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8  structures 1332  species 0  interactions 2146  sequences 14  architectures

Family: Prok-JAB (PF14464)

Summary: Prokaryotic homologs of the JAB domain

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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.

Prokaryotic homologs of the JAB domain Provide feedback

These are metalloenzymes that function as the ubiquitin isopeptidase/ deubiquitinase in the ubiquitin-based signaling and protein turnover pathways in eukaryotes [1]. Prokaryotic JAB domains are predicted to have a similar role in their cognates of the ubiquitin modification pathway [2,3]. The domain is widely found in bacteria, archaea and phages where they are present in several gene contexts in addition to those that correspond to the prokaryotic cognates of the eukaryotic Ub pathway. Other contexts in which JAB domains are present include gene neighbor associations with ubiquitin fold domains in cysteine and siderophore biosynthesis, and phage tail morphogenesis, where they are shown or predicted to process the associated ubiquitin [2,4]. A distinct family, the RadC-like JAB domains are widespread in bacteria and are predicted to function as nucleases [5]. In halophilic archaea the JAB domain shows strong gene-neighborhood associations with a nucleotidyltransferase suggesting a role in nucleotide metabolism [5].

Literature references

  1. Verma R, Aravind L, Oania R, McDonald WH, Yates JR 3rd, Koonin EV, Deshaies RJ;, Science. 2002;298:611-615.: Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome. PUBMED:12183636 EPMC:12183636

  2. Iyer LM, Burroughs AM, Aravind L; , Genome Biol. 2006;7:R60.: The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains. PUBMED:16859499 EPMC:16859499

  3. Iyer LM, Burroughs AM, Aravind L; , Genome Biol. 2006;7:R60.: The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains. PUBMED:16859499 EPMC:16859499

  4. Burns KE, Baumgart S, Dorrestein PC, Zhai H, McLafferty FW, Begley TP;, J Am Chem Soc. 2005;127:11602-11603.: Reconstitution of a new cysteine biosynthetic pathway in Mycobacterium tuberculosis. PUBMED:16104727 EPMC:16104727

  5. Iyer LM, Zhang D, Rogozin IB, Aravind L;, Nucleic Acids Res. 2011; [Epub ahead of print]: Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems. PUBMED:21890906 EPMC:21890906


External database links

This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

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 JAB (CL0366), which has the following description:

This superfamily includes a number of proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits, regulators of transcription factors and ubiquitination-assisting protein families. In eukaryotes and in prokaryotic cognates of the ubiquitin-based modification pathway, they function as ubiquitin isopeptidases/ deubiquitinases. JAB domains are also found in diverse metabolic pathways in prokaryotes such as siderophore and cysteine biosynthesis. Other distinct versions of the JAB domain, such as RadC are predicted to function as nucleases. Structurally, the JAB domain is related to the nucleotide deaminase and binds a Zinc ion in a similar structural location.

The clan contains the following 6 members:

JAB NPL4 Prok-JAB RadC Toxin-JAB1 UPF0172

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...

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
(111)
Full
(2146)
Representative proteomes NCBI
(3074)
Meta
(346)
RP15
(149)
RP35
(304)
RP55
(409)
RP75
(470)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(111)
Full
(2146)
Representative proteomes NCBI
(3074)
Meta
(346)
RP15
(149)
RP35
(304)
RP55
(409)
RP75
(470)
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
(111)
Full
(2146)
Representative proteomes NCBI
(3074)
Meta
(346)
RP15
(149)
RP35
(304)
RP55
(409)
RP75
(470)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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: Manual
Previous IDs: none
Type: Family
Author: Iyer LM, Burroughs AM, Aravind L
Number in seed: 111
Number in full: 2146
Average length of the domain: 105.60 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 49.36 %

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 25.0 25.0
Trusted cut-off 25.0 25.0
Noise cut-off 24.9 24.9
Model length: 105
Family (HMM) version: 1
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 Prok-JAB 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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