Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
9  structures 7727  species 0  interactions 19253  sequences 74  architectures

Family: UPF0004 (PF00919)

Summary: Uncharacterized protein family UPF0004

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.

Uncharacterized protein family UPF0004 Provide feedback

This family is the N terminal half of the Prosite family. The C-terminal half has been shown to be related to MiaB proteins [1,2]. This domain is a nearly always found in conjunction with PF04055 and PF01938 although its function is uncertain.

Literature references

  1. Anantharaman V, Koonin EV, Aravind L; , FEMS Microbiol Lett 2001;197:215-221.: TRAM, a predicted RNA-binding domain, common to tRNA uracil methylation and adenine thiolation enzymes. PUBMED:11313137 EPMC:11313137

  2. Pierrel F, Bjork GR, Fontecave M, Atta M; , J Biol Chem 2002;277:13367-13370.: Enzymatic modification of tRNAs: MiaB is an iron-sulfur protein. PUBMED:11882645 EPMC:11882645

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013848

The methylthiotransferase (MTTase) or miaB-like family is named after the (dimethylallyl)adenosine tRNA MTTase miaB protein, which catalyses a C-H to C-S bond conversion in the methylthiolation of tRNA. A related bacterial enzyme rimO performs a similar methylthiolation, but on a protein substrate. RimO acts on the ribosomal protein S12 and forms a separate MTTase subfamily. The miaB-subfamily includes mammalian CDK5 regulatory subunit-associated proteins and similar proteins in other eukaryotes. Two other subfamilies, yqeV and CDKAL1, are named after a Bacillus subtilis and a human protein, respectively. While yqeV-like proteins are found in bacteria, CDKAL1 subfamily members occur in eukaryotes and in archaebacteria. The likely MTTases from these 4 subfamilies contain an N-terminal MTTase domain, a central radical generating fold and a C-terminal TRAM domain (see PROSITEDOC ). The core forms a radical SAM fold (or AdoMet radical), containing a cysteine motif CxxxCxxC that binds a [4Fe-4S] cluster [ PUBMED:11882645 , PUBMED:18252828 , PUBMED:11222759 ]. A reducing equivalent from the [4Fe-4S]+ cluster is used to cleave S-adenosylmethionine (SAM) to generate methionine and a 5'-deoxyadenosyl radical. The latter is thought to produce a reactive substrate radical that is amenable to sulphur insertion [ PUBMED:18252828 , PUBMED:11222759 ]. The N-terminal MTTase domain contains 3 cysteines that bind a second [4Fe-4S] cluster, in addition to the radical-generating [4Fe-4S] cluster, which could be involved in the thiolation reaction. The C-terminal TRAM domain is not shared with other radical SAM proteins outside the MTTase family. The TRAM domain can bind to RNA substrate and seems to be important for substrate recognition. The tertiary structure of the central radical SAM fold has six beta/alpha motifs resembling a three-quarter TIM barrel core (see PROSITEDOC ) [ PUBMED:15289575 ]. The N-terminal MTTase domain might form an additional [beta/alpha]2 TIM barrel unit [ PUBMED:18252828 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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

Loading domain graphics...

Pfam Clan

This family is a member of clan CheY (CL0304), which has the following description:

This clan includes the CheY-like response regulators from bacteria [1-2].

The clan contains the following 11 members:

cREC_REC FleQ NARF OKR_DC_1_N RcsC RcsD_ABL Response_reg Response_reg_2 TadZ_N UPF0004 VpsR


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.

Representative proteomes UniProt
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

Representative proteomes UniProt

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.

Representative proteomes UniProt
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...


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: Pfam-B_1257 (release 3.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A , Moxon SJ
Number in seed: 109
Number in full: 19253
Average length of the domain: 97.30 aa
Average identity of full alignment: 32 %
Average coverage of the sequence by the domain: 20.78 %

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 27.0 27.0
Trusted cut-off 27.0 27.1
Noise cut-off 26.7 26.7
Model length: 98
Family (HMM) version: 23
Download: download the raw HMM for this family

Species distribution

Sunburst controls


Weight segments by...

Change the size of the sunburst


Colour assignments

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


Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls


The tree shows the occurrence of this domain across different species. More...


Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.


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 UPF0004 domain has been found. There are 9 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
A0A1D6F795 View 3D Structure Click here
A0A2R8PW25 View 3D Structure Click here
A0A2R8PX77 View 3D Structure Click here
A0JUY6 View 3D Structure Click here
A0KHZ9 View 3D Structure Click here
A0KN81 View 3D Structure Click here
A0L7K3 View 3D Structure Click here
A0L887 View 3D Structure Click here
A0LFB7 View 3D Structure Click here
A0LIM0 View 3D Structure Click here
A0LV00 View 3D Structure Click here
A0LV11 View 3D Structure Click here
A0Q0M5 View 3D Structure Click here
A0Q0P6 View 3D Structure Click here
A0QVX5 View 3D Structure Click here
A1A280 View 3D Structure Click here
A1APR6 View 3D Structure Click here
A1ATL9 View 3D Structure Click here
A1AX14 View 3D Structure Click here
A1B3K8 View 3D Structure Click here
A1B8C4 View 3D Structure Click here
A1BHA0 View 3D Structure Click here
A1BIX2 View 3D Structure Click here
A1K3J0 View 3D Structure Click here
A1K487 View 3D Structure Click here
A1R550 View 3D Structure Click here
A1S2T9 View 3D Structure Click here
A1S8S1 View 3D Structure Click here
A1SJ39 View 3D Structure Click here
A1SNG0 View 3D Structure Click here
A1SSC4 View 3D Structure Click here
A1T7U2 View 3D Structure Click here
A1TKI5 View 3D Structure Click here
A1TMP4 View 3D Structure Click here
A1UEZ3 View 3D Structure Click here
A1UU39 View 3D Structure Click here
A1VQ18 View 3D Structure Click here
A1VSP2 View 3D Structure Click here
A1WAJ7 View 3D Structure Click here
A1WBW2 View 3D Structure Click here