG_box
Homeodomain
PD-C2-AF1
Pou
Pox_D5 Pox_D5
Pribosyltran PuR_N
Pterin_4a HNF-1_N
PuR_N Pribosyltran
PuR_N
Put_DNA-bind_N CoA_binding
Put_DNA-bind_N
Rep_3 Rep_3
Rep_fac-A_3 RPA_C
Resolvase HTH_7
Response_reg GerE
HTH_8
Trans_reg_C
RFX_DNA_binding RFXA_RFXANK_bdg
RHD_DNA_bind Forkhead
Ribosomal_S11 Ribosomal_S18
Ribosomal_S13 Ribosomal_S19e
Ribosomal_S25
Ribosomal_S14 S10_plectin
Ribosomal_S18 KOW
Ribosomal_S21
Ribosomal_S6
RMF
Ribosomal_S19e Ribosomal_S7
Ribosomal_S9
Ribosomal_S25 EFG_C
GTP_EFTU
GTP_EFTU_D2
Ribosomal_S13
Ribosomal_S7
Ribosomal_S27 Ribosomal_S25
Ribosomal_S6 Ribosomal_S18
Ribosomal_S7 Ribosomal_S25
Ribosomal_S9 Ribosomal_S19e
Ribosomal_S25
Rio2_N RIO1
RNA_pol_A_CTD Sigma70_r4
RNA_pol_Rpb1_1 Sigma70_ner
Sigma70_r2
Sigma70_r3
Sigma70_r4
RNA_pol_Rpb1_2 Sigma70_r3
RNA_pol_Rpb2_1 CarD_CdnL_TRCF
Sigma70_r3
RNA_pol_Rpb2_6 Sigma70_r3
Sigma70_r4
RNA_pol_Rpb2_7 Sigma70_r3
RNase_H2-Ydr279 PCNA_N
RNase_H2-Ydr279
RNase_H2_suC
RNase_HII RNase_H2-Ydr279
RPA_C Rep_fac-A_3
Rep_fac-A_C
RPA_C
T_Ag_DNA_bind
RPN7 PCI
RQC DEAD
Helicase_C
Rrf2 Rrf2
Rsd_AlgQ Sigma70_r4
RseA_N Sigma70_r2
Sigma70_r4_2
RTP RTP
RuvB_C RuvB_C
RuvB_N RuvB_C
S10_plectin HABP4_PAI-RBP1
KH_2
Ribosomal_L7Ae
Ribosomal_S14
Ribosomal_S7e
SAC3_GANP DSS1_SEM1
PCI
SbcCD_C MukE
SBP_bac_1 Homeodomain
SelB-wing_1 SelB-wing_2
Sigma70_ner Sigma70_r2
Sigma70_r1_2 Sigma70_ner
Sigma70_r2
Sigma70_r3
Sigma70_r2 Cupin_7
FlgM
RseA_N
Sigma70_r2
Sigma70_r3
Sigma70_r4
zf-HC2
Sigma70_r3 FlgM
Sigma70_r1_2
Sigma70_r2
Sigma70_r3
Sigma70_r4
Sigma70_r4 Cupin_7
FlgM
HTH_3
Sigma70_r2
Sigma70_r4
TFX_C
zf-HC2
Sigma70_r4_2 RseA_N
Sigma70_r4_2
Ski_Sno Ski_Sno
SLIDE WHIM1
SMC_Nse1 zf-RING-like
SMC_ScpA SMC_ScpB
SMC_ScpB SMC_ScpB
Snf7 ESCRT-II
SRF-TF Ets
Homeodomain
SRP19 7tm_1
SRP19
SRP_SPB
SRP54 SRP_SPB
SRP54_N SRP_SPB
SRP_SPB 7tm_1
Ribosomal_L22
Ribosomal_L23
SRP54
SRP54_N
SRP_SPB
Sugar-bind HTH_38
SWIRM Amino_oxidase
Tau95 TFIIIC_sub6
TEA TEA
TetR_C_1 TetR_N
TetR_C_2 TetR_N
TetR_C_33 TetR_N
TetR_C_4 TetR_N
TetR_C_5 TetR_N
TetR_C_6 TetR_N
TetR_N CecR_C
TetR
TetR_C_1
TetR_C_2
TetR_C_3
TetR_C_33
TetR_C_4
TetR_C_5
TetR_C_6
TetR_N
TFIIE_alpha TF_Zn_Ribbon
TFIIF_alpha FCP1_C
TFIIF_alpha
TFIIF_beta
TFIIF_beta TFIIF_alpha
TFIIF_beta
TIG Forkhead
Tn7_Tnp_TnsA_C Tn7_TnsC_Int
Tn7_Tnp_TnsA_N Tn7_Tnp_TnsA_C
TPR_15 PCI
Trans_reg_C BTAD
FHA
Trans_reg_C
TrmB TrmB
tRNA-synt_2d B5
tRNA_anti-codon STN1_2
Trp_repressor Trp_repressor
ubiquitin Cullin_Nedd8
UPF0122 UPF0122
UTRA GntR
Vg_Tdu TEA
z-alpha z-alpha
zf-HC2 Sigma70_r2
zf-rbx1 Cullin_Nedd8

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the MSD group, to allow us to map Pfam domains onto UniProt three-dimensional structures. The table below shows the mapping between the Pfam families in this clan, the corresponding UniProt entries, and the region of the three-dimensional structures that are available for that sequence.

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