Entry: AAA (PF00004)

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Very fast search for clan entries. The
search can be done either by clan ID
(e.g. CL0192) or by clan name (e.g. GPCR_A).

Pfam summary


ATPase family associated with various cellular activities (AAA)

AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes [2].
Literature1. Confalonieri F, Duguet M; Bioessays 1995;17:639-650.A 200-amino acid ATPase module in search of a basic function. PUBMED:7646486
2. Neuwald AF, Aravind L, Spouge JL, Koonin EV; Genome Res 1999;9:27-43.AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. PUBMED:9927482

CL0023 (AAA)

The clan contains the following members: PF00004(AAA); PF03029(ATP_bind_1); PF02492(cobW); PF00270(DEAD); PF03796(DnaB_C); PF05127(DUF699); PF00009(GTP_EFTU); PF00271(Helicase_C); PF00225(Kinesin); PF03354(Terminase_1); PF02463(SMC_N); PF00448(SRP54); PF00685(Sulfotransfer_1); PF03567(Sulfotransfer_2); PF01591(6PF2K); PF00005(ABC_tran); PF02456(Adeno_IVa2); PF00709(Adenylsucc_synt); PF00406(ADK); PF03969(AFG1_ATPase); PF04548(AIG1); PF01583(APS_kinase); PF01637(Arch_ATPase); PF00025(Arf); PF03308(ArgK); PF02374(ArsA_ATPase); PF00006(ATP-synt_ab); PF00308(Bac_DnaA); PF01656(CbiA); PF01121(CoaE); PF02572(CobA_CobO_BtuR); PF02283(CobU); PF02224(Cytidylate_kin); PF02499(DNA_pack_C); PF02500(DNA_pack_N); PF01712(dNK); PF03193(DUF258); PF03237(DUF264); PF03266(DUF265); PF03976(PPK2); PF01935(DUF87); PF00350(Dynamin_N); PF00519(PPV_E1_C); PF04257(Exonuc_V_gamma); PF02421(FeoB_N); PF00142(Fer4_NifH); PF01268(FTHFS); PF01580(FtsK_SpoIIIE); PF00503(G-alpha); PF04466(Terminase_3); PF02263(GBP); PF00437(GSPII_E); PF00735(GTP_CDC); PF04670(Gtr1_RagA); PF00625(Guanylate_kin); PF02689(Herpes_Helicase); PF02399(Herpes_ori_bp); PF05049(IIGP); PF01715(IPPT); PF01745(IPT); PF01695(IstB); PF02606(LpxK); PF00493(MCM); PF01078(Mg_chelatase); PF01926(MMR_HSR1); PF03205(MobB); PF00488(MutS_V); PF00063(Myosin_head); PF00931(NB-ARC); PF01057(Parvo_NS1); PF02562(PhoH); PF04665(Pox_A32); PF00485(PRK); PF03215(Rad17); PF00071(Ras); PF00154(RecA); PF04851(ResIII); PF00910(RNA_helicase); PF00158(Sigma54_activat); PF01202(SKI); PF00176(SNF2_N); PF02223(Thymidylate_kin); PF00265(TK); PF00693(Herpes_TK); PF02534(TraG); PF03668(ATP_bind_2); PF02367(UPF0079); PF00580(UvrD-helicase); PF01443(Viral_helicase1); PF05496(RuvB_N); PF05621(TniB); PF05625(PAXNEB); PF05673(DUF815); PF05707(Zot); PF05729(NACHT); PF05783(DLIC); PF05872(DUF853); PF05876(Terminase_GpA); PF05879(RHD3); PF05894(Podovirus_Gp16); PF05970(DUF889); PF06068(TIP49); PF06144(DNA_pol3_delta); PF06309(Torsin); PF06414(Zeta_toxin); PF06418(CTP_synth_N); PF06431(Polyoma_lg_T_C); PF06733(DEAD_2); PF06745(KaiC); PF06858(NOG1); PF06862(DUF1253); PF06990(Gal-3-0_sulfotr); PF07015(VirC1); PF07088(GvpD); PF07517(SecA_DEAD); PF07652(Flavi_DEAD); PF07693(KAP_NTPase); PF07724(AAA_2); PF07726(AAA_3); PF07728(AAA_5); PF07755(DUF1611); PF07931(CPT);
InterPro entry IPR003959


