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8  structures 266  species 0  interactions 354  sequences 8  architectures

Family: Pam16 (PF03656)

Summary: Pam16

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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.

Pam16 Provide feedback

The Pam16 protein (P42949) is the fifth essential subunit of the pre-sequence translocase-associated protein import motor (PAM) [1]. In Saccharomyces cerevisiae, Pam16 is required for preprotein translocation into the matrix, but not for protein insertion into the inner membrane [1]. Pam16 has a degenerate J domain. J-domain proteins play important regulatory roles as co-chaperones, recruiting Hsp70 partners and accelerating the ATP-hydrolysis step of the chaperone cycle [2]. Pam16's J-like domain strongly interacts with Pam18's J domain, leading to a productive interaction of Pam18 with mtHsp70 at the mitochondria import channel [3]. Pam18 stimulates the ATPase activity of mtHsp70.

Literature references

  1. Frazier AE, Dudek J, Guiard B, Voos W, Li Y, Lind M, Meisinger C, Geissler A, Sickmann A, Meyer HE, Bilanchone V, Cumsky MG, Truscott KN, Pfanner N, Rehling P; , Nat Struct Mol Biol 2004;11:226-233.: Pam16 has an essential role in the mitochondrial protein import motor. PUBMED:14981507 EPMC:14981507

  2. Kelley WL; , Trends Biochem Sci 1998;23:222-227.: The J-domain family and the recruitment of chaperone power. PUBMED:9644977 EPMC:9644977

  3. D'Silva PR, Schilke B, Walter W, Craig EA; , Proc Natl Acad Sci U S A 2005;102:12419-12424.: Role of Pam16's degenerate J domain in protein import across the mitochondrial inner membrane. PUBMED:16105940 EPMC:16105940


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005341

The Pam16 protein is the fifth essential subunit of the pre-sequence translocase-associated protein import motor (PAM) [PUBMED:14981507]. In Saccharomyces cerevisiae (Baker's yeast), Pam16 is required for preprotein translocation into the matrix, but not for protein insertion into the inner membrane [PUBMED:14981507].

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 Chaperone-J (CL0392), which has the following description:

The J-domain is found in a number of stress-response proteins. It is found at the N-terminal of Hsc20, DnaJ-chaperone in E. coli, and viral large T-antigen proteins; it is also in Hsc40, mammalian auxilin and in both animal and plant DnaJ proteins. It is also found in degenerate form in Pam16 proteins.

The clan contains the following 2 members:

DnaJ Pam16

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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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
(3)
Full
(354)
Representative proteomes NCBI
(368)
Meta
(4)
RP15
(84)
RP35
(143)
RP55
(214)
RP75
(259)
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Format an alignment

  Seed
(3)
Full
(354)
Representative proteomes NCBI
(368)
Meta
(4)
RP15
(84)
RP35
(143)
RP55
(214)
RP75
(259)
Alignment:
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Sequence:
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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
(3)
Full
(354)
Representative proteomes NCBI
(368)
Meta
(4)
RP15
(84)
RP35
(143)
RP55
(214)
RP75
(259)
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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: SWISS-PROT
Previous IDs: UPF0108;
Type: Family
Author: Bateman A, Wood V, Studholme DJ, Mistry J
Number in seed: 3
Number in full: 354
Average length of the domain: 119.10 aa
Average identity of full alignment: 36 %
Average coverage of the sequence by the domain: 83.90 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 29.1 29.1
Trusted cut-off 29.1 29.2
Noise cut-off 28.9 28.9
Model length: 127
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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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 Pam16 domain has been found. There are 8 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 seqence.

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