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28  structures 1431  species 0  interactions 1812  sequences 11  architectures

Family: Lip_prot_lig_C (PF10437)

Summary: Bacterial lipoate protein ligase C-terminus

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Cofactor transferase family". More...

Cofactor transferase family Edit Wikipedia article

Richard Durbin (born 30th December 1960) is a computational biologist at the Wellcome Trust Sanger Institute. He was a joint winner of the Mullard Award of the Royal Society in 1994 (for work on the confocal microscope), won the Lord Lloyd of Kilgerran Award of the Foundation for Science and Technology in 2004, and was elected a Fellow of the Royal Society in 2004.

contributions to computational and genomic biology

Early work included developing the primary instrument software for one of the first X-ray crystallography area detectors (Durbin et al, Science 1986) and the MRC Biorad confocal microscope, alongside contributions to neural modelling (Durbin and Willshaw, Nature 1987; Durbin and Mitchison, Nature 1990).

He then led the informatics for the C. elegans genome project (Science 1998), and alongside Jean Thierry-Mieg developed the genome database Acedb, which evolved into the WormBase web resource. Following this he played an important role in data collection for and interpretation of the human genome sequence (Nature 2001).

He has developed methods for computational sequence analysis, including for gene finding (e.g. GeneWise: Birney and Durbin, Genome Research, 2000) and with Sean Eddy and Graeme Mitchison hidden Markov model and related methods for protein and nucleic acid alignment and matching (e.g. HMMER), leading to the standard textbook "Biological Sequence Analysis" coauthored with Sean Eddy, Anders Krogh and Graeme Mitchison. Using these methods Durbin worked with colleagues to build a series of important genomic data resources, including the protein family database Pfam (Proteins, 1997), the genome database Ensembl (Hubbard et al, NAR, 2002), and the gene family database TreeFam (Li et al, NAR 2006).

More recently Durbin has returned to sequencing and has developed low coverage approaches to population genome sequencing, applied first to yeast (Liti et al, Nature 2009), and have been one of the leaders in the application of new sequencing technology to study human genome variation (Li et al, 2008; Bentley et al., Nature 2008). Durbin currently co-leads the international 1000 Genomes Project to characterise variation down to 1% allele frequency as a foundation for human genetics.

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

Bacterial lipoate protein ligase C-terminus Provide feedback

This is the C-terminal domain of a bacterial lipoate protein ligase. There is no conservation between this C-terminus and that of vertebrate lipoate protein ligase C-termini, but both are associated with the domain BPL_LipA_LipB PF03099 further upstream. This domain is required for adenylation of lipoic acid by lipoate protein ligases. The domain is not required for transfer of lipoic acid from the adenylate to the lipoyl domain. Upon adenylation, this domain rotates 180 degrees away from the active site cleft. Therefore, the domain does not interact with the lipoyl domain during transfer.

Literature references

  1. McManus E, Luisi BF, Perham RN; , J Mol Biol. 2006;356:625-637.: Structure of a putative lipoate protein ligase from Thermoplasma acidophilum and the mechanism of target selection for post-translational modification. PUBMED:16384580 EPMC:16384580

  2. Christensen QH, Cronan JE;, J Biol Chem. 2009;284:21317-21326.: The Thermoplasma acidophilum LplA-LplB complex defines a new class of bipartite lipoate-protein ligases. PUBMED:19520844 EPMC:19520844

  3. Fujiwara K, Maita N, Hosaka H, Okamura-Ikeda K, Nakagawa A, Taniguchi H;, J Biol Chem. 2010;285:9971-9980.: Global conformational change associated with the two-step reaction catalyzed by Escherichia coli lipoate-protein ligase A. PUBMED:20089862 EPMC:20089862

This tab holds annotation information from the InterPro database.

InterPro entry IPR019491

This is the C-terminal domain of a bacterial lipoate protein ligase [ PUBMED:16043486 ]. There is no conservation between this C terminus and that of vertebrate lipoate protein ligase C-termini, but both are associated with INTERPRO , further upstream. This C-terminal domain is more stable than INTERPRO and the hypothesis is that the C-terminal domain has a role in recognising the lipoyl domain and/or transferring the lipoyl group onto it from the lipoyl-AMP intermediate. C-terminal fragments of length 172 to 193 amino acid residues are observed in the eubacterial enzymes whereas in their archaeal counterparts the C-terminal segment is significantly smaller, ranging in size from 87 to 107 amino acid residues.

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 SufE_NifU (CL0233), which has the following description:

This clan includes iron sulfur cluster assembly proteins.

The clan contains the following 4 members:

CO_deh_flav_C Lip_prot_lig_C NifU_N SufE


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...

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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.

Representative proteomes UniProt
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Representative proteomes UniProt

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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.

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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: Gene3D, pdb_1vqz
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Coggill P
Number in seed: 205
Number in full: 1812
Average length of the domain: 84.1 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 25.41 %

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 24.0 24.0
Trusted cut-off 24.0 24.0
Noise cut-off 23.9 23.9
Model length: 85
Family (HMM) version: 12
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


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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...

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


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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 Lip_prot_lig_C domain has been found. There are 28 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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