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0  structures 391  species 0  interactions 3319  sequences 122  architectures

Family: DUF642 (PF04862)

Summary: Protein of unknown function (DUF642)

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 "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

  1. ^ 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. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  2. ^ Jaroszewski L, Li Z, Krishna SS; et al. (2009). "Exploration of uncharted regions of the protein universe". PLoS Biol. 7 (9): e1000205. doi:10.1371/journal.pbio.1000205. PMC 2744874. PMID 19787035. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)

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

"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.

Protein of unknown function (DUF642) Provide feedback

This family represents a duplicated conserved region found in a number of uncharacterised plant proteins, potentially in the stem. There is a conserved CGP sequence motif.

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006946

This entry represents a duplicated conserved region found in a number of uncharacterised plant proteins, potentially in the stem. There is a conserved CGP sequence motif.

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 GBD (CL0202), which has the following description:

This large superfamily contains beta sandwich domains with a jelly roll topology. Many of these families are involved in carbohydrate recognition. Despite sharing little sequence similarity they do share a weak sequence motif, with a conserved bulge in the C-terminal beta sheet. The probable role of this bulge is in bending of the beta sheet that contains the bulge. This enables the curvature of the sheet forming the sugar binding site [1].

The clan contains the following 71 members:

7TMR-DISMED2 Agarase_CBM Allantoicase ANAPC10 Arabino_trans_C Bac_rhamnosid_N BcsB BetaGal_dom4_5 BPA_C Calpain_III CBM-like CBM27 CBM32 CBM46 CBM60 CBM65_1 CBM_11 CBM_15 CBM_17_28 CBM_26 CBM_35 CBM_4_9 CBM_6 CE2_N CIA30 Clenterotox Cry1Ac_D5 DUF1883 DUF4465 DUF4627 DUF5000 DUF5010_C DUF5077 DUF5625 DUF642 Endotoxin_C Ephrin_lbd Exop_C F5_F8_type_C FBA FlhE GH101_N GH115_C Glft2_N Glyco_hydro_2_N GxDLY HA70_C Laminin_B Laminin_N Lectin_like Lipl32 Lyase_N Malectin Malectin_like Muskelin_N NPCBM P_proprotein PA-IL PAW PCMD PepX_C PINIT PITH PPC PulA_N1 Sad1_UNC SGBP_B_XBD TcA_TcB_BD Thioredoxin_10 XRCC1_N YpM

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
(50)
Full
(3319)
Representative proteomes UniProt
(5743)
RP15
(467)
RP35
(1662)
RP55
(2976)
RP75
(3987)
Jalview View  View  View  View  View  View  View 
HTML View  View           
PP/heatmap 1 View           

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(50)
Full
(3319)
Representative proteomes UniProt
(5743)
RP15
(467)
RP35
(1662)
RP55
(2976)
RP75
(3987)
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
(50)
Full
(3319)
Representative proteomes UniProt
(5743)
RP15
(467)
RP35
(1662)
RP55
(2976)
RP75
(3987)
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_4723 (release 7.6)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Mifsud W
Number in seed: 50
Number in full: 3319
Average length of the domain: 156.9 aa
Average identity of full alignment: 33 %
Average coverage of the sequence by the domain: 54.8 %

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 20.0
Trusted cut-off 27.0 20.3
Noise cut-off 26.9 19.9
Model length: 157
Family (HMM) version: 15
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

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.

Protein Predicted structure External Information
A0A0P0V3K7 View 3D Structure Click here
A0A0P0VJV0 View 3D Structure Click here
A0A0P0VWX1 View 3D Structure Click here
A0A0P0WBZ8 View 3D Structure Click here
A0A0R0IVF1 View 3D Structure Click here
A0A1D6E7A4 View 3D Structure Click here
A0A1D6E7A5 View 3D Structure Click here
A0A1D6E7A6 View 3D Structure Click here
A0A1D6E7A7 View 3D Structure Click here
A0A1D6E7A9 View 3D Structure Click here
A0A1D6GBD6 View 3D Structure Click here
A0A1D6H3D4 View 3D Structure Click here
A0A1D6L8I2 View 3D Structure Click here
B4FRA6 View 3D Structure Click here
B4FVN8 View 3D Structure Click here
C6T8R3 View 3D Structure Click here
C6TJT0 View 3D Structure Click here
I1K8X9 View 3D Structure Click here
I1K8Y0 View 3D Structure Click here
I1L5M2 View 3D Structure Click here
I1LNW8 View 3D Structure Click here
I1M1F0 View 3D Structure Click here
I1M5Q9 View 3D Structure Click here
I1M9K9 View 3D Structure Click here
I1MCI8 View 3D Structure Click here
I1MF39 View 3D Structure Click here
I1MWQ0 View 3D Structure Click here
K7TQE7 View 3D Structure Click here
O22939 View 3D Structure Click here
O22940 View 3D Structure Click here
O64696 View 3D Structure Click here
Q0E2X7 View 3D Structure Click here
Q0JC33 View 3D Structure Click here
Q0JC34 View 3D Structure Click here
Q7XT45 View 3D Structure Click here
Q7XU61 View 3D Structure Click here
Q84M59 View 3D Structure Click here
Q8LAR0 View 3D Structure Click here
Q8S0T6 View 3D Structure Click here
Q94F20 View 3D Structure Click here

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.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;