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0  structures 3  species 0  interactions 3  sequences 1  architecture

Family: Gp79 (PF17463)

Summary: Gene Product 79

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Gene Product 79 Provide feedback

This is a domain of unknown function found in Mycobacterium phage. Family members include the full Gp79 protein found in Mycobacteriophage L5 Q05294. Mycobacteriophage L5, is a phage isolated from Mycobacterium smegmatis. It forms stable lysogens in M. smegmatis and has a broad host range among the pathogenic mycobacteria. L5 encodes gene products (gp) toxic to the host M. smegmatis. Expression of gp79 interferes with the cell membrane or cell-wall synthesis of M. smegmatis, leading to altered cell morphology. It also has a bactericidal effect on E. coli. The N-terminal segment of gp79 (amino acids 1–41) shares sequence similarity with the signal peptide of the D-alanylD-alanine carboxypeptidase of Bacillus licheniformis. This enzyme removes C-terminal D-alanyl residues from sugarpeptide cell-wall precursors and is also a penicillin-binding protein (PBP). The homology of the hydrophobic N-terminal part of gp79 to a PBP (penicillin-binding protein) signal peptide may indicate an interaction of gp79 with proteins or metabolites involved in the peptidoglycan synthesis of M. smegmatis [1].

Literature references

  1. Rybniker J, Plum G, Robinson N, Small PL, Hartmann P;, Microbiology. 2008;154:2304-2314.: Identification of three cytotoxic early proteins of mycobacteriophage L5 leading to growth inhibition in Mycobacterium smegmatis. PUBMED:18667563 EPMC:18667563


This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

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 (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
(3)
Full
(3)
Representative proteomes UniProt
(109)
NCBI
(84)
Meta
(0)
RP15
(2)
RP35
(2)
RP55
(3)
RP75
(3)
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PP/heatmap 1 View               

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(3)
Full
(3)
Representative proteomes UniProt
(109)
NCBI
(84)
Meta
(0)
RP15
(2)
RP35
(2)
RP55
(3)
RP75
(3)
Alignment:
Format:
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Sequence:
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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
(3)
Full
(3)
Representative proteomes UniProt
(109)
NCBI
(84)
Meta
(0)
RP15
(2)
RP35
(2)
RP55
(3)
RP75
(3)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download    
Gzipped Download   Download   Download   Download   Download   Download   Download   Download    

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 View help on the curation process

This family is new in this Pfam release.

Seed source: PRODOM:PD475322
Previous IDs: none
Type: Family
Author: El-Gebali S
Number in seed: 3
Number in full: 3
Average length of the domain: 50.30 aa
Average identity of full alignment: 60 %
Average coverage of the sequence by the domain: 68.95 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 35.4 107.0
Noise cut-off 24.0 23.0
Model length: 51
Family (HMM) version: 1
Download: download the raw HMM for this family

Species distribution

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