Summary: Surface lipoprotein assembly modifier
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This is the Wikipedia entry entitled "Domain of unknown function". More...
Domain of unknown function Edit Wikipedia article
A Domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF188 and DUF1000. There are now over 3,000 DUF families within the Pfam database representing over 20% of known families.
History
The DUF naming scheme was introduced by Chris Ponting, through the addition of DUF1 and DUF2 to the SMART database.[1] These two domains were found to be widely distributed in bacterial signaling proteins. Subsequently, the functions of these domains were identified and they have since been renamed as the GGDEF domain and EAL domain respectively.
Structure
Structural genomics programmes have attempted to understand the function of DUFs through structure determination. The structures of over 250 DUF families have been solved.[2]
External Links
List of Pfam familes beginning with the letter D, including DUF families
References
- ^ Schultz J, Milpetz F, Bork P, Ponting CP (1998). "SMART, a simple modular architecture research tool: identification of signaling domains". Proc. Natl. Acad. Sci. U.S.A. 95 (11): 5857–64. PMC 34487. PMID 9600884.
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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.
Surface lipoprotein assembly modifier Provide feedback
Surface lipoprotein assembly modifier (Slam) is a surface lipoprotein that may have a role in virulence [1]. In Neisseria, it is required for the surface display of lipidated virulence factors [2]. Proteins in this family contain an eight-stranded beta-barrel domain [1].
Literature references
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Hooda Y, Lai CCL, Moraes TF;, Front Cell Infect Microbiol. 2017;7:207.: Identification of a Large Family of Slam-Dependent Surface Lipoproteins in Gram-Negative Bacteria. PUBMED:28620585 EPMC:28620585
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Hooda Y, Lai CC, Judd A, Buckwalter CM, Shin HE, Gray-Owen SD, Moraes TF;, Nat Microbiol. 2016;1:16009.: Slam is an outer membrane protein that is required for the surface display of lipidated virulence factors in Neisseria. PUBMED:27572441 EPMC:27572441
Internal database links
SCOOP: | BBP2_2 DUF2860 |
Similarity to PfamA using HHSearch: | BBP2_2 DUF2860 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR007655
Slam, also known as NTHI1171 in Haemophilus influenzae, is a surface lipoprotein that may have a role in virulence [ PUBMED:28620585 ]. In Neisseria, it is required for the surface display of lipidated virulence factors [ PUBMED:27572441 ]. Proteins in this family contain an eight-stranded beta-barrel domain [ PUBMED:28620585 ].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Cellular component | cell outer membrane (GO:0009279) |
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 MBB (CL0193), which has the following description:
This clan gathers together a large set of beta barrel membrane proteins.Although these proteins have different numbers of beta strands in the barrel they have significant sequence similarity between families.
The clan contains the following 117 members:
Ail_Lom Alginate_exp Attacin_C Attacin_N Autotransporter BBP2 BBP2_2 BBP7 BCSC_C Campylo_MOMP Caps_assemb_Wzi CBP_BcsS Channel_Tsx Chlam_OMP CopB CymA DcaP DUF1207 DUF1302 DUF1842 DUF2219 DUF2490 DUF2715 DUF2860 DUF3034 DUF3078 DUF3138 DUF3187 DUF3373 DUF3570 DUF3573 DUF3575 DUF3769 DUF3996 DUF4421 DUF4595 DUF481 DUF4840 DUF5020 DUF5686 DUF5723 DUF5777 DUF5916 DUF6048 DUF6089 DUF6268 Gcw_chp GrlR HP_OMP HP_OMP_2 HpuA IAT_beta KdgM LamB Legionella_OMP Lipoprot_C LptD LptD_2 MDM10 MipA MOSP_C MSP MtrB_PioB NfrA_C Omp85 Omp85_2 Omp_AT OMP_b-brl OMP_b-brl_2 OMP_b-brl_3 OmpA_like OmpA_membrane Omptin OmpW Opacity OpcA OprB OprD OprF PagL PagP Phenol_MetA_deg PLA1 Pom Porin_1 Porin_10 Porin_2 Porin_3 Porin_4 Porin_5 Porin_6 Porin_7 Porin_8 Porin_O_P Porin_OmpG Porin_OmpG_1_2 Porin_OmpL1 PorP_SprF PorV Serpulina_VSP ShlB SlipAM Surface_Ag_2 TbpB_B_D Toluene_X TonB_dep_Rec TraF_2 TraO TSA UPF0164 UPF0257 Usher Usher_TcfC YadA_anchor YaiO YfaZ YjbHAlignments
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 (11) |
Full (676) |
Representative proteomes | UniProt (3314) |
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RP15 (60) |
RP35 (285) |
RP55 (682) |
RP75 (1226) |
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Jalview | |||||||
HTML | |||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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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 (11) |
Full (676) |
Representative proteomes | UniProt (3314) |
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RP15 (60) |
RP35 (285) |
RP55 (682) |
RP75 (1226) |
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Raw Stockholm | |||||||
Gzipped |
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
Seed source: | Pfam-B_4010 (release 7.5) |
Previous IDs: | DUF560; |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Waterfield DI |
Number in seed: | 11 |
Number in full: | 676 |
Average length of the domain: | 270.3 aa |
Average identity of full alignment: | 16 % |
Average coverage of the sequence by the domain: | 61.19 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 288 | ||||||||||||
Family (HMM) version: | 16 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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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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.
trRosetta Structure
The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.
The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.
- View the contact map and structural model in InterPro
- Download the model in PDB format
- Download all the data from the Pfam FTP site