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0  structures 345  species 0  interactions 925  sequences 28  architectures

Family: TIC20 (PF16166)

Summary: Chloroplast import apparatus Tic20-like

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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.

Chloroplast import apparatus Tic20-like Provide feedback

Chloroplast function requires the import of nuclear encoded proteins from the cytoplasm across the chloroplast double membrane. This is accomplished by two protein complexes, the Toc complex located at the outer membrane and the Tic complex located at the inner membrane. 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 Tic20, a core member of the Tic complex. This protein is deeply embedded in the inner envelope membrane and is thought to function as a protein- conducting component of the Tic complex.

Literature references

  1. Kouranov A, Chen X, Fuks B, Schnell DJ;, J Cell Biol. 1998;143:991-1002.: Tic20 and Tic22 are new components of the protein import apparatus at the chloroplast inner envelope membrane. PUBMED:9817756 EPMC:9817756

  2. Dutta S, Mohanty S, Tripathy BC;, Plant Physiol. 2009;150:1050-1061.: Role of temperature stress on chloroplast biogenesis and protein import in pea. PUBMED:19403728 EPMC:19403728

  3. Kovacs-Bogdan E, Soll J, Bolter B;, Biochim Biophys Acta. 2010;1803:740-747.: Protein import into chloroplasts: the Tic complex and its regulation. PUBMED:20100520 EPMC:20100520


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005691

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 Tic20, a core member of the Tic complex. This protein is deeply embedded in the inner envelope membrane and is thought to function as a protein conducting component of the Tic complex [ PUBMED:9817756 ].

Domain organisation

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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...

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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.

  Seed
(13)
Full
(925)
Representative proteomes UniProt
(2545)
RP15
(146)
RP35
(526)
RP55
(822)
RP75
(1149)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

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  Seed
(13)
Full
(925)
Representative proteomes UniProt
(2545)
RP15
(146)
RP35
(526)
RP55
(822)
RP75
(1149)
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  Seed
(13)
Full
(925)
Representative proteomes UniProt
(2545)
RP15
(146)
RP35
(526)
RP55
(822)
RP75
(1149)
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

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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.

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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

Seed source: PF09685
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Coggill P
Number in seed: 13
Number in full: 925
Average length of the domain: 160.80 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 65.36 %

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 28.6 28.6
Trusted cut-off 28.6 28.9
Noise cut-off 28.5 28.3
Model length: 181
Family (HMM) version: 7
Download: download the raw HMM for this family

Species distribution

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