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2812  structures 10949  species 97  interactions 1020775  sequences 5699  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 202 families and the total number of domains in the clan is 1020775. 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 202 member families:

AphA_like Arg_repressor B-block_TFIIIC Bac_DnaA_C BetR Bot1p BrkDBD CENP-B_N Cro Crp DDRGK Dimerisation DUF1133 DUF1153 DUF1323 DUF134 DUF1441 DUF1492 DUF1495 DUF1670 DUF1804 DUF1836 DUF1870 DUF2089 DUF2250 DUF2316 DUF3116 DUF3853 DUF387 DUF3908 DUF4095 DUF4364 DUF739 DUF742 DUF977 E2F_TDP ELK Ets Exc F-112 FaeA Fe_dep_repr_C Fe_dep_repress FeoC Ftsk_gamma FUR GcrA GerE GntR HARE-HTH HemN_C Homeobox Homeobox_KN Homez 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_5 HTH_6 HTH_7 HTH_8 HTH_9 HTH_AraC HTH_AsnC-type HTH_CodY HTH_Crp_2 HTH_DeoR HTH_IclR HTH_Mga HTH_OrfB_IS605 HTH_psq 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 IF2_N KorB LacI LexA_DNA_bind LZ_Tnp_IS481 MADF_DNA_bdg MarR MarR_2 Med9 MerR MerR-DNA-bind MerR_1 MerR_2 Mga Mnd1 Mor MotA_activ MRP-L20 Myb_DNA-bind_2 Myb_DNA-bind_3 Myb_DNA-bind_4 Myb_DNA-bind_5 Myb_DNA-bind_6 Myb_DNA-binding Neugrin NUMOD1 OST-HTH P22_Cro PaaX PadR PAX PCI PCI_Csn8 Penicillinase_R Phage_AlpA Phage_antitermQ Phage_CI_repr Phage_CII Phage_rep_org_N Phage_terminase Pou Pox_D5 PuR_N Put_DNA-bind_N Rap1-DNA-bind Rep_3 RepA_C RepA_N RepC RepL Replic_Relax RFX_DNA_binding Ribosomal_S25 Rio2_N RNA_pol_Rpc34 RP-C RPA RPA_C RQC Rrf2 RTP SAC3_GANP SgrR_N Sigma54_CBD Sigma54_DBD Sigma70_ECF Sigma70_r2 Sigma70_r3 Sigma70_r4 Sigma70_r4_2 SpoIIID Sulfolobus_pRN TBPIP Terminase_5 TetR_N TFIIE_alpha Tn916-Xis Trans_reg_C TrfA TrmB Trp_repressor UPF0122 z-alpha

External database links

Domain organisation

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

Loading domain graphics...

