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36  structures 4668  species 0  interactions 23771  sequences 868  architectures

Family: AAA_12 (PF13087)

Summary: AAA domain

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

This is the Wikipedia entry entitled "AAA proteins". More...

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

AAA domain Provide feedback

This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR041679

This domain contains a P-loop motif that is characteristic of the AAA superfamily. Proteins containing this domain are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA [ PUBMED:10322435 , PUBMED:1552844 , PUBMED:16935882 ].

Proteins containing this domain include helicases, such as Dna2 an Nam7. Dna2 is a DNA replication factor with single-stranded DNA-dependent ATPase, ATP-dependent nuclease, (5'-flap endonuclease) and helicase activities [ PUBMED:10880469 , PUBMED:22570407 ]. Nam7 (also known as Upf1) is an ATP-dependent RNA helicase involved in the nonsense-mediated mRNA decay (NMD) pathway [ PUBMED:29236296 ].

This domain can also be found in some virus polyproteins. This domain is also known as HelicC.

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 243 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 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 DBINO DEAD DEAD_2 DLIC DNA_pack_C DNA_pack_N DNA_pol3_delta DNA_pol3_delta2 DnaB_C dNK DO-GTPase1 DO-GTPase2 DUF1611 DUF1726 DUF2075 DUF2326 DUF2478 DUF257 DUF2791 DUF2813 DUF3584 DUF463 DUF5906 DUF6079 DUF815 DUF853 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 GTP_EFTU Gtr1_RagA Guanylate_kin GvpD HDA2-3 Helicase_C Helicase_C_2 Helicase_C_4 Helicase_RecD Herpes_Helicase Herpes_ori_bp Herpes_TK HSA HydF_dimer HydF_tetramer Hydin_ADK IIGP IPPT IPT iSTAND IstB_IS21 KAP_NTPase KdpD Kinase-PPPase Kinesin KTI12 LAP1C Lon_2 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 OPA1_C 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 RhoGAP_pG1_pG2 RHSP RNA12 RNA_helicase Roc RsgA_GTPase RuvB_N SbcCD_C SecA_DEAD Septin Sigma54_activ_2 Sigma54_activat SKI SMC_N SNF2-rel_dom Spore_III_AA Spore_IV_A SRP54 SRPRB SulA Sulfotransfer_1 Sulfotransfer_2 Sulfotransfer_3 Sulfotransfer_4 Sulfotransfer_5 Sulphotransf SWI2_SNF2 T2SSE T4SS-DNA_transf Terminase_1 Terminase_3 Terminase_6N Terminase_GpA Thymidylate_kin TIP49 TK 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
(98)
Full
(23771)
Representative proteomes UniProt
(60461)
RP15
(4681)
RP35
(11538)
RP55
(20391)
RP75
(29138)
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
(98)
Full
(23771)
Representative proteomes UniProt
(60461)
RP15
(4681)
RP35
(11538)
RP55
(20391)
RP75
(29138)
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
(98)
Full
(23771)
Representative proteomes UniProt
(60461)
RP15
(4681)
RP35
(11538)
RP55
(20391)
RP75
(29138)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   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: Jackhmmer:O25195
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 98
Number in full: 23771
Average length of the domain: 192.60 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 15.82 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 199
Family (HMM) version: 8
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 AAA_12 domain has been found. There are 36 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
A0A0G2K7P1 View 3D Structure Click here
A0A0K2WNK1 View 3D Structure Click here
A0A0N7KJL1 View 3D Structure Click here
A0A0N7KTA4 View 3D Structure Click here
A0A0P0VN81 View 3D Structure Click here
A0A0P0VZ57 View 3D Structure Click here
A0A0P0WAJ1 View 3D Structure Click here
A0A0P0WDV7 View 3D Structure Click here
A0A0P0WDV7 View 3D Structure Click here
