TABLE 1.

Differential biomarkers for old (isolated before 1980) and new (isolated after 1980) M1 and M28 strains and their putative functions

Clustera	Phageb	Accession no.	Biomarker	Coordinates (beginning … end)	Name	Function
1	6180.2 (SpeK and Sla)	NC_007296	1	1266943 … 1267323	M28_Spy1283	Phage protein
			1266570 … 1266929	M28_Spy1282	Phage transcriptional regulator, Cro/CI family
			2	1265583 … 1265774	M28_Spy1281	Phage protein
			3	1264844 … 1265572	M28_Spy1280	Phage antirepressor protein
			4	1256286 … 1256507	M28_Spy1257	Phage protein
			5	1255757 … 1256014	M28_Spy1256	Phage protein
			6	1251854 … 1253065	M28_Spy1250	Terminase large subunit
			7	1246284 … 1246700	M28_Spy1243	Phage protein
						8	1239705 … 1240421	M28_Spy1235	Phage protein
						9	1240418 … 1243699	M28_Spy1235	Phage protein
						10	1237561 … 1239708	M28_Spy1234	Phage endopeptidase
						11	1234137 … 1236023	M28_Spy1231	Phage protein
							1232591 … 1232776	M28_Spy1227	Phage protein
							1231278 … 1232480	M28_Spy1226	Phage-associated cell wall hydrolase
						12	1228677 … 1229471	M28_Spy1223	SpeK
2	6180.1 (SpeC)	NC_007296	13	1001137 … 1001460	M28_Spy0981	Phage protein
			14	997487 … 1001122	M28_Spy0980	Phage protein
			15	994625 … 996679	M28_Spy0977	Phage protein
3	315.6 (Sdn)	NC_004589	16	32577 … 34589	SpyM3_1417	Phage infection protein
			17	36745 … 37476	SpyM3_1411	Phage-associated cell wall hydrolase
4	315.6 (Sdn)	NC_004589	18	2307 … 1927	SpyM3_1456	Phage protein
			2695 … 2324	SpyM3_1455	Phage transcriptional regulator, Cro/CI family
			19	5022 … 5222	SpyM3_1447	Phage protein
			5313 … 5609	SpyM3_1446	Phage protein
			20	7389 … 9308	SpyM3_1443	Phage-encoded DNA polymerase
			21	9316 … 11697	SpyM3_1442	DNA primase
			22	20647 … 21531	SpyM3_1429	Phage protein
			23	24338 … 28717	SpyM3_1421	Phage protein
						24	28732 … 29571	SpyM3_1420	Phage protein
						25	29584 … 31560	SpyM3_1419	Phage endopeptidase
		5005.3 (SdaD2)	NC_007297	18	1423403 … 1423804	M5005_Spy_1465	Phage protein
	M5005_Spy_1464			Phage transcriptional regulator, Cro/CI family
	19			1420497 … 1420796	M5005_Spy_1454	Phage protein
	M5005_Spy_1453			Phage protein
	20			1416408 … 1418330	M5005_Spy_1450	Phage-encoded DNA polymerase
	21			1414019 … 1416403	M5005_Spy_1449	DNA primase
	22			1404178 … 1404747	M5005_Spy_1435	Phage scaffold protein
	1403278 … 1404165			M5005_Spy_1434	Phage protein
						23	1396092 … 1400474	M5005_Spy_1426	Phage protein
			24	1395238 … 1396080	M5005_Spy_1425	Phage protein
			25	1393246 … 1395228	M5005_Spy_1424	Phage endopeptidase
					M5005_Spy_1423	Hyaluronoglucosaminidase
5	5005.3 (SdaD2)		26	1389641 … 1391548	M5005_Spy_1422	Phage protein
		27	1389641 … 1391548	M5005_Spy_1421	Phage infection protein
		28	1389471 … 1389632	M5005_Spy_1420	Phage protein
		1388848 … 1389468	M5005_Spy_1419	Phage protein
		29	1387049 … 1388245	M5005_Spy_1416	Phage-associated cell wall hydrolase
		30	1385761 … 1386933	M5005_Spy_1415	SdaD2
6	5005.1 (SpeA2)	NC_007297	31	989426 … 991177	M5005_Spy_1006	Phage structural protein
			32	991293 … 994733	M5005_Spy_1007	Phage protein
			33	996219 … 998024	M5005_Spy_1009	Phage protein
			34	996219 … 998024	M5005_Spy_1010	Phage protein
			35	1001072 … 1001962	M5005_Spy_1018	Phage protein
			M5005_Spy_1019	Phage scaffold protein
			36	1003948 … 1005273	M5005_Spy_1021	Phage protein
			M5005_Spy_1022	Portal protein
			37	1006537 … 1006917	M5005_Spy_1023	Terminase large subunit
			38	1006537 … 1006917	M5005_Spy_1024	phage protein
					M5005_Spy_1025	Phage-encoded transcriptional regulator, ArpU

^aClusters of biomarkers shown in Fig. 1.

^bSuperantigens, streptodornases, and a phospholipase, encoded on the different prophages, are indicated in parentheses.