1.E.43 The Putative 3-4 TMS Transglycosylase-associated Holin (T-A Hol) Family Thousands of diverse phage and bacterial proteins of 80-140aas with 3-4 TMSs prove to be homologous. They are holin-like and are designated 'Transglycosylase-associated', 'Putative holin' 'Phage-like transmembrane protein', 'YeaQ protein', etc. in the NCBI protein database. Their functions appear to be unknown. 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 CDD (> 15 SD with the GSAT program with 20,000 random shuffles). The RDD (pfam06271) family includes members with these highly conserved residues Arg, Asp and Asp, hence the name. This region contains the first two predicted TMSs of a total of 3 or 4 TMSs. The R is at the N-terminus of the first TMS and the first D is in the middle of this helix. This region of the protein may be involved in the transport of an unknown set of ligands (A Bateman, pers. observation; see CDD). Some members are fused to other domains of recognized function.
This family belongs to the Holin IV Superfamily .
References:
Deutschbauer, A., M.N. Price, K.M. Wetmore, W. Shao, J.K. Baumohl, Z. Xu, M. Nguyen, R. Tamse, R.W. Davis, and A.P. Arkin. (2011). Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions. PLoS Genet 7: e1002385.
Hug, L.A., B.J. Baker, K. Anantharaman, C.T. Brown, A.J. Probst, C.J. Castelle, C.N. Butterfield, A.W. Hernsdorf, Y. Amano, K. Ise, Y. Suzuki, N. Dudek, D.A. Relman, K.M. Finstad, R. Amundson, B.C. Thomas, and J.F. Banfield. (2016). A new view of the tree of life. Nat Microbiol 1: 16048.
Examples:
TC#	Name	Organismal Type	Example
1.E.43.1.1	YeaQ of 82 aas and 3 TMSs	Proteobacteria	*YeaQ of Klebsiella pneumoniae* (A6TAG3)**

1.E.43.1.10	Putative holin of 83 aas and 3 TMSs	Bacteroidetes	Putative holin of Bacteroides vulgatus

1.E.43.1.11	Putative transglycosylase-associated holin of 115 aas and 3 TMSs		holin of Burkholderia pseudomallei

1.E.43.1.12	Transglycosylase, putative holin of 126 aas and 3 TMSs.		Putative holin of Planctopirus limnophila

1.E.43.1.13	Putative holin of 97 aas and 3 TMSs.		Holin of Bdellovibrio bacteriovorus

1.E.43.1.14	*Putative holin of 80 aas and 2 TMSs (Hug et al.* 2016).**		Holin of Candidatus Peribacter riflensis

1.E.43.1.15	GlsB/YeaQ/YmgE family stress response membrane protein.		*UP of Nostoc* sp. PCC 7107**

1.E.43.1.16	Antiholin/holin protein of 135 aas and 3 TMSs.		Putative holin of Pectobacterium phage MA12

1.E.43.1.2	Transglycosylase-associated protein of 86 aas and 3 TMSs	Thermobaculum	*T-A protein of Thermobaculum terrenum* (D1CIE6)**

1.E.43.1.3	Putative holin of 144 aas and 4 TMSs	Proteobacteria	*Putative holin of E. coli* (B6IAY2)**

1.E.43.1.4	Uncharacterized protein of 104 aas and 3 TMSs	Planctomycetes	*UP of Blastopirellula* marina (A3ZS55)**

1.E.43.1.5	Putative holin of 124 aas and 3 or 4 TMSs.	Proteobacteria	*Putative holin of Pseudomonas aeruginosa* (Q9I549)**

1.E.43.1.6	Putative holin	Proteobacterial phage	*Putative holin of Pseudomonas* phage phiCTX**

1.E.43.1.7	Transglycosylase associated protein of 146 aas and 3 or 4 TMSs	Deinococcus/Thermus	*T-A protein of Deinococcus radiodurans* (Q9RRU6)**

1.E.43.1.8	Uncharacterized protein of 88 aas and 3 TMSs	Actinobacteria	*Uncharacterized protein of Gordonia polyisoprenivorans* (H6N4M5)**

1.E.43.1.9	Membrane protein of 82 aas and 3 TMSs	Firmicutes	*Membrane protein of Bacillus cereus* (J8Z3M3)**

Examples:
TC#	Name	Organismal Type	Example
1.E.43.2.1	Hypothetical protein of 134 aas and 4 TMSs	Archaea	*HP of Natronobacterium gregoryi* (G4G4E5)**

1.E.43.2.2	Hypothetical Protein of 110 aas and 3 TMSs	Archaea	*HP of Pyrolobus fumarii* (G0EH17)**

1.E.43.2.3	Putative holin of 119 aas and 4 TMSs.	Euryarchaea	Putative holin of Methanobacterium paludis

1.E.43.2.4	Putative holin of 142 aas and 3 TMSs.	Euryarchaea	putative holin of Haloferax denitrificans

1.E.43.2.5	Putative holin of 112 aas and 3 TMSs.	Euryarchaea	Putative holin of Methanoculleus marisnigri

1.E.43.2.6	Putative holin of 124 aas and 4 TMSs.	Crenarchaea	Putative holin of Pyrobaculum aerophilum

1.E.43.2.7	Putative holin of 123 aas and 4 TMSs. There appears to be a 2 TMS repeat unit, so that TMSs 1 - 2 are homolous to TMSs 3 - 4.		Putative holin of Methanobacterium lacus

1.E.43.2.8	Uncharacterized protein of 168 aas and 4 TMSs, YckC3.		YckC3 of Desulfovibrio gigas

1.E.43.2.9	Putative holin of 103 aas and 3 TMSs.		Putative holin of Klebsiella pneumoniae

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