Summary: gag-polypeptide of LTR copia-type
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gag-polypeptide of LTR copia-type Provide feedback
This family is found in Plants and fungi, and contains LTR-polyproteins, or retrotransposons of the copia-type.
Internal database links
|Similarity to PfamA using HHSearch:||UBN2|
External database links
This tab holds annotation information from the InterPro database.
No InterPro data for this Pfam family.
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
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This superfamily is characterised by family members that ar derived from retrotransposons of the copia-type.
The clan contains the following 7 members:DUF1759 DUF4219 PNMA Retrotrans_gag UBN2 UBN2_2 UBN2_3
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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Curation and family details
|Number in seed:||97|
|Number in full:||1112|
|Average length of the domain:||105.80 aa|
|Average identity of full alignment:||19 %|
|Average coverage of the sequence by the domain:||15.57 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||1|
|Download:||download the raw HMM for this family|
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