Summary: Domain of unknown function (DUF4198)
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"DUF" families are annotated with the Domain of unknown function Wikipedia article. This is a general article, with no specific information about individual Pfam DUFs. If you have information about this particular DUF, please let us know using the "Add annotation" button below.
Domain of unknown function (DUF4198) Provide feedback
This family was previously missannotated in Pfam as NikM.
Internal database links
SCOOP: | Big_1 bMG3 CarbopepD_reg_2 CarboxypepD_reg Dioxygenase_C SdrD_B SpaA |
Similarity to PfamA using HHSearch: | Dioxygenase_C bMG3 CarboxypepD_reg |
This tab holds annotation information from the InterPro database.
InterPro entry IPR019613
This family, which includes Haemophilus influenzae protein HI_1624, is functionally uncharacterised. Some family members were previously annotated as prokaryotic transmembrane nickel uptake transporters, NikM. This has been shown to be incorrect, as the proteins matched do not exhibit transmembrane properties, nor do they contain conserved residues associated with NikM proteins [PUBMED:16352848].
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 Transthyretin (CL0287), which has the following description:
This clan unifies several SCOP superfamilies that all share a 7 stranded beta sandwich fold.
The clan contains the following 33 members:
CarbopepD_reg_2 CarboxypepD_reg Cna_B CooC_C Dioxygenase_C DUF1416 DUF2012 DUF2606 DUF3823 DUF3869 DUF4139 DUF4198 DUF4458 DUF5300 FctA Fimbrillin_C fn3_3 GramPos_pilinD1 GramPos_pilinD3 Lipase_C MetallophosN PapC_C PEGA phage_tail_N Pollen_Ole_e_1 PUD SdrD_B SpaA T6_Ig_like T6SS-SciN Transthyretin TTR-52 VHLAlignments
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, the UniProtKB sequence database, 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 (202) |
Full (1806) |
Representative proteomes | UniProt (7775) |
NCBI (11120) |
Meta (239) |
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RP15 (231) |
RP35 (834) |
RP55 (1796) |
RP75 (3121) |
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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.
Format an alignment
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 (202) |
Full (1806) |
Representative proteomes | UniProt (7775) |
NCBI (11120) |
Meta (239) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (231) |
RP35 (834) |
RP55 (1796) |
RP75 (3121) |
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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_42996 (release 22.0) |
Previous IDs: | NikM; |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Coggill P |
Number in seed: | 202 |
Number in full: | 1806 |
Average length of the domain: | 214.00 aa |
Average identity of full alignment: | 20 % |
Average coverage of the sequence by the domain: | 80.70 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 213 | ||||||||||||
Family (HMM) version: | 10 | ||||||||||||
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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