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 putative actinobacterial holin-X (Hol-X) family was retrieved as a distant member of TC family 1.E.20, suggesting membership of the holin superfamily III. Most Hol-X proteins are less than 200 amino acyl residues (aas) in length and possess two transmembrane segments (TMSs). A representative list of proteins belonging to this family can be found in the Transporter Classification Database.
The Pseudomonas aeruginosa Hol Holin Family is a group of transporters belonging to the Holin Superfamily III.
The Holin superfamily V is a superfamily of integral membrane transport proteins. It is one of the seven different holin superfamilies in total. In general, these proteins are thought to play a role in regulated cell death, although functionality varies between families and individual members. The Holin superfamily V includes the TC families:
The Holin superfamily VII is a superfamily of integral membrane transport proteins. It is one of the seven different holin superfamilies in total. In general, these proteins are thought to play a role in regulated cell death, although functionality varies between families and individual members.
The Listeria Phage A118 Holin (Hol118) Family is a group of transporters belonging to the Holin Superfamily V. A representative list of proteins belonging to the Hol118 family can be found in the Transporter Classification Database.
The Holin Hol44 (Hol44) Family is a group of transporters belonging to the Holin Superfamily V. A representative list of proteins belonging to the Hol44 family from caudovirales and firmicutes 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 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 Prophage Hp1 Hol (Hp1Hol) Family consists of a single putative holin of 69 amino acyl residues in length, exhibiting what appears to be a single transmembrane segment (TMS). It is derived from the firmicute, Clostridium hathewayi DSM 13479. This protein is functionally uncharacterized and does not appear to be homologous to other holins. It does, however, show 31% identity to a heavy metal transporter from Dethiosulfovibrio peptidovorans.
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.