A0A0P0WDW2 View 3D Structure Click here
A0A0P0WDY1 View 3D Structure Click here
A0A0P0WE98 View 3D Structure Click here
A0A0P0Y4W4 View 3D Structure Click here
A0A0P0Y503 View 3D Structure Click here
A0A0R0EH31 View 3D Structure Click here
A0A0R0EVT1 View 3D Structure Click here
A0A0R0EVT1 View 3D Structure Click here
A0A0R0FU35 View 3D Structure Click here
A0A0R0GQI2 View 3D Structure Click here
A0A0R0IIL5 View 3D Structure Click here
A0A0R0IXD0 View 3D Structure Click here
A0A0R0JI10 View 3D Structure Click here
A0A0R0K131 View 3D Structure Click here
A0A0R4IPD8 View 3D Structure Click here
A0A0U1RS25 View 3D Structure Click here
A0A143ZY29 View 3D Structure Click here
A0A1D6E1M0 View 3D Structure Click here
A0A1D6E1W7 View 3D Structure Click here
A0A1D6EWB9 View 3D Structure Click here
A0A1D6F4A6 View 3D Structure Click here
A0A1D6FS17 View 3D Structure Click here
A0A1D6G1P6 View 3D Structure Click here
A0A1D6GCN3 View 3D Structure Click here
A0A1D6GH93 View 3D Structure Click here
A0A1D6GQJ9 View 3D Structure Click here
A0A1D6GSG6 View 3D Structure Click here
A0A1D6HZL3 View 3D Structure Click here
A0A1D6I7H4 View 3D Structure Click here
A0A1D6IBD8 View 3D Structure Click here
A0A1D6IC41 View 3D Structure Click here
A0A1D6IXA7 View 3D Structure Click here
A0A1D6IXA9 View 3D Structure Click here
A0A1D6JBM7 View 3D Structure Click here
A0A1D6JBM7 View 3D Structure Click here
A0A1D6JP79 View 3D Structure Click here
A0A1D6K4P0 View 3D Structure Click here
A0A1D6K7K7 View 3D Structure Click here
A0A1D6K996 View 3D Structure Click here
A0A1D6KB54 View 3D Structure Click here
A0A1D6KKC2 View 3D Structure Click here
A0A1D6KKC2 View 3D Structure Click here
A0A1D6KWD6 View 3D Structure Click here
A0A1D6MMZ0 View 3D Structure Click here
A0A1D6MSC2 View 3D Structure Click here
A0A1D6NUT5 View 3D Structure Click here
A0A1D6Q257 View 3D Structure Click here
A0A1D8PPB3 View 3D Structure Click here
A0A1D8PT99 View 3D Structure Click here
A0A1P8ASY1 View 3D Structure Click here
A0A1P8AT95 View 3D Structure Click here
A0A1P8BAQ8 View 3D Structure Click here
A0A2R8Q1I5 View 3D Structure Click here
A0A2R8QJS2 View 3D Structure Click here
A0A2R8QMX1 View 3D Structure Click here
A0A5K1K9F2 View 3D Structure Click here
A0A5K1K9F2 View 3D Structure Click here
A1Z9K0 View 3D Structure Click here
A1ZAP7 View 3D Structure Click here
A2AKX3 View 3D Structure Click here
A3KNA0 View 3D Structure Click here
A4HU46 View 3D Structure Click here
A4I4R9 View 3D Structure Click here
B6SFA4 View 3D Structure Click here
B7Z0D7 View 3D Structure Click here
C0P7X4 View 3D Structure Click here
C7G036 View 3D Structure Click here
C7J1S0 View 3D Structure Click here
D3ZG52 View 3D Structure Click here
D3ZH42 View 3D Structure Click here
D3ZUC2 View 3D Structure Click here
D4ADC2 View 3D Structure Click here
D4ADZ6 View 3D Structure Click here
D4AEB3 View 3D Structure Click here
E7FAV9 View 3D Structure Click here
E7FBJ2 View 3D Structure Click here
E9P860 View 3D Structure Click here
F1Q892 View 3D Structure Click here
F1QAI5 View 3D Structure Click here
F1QQV6 View 3D Structure Click here
F1RCY6 View 3D Structure Click here
F4IBK4 View 3D Structure Click here
F4IBK8 View 3D Structure Click here
F4JGH5 View 3D Structure Click here
F4K1G7 View 3D Structure Click here
F4K5V7 View 3D Structure Click here
F4K5W4 View 3D Structure Click here
F4K5W5 View 3D Structure Click here
I1J424 View 3D Structure Click here
I1J9N5 View 3D Structure Click here
I1JB43 View 3D Structure Click here
I1JNF0 View 3D Structure Click here
I1L7B1 View 3D Structure Click here
I1LGX2 View 3D Structure Click here
I1N930 View 3D Structure Click here
I1NCV6 View 3D Structure Click here
K7K5I1 View 3D Structure Click here
