Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
0  structures 702  species 0  interactions 1018  sequences 2  architectures

Family: Cad (PF03596)

Summary: Cadmium resistance transporter

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 "Cadmium resistance transporter". More...

Cadmium resistance transporter Edit Wikipedia article

Cadmium Resistance Protein
Identifiers
Symbol CadD
Pfam PF03596
InterPro IPR004676

The cadmium resistance (CadD) protein family (TC# 2.A.77) belongs to the Lysine exporter (LysE) superfamily.[1] CadD members facilitate the export of cationic compounds such as cadmium ions.[2]

Members

Currently, many sequenced proteins comprise the CadD family. Two are close orthologues in two Staphylococcus species that have been reported to function in cadmium resistance, a fourth has been reported to function in quaternary ammonium cation export, and the fourth is a distant open reading frame (ORF) in Staphylococcus aureus.[3] These proteins are found in Gram-positive bacteria. Their mode of energy coupling has not been investigated, but is hypothesized to include a proton antiport mechanism. This family is distantly related to members of the LysE family (TC #2.A.75) and the RhtB family (TC #2.A.76). These three families, which are included in the LysE superfamily, all consist of proteins of similar sizes (about 200 residues) and topologies (6 putative transmembrane α-helical segments; 5 experimentally determined TMSs).[4]

General Transport Reaction

The probable reaction catalyzed by these proteins is:[2]

Cationic compound (in) + nH+ (out) → Cationic compound (out) + nH+ (in).

Further reading

References

  1. ^ Tsu BV, Saier MH (2015-01-01). "The LysE Superfamily of Transport Proteins Involved in Cell Physiology and Pathogenesis". PLOS One. 10 (10): e0137184. doi:10.1371/journal.pone.0137184. PMC 4608589Freely accessible. PMID 26474485. 
  2. ^ a b "2.A.77 The Cadmium Resistance (CadD) Family". Transporter Classification Database. Retrieved 2016-02-25. 
  3. ^ Crupper SS, Worrell V, Stewart GC, Iandolo JJ (July 1999). "Cloning and expression of cadD, a new cadmium resistance gene of Staphylococcus aureus". Journal of Bacteriology. 181 (13): 4071–5. PMC 93898Freely accessible. PMID 10383976. 
  4. ^ Cao Y, Jin X, Levin EJ, Huang H, Zong Y, Quick M, Weng J, Pan Y, Love J, Punta M, Rost B, Hendrickson WA, Javitch JA, Rajashankar KR, Zhou M (May 2011). "Crystal structure of a phosphorylation-coupled saccharide transporter". Nature. 473 (7345): 50–4. doi:10.1038/nature09939. PMC 3201810Freely accessible. PMID 21471968. 

As of 25 February 2016, this article is derived in whole or in part from Transporter Classification Database. The copyright holder has licensed the content in a manner that permits reuse under CC BY-SA 3.0 and GFDL. All relevant terms must be followed. The original text was at "2.A.77 The Cadmium Resistance (CadD) Family".


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

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.

Cadmium resistance transporter Provide feedback

No Pfam abstract.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004676

These proteins are members of the Cadmium Resistance (CadD) family. The CadD family includes two close orthologues in two Staphylococcus species that have been reported to function in cadmium resistance [PUBMED:10383976].

Domain organisation

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

Loading domain graphics...

Pfam Clan

This family is a member of clan LysE (CL0292), which has the following description:

This clan includes a diverse range of transporter families [1].

The clan contains the following 18 members:

BacA Cad Colicin_V DsbD DsbD_2 DUF475 FTR1 HupE_UreJ HupE_UreJ_2 LysE MarC Mntp NicO OFeT_1 SfLAP TauE TerC UPF0016

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, 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
(4)
Full
(1018)
Representative proteomes UniProt
(3037)
NCBI
(4322)
Meta
(3)
RP15
(129)
RP35
(548)
RP55
(970)
RP75
(1505)
Jalview View  View  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
(4)
Full
(1018)
Representative proteomes UniProt
(3037)
NCBI
(4322)
Meta
(3)
RP15
(129)
RP35
(548)
RP55
(970)
RP75
(1505)
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
(4)
Full
(1018)
Representative proteomes UniProt
(3037)
NCBI
(4322)
Meta
(3)
RP15
(129)
RP35
(548)
RP55
(970)
RP75
(1505)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   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: TIGRFAMs
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: TIGRFAMs, Griffiths-Jones SR
Number in seed: 4
Number in full: 1018
Average length of the domain: 185.60 aa
Average identity of full alignment: 33 %
Average coverage of the sequence by the domain: 88.37 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.2 26.2
Trusted cut-off 26.8 26.3
Noise cut-off 26.1 26.1
Model length: 192
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.