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1080  structures 8707  species 0  interactions 59233  sequences 853  architectures

Family: AAA_lid_3 (PF17862)

Summary: AAA+ lid 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.

AAA+ lid domain Provide feedback

This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains.

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR041569

This entry represents the alpha helical AAA+ lid domain that is found to the C terminus of AAA domains.

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 AAA_lid (CL0671), which has the following description:

Many AAA+ proteins have a C-terminal alpha-helical bundle in addition to the AAA core [1]. The functional roles of the helical bundle are varied and include the formation of a lid over the nucleotide binding site and mediation of subunit interactions in oligomeric protein complexes [1].

The clan contains the following 22 members:

AAA_assoc_2 AAA_lid_1 AAA_lid_10 AAA_lid_11 AAA_lid_2 AAA_lid_3 AAA_lid_4 AAA_lid_5 AAA_lid_6 AAA_lid_7 AAA_lid_8 AAA_lid_9 CbbQ_C ClpB_D2-small Dpoe2NT MCM_lid Mg_chelatase_C ORC4_C PCP_red TIP49_C UVR Vps4_C

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
(586)
Full
(59233)
Representative proteomes UniProt
(147948)
RP15
(10224)
RP35
(28147)
RP55
(50747)
RP75
(73087)
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
(586)
Full
(59233)
Representative proteomes UniProt
(147948)
RP15
(10224)
RP35
(28147)
RP55
(50747)
RP75
(73087)
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
(586)
Full
(59233)
Representative proteomes UniProt
(147948)
RP15
(10224)
RP35
(28147)
RP55
(50747)
RP75
(73087)
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: ECOD:EUF01103
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 586
Number in full: 59233
Average length of the domain: 47.70 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 8.01 %

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 27.2 27.2
Trusted cut-off 27.2 27.2
Noise cut-off 27.1 27.1
Model length: 45
Family (HMM) version: 3
Download: download the raw HMM for this family

Species distribution

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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_lid_3 domain has been found. There are 1080 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.

Loading structure mapping...