K7KYE7 View 3D Structure Click here
K7KZI7 View 3D Structure Click here
K7LRE4 View 3D Structure Click here
K7MEG5 View 3D Structure Click here
K7MPX5 View 3D Structure Click here
O01976 View 3D Structure Click here
O50466 View 3D Structure Click here
O60306 View 3D Structure Click here
O64476 View 3D Structure Click here
O74465 View 3D Structure Click here
O76512 View 3D Structure Click here
O81047 View 3D Structure Click here
O94247 View 3D Structure Click here
O94387 View 3D Structure Click here
O94508 View 3D Structure Click here
P23249 View 3D Structure Click here
P30771 View 3D Structure Click here
P32644 View 3D Structure Click here
P34243 View 3D Structure Click here
P38859 View 3D Structure Click here
P38935 View 3D Structure Click here
P39369 View 3D Structure Click here
P40694 View 3D Structure Click here
P42694 View 3D Structure Click here
P51530 View 3D Structure Click here
Q00416 View 3D Structure Click here
Q09594 View 3D Structure Click here
Q09820 View 3D Structure Click here
Q0D6B1 View 3D Structure Click here
Q0DRG6 View 3D Structure Click here
Q0DYB5 View 3D Structure Click here
Q0IW26 View 3D Structure Click here
Q0IZ90 View 3D Structure Click here
Q0J3D0 View 3D Structure Click here
Q0VGT4 View 3D Structure Click here
Q10RG1 View 3D Structure Click here
Q18633 View 3D Structure Click here
Q1LXK4 View 3D Structure Click here
Q1LXK5 View 3D Structure Click here
Q2G1Q4 View 3D Structure Click here
Q4D7X5 View 3D Structure Click here
Q4DWK2 View 3D Structure Click here
Q4E3J9 View 3D Structure Click here
Q4E556 View 3D Structure Click here
Q54HF3 View 3D Structure Click here
Q54HF4 View 3D Structure Click here
Q54I89 View 3D Structure Click here
Q54P97 View 3D Structure Click here
Q54XT3 View 3D Structure Click here
Q553Q0 View 3D Structure Click here
Q555Z2 View 3D Structure Click here
Q55F22 View 3D Structure Click here
Q55F23 View 3D Structure Click here
Q55F26 View 3D Structure Click here
Q57568 View 3D Structure Click here
Q5A507 View 3D Structure Click here
Q5AAW1 View 3D Structure Click here
Q5ANG6 View 3D Structure Click here
Q5JLH1 View 3D Structure Click here
Q5JLH1 View 3D Structure Click here
Q6DFV5 View 3D Structure Click here
Q6F2U8 View 3D Structure Click here
Q6J5K9 View 3D Structure Click here
Q6NYU2 View 3D Structure Click here
Q6ZQJ5 View 3D Structure Click here
Q75JA0 View 3D Structure Click here
Q7KSN8 View 3D Structure Click here
Q7TP99 View 3D Structure Click here
Q7Z333 View 3D Structure Click here
Q869R3 View 3D Structure Click here
Q86AS0 View 3D Structure Click here
Q86IV6 View 3D Structure Click here
Q86YA3 View 3D Structure Click here
Q8CFQ3 View 3D Structure Click here
Q8GYD9 View 3D Structure Click here
Q8IC35 View 3D Structure Click here
Q8IDH3 View 3D Structure Click here
Q8IIT6 View 3D Structure Click here
Q8IIT6 View 3D Structure Click here
Q8IJU3 View 3D Structure Click here
Q8IRL9 View 3D Structure Click here
Q8L5Y4 View 3D Structure Click here
Q8R151 View 3D Structure Click here
Q92355 View 3D Structure Click here
Q92900 View 3D Structure Click here
Q99MV5 View 3D Structure Click here
Q9BXT6 View 3D Structure Click here
Q9BYK8 View 3D Structure Click here
Q9BYK8 View 3D Structure Click here
Q9EPU0 View 3D Structure Click here
Q9EQN5 View 3D Structure Click here
Q9FJ83 View 3D Structure Click here
Q9FJR0 View 3D Structure Click here
Q9HCE1 View 3D Structure Click here
Q9P2E3 View 3D Structure Click here
Q9SZW3 View 3D Structure Click here
Q9U1Q7 View 3D Structure Click here
Q9U3F2 View 3D Structure Click here
Q9URU2 View 3D Structure Click here
Q9VCB7 View 3D Structure Click here
Q9VUH9 View 3D Structure Click here
Q9VYS3 View 3D Structure Click here
X1WF29 View 3D Structure Click here
X1WF29 View 3D Structure Click here