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756  structures 9998  species 0  interactions 272115  sequences 4309  architectures

Family: Helicase_C (PF00271)

Summary: Helicase conserved C-terminal domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Helicase conserved C-terminal domain Provide feedback

The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001650

Helicases have been classified in 5 superfamilies (SF1-SF5). For the two largest groups, commonly referred to as SF1 and SF2, a total of seven characteristic motifs has been identified [ PUBMED:2546125 ]. These two superfamilies encompass a large number of DNA and RNA helicases from archaea, eubacteria, eukaryotes and viruses.

This entry represents the C-terminal domain found in proteins belonging to the helicase superfamilies 1 and 2. Included in this group is the eukaryotic translation initiation factor 4A (eIF4A), a member of the DEA(D/H)-box RNA helicase family. The structure of the carboxyl-terminal domain of eIF4A has been determined; it has a parallel alpha-beta topology that superimposes, with minor variations, on the structures and conserved motifs of the equivalent domain in other, distantly related helicases [ PUBMED:11087862 ].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan P-loop_NTPase (CL0023), which has the following description:

AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes [2].

The clan contains the following 245 members:

6PF2K AAA AAA-ATPase_like AAA_10 AAA_11 AAA_12 AAA_13 AAA_14 AAA_15 AAA_16 AAA_17 AAA_18 AAA_19 AAA_2 AAA_21 AAA_22 AAA_23 AAA_24 AAA_25 AAA_26 AAA_27 AAA_28 AAA_29 AAA_3 AAA_30 AAA_31 AAA_32 AAA_33 AAA_34 AAA_35 AAA_5 AAA_6 AAA_7 AAA_8 AAA_9 AAA_PrkA ABC_ATPase ABC_tran ABC_tran_Xtn Adeno_IVa2 Adenylsucc_synt ADK AFG1_ATPase AIG1 APS_kinase Arf ArsA_ATPase ATP-synt_ab ATP_bind_1 ATP_bind_2 ATPase ATPase_2 Bac_DnaA BCA_ABC_TP_C Beta-Casp bpMoxR BrxC_BrxD BrxL_ATPase Cas_Csn2 Cas_St_Csn2 CbiA CBP_BcsQ CDC73_C CENP-M CFTR_R CLP1_P CMS1 CoaE CobA_CobO_BtuR CobU cobW CPT CSM2 CTP_synth_N Cytidylate_kin Cytidylate_kin2 DAP3 DEAD DEAD_2 divDNAB DLIC DNA_pack_C DNA_pack_N DNA_pol3_delta DNA_pol3_delta2 DnaB_C dNK DO-GTPase1 DO-GTPase2 DUF1611 DUF2075 DUF2326 DUF2478 DUF257 DUF2813 DUF3584 DUF463 DUF4914 DUF5906 DUF6079 DUF815 DUF835 DUF87 DUF927 Dynamin_N Dynein_heavy Elong_Iki1 ELP6 ERCC3_RAD25_C Exonuc_V_gamma FeoB_N Fer4_NifH Flavi_DEAD FTHFS FtsK_SpoIIIE G-alpha Gal-3-0_sulfotr GBP GBP_C GpA_ATPase GpA_nuclease GTP_EFTU Gtr1_RagA Guanylate_kin GvpD_P-loop HDA2-3 Helicase_C Helicase_C_2 Helicase_C_4 Helicase_RecD HerA_C Herpes_Helicase Herpes_ori_bp Herpes_TK HydF_dimer HydF_tetramer Hydin_ADK IIGP IPPT IPT iSTAND IstB_IS21 KAP_NTPase KdpD Kinase-PPPase Kinesin KTI12 LAP1_C LpxK MCM MeaB MEDS Mg_chelatase Microtub_bd MipZ MMR_HSR1 MMR_HSR1_C MobB MukB Mur_ligase_M MutS_V Myosin_head NACHT NAT_N NB-ARC NOG1 NTPase_1 NTPase_P4 ORC3_N P-loop_TraG ParA Parvo_NS1 PAXNEB PduV-EutP PhoH PIF1 Ploopntkinase1 Ploopntkinase2 Ploopntkinase3 Podovirus_Gp16 Polyoma_lg_T_C Pox_A32 PPK2 PPV_E1_C PRK PSY3 Rad17 Rad51 Ras RecA ResIII RHD3_GTPase RhoGAP_pG1_pG2 RHSP RNA12 RNA_helicase Roc RsgA_GTPase RuvB_N SbcC_Walker_B SecA_DEAD Senescence Septin Sigma54_activ_2 Sigma54_activat SKI SMC_N SNF2-rel_dom SpoIVA_ATPase Spore_III_AA SRP54 SRPRB SulA Sulfotransfer_1 Sulfotransfer_2 Sulfotransfer_3 Sulfotransfer_4 Sulfotransfer_5 Sulphotransf SWI2_SNF2 T2SSE T4SS-DNA_transf TerL_ATPase Terminase_3 Terminase_6N Thymidylate_kin TIP49 TK TmcA_N TniB Torsin TraG-D_C tRNA_lig_kinase TrwB_AAD_bind TsaE UvrB UvrD-helicase UvrD_C UvrD_C_2 Viral_helicase1 VirC1 VirE YqeC Zeta_toxin Zot