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
A0A096S2Q4 View 3D Structure Click here
A0A0B4KFL3 View 3D Structure Click here
A0A0G2K0I1 View 3D Structure Click here
A0A0N7KH90 View 3D Structure Click here
A0A0P0VPG0 View 3D Structure Click here
A0A0P0WUI4 View 3D Structure Click here
A0A0P0XFK3 View 3D Structure Click here
A0A0P0XFK3 View 3D Structure Click here
A0A0P0XIR9 View 3D Structure Click here
A0A0R0EK57 View 3D Structure Click here
A0A0R0ERR0 View 3D Structure Click here
A0A0R0EUY8 View 3D Structure Click here
A0A0R0EW30 View 3D Structure Click here
A0A0R0EXN2 View 3D Structure Click here
A0A0R0EXN2 View 3D Structure Click here
A0A0R0EXW6 View 3D Structure Click here
A0A0R0F8H1 View 3D Structure Click here
A0A0R0G1R8 View 3D Structure Click here
A0A0R0G760 View 3D Structure Click here
A0A0R0GHN2 View 3D Structure Click here
A0A0R0GL56 View 3D Structure Click here
A0A0R0GYQ0 View 3D Structure Click here
A0A0R0H4L9 View 3D Structure Click here
A0A0R0H540 View 3D Structure Click here
A0A0R0I7T2 View 3D Structure Click here
A0A0R0JA66 View 3D Structure Click here
A0A0R0JPK0 View 3D Structure Click here
A0A0R0K5N2 View 3D Structure Click here
A0A0R0KQA1 View 3D Structure Click here
A0A0R0KQA1 View 3D Structure Click here
A0A0R0LFC3 View 3D Structure Click here
A0A0R4IFE2 View 3D Structure Click here
A0A0R4IJC7 View 3D Structure Click here
A0A0R4ILA8 View 3D Structure Click here
A0A0R4IPF0 View 3D Structure Click here
A0A0R4IPK7 View 3D Structure Click here
A0A0R4J302 View 3D Structure Click here
A0A0R4J305 View 3D Structure Click here
A0A0R4J3N1 View 3D Structure Click here
A0A0R4J3Y6 View 3D Structure Click here
A0A0R4J439 View 3D Structure Click here
A0A0R4J4L8 View 3D Structure Click here
A0A0R4J4W3 View 3D Structure Click here
A0A1D6E3T3 View 3D Structure Click here
A0A1D6E8V8 View 3D Structure Click here
A0A1D6F461 View 3D Structure Click here
A0A1D6F4V7 View 3D Structure Click here
A0A1D6F810 View 3D Structure Click here
A0A1D6FKF0 View 3D Structure Click here
A0A1D6FLN2 View 3D Structure Click here
A0A1D6G1D0 View 3D Structure Click here
A0A1D6GG87 View 3D Structure Click here
A0A1D6GQ42 View 3D Structure Click here
A0A1D6GQ42 View 3D Structure Click here
A0A1D6H7Z8 View 3D Structure Click here
A0A1D6HH77 View 3D Structure Click here
A0A1D6HNL9 View 3D Structure Click here
A0A1D6IJ43 View 3D Structure Click here
A0A1D6IJ43 View 3D Structure Click here
A0A1D6IP54 View 3D Structure Click here
A0A1D6J9M9 View 3D Structure Click here
A0A1D6JEJ9 View 3D Structure Click here
A0A1D6JJB1 View 3D Structure Click here
A0A1D6JNX1 View 3D Structure Click here
A0A1D6JNX1 View 3D Structure Click here
A0A1D6K2P8 View 3D Structure Click here
A0A1D6KUI9 View 3D Structure Click here
A0A1D6KUI9 View 3D Structure Click here
A0A1D6LJK2 View 3D Structure Click here
A0A1D6LJK2 View 3D Structure Click here
A0A1D6LMZ3 View 3D Structure Click here
A0A1D6LPZ6 View 3D Structure Click here
A0A1D6MF68 View 3D Structure Click here
A0A1D6MTY9 View 3D Structure Click here
A0A1D6NB66 View 3D Structure Click here
A0A1D6NFE4 View 3D Structure Click here
A0A1D6NGA0 View 3D Structure Click here
A0A1D6NGB6 View 3D Structure Click here
A0A1D6NJI2 View 3D Structure Click here
A0A1D6NK09 View 3D Structure Click here
A0A1D6NU47 View 3D Structure Click here
A0A1D6NW80 View 3D Structure Click here
A0A1D6NX03 View 3D Structure Click here
A0A1D6NX03 View 3D Structure Click here
A0A1D6P390 View 3D Structure Click here
A0A1D6P5R0 View 3D Structure Click here
A0A1D6PAG0 View 3D Structure Click here
A0A1D6PNJ3 View 3D Structure Click here
A0A1D6PSJ1 View 3D Structure Click here
A0A1D6PSJ1 View 3D Structure Click here
A0A1D6PZ26 View 3D Structure Click here
A0A1D6Q4D3 View 3D Structure Click here
A0A1D6Q604 View 3D Structure Click here
A0A1D6QCY8 View 3D Structure Click here
A0A1D6QEJ7 View 3D Structure Click here
A0A1D6QU92 View 3D Structure Click here
A0A1D8PFN6 View 3D Structure Click here
A0A1D8PI93 View 3D Structure Click here
A0A1D8PIV7 View 3D Structure Click here
A0A1D8PME0 View 3D Structure Click here
A0A1D8PMQ4 View 3D Structure Click here
A0A1D8PND0 View 3D Structure Click here
A0A1D8PND0 View 3D Structure Click here
