The PRD1 Phage P35 Holin Family is a member of Holin Superfamily III. The prototype for this family is the lipid-containing PRD1 enterobacterial phage holin protein P35 encoded by gene XXXV (orfT). It is a component of a typical holin-endolysin system which functions to lyse the host bacterial cell.
The Actinobacterial 1 TMS Holin Family consists of proteins found in actinobacteria, their conjugative plasmids and their phage. They are usually between 90 and 140 amino acyl residues (aas) in length and exhibit 1 or sometimes even 2 transmembrane segments despite the families name. Although some are annotated as phage proteins or holins, members of the A-1 family are not yet functionally characterized. A representative list of proteins belonging to the A-1 Holin family can be found in the Transporter Classification Database (TCDB).
The 2 or 3 TMS Putative Holin Family consists of many proteobacterial proteins ranging in size from about 70 to 120 amino acyl residues (aas) in length that exhibit 2 or 3 predicted transmembrane segments (TMSs). Although annotated as holins, these proteins are not yet functionally characterized. A representative list of proteins belonging to the 2/3 Holin family can be found in the Transporter Classification Database.
The Phage T1 Holin Family is represented in enterobacterial phages T1, RTP and F20, Klebsiella phage KP36, and Escherichia phage ADB-2. All of these possess a putative holin that share a high level of identity. Additionally, Gp9 of E. coli phage phiE49 is similar in sequence. These proteins are short, 55 to 71 amino acyl residues (aas) in length, and exhibit a single transmembrane segment (TMS). A representative list of proteins belonging to the T1 Holin family can be found in the Transporter Classification Database.
The Staphylococcusphage P68 Putative Holin Family consists of a single putative holin from Staphylococcus aureus phage P68 that is 92 amino acyl residues (aas) in length and exhibits 2 transmembrane segments (TMSs). While annotated as a holin, this protein has not been functionally characterized.[2]
The Mycobacterial Phage PBI1 Gp36 Holin Family consists of a single protein, Gp36 of Mycobacterial phage PBI1 identified by Castalao et al. (2012). Gp36 is 116 amino acyl residues (aas) in length and exhibits 2 transmembrane segments (TMSs). While annotated as a holin, this protein has not been functionally characterized.
The putative holin-like toxin (Hol-Tox) family consists of many small proteins, between 34 and 48 amino acyl residues (aas) with a single transmembrane segment (TMSs). Rajesh et al. first identified the gene and designated it tmp1, which coded for a 34 amino acyl peptide that acts as an antibacterial agent on gram-positive bacteria. This peptide exhibits a single transmembrane domain (TMD) that is believed to play a role in facilitating the antibacterial activity. A representative list of proteins belonging to the Hol-Tox family can be found in the Transporter Classification Database.
The Putative 3-4 TMS Transglycosylase-associated Holin Family is believed to be a group of holins that does not belong to one of the seven holin superfamilies. Homologues include thousands of diverse phage and bacterial proteins between 80 and 140 amino acyl residues (aas) in length that exhibit 3 to 4 transmembrane segments (TMSs). These proteins are holin-like in their size and topology and are designated 'Transglycosylase-associated', 'Putative holin', 'Phage-like transmembrane protein', 'YeaQ protein', etc. in the NCBI protein database. As of early 2016, they remain functionally uncharacterized. They derive from a wide range of bacterial and archaeal phyla including both Gram-negative and Gram-positive bacteria. These proteins are related to the RDD family in the conserved domain database. A representative list of proteins belonging to the T-A Hol family can be found in the Transporter Classification Database.
The Putative Lactococcus lactis Holin (LLHol) Family consists of just a few proteins from Lactococcus lactis species and their phage. These proteins are small, between 61 and 78 amino acyl residues (aas) in length, and exhibit one or two transmembrane segments (TMSs). As of March 2016, LLHol proteins remain functionally uncharacterized. They are not demonstrably homologous to members of other holin families and thus do not belong to one of the seven holin superfamilies. A representative list of proteins belonging to the LLHol family can be found in the Transporter Classification Database.
The XanthomonasPhage Holin (XanPHol) Family consists of a single protein of 64 amino acyl residues (aas) in length with 2 transmembrane segments (TMSs). It is a putative uncharacterized protein from Xanthomonas phage Xp15. This protein corresponds to sequence 68 from patent US 7919601. As of March 2016, this protein does not show appreciable sequence similarity to any other proteins in the NCBI protein database.
The CaulobacterPhage Holin (CauHol) Family consists of several putative holins of 157 to 159 amino acyl residues (aas) in length that exhibit 2 transmembrane segments (TMSs). They derive from phage specific for Caulobacter species. These proteins are not functionally characterized. A representative list of proteins belonging to the CauHol family can be found in the Transporter Classification Database.