Alignments

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

Pfam family Num. domains Alignment
HTH_1 (PF00126) 86700 (8.5%) View
TetR_N (PF00440) 63222 (6.2%) View
HTH_18 (PF12833) 57814 (5.7%) View
Trans_reg_C (PF00486) 52522 (5.1%) View
GntR (PF00392) 49014 (4.8%) View
Sigma70_r2 (PF04542) 39743 (3.9%) View
GerE (PF00196) 38873 (3.8%) View
HTH_3 (PF01381) 36941 (3.6%) View
LacI (PF00356) 29289 (2.9%) View
Homeobox (PF00046) 25115 (2.5%) View
Sigma70_r4_2 (PF08281) 24630 (2.4%) View
MarR (PF01047) 19890 (1.9%) View
HTH_8 (PF02954) 19848 (1.9%) View
MerR_1 (PF13411) 18606 (1.8%) View
Sigma70_r4 (PF04545) 17028 (1.7%) View
HTH_DeoR (PF08220) 15183 (1.5%) View
HTH_19 (PF12844) 14559 (1.4%) View
HTH_Tnp_1 (PF01527) 12930 (1.3%) View
Myb_DNA-binding (PF00249) 12500 (1.2%) View
HTH_11 (PF08279) 12449 (1.2%) View
HTH_24 (PF13412) 12234 (1.2%) View
HTH_IclR (PF09339) 11639 (1.1%) View
HTH_21 (PF13276) 11498 (1.1%) View
MarR_2 (PF12802) 11347 (1.1%) View
Sigma70_r3 (PF04539) 10957 (1.1%) View
HTH_31 (PF13560) 10133 (1.0%) View
HTH_20 (PF12840) 9773 (1.0%) View
HTH_6 (PF01418) 9722 (1.0%) View
FUR (PF01475) 9302 (0.9%) View
HTH_5 (PF01022) 9132 (0.9%) View
PadR (PF03551) 8479 (0.8%) View
HTH_Crp_2 (PF13545) 8343 (0.8%) View
HxlR (PF01638) 8192 (0.8%) View
Rrf2 (PF02082) 8068 (0.8%) View
HTH_17 (PF12728) 7911 (0.8%) View
IF2_N (PF04760) 7695 (0.8%) View
HTH_28 (PF13518) 5836 (0.6%) View
Mga (PF05043) 5627 (0.6%) View
HTH_AsnC-type (PF13404) 5527 (0.5%) View
HTH_30 (PF13556) 5435 (0.5%) View
HemN_C (PF06969) 5381 (0.5%) View
Ftsk_gamma (PF09397) 5039 (0.5%) View
Bac_DnaA_C (PF08299) 4828 (0.5%) View
HTH_26 (PF13443) 4823 (0.5%) View
Myb_DNA-bind_6 (PF13921) 4769 (0.5%) View
PCI (PF01399) 4727 (0.5%) View
HTH_38 (PF13936) 4579 (0.4%) View
Arg_repressor (PF01316) 4229 (0.4%) View
Homeobox_KN (PF05920) 3978 (0.4%) View
HTH_OrfB_IS605 (PF12323) 3827 (0.4%) View
HTH_7 (PF02796) 3816 (0.4%) View
HTH_29 (PF13551) 3523 (0.3%) View
LexA_DNA_bind (PF01726) 3433 (0.3%) View
Fe_dep_repr_C (PF02742) 3389 (0.3%) View
Fe_dep_repress (PF01325) 3362 (0.3%) View
HTH_Tnp_ISL3 (PF13542) 3356 (0.3%) View
RQC (PF09382) 3296 (0.3%) View
MerR (PF00376) 3063 (0.3%) View
DUF387 (PF04079) 3001 (0.3%) View
HTH_25 (PF13413) 2987 (0.3%) View
Penicillinase_R (PF03965) 2958 (0.3%) View
Phage_AlpA (PF05930) 2885 (0.3%) View
Sigma54_CBD (PF04963) 2858 (0.3%) View
Sigma54_DBD (PF04552) 2839 (0.3%) View
MerR-DNA-bind (PF09278) 2740 (0.3%) View
HTH_23 (PF13384) 2487 (0.2%) View
Ets (PF00178) 2375 (0.2%) View
Crp (PF00325) 2310 (0.2%) View
KorB (PF08535) 2280 (0.2%) View
DUF4095 (PF13338) 2088 (0.2%) View
HTH_Tnp_Tc5 (PF03221) 2088 (0.2%) View
HTH_27 (PF13463) 2080 (0.2%) View
Rep_3 (PF01051) 2007 (0.2%) View
HSF_DNA-bind (PF00447) 1989 (0.2%) View
HTH_WhiA (PF02650) 1969 (0.2%) View
HTH_22 (PF13309) 1886 (0.2%) View
Myb_DNA-bind_4 (PF13837) 1844 (0.2%) View
HTH_36 (PF13730) 1833 (0.2%) View
Put_DNA-bind_N (PF06971) 1817 (0.2%) View
SgrR_N (PF12793) 1737 (0.2%) View
HTH_Tnp_IS630 (PF01710) 1697 (0.2%) View
OST-HTH (PF12872) 1690 (0.2%) View
ELK (PF03789) 1671 (0.2%) View
TrmB (PF01978) 1668 (0.2%) View
HTH_42 (PF06224) 1653 (0.2%) View
PAX (PF00292) 1629 (0.2%) View
Trp_repressor (PF01371) 1612 (0.2%) View
HTH_Tnp_4 (PF13613) 1593 (0.2%) View
HARE-HTH (PF05066) 1524 (0.1%) View
MADF_DNA_bdg (PF10545) 1496 (0.1%) View
UPF0122 (PF04297) 1476 (0.1%) View
E2F_TDP (PF02319) 1416 (0.1%) View
Pou (PF00157) 1357 (0.1%) View
HTH_Tnp_IS1 (PF12759) 1328 (0.1%) View
HTH_psq (PF05225) 1317 (0.1%) View
RepA_N (PF06970) 1268 (0.1%) View
HTH_Tnp_Tc3_2 (PF01498) 1241 (0.1%) View
DUF1836 (PF08876) 1171 (0.1%) View
PuR_N (PF09182) 1165 (0.1%) View