New Hampshire tree

The seed alignment for this family in the PANDIT database contains 245 aligned sequences:

  AFG2_YEAST/281-470   AFG2_YEAST/552-737   AFG3_YEAST/323-518   BCS1_SCHPO/244-422   BCS1_YEAST/262-444   CD48B_ARATH/322-510   CD48B_ARATH/58-248   CDAT_PLAF7/563-747   CDC48_SOYBN/517-704   CDC48_YEAST/523-710   CDC6_HUMAN/197-403   CDCH_HALSA/225-409   CDCH_HALSA/498-683   CLPA_ECOLI/209-403   CLPB_AQUAE/335-528   CLPB_HELPY/199-392   CLPB_MYCPN/55-240   CLPB_RICPR/202-396   CLPX_AQUAE/112-363   CLPX_BACSU/111-358   CLPX_BORBU/112-285   CLPX_CHLTR/116-322   CLPX_HAEIN/112-366   CLPX_HUMAN/288-485   CLPX_MYCTU/116-323   CLPX_SYNP7/141-349   CLPX_SYNY3/136-368   CLPX_TREPA/112-331   DPA4_BPR69/45-217   DPA4_BPT4/45-217   FTSH1_ARATH/297-484   FTSH1_HAEIN/186-373   FTSH2_SYNY3/246-433   FTSH3_SYNY3/209-398   FTSH_AQUAE/190-378   FTSH_HELPY/205-394   FTSH_LACLA/228-416   FTSH_MYCLE/198-385   FTSH_MYCPN/263-450   FTSH_ODOSI/221-408   FTSH_RICPR/190-377   FTSH_TREPA/176-362   LON1_BACSU/349-544   LON1_MAIZE/404-599   LON1_MYXXA/363-558   LON2_BACSU/92-318   LON2_BORBU/364-559   LON2_MAIZE/450-645   LON2_MYXXA/373-568   LON_AQUAE/365-560   LON_BORBU/384-579   More...

The full alignment for this family in the Pfam database contains 24097 aligned sequences

Species in the seed alignment

List of species covered in the seed alignment. The number in brackets denotes the number of sequences taken from each organism.

  Saccharomyces cerevisiae (24);   Arabidopsis thaliana (18);   Schizosaccharomyces pombe (17);   Caenorhabditis elegans (15);   Homo sapiens (13);   Archaeoglobus fulgidus (7);   Mycobacterium tuberculosis (7);   Borrelia burgdorferi (6);   Bacillus subtilis (6);   Treponema pallidum (5);   Mus musculus (5);   Rickettsia prowazekii (5);   Synechocystis sp. PCC 6803 (5);   Drosophila melanogaster (5);   Aquifex aeolicus (4);   Mycobacterium leprae (4);   Methanocaldococcus jannaschii (4);   Methanothermobacter thermautotrophicus str. Delta H (4);   Haemophilus influenzae (4);   Pyrococcus horikoshii (4);   Rattus norvegicus (3);   Xenopus laevis (3);   Helicobacter pylori J99 (3);   Helicobacter pylori (3);   Escherichia coli K12 (3);   Chlamydia trachomatis (3);   Mycoplasma pneumoniae (3);   Halobacterium salinarum (2);   Bacillus cereus (2);   Sulfolobus acidocaldarius (2);   Chlamydophila pneumoniae (2);   Myxococcus xanthus (2);   Odontella sinensis (2);   Yarrowia lipolytica (2);   Thermoplasma acidophilum (2);   Pichia pastoris (2);   Plasmodium falciparum 3D7 (2);   Strongylocentrotus purpuratus (2);   Zea mays (2);   Loligo pealei (1);   Marchantia polymorpha (1);   Coxiella burnetii (1);   Enterobacteria phage T4 (1);   Glycine max (1);   Thermotoga maritima (1);   Synechococcus elongatus PCC 7942 (1);   Candida albicans (1);   Mycoplasma genitalium (1);   Phaseolus vulgaris (1);   Bacillus sp. (1);   Streptomyces coelicolor (1);   More...

