Multiple sequence alignments of representative sequences of COG3926/DUF847 (a), T4 lysozyme family (b), COG5526 (c), and lytic transglycosylases (d). The sequence identifiers on the left are NCBI gene identification (gi) numbers. The red gi numbers indicate sequences with known three-dimensional structures, with Protein Data Bank (PDB) IDs (Berman et al. 2002) following them. The blue gi number(s) in italic, underlines, and bold letters correspond to proteins with signal peptide, LATM1, and LATM2, respectively. The species name abbreviations are shown after the gi numbers, with bacteriophage species in blue letters. The first and the last residue numbers and the sequence length are shown. The numbers of residues between core blocks are shown in parentheses, with the exception of gi|433223, where there are seven residues inserted between the underlined “N” and “G.” The catalytic glutamate and aspartate, as well as the second residue in motif Pho-[Asn|Gln] are highlighted as white letters on black background. They are also marked under the alignments of T4 lysozyme family and lytic transglycosylase family with known structures (catalytic residues, triangles; Pho-[Asn|Gln] motif, stars). Conserved positions with mainly glycines are shaded in gray. Positions occupied by mainly hydrophobic residues are shaded in yellow. Two sequence signatures characteristic of peptidoglycan-binding motif are colored pink (Leu–Gln in α-helix A4 and Asp–Gly in the loop after it). Real secondary structural elements of T4 lysozyme (PDB ID 4lzm) and a lytic transglycosylase (PDB ID 1qsa) are shown as cartoon diagrams: cylinders as α-helices and arrows as β-strands. Blue α-helices are essential elements present in all lysozyme-like families and gray α-helices are not present in all of them. The predicted secondary structures for the COG3926/DUF847 family and COG5526 family are shown above their alignments. Species name abbreviations are 44RR2, Bacteriophage 44RR2.8t; Aa, Aquifex aeolicus; Aeh1, Bacteriophage Aeh1; Ba, Brucella abortus; Bf, Burkholderia fungorum; BIP1, Bordetella phage BIP1; Bj, Bradyrhizobium japonicum; Bm, Brucella melitensis; Bq, Bartonella quintana; Cb, Coxiella burnetii; Cc, Caulobacter crescentus; Dd, Dictyostelium discoideum; Dh, Desulfitobacterium hafniense; Dv, Desulfovibrio vulgaris; Ec, Escherichia coli; Eca, Erwinia carotovora; Hp, Helicobacter pylori; KMV, Bacteriophage φKMV; Md, Microbulbifer degradans; Ml, Mesorhizobium loti; Mm, Magnetospirillum magnetotacticum; Ms, Mannheimia succiniciproducens; Na, Novosphingobium aromaticivorans; Nm, Neisseria meningitidis; Ns, Nostoc sp.; PaP3, Pseudomonas aeruginosa phage PaP3; Pg, Porphyromonas gingivalis; φ8, Bacteriophage φ8; Re, Ralstonia eutropha; Rr, Rhodospirillum rubrum; Rs, Rhodobacter sphaeroides; Sen, Salmonella enterica; Sel, Synechococcus elongatus; Sp, Silicibacter pomeroyi; Ss, Silicibacter sp.; T4, Enterobacteria phage T4; Te, Trichodesmium erythraeum; Tp, Treponema pallidum; VHML, Vibrio harveyi bacteriophage VHML; VP16T, Vibrio parahaemolyticus phage VP16T; Vv, Vibrio vulnificus; Xa, Xanthomonas axonopodis; Zm, Zymomonas mobilis.

Domain architecture of COG3926/DUF847 and COG5526 proteins. The lengths of domains are approximately to scale. Horizontal braces together with the arrows under them suggest homology relationship between domains that can be linked by PSI-BLAST with significant e-values. The two lysozyme-associated transmembrane modules are shown with dotted boundary lines. Predicted transmembrane regions are marked rectangles, with one low confidence prediction shown with dotted boundary line. NCBI gene identification (gi) numbers and species names of representative sequences are shown. The number of proteins with a domain architecture is shown in parentheses after the domain diagram. (a) Single-domain proteins of COG3926/DUF847; (b) the COG3926/DUF847 member with a signal peptide; (c) COG3926/DUF847 members with LATM1; (d) T4 lysozyme family members with LATM1; (e) the COG3926/DUF847 member with LATM2; (f) COG5526 members with PGB and LATM2; (g) single-domain COG5526 members.