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489  structures 7794  species 0  interactions 17375  sequences 205  architectures

Family: IMS_C (PF11799)

Summary: impB/mucB/samB family C-terminal domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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.

impB/mucB/samB family C-terminal domain Provide feedback

These proteins are involved in UV protection (Swiss).

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR017961

This entry represents the little finger domain found in Y-family (lesion bypass) DNA polymerases. Y-family polymerases were originally known as UmuC/DinB/Rev1/Rad30 after each branch of the family. These enzymes are characterised by their low-fidelity synthesis on undamaged DNA templates and by their ability to traverse replication-blocking lesions. By contrast, high-fidelity polymerases (such as DNA polymerase III) are sensitive to distortions in the DNA template. As a result, Y-family polymerases can extend primer strands across DNA strand lesions that would otherwise stall replicative polymerases. To minimize mutations through their low fidelity synthesis, these enzymes are regulated, and are thought to interact with processivity factors, beta-clamp or proliferating cell nuclear antigen (PCNA), which are also essential for the function of replicative DNA polymerases [ PUBMED:14592985 ]. Organisms can contain more than one Y-family polymerase, each with a unique DNA damage bypass and fidelity profile. For example, humans posses four Y-family polymerases: DNA polymerases kappa, iota, eta and Rev1. Y-family polymerases show no homology to DNA polymerases from the A-, B-, C-, D- or X-families [ PUBMED:11595188 ].

The Y-family of DNA polymerases includes the following enzymes:

Human DNA polymerase kappa is a right-handed shaped molecule with palm, fingers, thumb, little finger and wrist subdomains [ PUBMED:15296733 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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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
(700)
Full
(17375)
Representative proteomes UniProt
(72573)
RP15
(2192)
RP35
(7798)
RP55
(16471)
RP75
(27863)
Jalview View  View  View  View  View  View  View 
HTML View             
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
(700)
Full
(17375)
Representative proteomes UniProt
(72573)
RP15
(2192)
RP35
(7798)
RP55
(16471)
RP75
(27863)
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
(700)
Full
(17375)
Representative proteomes UniProt
(72573)
RP15
(2192)
RP35
(7798)
RP55
(16471)
RP75
(27863)
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_1349 (release 2.1)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 700
Number in full: 17375
Average length of the domain: 117.10 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 22.23 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.7 20.7
Trusted cut-off 20.7 20.7
Noise cut-off 20.6 20.6
Model length: 113
Family (HMM) version: 10
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 IMS_C domain has been found. There are 489 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
A0A0G2K4L7 View 3D Structure Click here
A0A0R0LFA9 View 3D Structure Click here
A0A1D6GLR1 View 3D Structure Click here
A0A1D6GU80 View 3D Structure Click here
A0A1D6NB48 View 3D Structure Click here
A2CEB0 View 3D Structure Click here
A3EWL3 View 3D Structure Click here
A4HZ62 View 3D Structure Click here
A4I3M0 View 3D Structure Click here
A4I3M1 View 3D Structure Click here
A4ICX7 View 3D Structure Click here
B0UY97 View 3D Structure Click here
D3ZRU9 View 3D Structure Click here
D4A8I8 View 3D Structure Click here
D4ADZ0 View 3D Structure Click here
E7F6Y7 View 3D Structure Click here
F1Q7Z9 View 3D Structure Click here
G5EFY1 View 3D Structure Click here
I1JB00 View 3D Structure Click here
I1KRK8 View 3D Structure Click here
I1LFP9 View 3D Structure Click here
O74944 View 3D Structure Click here
O94623 View 3D Structure Click here
P04152 View 3D Structure Click here
P12689 View 3D Structure Click here
P34409 View 3D Structure Click here
P9WNT1 View 3D Structure Click here
P9WNT3 View 3D Structure Click here
Q04049 View 3D Structure Click here
Q09615 View 3D Structure Click here
Q0DQB4 View 3D Structure Click here
Q2FWZ5 View 3D Structure Click here
Q2FYS2 View 3D Structure Click here
Q47155 View 3D Structure Click here
Q4D0M0 View 3D Structure Click here
Q4D0M2 View 3D Structure Click here
Q4D5H8 View 3D Structure Click here
Q4D5I0 View 3D Structure Click here
Q4DLJ0 View 3D Structure Click here
Q4DQV1 View 3D Structure Click here
Q59Q77 View 3D Structure Click here
Q5JLR9 View 3D Structure Click here
Q654Y6 View 3D Structure Click here
Q6JDV7 View 3D Structure Click here
Q6R3M4 View 3D Structure Click here
Q8H2D5 View 3D Structure Click here
Q920Q2 View 3D Structure Click here
Q9JJN0 View 3D Structure Click here
Q9QUG2 View 3D Structure Click here
Q9UBT6 View 3D Structure Click here
Q9UBZ9 View 3D Structure Click here
Q9UNA4 View 3D Structure Click here
Q9VHV1 View 3D Structure Click here
Q9VNX1 View 3D Structure Click here
Q9W0P2 View 3D Structure Click here
Q9Y253 View 3D Structure Click here