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0  structures 99  species 0  interactions 154  sequences 1  architecture

Family: Adeno_52K (PF03052)

Summary: Adenoviral protein L1 52/55-kDa

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Adenoviral protein L1 52/55-kDa Provide feedback

The adenoviral protein L1 52/55-kDa is expressed in both the early and late stages of infection which suggests that it could play multiple roles in the viral life cycle. The L1 52/55 kDa protein interacts with the viral IVa2 protein and is required for DNA packaging [2]. L1 53/55-kDa is required to mediate stable association between the viral DNA and empty capsid [2].

Literature references

  1. Chiocca S, Kurzbauer R, Schaffner G, Baker A, Mautner V, Cotten M; , J Virol 1996;70:2939-2949.: The complete DNA sequence and genomic organization of the avian adenovirus CELO. PUBMED:8627769 EPMC:8627769

  2. Gustin KE, Lutz P, Imperiale MJ; , J Virol. 1996;70:6463-6467.: Interaction of the adenovirus L1 52/55-kilodalton protein with the IVa2 gene product during infection. PUBMED:8709283 EPMC:8709283

  3. Gustin KE, Imperiale MJ; , J Virol. 1998;72:7860-7870.: Encapsidation of viral DNA requires the adenovirus L1 52/55-kilodalton protein. PUBMED:9733823 EPMC:9733823


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004292

The adenoviral protein 52K (named after the earliest known 52kDa members) is a DNA-binding protein [PUBMED:8627769]. The adenoviral 52K protein is encoded by a late gene [PUBMED:9791022] in various adenoviruses including the avian adenovirus: chicken embryo lethal orphan (CELO) virus [PUBMED:8627769].

The adenoviral protein L1 52/55 kDa is expressed in both the early and late stages of infection which suggests that it could play multiple roles in the viral life cycle. The L1 52/55 kDa protein interacts with the viral IVa2 protein and is required for DNA packaging [PUBMED:8709283, PUBMED:9733823]. L1 53/55 kDa is required to mediate stable association between the viral DNA and empty capsid [PUBMED:8709283].

This entry represents the adenoviral 52kDa-like protein and includes proteins involved in virion assembly.

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

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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.

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(18)
Full
(154)
Representative proteomes NCBI
(150)
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(0)
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RP35
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RP55
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RP75
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  Seed
(18)
Full
(154)
Representative proteomes NCBI
(150)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
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  Seed
(18)
Full
(154)
Representative proteomes NCBI
(150)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
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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:

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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: Pfam-B_2151 (release 6.4)
Previous IDs: none
Type: Family
Author: Mifsud W
Number in seed: 18
Number in full: 154
Average length of the domain: 187.10 aa
Average identity of full alignment: 52 %
Average coverage of the sequence by the domain: 54.87 %

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 25.0 25.0
Trusted cut-off 47.2 46.8
Noise cut-off 21.7 17.9
Model length: 201
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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