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0  structures 905  species 0  interactions 1883  sequences 4  architectures

Family: Gemini_AL2 (PF01440)

Summary: Geminivirus AL2 protein

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Geminivirus AL2 protein Provide feedback

Geminiviruses are small, ssDNA-containing plant viruses. Geminiviruses contain three ORFs (designated AL1, AL2, and AL3) that overlap and are specified by multiple polycistronic mRNAs. The AL2 gene product transactivates expression of TGMV coat protein gene [1] and BR1 movement protein.

Literature references

  1. Sunter G, Bisaro DM; , Virology 1991;180:416-419.: Transactivation in a geminivirus: AL2 gene product is needed for coat protein expression. PUBMED:1984661 EPMC:1984661


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000942

Geminiviruses are characterised by a genome of circular single-stranded DNA encapsidated in twinned (geminate) quasi-isometric particles, from which the group derives its name [PUBMED:16453696]. Most geminiviruses can be divided into two subgroups on the basis of host range and/or insect vector: i.e. those that infect dicotyledenous plants and are transmitted by the same whitefly species, and those that infect monocotyledenous plants and are transmitted by different leafhopper vectors. The genomes of the whitefly-transmitted African cassava mosaic virus, Tomato golden mosaic virus (TGMV) and Bean golden mosaic virus (BGMV) possess a bipartite genome. By contrast, only a single DNA component has been identified for the leafhopper-transmitted Maize streak virus (MSV) and Wheat dwarf virus (WDV) [PUBMED:6526009, PUBMED:2829117]. Beet curly top virus (BCTV), and Tobacco yellow dwarf virus belong to a third possible subgroup. Like MSV and WDV, BCTV is transmitted by a specific leafhopper species, yet like the whitefly-transmitted geminiviruses it has a host range confined to dicotyledenous plants.

Sequence comparison of the whitefly-transmitted Squash leaf curl virus (SqLCV) and Tomato yellow leaf curl virus (TYLCV) with the genomic components of TGMV and BGMV reveals a close evolutionary relationship [PUBMED:1840676, PUBMED:1984668, PUBMED:1926771]. Amino acid sequence alignments of Potato yellow mosaic virus (PYMV) proteins with those encoded by other geminiviruses show that PYMV is closely related to geminiviruses isolated from the New World, especially in the putative coat protein gene regions [PUBMED:1926771]. Comparison of MSV DNA-encoded proteins with those of other geminiviruses infecting monocotyledonous plants, including Panicum streak virus [PUBMED:1588314] and Miscanthus streak virus (MiSV) [PUBMED:1919519], reveal high levels of similarity.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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Alignments

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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
(116)
Full
(1883)
Representative proteomes NCBI
(1605)
Meta
(0)
RP15
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RP35
(0)
RP55
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RP75
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Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(116)
Full
(1883)
Representative proteomes NCBI
(1605)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
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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
(116)
Full
(1883)
Representative proteomes NCBI
(1605)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
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Gzipped Download   Download           Download    

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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: Prodom_1117 (release 99.1)
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 116
Number in full: 1883
Average length of the domain: 131.50 aa
Average identity of full alignment: 56 %
Average coverage of the sequence by the domain: 96.44 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.6 25.6
Trusted cut-off 25.8 27.5
Noise cut-off 25.5 25.5
Model length: 134
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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