A0A1D8PP04 View 3D Structure Click here
A0A1D8PR43 View 3D Structure Click here
A0A1P8AX50 View 3D Structure Click here
A0A1P8B5P0 View 3D Structure Click here
A0A2R8PVN0 View 3D Structure Click here
A0A368UI19 View 3D Structure Click here
A0A368UI45 View 3D Structure Click here
A2ZVG7 View 3D Structure Click here
A4HV00 View 3D Structure Click here
A4HVM4 View 3D Structure Click here
A4HVN7 View 3D Structure Click here
A4HWE8 View 3D Structure Click here
A4HYS3 View 3D Structure Click here
A4HZT4 View 3D Structure Click here
A4HZT9 View 3D Structure Click here
A4I2Q7 View 3D Structure Click here
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A4I3C0 View 3D Structure Click here
A4I4W4 View 3D Structure Click here
A4I5S8 View 3D Structure Click here
A4I6G4 View 3D Structure Click here
A4I9Q6 View 3D Structure Click here
A4IB20 View 3D Structure Click here
A4ICJ9 View 3D Structure Click here
A4ICJ9 View 3D Structure Click here
A4IE38 View 3D Structure Click here
A8MPR5 View 3D Structure Click here
A9JRG9 View 3D Structure Click here
B0R1D0 View 3D Structure Click here
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B3DGU1 View 3D Structure Click here
B4F988 View 3D Structure Click here
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B4FSF1 View 3D Structure Click here
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B4G124 View 3D Structure Click here
B7E390 View 3D Structure Click here
B7ZV62 View 3D Structure Click here
B8A0A6 View 3D Structure Click here
B8A4A1 View 3D Structure Click here
B8A4A1 View 3D Structure Click here
B9DGC0 View 3D Structure Click here
C0P406 View 3D Structure Click here
C0P882 View 3D Structure Click here
C0PIH1 View 3D Structure Click here
C4J917 View 3D Structure Click here
C6KT34 View 3D Structure Click here
C6KT34 View 3D Structure Click here
C6TE07 View 3D Structure Click here
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D3ZZ20 View 3D Structure Click here
D3ZZB2 View 3D Structure Click here
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E7EXJ5 View 3D Structure Click here
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E7F2S4 View 3D Structure Click here
E7F6D6 View 3D Structure Click here
E7FE14 View 3D Structure Click here
E9AG43 View 3D Structure Click here
E9AGB0 View 3D Structure Click here
E9Q166 View 3D Structure Click here
F1LN92 View 3D Structure Click here
F1M5A4 View 3D Structure Click here
F1Q8W3 View 3D Structure Click here
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F1QGG3 View 3D Structure Click here
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F4JRR2 View 3D Structure Click here
F4KF14 View 3D Structure Click here
F4KHN5 View 3D Structure Click here
F6M9W9 View 3D Structure Click here
G3V6W6 View 3D Structure Click here
G5ED99 View 3D Structure Click here
G5EDB6 View 3D Structure Click here
G5EGR7 View 3D Structure Click here
I1J3Y7 View 3D Structure Click here
I1JEF9 View 3D Structure Click here
I1JEF9 View 3D Structure Click here
I1JFH9 View 3D Structure Click here
I1JHB5 View 3D Structure Click here
I1JPP3 View 3D Structure Click here
I1JPP3 View 3D Structure Click here
I1JRA0 View 3D Structure Click here
I1JS66 View 3D Structure Click here
I1JSX4 View 3D Structure Click here
I1JXA0 View 3D Structure Click here
I1JXA0 View 3D Structure Click here
I1JYM1 View 3D Structure Click here
I1K345 View 3D Structure Click here
I1K360 View 3D Structure Click here
I1K743 View 3D Structure Click here
I1K7F0 View 3D Structure Click here
I1KAX2 View 3D Structure Click here
I1KCD7 View 3D Structure Click here
I1KCD7 View 3D Structure Click here
I1KH58 View 3D Structure Click here
I1KLJ1 View 3D Structure Click here
I1KMB2 View 3D Structure Click here
I1KPL2 View 3D Structure Click here
I1KRH0 View 3D Structure Click here
I1KRI0 View 3D Structure Click here
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I1KUM2 View 3D Structure Click here
I1KV99 View 3D Structure Click here
I1L2Y3 View 3D Structure Click here
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I1L8Z3 View 3D Structure Click here
I1LBA2 View 3D Structure Click here
I1LDK4 View 3D Structure Click here
I1LLZ2 View 3D Structure Click here
I1LQN8 View 3D Structure Click here
