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2  structures 262  species 0  interactions 714  sequences 14  architectures

Family: Tic22 (PF04278)

Summary: Tic22-like family

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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.

Tic22-like family Provide feedback

The preprotein translocation at the inner envelope membrane of chloroplasts so far involves five proteins: Tic110, Tic55, Tic40, Tic22 (this family) and Tic20. The molecular function of these proteins has not yet been established [1].

Literature references

  1. Heins L, Mehrle A, Hemmler R, Wagner R, Kuchler M, Hormann F, Sveshnikov D, Soll J; , EMBO J 2002;21:2616-2625.: The preprotein conducting channel at the inner envelope membrane of plastids. PUBMED:12032074 EPMC:12032074


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007378

Chloroplast function requires the import of nuclear encoded proteins from the cytoplasm across the chloroplast double membrane. This is accompished by two protein complexes, the Toc complex located at the outer membrane and the Tic complex loacted at the inner membrane [PUBMED:11315189]. The Toc complex recognises specific proteins by a cleavable N-terminal sequence and is primarily responsible for translocation through the outer membrane, while the Tic complex translocates the protein through the inner membrane.

This entry represents Tic22, a core member of the Tic complex. Tic22 is a soluble protein and the only Tic complex component of the intermembrane space that has been shown to interact with preproteins during import. It may also act as a chaperone that prevent misfolding or missorting of the preprotein to the intermembrane space and potentially serve as a component that links the Toc and Tic complexes [PUBMED:25174336].

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, 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
(7)
Full
(714)
Representative proteomes UniProt
(1317)
NCBI
(1625)
Meta
(0)
RP15
(67)
RP35
(401)
RP55
(622)
RP75
(810)
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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
(7)
Full
(714)
Representative proteomes UniProt
(1317)
NCBI
(1625)
Meta
(0)
RP15
(67)
RP35
(401)
RP55
(622)
RP75
(810)
Alignment:
Format:
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Sequence:
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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
(7)
Full
(714)
Representative proteomes UniProt
(1317)
NCBI
(1625)
Meta
(0)
RP15
(67)
RP35
(401)
RP55
(622)
RP75
(810)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download    
Gzipped 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 (release 2.0);
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: TIGRFAMs, Finn RD
Number in seed: 7
Number in full: 714
Average length of the domain: 195.60 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 62.71 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.1 20.1
Trusted cut-off 20.3 20.4
Noise cut-off 19.8 19.2
Model length: 244
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

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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 Tic22 domain has been found. There are 2 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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