The Putative Treponema 4 TMS Holin (Tre4Hol) Family consists of several proteins from Treponema species. They range in size from 100 to 110 amino acyl residues (aas) in length and exhibit 4 transmembrane segments (TMSs). A fragment has been sequenced from Treponema phage Phi td1 (D2ECI8) and was designated a putative holin.
The β-proteobacterial holin (BP-Hol) family is a small family that includes members derived from a number of Burkholderia phage as well as a Poloromonas species. As of April 3, 2016, this family belongs to the Holin superfamily II. Members of Saier Bioinformatics Lab at University of California, San Diego found that the BP-Hol family is most closely related to the T7 holin family. These proteins are of 60 to 110 amino acyl residues (aas) in length and exhibit 1 or 2 transmembrane segments (TMSs). Some are annotated as type II hollins and may be related to members of the T7 Holin family, although BP-Hol proteins remain functionally uncharacterized. A representative list of the proteins belonging to the BP-Hol family can be found in the Transporter Classification Database.
The Putative Listeria Phage Holin (LP-Hol) Family consists of several small proteins of 41 amino acyl residues (aas) and 1 transmembrane segment (TMS). They can be found in several Listeria phage as well as in Listeria monocytogenes. While annotated as holins, these proteins remain functionally uncharacterized. A representative list of proteins belonging to the LP-Hol family can be found in the Transporter Classification Database.
The Flp/Fap Pilin Putative Holin (FFPP-Hol) Family is a large diverse family with members from many bacterial phyla. Some members are annotated as Flp or Fap pilin subunits; others are identified as Holin BlyA family members. They range in size of 50 to 80 amino acyl residues (aas) with a single N-terminal transmembrane segment (TMS) although one member has 99 aas and 2 TMSs. Flp homologues are included in TCDB under TC# 3.A.7.13.1 (pXO1-63) and TC# 3.A.7.15.1 (Flp-1). As on March 2016, their precise functions appear to be unknown. A representative list of proteins belonging to the FFPP-Hol family can be found in the Transporter Classification Database.
The Putative 3 TMS Holin (3-Hol) Family is large, consisting of many members derived from proteobacteria and their phage, all of small size and usually with 3 transmembrane segments (TMSs). A representative list of the proteins belonging to this family can be found in the Transporter Classification Database. While many of the proteins belonging to this family are annotated in holins, they remain functionally uncharacterized.
The Putative Archaeal 2 TMS Holin (A2-Hol) Family consists of a few putative holins from Thaumarchaeota ranging in size from about 130 to 165 amino acyl residues (aas) and exhibiting 2 transmembrane segments (TMSs). A representative list of proteins belonging to the A2-Hol family can be found in the Transporter Classification Database. The archaeon, Candidatus Nitrosoarchaeum limnia, encodes adjacent genes designated Toxin Secretion/Lysis Holin. The "toxin" gene encodes a soluble protein of 325 aas stated as belonging to the "Glycosyltransferase GBT-type Superfamily". This protein brings up other glycosyltransferases in a NCBI BLAST search. The adjacent gene encodes a small protein of 132 aas and 2 TMSs that could be a holin, based on its size and topology. This protein has the UniProt accession number of S2E3C4. Paralogues are found in this same organism and other closely related species.
The Putative Bacterial Archaeal Holin(BAH) Family consists of several uncharacterized proteins. However, these proteins were retrieved when functionally characterized holins from the T-A Hol family were BLASTED against the NCBI database, and thus may be related to the T-A Hol family. Most BAH proteins are between 125 and 140 amino acyl residues (aas) in length and exhibit 4 transmembrane segments (TMSs), although at least one putative holin is almost 260 aas long. A representative list of proteins belonging to the BAH family can be found in the Transporter Classification Database.
The BhlA Holin Family is named after putative holin-like peptides encoded in bacteria with bacteriocin similarities. BhlA proteins are generally about 67 to 80 amino acyl residues (aas) in length and exhibit a single N-terminal transmembrane segment (TMS). BhlA. It has an antibacterial activity against Gram-positive bacteria. A representative list of proteins belonging to this family can be found in the Transporter Classification Database.
The Firmicute PhageφU53 Holin Family consists of putative holins that range in size from 117 to 124 amino acyl residues (aas) in length and exhibit 3 transmembrane segments (TMSs) found in Firmicute phage. While annotated as holins, it appears as though many members of the φU53 holin family are not yet functionally characterized. A representative list of homologues can be found in the Transporter Classification Database.