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(421)
Full
(272115)
Representative proteomes UniProt
(807618)
RP15
(45798)
RP35
(124378)
RP55
(238299)
RP75
(365087)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(421)
Full
(272115)
Representative proteomes UniProt
(807618)
RP15
(45798)
RP35
(124378)
RP55
(238299)
RP75
(365087)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(421)
Full
(272115)
Representative proteomes UniProt
(807618)
RP15
(45798)
RP35
(124378)
RP55
(238299)
RP75
(365087)
Raw Stockholm Download     Download   Download        
Gzipped Download     Download   Download        

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Published_alignment
Previous IDs: helicase_C;
Type: Domain
Sequence Ontology: SO:0000417
Author: Sonnhammer ELL , Eberhardt R
Number in seed: 421
Number in full: 272115
Average length of the domain: 117.2 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 12.69 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.5 23.5
Trusted cut-off 23.5 23.5
Noise cut-off 23.4 23.4
Model length: 111
Family (HMM) version: 34
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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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 PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Helicase_C domain has been found. There are 756 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A044QLS4 View 3D Structure Click here
A0A044QSY4 View 3D Structure Click here
A0A044R340 View 3D Structure Click here
A0A044R795 View 3D Structure Click here
A0A044R7T5 View 3D Structure Click here
A0A044R9U0 View 3D Structure Click here
A0A044RDT9 View 3D Structure Click here
A0A044REY8 View 3D Structure Click here
A0A044RFE1 View 3D Structure Click here
A0A044RGV7 View 3D Structure Click here
A0A044RH56 View 3D Structure Click here
A0A044RHY8 View 3D Structure Click here
A0A044RKK3 View 3D Structure Click here
A0A044S261 View 3D Structure Click here
A0A044S5D8 View 3D Structure Click here
A0A044S702 View 3D Structure Click here
A0A044S759 View 3D Structure Click here
A0A044SEX9 View 3D Structure Click here
A0A044SF33 View 3D Structure Click here
A0A044SGP8 View 3D Structure Click here
A0A044SGY4 View 3D Structure Click here
A0A044SHS3 View 3D Structure Click here
A0A044SKU1 View 3D Structure Click here
A0A044SQ82 View 3D Structure Click here
A0A044SRH8 View 3D Structure Click here
A0A044SSK0 View 3D Structure Click here
A0A044ST80 View 3D Structure Click here
A0A044T0S0 View 3D Structure Click here
A0A044T0V6 View 3D Structure Click here
A0A044T5L8 View 3D Structure Click here
A0A044TET3 View 3D Structure Click here
A0A044TLK9 View 3D Structure Click here
A0A044U202 View 3D Structure Click here
A0A044U482 View 3D Structure Click here
A0A044UC07 View 3D Structure Click here
A0A044UGH5 View 3D Structure Click here
A0A044UJ42 View 3D Structure Click here
A0A044UQB4 View 3D Structure Click here
A0A044URA8 View 3D Structure Click here
A0A044US53 View 3D Structure Click here