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49  structures 3555  species 0  interactions 6729  sequences 18  architectures

Family: Lipoprotein_9 (PF03180)

Summary: NlpA lipoprotein

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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.

NlpA lipoprotein Provide feedback

This entry represents bacterial lipoproteins that belong to the NlpA family [1,2]. It contains several antigenic members, that may be involved in bacterial virulence. This entry includes the D-methionine binding lipoprotein MetQ, which is the substrate-binding component of a D-methionine permease, a binding protein-dependent, ATP-driven transport system [2,3]. Other members of this family, such as NlpA, have been identified as putative substrate-binding components of ABC transporters. NlpA, is an inner-membrane-anchored lipoprotein that has been shown to have a minor role in methionine import [4,5].

Literature references

  1. Yu F, Inouye S, Inouye M; , J Biol Chem 1986;261:2284-2288.: Lipoprotein-28, a cytoplasmic membrane lipoprotein from Escherichia coli. Cloning, DNA sequence, and expression of its gene. PUBMED:3003106 EPMC:3003106

  2. Gal J, Szvetnik A, Schnell R, Kalman M;, J Bacteriol. 2002;184:4930-4932.: The metD D-methionine transporter locus of Escherichia coli is an ABC transporter gene cluster. PUBMED:12169620 EPMC:12169620

  3. Nguyen PT, Lai JY, Lee AT, Kaiser JT, Rees DC;, Proc Natl Acad Sci U S A. 2018;115:E10596.: Noncanonical role for the binding protein in substrate uptake by the MetNI methionine ATP Binding Cassette (ABC) transporter. PUBMED:30352853 EPMC:30352853

  4. Schwechheimer C, Kuehn MJ;, J Bacteriol. 2013;195:4161-4173.: Synthetic effect between envelope stress and lack of outer membrane vesicle production in Escherichia coli. PUBMED:23852867 EPMC:23852867

  5. Zhang Z, Feige JN, Chang AB, Anderson IJ, Brodianski VM, Vitreschak AG, Gelfand MS, Saier MH Jr;, Arch Microbiol. 2003;180:88-100.: A transporter of Escherichia coli specific for L- and D-methionine is the prototype for a new family within the ABC superfamily. PUBMED:12819857 EPMC:12819857


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004872

The lipoproteins in this group belong to the NlpA family. D-methionine binding lipoprotein MetQ is the main member of this group. This protein is a component of a D-methionine permease, a binding protein-dependent, ATP-driven transport system [ PUBMED:12169620 ].

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 PBP (CL0177), which has the following description:

Periplasmic binding proteins (PBPs) consist of two large lobes that close around the bound ligand. This architecture is reiterated in transcriptional regulators, such as the lac repressors. In the process of evolution, genes encoding the PBPs have fused with genes for integral membrane proteins. Thus, diverse mammalian receptors contain extracellular ligand binding domains that are homologous to the PBPs; these include glutamate/glycine-gated ion channels such as the NMDA receptor, G protein-coupled receptors, including metabotropic glutamate, GABA-B, calcium sensing, and pheromone receptors, and atrial natriuretic peptide-guanylate cyclase receptors [2].

The clan contains the following 27 members:

CypI DctP DUF3834 HisG Lig_chan-Glu_bd Lipoprotein_8 Lipoprotein_9 LysR_substrate NMT1 NMT1_2 NMT1_3 OpuAC PBP_like PBP_like_2 PDT Phosphonate-bd Porphobil_deam SBP_bac_1 SBP_bac_11 SBP_bac_3 SBP_bac_5 SBP_bac_6 SBP_bac_8 TctC Transferrin VitK2_biosynth YhfZ_C

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
(29)
Full
(6729)
Representative proteomes UniProt
(40190)
RP15
(588)
RP35
(2985)
RP55
(6945)
RP75
(14067)
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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
(29)
Full
(6729)
Representative proteomes UniProt
(40190)
RP15
(588)
RP35
(2985)
RP55
(6945)
RP75
(14067)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(29)
Full
(6729)
Representative proteomes UniProt
(40190)
RP15
(588)
RP35
(2985)
RP55
(6945)
RP75
(14067)
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...

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_1418 (release 6.5)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Mifsud W
Number in seed: 29
Number in full: 6729
Average length of the domain: 233.10 aa
Average identity of full alignment: 36 %
Average coverage of the sequence by the domain: 85.04 %

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 27.0
Noise cut-off 26.9 26.9
Model length: 237
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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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 Lipoprotein_9 domain has been found. There are 49 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
P04846 View 3D Structure Click here
P28635 View 3D Structure Click here
Q2FZZ0 View 3D Structure Click here
Q2G0V0 View 3D Structure Click here