The full alignment covers 1576 species.

Pre-computed estimates from Markov codon substitution models (explanation)

Following are maximum-likelihood estimates and log-likelihood scores from codon models M0, M1, M2, M7 and M8, implemented in PAML v.4.1

Model name  

Model M0

Model M1

Model M2

Model M7

Model M8

Log-likelihood score  


Tree Length  





ω=0.01198p0=0.966645 ~ ω0=0.012395
p1=0.033355 ~ ω1=1
p0=0.966691 ~ ω0=0.012394
p1=0.033309 ~ ω1=1
p2=0 ~ ω2=25.801053
ω~Β(1.043901,75.708602)p0=0.999999 ~ ω~Β(1.043907,75.708957)
p1=1e-06 ~ ω=1.861012

P-value for testing  
positive selection  

M1 vs M2: P-value=1
family classification: conserved
M7 vs M8: P-value=1
family classification: conserved

Maximum-likelihood estimates and log-likelihood scores from codon models Nonsynonymous and Dual implemented in HYPHY

Model name  

Model Nonsynonymous

Model Dual

Log-likelihood score  


Mean ω-ratio  

ω = 0.94175ω = 1.28927

Coeff. of variation  
of ω-ratio  

CVω = 0.54765CVω = 1.01893


InteractionsThis family has 13 known interactions:
PF00004; PF01434; PF02359; PF02861; PF02933; PF05491; PF05496; PF06068; PF06144; PF07499; PF07724; PF08542; PF09336;

StructuresThis family has 247 structures:
Notation: PDB_ID (PDB chain, PDB residues)

Gene Ontologies
Molecular Function
 ATP binding[GO:0005524]

KEGG Pathways - for genes coding for sequences from full alignment
Carbohydrate Metabolism
Glycolysis / Gluconeogenesis [KEGG]
Pentose phosphate pathway [KEGG]
Pentose and glucuronate interconversions [KEGG]
Fructose and mannose metabolism [KEGG]
Galactose metabolism [KEGG]
Ascorbate and aldarate metabolism [KEGG]
Starch and sucrose metabolism [KEGG]
Nucleotide sugars metabolism [KEGG]
Aminosugars metabolism [KEGG]
Inositol phosphate metabolism [KEGG]
Pyruvate metabolism [KEGG]
Glyoxylate and dicarboxylate metabolism [KEGG]
Butanoate metabolism [KEGG]
Energy Metabolism
Oxidative phosphorylation [KEGG]
Photosynthesis [KEGG]
Methane metabolism [KEGG]
Carbon fixation in photosynthetic organisms [KEGG]
Reductive carboxylate cycle (CO2 fixation) [KEGG]
Nitrogen metabolism [KEGG]
Sulfur metabolism [KEGG]
Lipid Metabolism
Fatty acid biosynthesis [KEGG]
Nucleotide Metabolism
Purine metabolism [KEGG]
Pyrimidine metabolism [KEGG]
Amino Acid Metabolism
Glutamate metabolism [KEGG]
Alanine and aspartate metabolism [KEGG]
Glycine, serine and threonine metabolism [KEGG]
Lysine biosynthesis [KEGG]
Lysine degradation [KEGG]
Arginine and proline metabolism [KEGG]
Phenylalanine metabolism [KEGG]
Phenylalanine, tyrosine and tryptophan biosynthesis [KEGG]
Metabolism of Other Amino Acids
beta-Alanine metabolism [KEGG]
Selenoamino acid metabolism [KEGG]
D-Glutamine and D-glutamate metabolism [KEGG]
Glutathione metabolism [KEGG]
Glycan Biosynthesis and Metabolism
Lipopolysaccharide biosynthesis [KEGG]
Peptidoglycan biosynthesis [KEGG]
Metabolism of Cofactors and Vitamins
Thiamine metabolism [KEGG]
Riboflavin metabolism [KEGG]
Vitamin B6 metabolism [KEGG]
Pantothenate and CoA biosynthesis [KEGG]
Biotin metabolism [KEGG]
Folate biosynthesis [KEGG]
Porphyrin and chlorophyll metabolism [KEGG]
Biosynthesis of Secondary Metabolites
Streptomycin biosynthesis [KEGG]
Xenobiotics Biodegradation and Metabolism
Benzoate degradation via CoA ligation [KEGG]
Drug metabolism - other enzymes [KEGG]
Genetic Information Processing
RNA polymerase [KEGG]
Basal transcription factors [KEGG]
Aminoacyl-tRNA biosynthesis [KEGG]
Ribosome [KEGG]
Folding, Sorting and Degradation
Proteasome [KEGG]
Protein export [KEGG]
Type III secretion system [KEGG]
Type IV secretion system [KEGG]
Type II secretion system [KEGG]
Replication and Repair
DNA replication [KEGG]
Base excision repair [KEGG]
Nucleotide excision repair [KEGG]
Mismatch repair [KEGG]
Homologous recombination [KEGG]
Non-homologous end-joining [KEGG]
Environmental Information Processing
Membrane Transport
ABC transporters [KEGG]
Signal Transduction
Two-component system [KEGG]
Wnt signaling pathway [KEGG]
Hedgehog signaling pathway [KEGG]
Cellular Processes
Cell Motility
Bacterial chemotaxis [KEGG]
Flagellar assembly [KEGG]
Cell Growth and Death
Cell cycle [KEGG]
Cell cycle - yeast [KEGG]
p53 signaling pathway [KEGG]
Apoptosis [KEGG]
Immune System
Antigen processing and presentation [KEGG]
Human Diseases
Immune Disorders
Primary immunodeficiency [KEGG]
Neurodegenerative Diseases
Huntington's disease [KEGG]
Infectious Diseases
Vibrio cholerae phathogenic cycle [KEGG]