I1LTL9 View 3D Structure Click here
I1LTL9 View 3D Structure Click here
I1LWY7 View 3D Structure Click here
I1LZ82 View 3D Structure Click here
I1LZ82 View 3D Structure Click here
I1M0B2 View 3D Structure Click here
I1M344 View 3D Structure Click here
I1M5H4 View 3D Structure Click here
I1M934 View 3D Structure Click here
I1MAC5 View 3D Structure Click here
I1MB96 View 3D Structure Click here
I1MCK1 View 3D Structure Click here
I1MPD2 View 3D Structure Click here
I1MXZ0 View 3D Structure Click here
I1N3G3 View 3D Structure Click here
I1N4D7 View 3D Structure Click here
I1N6J7 View 3D Structure Click here
I1NAA5 View 3D Structure Click here
I1NAA5 View 3D Structure Click here
I1NCS8 View 3D Structure Click here
I1NGZ3 View 3D Structure Click here
K7K8K0 View 3D Structure Click here
K7KL57 View 3D Structure Click here
K7KLH4 View 3D Structure Click here
K7KUR7 View 3D Structure Click here
K7KV74 View 3D Structure Click here
K7L4G7 View 3D Structure Click here
K7L8H2 View 3D Structure Click here
K7LFQ9 View 3D Structure Click here
K7LGX4 View 3D Structure Click here
K7LMM0 View 3D Structure Click here
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K7LQC6 View 3D Structure Click here
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K7LSQ6 View 3D Structure Click here
K7LT69 View 3D Structure Click here
K7LTB1 View 3D Structure Click here
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K7LWF1 View 3D Structure Click here
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K7M691 View 3D Structure Click here
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K7MNG0 View 3D Structure Click here
K7MQB0 View 3D Structure Click here
K7MRG3 View 3D Structure Click here
K7TUL7 View 3D Structure Click here
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K7TYZ8 View 3D Structure Click here
K7UEH4 View 3D Structure Click here
K7UEH4 View 3D Structure Click here
K7UTR3 View 3D Structure Click here
K7V321 View 3D Structure Click here
K7V3I7 View 3D Structure Click here
K7VBI0 View 3D Structure Click here
K7VGG8 View 3D Structure Click here
K7VQA7 View 3D Structure Click here
K7VQA7 View 3D Structure Click here
O04019 View 3D Structure Click here
O13764 View 3D Structure Click here
O14114 View 3D Structure Click here
O14126 View 3D Structure Click here
O14325 View 3D Structure Click here
O14325 View 3D Structure Click here
O15381 View 3D Structure Click here
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O16299 View 3D Structure Click here
O16368 View 3D Structure Click here
O17071 View 3D Structure Click here
O18413 View 3D Structure Click here
O22993 View 3D Structure Click here
O42931 View 3D Structure Click here
O43078 View 3D Structure Click here
O43933 View 3D Structure Click here
O59824 View 3D Structure Click here
O60058 View 3D Structure Click here
O60058 View 3D Structure Click here
O74445 View 3D Structure Click here
O75351 View 3D Structure Click here
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O76371 View 3D Structure Click here
O77313 View 3D Structure Click here
O80860 View 3D Structure Click here
O80983 View 3D Structure Click here
O88685 View 3D Structure Click here
O88967 View 3D Structure Click here
P0AAI3 View 3D Structure Click here
P0DKJ9 View 3D Structure Click here
P0DKK0 View 3D Structure Click here
P17980 View 3D Structure Click here
P18759 View 3D Structure Click here
P24004 View 3D Structure Click here
P25694 View 3D Structure Click here
P25694 View 3D Structure Click here
P28737 View 3D Structure Click here
P32794 View 3D Structure Click here
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P54812 View 3D Structure Click here
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P62333 View 3D Structure Click here
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P90532 View 3D Structure Click here
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P91025 View 3D Structure Click here
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P96281 View 3D Structure Click here
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Q01939 View 3D Structure Click here
Q07844 View 3D Structure Click here
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