Summary: FANCL C-terminal domain
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FANCL C-terminal domain Provide feedback
This domain is found at the C-terminus of the Fancl protein in humans which is the putative E3 ubiquitin ligase subunit of the FA complex (Fanconi anaemia). Eight subunits of the Fanconi anaemia gene products form a multisubunit nuclear complex which is required for mono-ubiquitination of a downstream FA protein, FANCD2.
Literature references
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Gurtan AM, Stuckert P, D'Andrea AD; , J Biol Chem. 2006;281:10896-10905.: The WD40 repeats of FANCL are required for Fanconi anemia core complex assembly. PUBMED:16474167 EPMC:16474167
Internal database links
SCOOP: | Baculo_RING PHD Prok-RING_1 Prok-RING_4 RINGv zf-ANAPC11 zf-C3HC4 zf-C3HC4_2 zf-C3HC4_3 zf-HC5HC2H zf-rbx1 zf-RING_11 zf-RING_2 zf-RING_5 zf-RING_UBOX Zn_ribbon_17 |
Similarity to PfamA using HHSearch: | zf-RING-like zf-rbx1 zf-ANAPC11 zf-RING_2 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR026850
This entry represents the C-terminal domain of the FANCL, which is the E3 ubiquitin ligase subunit of the FA (Fanconi anaemia) complex [PUBMED:16474167, PUBMED:21775430, PUBMED:24389026, PUBMED:20154706]. This entry also consists of structure-specific endonuclease subunit slx1.
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan RING (CL0229), which has the following description:
This clan includes the Ring zinc finger domains as well as the U-box domain that appears to have lost the zinc coordinating cysteine residues [1].
The clan contains the following 43 members:
Baculo_IE-1 Baculo_RING DUF1644 FANCL_C IBR Prok-RING_1 Prok-RING_2 Prok-RING_4 RINGv Rtf2 T3SS_NleG U-box UPF1_Zn_bind VATC zf-ANAPC11 zf-C3H2C3 zf-C3HC4 zf-C3HC4_2 zf-C3HC4_3 zf-C3HC4_4 zf-C3HC4_5 zf-MIZ zf-NOSIP zf-Nse zf-P11 zf-rbx1 zf-RING-like zf-RING_10 zf-RING_11 zf-RING_12 zf-RING_13 zf-RING_14 zf-RING_2 zf-RING_4 zf-RING_5 zf-RING_6 zf-RING_9 zf-RING_UBOX zf-UBP zf-UBP_var zf-UDP zinc_ribbon_16 Zn_ribbon_17Alignments
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...
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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 (9) |
Full (874) |
Representative proteomes | UniProt (1407) |
NCBI (3785) |
Meta (15) |
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RP15 (137) |
RP35 (325) |
RP55 (570) |
RP75 (871) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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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 (9) |
Full (874) |
Representative proteomes | UniProt (1407) |
NCBI (3785) |
Meta (15) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (137) |
RP35 (325) |
RP55 (570) |
RP75 (871) |
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Raw Stockholm | |||||||||
Gzipped |
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
Seed source: | KOGs (KOG3268) |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
KOGs, Finn RD |
Number in seed: | 9 |
Number in full: | 874 |
Average length of the domain: | 68.40 aa |
Average identity of full alignment: | 36 % |
Average coverage of the sequence by the domain: | 14.93 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 70 | ||||||||||||
Family (HMM) version: | 9 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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 FANCL_C domain has been found. There are 5 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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