HTH_37 (PF13744) 1158 (0.1%) View
HTH_40 (PF14493) 1114 (0.1%) View
SAC3_GANP (PF03399) 1100 (0.1%) View
continued
Pfam family Num. domains Alignment
HTH_CodY (PF08222) 1097 (0.1%) View
Pox_D5 (PF03288) 1059 (0.1%) View
HrcA_DNA-bdg (PF03444) 1056 (0.1%) View
HTH_12 (PF08461) 1050 (0.1%) View
HTH_35 (PF13693) 1007 (0.1%) View
HTH_Mga (PF08280) 958 (0.1%) View
DUF1323 (PF07037) 925 (0.1%) View
MerR_2 (PF13591) 920 (0.1%) View
Dimerisation (PF08100) 919 (0.1%) View
Phage_antitermQ (PF06530) 887 (0.1%) View
Terminase_5 (PF06056) 859 (0.1%) View
Myb_DNA-bind_3 (PF12776) 836 (0.1%) View
HTH_10 (PF04967) 808 (0.1%) View
FeoC (PF09012) 803 (0.1%) View
HTH_33 (PF13592) 787 (0.1%) View
Mor (PF08765) 765 (0.1%) View
P22_Cro (PF14549) 735 (0.1%) View
RFX_DNA_binding (PF02257) 732 (0.1%) View
DUF742 (PF05331) 710 (0.1%) View
Phage_CI_repr (PF07022) 693 (0.1%) View
HTH_32 (PF13565) 664 (0.1%) View
DUF977 (PF06163) 656 (0.1%) View
PaaX (PF07848) 652 (0.1%) View
Phage_rep_org_N (PF09681) 638 (0.1%) View
PCI_Csn8 (PF10075) 621 (0.1%) View
HTH_16 (PF12645) 618 (0.1%) View
Ribosomal_S25 (PF03297) 591 (0.1%) View
DUF134 (PF02001) 568 (0.1%) View
HTH_34 (PF13601) 545 (0.1%) View
Myb_DNA-bind_5 (PF13873) 544 (0.1%) View
TFIIE_alpha (PF02002) 544 (0.1%) View
CENP-B_N (PF04218) 534 (0.1%) View
Phage_CII (PF05269) 497 (0.0%) View
RP-C (PF03428) 484 (0.0%) View
HTH_AraC (PF00165) 482 (0.0%) View
GcrA (PF07750) 480 (0.0%) View
Tn916-Xis (PF09035) 457 (0.0%) View
Rio2_N (PF09202) 449 (0.0%) View
DUF1870 (PF08965) 448 (0.0%) View
HTH_Tnp_Mu_1 (PF02316) 448 (0.0%) View
LZ_Tnp_IS481 (PF13011) 445 (0.0%) View
Replic_Relax (PF13814) 432 (0.0%) View
RNA_pol_Rpc34 (PF05158) 415 (0.0%) View
SpoIIID (PF12116) 411 (0.0%) View
RPA (PF10134) 404 (0.0%) View
DUF1441 (PF07278) 388 (0.0%) View
RPA_C (PF08784) 349 (0.0%) View
RepL (PF05732) 349 (0.0%) View
DUF1492 (PF07374) 341 (0.0%) View
HTH_41 (PF14502) 338 (0.0%) View
z-alpha (PF02295) 330 (0.0%) View
NUMOD1 (PF07453) 326 (0.0%) View
B-block_TFIIIC (PF04182) 324 (0.0%) View
FaeA (PF04703) 310 (0.0%) View
HTH_43 (PF09904) 301 (0.0%) View
DUF2089 (PF09862) 297 (0.0%) View
HTH_45 (PF14947) 290 (0.0%) View
Exc (PF07825) 289 (0.0%) View
HTH_9 (PF08221) 285 (0.0%) View
DUF1133 (PF06576) 284 (0.0%) View
DUF1153 (PF06627) 282 (0.0%) View
Mnd1 (PF03962) 274 (0.0%) View
DUF2316 (PF10078) 273 (0.0%) View
TBPIP (PF07106) 266 (0.0%) View
Sigma70_ECF (PF07638) 258 (0.0%) View
HTH_39 (PF14090) 254 (0.0%) View
DUF4364 (PF14277) 224 (0.0%) View
Neugrin (PF06413) 219 (0.0%) View
Phage_terminase (PF10668) 212 (0.0%) View
DDRGK (PF09756) 209 (0.0%) View
RepA_C (PF04796) 189 (0.0%) View
Med9 (PF07544) 187 (0.0%) View
TrfA (PF07042) 183 (0.0%) View
BetR (PF08667) 180 (0.0%) View
Bot1p (PF12298) 175 (0.0%) View
HTH_13 (PF11972) 171 (0.0%) View
Homez (PF11569) 166 (0.0%) View
Myb_DNA-bind_2 (PF08914) 164 (0.0%) View
HTH_Tnp_Tc3_1 (PF11427) 160 (0.0%) View
MRP-L20 (PF12824) 157 (0.0%) View
DUF1804 (PF08822) 154 (0.0%) View
Cro (PF09048) 146 (0.0%) View
HTH_Tnp_Mu_2 (PF09039) 131 (0.0%) View
HTH_15 (PF12324) 128 (0.0%) View
DUF3116 (PF11313) 124 (0.0%) View
BrkDBD (PF09607) 116 (0.0%) View
RepC (PF06504) 105 (0.0%) View
DUF2250 (PF10007) 100 (0.0%) View
DUF3908 (PF13048) 99 (0.0%) View
DUF3853 (PF12964) 97 (0.0%) View
DUF739 (PF05339) 78 (0.0%) View
DUF1495 (PF07381) 58 (0.0%) View
RTP (PF02334) 54 (0.0%) View
Rap1-DNA-bind (PF09197) 53 (0.0%) View
DUF1670 (PF07900) 52 (0.0%) View
Sulfolobus_pRN (PF05584) 48 (0.0%) View
HTH_Tnp_1_2 (PF13022) 30 (0.0%) View
MotA_activ (PF09114) 22 (0.0%) View
AphA_like (PF14557) 13 (0.0%) View
F-112 (PF09645) 4 (0.0%) View
Total: 202 Total: 1020775 Clan alignment
 

