Summary: Retrotransposon gag protein
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Retrotransposon gag protein Provide feedback
Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved .
Nakayashiki H, Matsuo H, Chuma I, Ikeda K, Betsuyaku S, Kusaba M, Tosa Y, Mayama S; , Nucleic Acids Res 2001;29:4106-4113.: Pyret, a Ty3/Gypsy retrotransposon in Magnaporthe grisea contains an extra domain between the nucleocapsid and protease domains. PUBMED:11600699 EPMC:11600699
This tab holds annotation information from the InterPro database.
InterPro entry IPR005162
Transposable elements (TEs) promote various chromosomal rearrangements more efficiently, and often more specifically, than other cellular processes. Retrotransposons are structurally similar to retroviruses and are bounded by long terminal repeats. This entry represents eukaryotic Gag or capsid-related retrotranspon-related proteins. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved [PUBMED:11600699].
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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 DUF4939 PNMA Retrotran_gag_2 Retrotran_gag_3 Retrotrans_gag
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Curation and family details
|Seed source:||Pfam-B_3194 (release 7.0)|
|Number in seed:||56|
|Number in full:||3711|
|Average length of the domain:||93.30 aa|
|Average identity of full alignment:||17 %|
|Average coverage of the sequence by the domain:||13.55 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 11927849 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||14|
|Download:||download the raw HMM for this family|
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