DisProt- disorder annotation inferred from homologous DisProt sequences

Expression data (explanation)

Bgee expression data - for genes coding for sequences from seed alignment     Click here for overview of Bgee data

The numbers in brackets correspond to the number of genes that are associated with the selected family and are expressed in the corresponding tissue. Click on the tissue to see all the families that possibly have function in that tissue and click on the genes to see the corresponding genes.

Homo sapiens
Drosophila melanogaster
Mus musculus

HumanProteinpedia expression data - for human genes coding for sequences from full alignment     Click here for overview of Human Proteinpedia data

The numbers in brackets correspond to the number of human genes that are associated with the selected family and are expressed in the corresponding tissue. Click on the tissue to see all the families that possibly have function in that tissue and click on the genes to see the corresponding genes.

Healthy tissues
Disease tissues

Human disease association

Genetic Association Database - data for human genes coding for sequences from full alignment

The numbers in brackets correspond to the number of genes that are associated with the selected family and are associated with the corresponding disease. Click on the disease name to see all the families possibly associated with that disease and click on the genes to see the corresponding genes.

Associated diseases and disorders

Links to OMIM - for human genes coding for sequences from full alignment
604788 (1) 609982 (1) 603056 (1) 602708 (1) 601023 (1) 608465 (1) 601633 (1) 186852 (1) 604857 (1) 609661 (1) 602638 (1) 608196 (1) 605459 (1) 607041 (1) 603336 (1) 609662 (1) 612316 (1) 601213 (1) 611628 (1) 603333 (1) 610388 (1) 171060 (1) 600405 (1) 607040 (1) 604581 (1) 605693 (1) 602136 (1) 603139 (1) 611260 (1) 605452 (1) 605454 (1) 602426 (1) 602707 (1) 600822 (1) 103000 (1) 602696 (1) 602706 (1) 604277 (1) 609983 (1) 600112 (1) 600502 (1) 609364 (1) 603647 (1) 604507 (1) 609650 (1) 611941 (1) 601215 (1) 102577 (1) 603449 (1) 606696 (1) 608050 (1) 601498 (1) 102579 (1) 609534 (1) 607472 (1) 608009 (1) 601902 (1) 601681 (1) 601686 (1) 606636 (1) 600355 (1) 154365 (1) 602783 (1) 602627 (1) 605884 (1) 116945 (1) 610337 (1) 179503 (1) 605490 (1) 603335 (1) 139270 (1) More...