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Family relationships

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

We could not retrieve a family relationship diagram for this clan.

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 97 interactions for this clan. More...

Interacting families
A B
HTH_5 HTH_5
Myb_DNA-binding Myb_DNA-binding
Amino_oxidase
HTH_IclR IclR
HTH_IclR
HTH_1 HTH_1
LysR_substrate
GerE Response_reg
GerE
HxlR HxlR
HTH_11 AsnC_trans_reg
BPL_LplA_LipB
HTH_11
Dimerisation Methyltransf_2
Phage_CII Phage_CII
HTH_8 HTH_8
HemN_C Radical_SAM
Bac_DnaA_C Bac_DnaA
Arg_repressor Arg_repressor
Arg_repressor_C
RQC DEAD
Cro Cro
PAX Ets
Penicillinase_R Penicillinase_R
MerR MerR-DNA-bind
TetR_N TetR_N
TetR_C
TetR_C_4
TetR_C_5
TetR_C_2
TetR_C_3
DUF1956
Trp_repressor Trp_repressor
HTH_3 HTH_3
Cupin_2
SinI
Ets Ets
SRF-TF
Crp cNMP_binding
MarR MarR
UPF0122 UPF0122
Trans_reg_C Response_reg
Trans_reg_C
FHA
BTAD
Fe_dep_repr_C Fe_dep_repress
Fe_dep_repr_C
FeoA
Rrf2 Rrf2
RTP RTP
Sigma70_r4_2 RseA_N
Sigma70_r4_2
FUR FUR
Sigma70_r3 RNA_pol_Rpb2_6
RNA_pol_Rpb1_2
Sigma70_r2
Sigma70_r4
RNA_pol_Rpb2_7
RNA_pol_Rpb2_1
RNA_pol_Rpb1_1
Put_DNA-bind_N CoA_binding
Put_DNA-bind_N
Pou Homeobox
Pou
HMG_box
DUF1870 DUF1870
Homeobox Homeobox
Pou
E2F_TDP E2F_TDP
GntR GntR
FCD
FadR_C
PadR Vir_act_alpha_C
PuR_N Pribosyltran
PuR_N
Sigma70_r2 Sigma70_r1_2
RseA_N
FlgM
Sigma70_r3
Sigma70_r2
Sigma70_r4
RNA_pol_Rpb1_1
MerR-DNA-bind MerR
MerR-DNA-bind
HTH_CodY HTH_CodY
TrmB TrmB
Fe_dep_repress Fe_dep_repress
Fe_dep_repr_C
FeoA
Sigma70_r4 RNA_pol_Rpb2_6
FlgM
Rsd_AlgQ
Sigma70_r3
Sigma70_r2
Sigma70_r4
RNA_pol_Rpb1_1
AsiA

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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