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4  structures 147  species 0  interactions 169  sequences 10  architectures

Family: Caps_syn_GfcC_N (PF20616)

Summary: Capsule biosynthesis GfcC, N-terminal

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Capsule biosynthesis GfcC, N-terminal Provide feedback

Many bacteria are covered in a layer of surface-associated polysaccharide called the capsule. These capsules can be divided into four groups depending upon the organisation of genes responsible for capsule assembly, the assembly pathway and regulation [1]. This family plays a role in group 4 capsule biosynthesis [2]. These proteins have a beta-grasp fold [3]. Two beta-grasp domains, D2 and D3, are arranged in tandem. There is a C-terminal amphipathic helix which packs against D3. A helical hairpin insert in D2 binds to D3 and constrains its position, a conserved arginine residue at the end of this hairpin is essential for structural integrity [4]. This entry represents D2 domain found at the N-terminal [4].

Literature references

  1. Whitfield C, Roberts IS;, Mol Microbiol. 1999;31:1307-1319.: Structure, assembly and regulation of expression of capsules in Escherichia coli. PUBMED:10200953 EPMC:10200953

  2. Peleg A, Shifrin Y, Ilan O, Nadler-Yona C, Nov S, Koby S, Baruch K, Altuvia S, Elgrably-Weiss M, Abe CM, Knutton S, Saper MA, Rosenshine I;, J Bacteriol. 2005;187:5259-5266.: Identification of an Escherichia coli operon required for formation of the O-antigen capsule. PUBMED:16030220 EPMC:16030220

  3. Burroughs AM, Balaji S, Iyer LM, Aravind L; , Biol Direct. 2007;2:4-4.: A novel superfamily containing the beta-grasp fold involved in binding diverse soluble ligands. PUBMED:17250770 EPMC:17250770

  4. Sathiyamoorthy K, Mills E, Franzmann TM, Rosenshine I, Saper MA;, Biochemistry 2011;0:0-0.: Crystal structure of E. coli group 4 capsule protein GfcC reveals a domain organization resembling Wza. PUBMED:21449614 EPMC:21449614

This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

Domain organisation

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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.

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Representative proteomes UniProt

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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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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.

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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

This family is new in this Pfam release.

Seed source: Pfam-B_9574 (release 9.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Sammut SJ , Bateman A , Eberhardt R
Number in seed: 6
Number in full: 169
Average length of the domain: 123 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 41.63 %

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 22.1 22.1
Trusted cut-off 22.1 22.1
Noise cut-off 22.0 21.9
Model length: 129
Family (HMM) version: 1
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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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 Caps_syn_GfcC_N domain has been found. There are 4 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
P32688 View 3D Structure Click here
P75883 View 3D Structure Click here
Q328Y3 View 3D Structure Click here
Q32HS2 View 3D Structure Click here
Q8ZKI2 View 3D Structure Click here