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23  structures 7845  species 0  interactions 27544  sequences 165  architectures

Family: UbiA (PF01040)

Summary: UbiA prenyltransferase family

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UbiA prenyltransferase family Provide feedback

No Pfam abstract.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000537

The UbiA family of prenyltransferases includes bacterial 4-hydroxybenzoate octaprenyltransferase (gene ubiA); yeast mitochondrial para-hydroxybenzoate--polyprenyltransferase (gene COQ2); protohaem IX farnesyltransferase (haem O synthase) from yeast and mammals (gene COX10), and from bacteria (genes cyoE or ctaB) [ PUBMED:8155731 , PUBMED:7885224 ]; and 2-acylphloroglucinol 4-prenyltransferase and 2-acyl-4-prenylphloroglucinol 6-prenyltransferase from plant chloroplasts which catalyze prenylation steps in the beta-bitter acid pathway [ PUBMED:22166201 , PUBMED:25564559 ]. These are integral membrane proteins, which probably contain seven transmembrane segments. Archaeal family members include lycopene elongase/hydratase - this type of enzyme has been shown to be involved in bacterioruberin synthesis in Halobacterium salinarum and Haloferax volcanii [ PUBMED:21840984 ].

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...

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Pfam Clan

This family is a member of clan Terp_synthase (CL0613), which has the following description:

This superfamily includes a diverse range of terpene synthase enzymes which share an alpha helical core.

The clan contains the following 7 members:

HEPPP_synt_1 polyprenyl_synt SQS_PSY Terpene_syn_C_2 Terpene_synth_C TRI5 UbiA

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
(884)
Full
(27544)
Representative proteomes UniProt
(112084)
RP15
(3756)
RP35
(12898)
RP55
(26720)
RP75
(44165)
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
(884)
Full
(27544)
Representative proteomes UniProt
(112084)
RP15
(3756)
RP35
(12898)
RP55
(26720)
RP75
(44165)
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
(884)
Full
(27544)
Representative proteomes UniProt
(112084)
RP15
(3756)
RP35
(12898)
RP55
(26720)
RP75
(44165)
Raw Stockholm Download   Download   Download   Download   Download   Download    
Gzipped 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: Pfam-B_1357 (release 3.0)
Previous IDs: CytC_assmbly_fac; COX10_ctaB_cyoE;
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD , Bateman A
Number in seed: 884
Number in full: 27544
Average length of the domain: 250.80 aa
Average identity of full alignment: 16 %
Average coverage of the sequence by the domain: 77.27 %

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 34.2 34.2
Trusted cut-off 34.2 34.2
Noise cut-off 34.1 34.1
Model length: 251
Family (HMM) version: 20
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 UbiA domain has been found. There are 23 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
A0A0P0XF65 View 3D Structure Click here
A0A0P0XFT7 View 3D Structure Click here
A0A0R0FM72 View 3D Structure Click here
A0A0R0FY91 View 3D Structure Click here
A0A0R0HE87 View 3D Structure Click here
A0A0R0HQD8 View 3D Structure Click here
A0A0R0I1T3 View 3D Structure Click here
A0A0R0I7K2 View 3D Structure Click here
A0A0R0ICK4 View 3D Structure Click here
A0A0R0IQ72 View 3D Structure Click here
A0A0R0J086 View 3D Structure Click here
A0A0R0J086 View 3D Structure Click here
A0A0R0LG31 View 3D Structure Click here
A0A0R4J5W6 View 3D Structure Click here
A0A1D6EVT3 View 3D Structure Click here
A0A1D6JQ27 View 3D Structure Click here
A0A1D6M2M1 View 3D Structure Click here
A0A1D6P5F1 View 3D Structure Click here
A0A1D8PNE8 View 3D Structure Click here
A0A1D8PU83 View 3D Structure Click here
A0A1R3P7B6 View 3D Structure Click here
A0A368UID1 View 3D Structure Click here
A3KNW5 View 3D Structure Click here
A4I0M3 View 3D Structure Click here
A4I3L1 View 3D Structure Click here
B6T4K7 View 3D Structure Click here
B7FA90 View 3D Structure Click here
B8A333 View 3D Structure Click here
B9A1Q4 View 3D Structure Click here
C0HG52 View 3D Structure Click here
C6KSS3 View 3D Structure Click here
C6TML7 View 3D Structure Click here
C7G049 View 3D Structure Click here
D3ZG27 View 3D Structure Click here
E7FB98 View 3D Structure Click here
F1LVF4 View 3D Structure Click here
F1QL30 View 3D Structure Click here
I1JFW4 View 3D Structure Click here
I1MSP5 View 3D Structure Click here
I1N2Z4 View 3D Structure Click here
I1NJ83 View 3D Structure Click here
I1NJA2 View 3D Structure Click here
K7LGE3 View 3D Structure Click here
K7LHV9 View 3D Structure Click here
K7LIZ8 View 3D Structure Click here
K7LWU9 View 3D Structure Click here
K7LXY1 View 3D Structure Click here
K7LZY0 View 3D Structure Click here
K7LZY1 View 3D Structure Click here
K7LZY3 View 3D Structure Click here
K7MGI0 View 3D Structure Click here
K7VHB7 View 3D Structure Click here
K7VIM4 View 3D Structure Click here
K8ES01 View 3D Structure Click here
O64886 View 3D Structure Click here
P0AEA5 View 3D Structure Click here
P0AGK1 View 3D Structure Click here
P21592 View 3D Structure Click here
P32166 View 3D Structure Click here
P32378 View 3D Structure Click here
P9WFR5 View 3D Structure Click here
P9WFR7 View 3D Structure Click here
P9WIP3 View 3D Structure Click here
Q0D576 View 3D Structure Click here
Q0DAK7 View 3D Structure Click here
Q0WUA3 View 3D Structure Click here
Q10252 View 3D Structure Click here
Q10QN3 View 3D Structure Click here
Q12887 View 3D Structure Click here
Q1ACB3 View 3D Structure Click here
Q2FZM0 View 3D Structure Click here
Q2G2B9 View 3D Structure Click here
Q38833 View 3D Structure Click here
Q499N4 View 3D Structure Click here
Q4D2X9 View 3D Structure Click here
Q4D596 View 3D Structure Click here
Q4DK79 View 3D Structure Click here
Q4DSC8 View 3D Structure Click here
Q54JB3 View 3D Structure Click here
Q54K99 View 3D Structure Click here
Q54U71 View 3D Structure Click here
Q55E99 View 3D Structure Click here
Q57727 View 3D Structure Click here
Q5QLH9 View 3D Structure Click here
Q5W6H5 View 3D Structure Click here
Q66JT7 View 3D Structure Click here
Q6ZAH2 View 3D Structure Click here
Q8CFY5 View 3D Structure Click here
Q8I0W6 View 3D Structure Click here
Q8I7J4 View 3D Structure Click here
Q8VWJ1 View 3D Structure Click here
Q93YP7 View 3D Structure Click here
Q96H96 View 3D Structure Click here
Q9DC60 View 3D Structure Click here
Q9V3R8 View 3D Structure Click here
Q9VHS7 View 3D Structure Click here
Q9VKZ1 View 3D Structure Click here
Q9Y5Z9 View 3D Structure Click here
Q9Y7Y4 View 3D Structure Click here