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What is a spanin?
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Spanins are a class of proteins usually encoded by phages (or prophages) that infect Gram-negative bacteria. These proteins function in the last step of lysis, disrupting the outer membrane and allowing phage progeny release from infected cells. Two broad classes of spanins are the unimolecular spanins, such as gp11 in phage T1 (Kongari et al. 2018), that consist of a single protein anchored by a transmembrane domain in the inner membrane, and the outer membrane by lipoylation, and the bimolecular spanins, such as Rz and Rz1 of phage lambda (Berry et al. 2008), which divide the anchors between two proteins.
Additional detailed information concerning spanin genetic architecture, mechanism of action, and diversity can be found in Kongari et al. 2018 and Cahill & Young 2019.
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How do I find and annotate spanins in my phage genome?
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The Center for Phage Technology has prepared two tutorials with background and detailed instructions on using Galaxy and Apollo for finding spanin genes within phage genomes. The first tutorial, Finding Lysis Genes, explains what kinds of spanins are known to exist, and how to spot them when annotating a phage genome in Apollo. The second tutorial, the Advanced Lysis Gene Search, gives pointers for hard-to-find spanins, such as those that might not have any BLAST hits to known spanins.
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Where did this data come from?
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Most of the spanins in this database were described in the bioinformatic study by Kongari et al. 2018. The actual data populating the pages here were retrieved from NCBI.
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Why are there alternate sequence versions for some spanins?
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Each spanin protein in this database was hand-curated. Care was taken to ensure that biologically relevant gene starts were selected, but sometimes bioinformatics is not sufficient to determine the correct gene start. In fact, some spanins may have multiple starts as a form of regulation (see Kongari et al. 2018). This can be the source of alternative sequences displayed.
A second source can be the protein used in the NCBI record, which may use a gene start that doesn't have an upstream Shine-Dalgarno sequence. Since these genes are called, and similar protein sequences will be in public databases, they are shown here for comparison.
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Can the spanin proteins from my phage be added to DBoP?
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Yes, high-quality annotations of spanin proteins with evidence for the transmembrane domain and/or lipobox for the lipoylation signal are accepted. Please send inquiries to CPT@tamu.edu, and be prepared to share spanin protein fasta files, NCBI genome/gene accessions and coordinates, and the source of evidence for the annotations for review.