Table 3.

Percent identity from tBLASTn searches of Staphylococcus aureus genomes using the polypeptide sequences for protein encoding genes from ED98.

Protein encoding gene				tBLASTn percent identity for isolate genome(s)																Count for NCBI S. aureus Desc
Protein encoding gene			29 human	Commensals		Pathogens										X22clade
PEG	Polypeptide annotation	Length		ch3	ch5	ch9	ED98	ch21	ch22	ch23	B2-15A	B3-17D	B4-59C	B8-13D	1519	pa3	ph2	X22	ch24
47	Hypothetical	638	54	93	93	100	100	100	100	100	100	100	67	100	100	93	93	0	0	25
*48	Hypothetical	56	0	0	0	100	100	100	100	100	100	100	95	100	100	0	0	0	0	28
49	Hypothetical	452	81	96	96	100	100	100	100	100	100	100	93	100	100	96	96	29	29	381
754	Methionine ABC transporter substrate-binding	274	100	100	100	100	100	100	100	100	100	100	100	100	100	99	99	99	99	1012
*755	Integrase SaPI	407	99	45	45	100	100	100	100	100	100	100	100	100	100	99	99	100	45	307
*756	SAP domain (DNA binding domain)	463	100	0	0	100	100	100	100	100	100	100	100	100	100	100	100	100	0	53
*757	Hypothetical in SaPI	191	100	0	0	100	100	100	100	100	100	100	100	100	100	98	98	100	30	53
*758	Hypothetical in SaPI	74	100	0	0	100	100	100	100	100	100	100	100	100	100	100	100	100	0	53
*759	Winged helix-turn-helix domain-Containing	91	100	0	0	100	100	100	100	100	100	100	100	100	100	100	100	100	41	394
*760	Hypothetical in SaPI	49	100	0	0	100	100	100	100	100	100	100	100	100	100	100	100	100	96	368
*761	Hypothetical in SaPI	71	41	0	0	45	100	100	100	100	100	100	100	100	100	42	42	100	0	89
*762	Hypothetical in SaPI	120	0	0	0	0	100	100	100	100	100	100	100	100	100	0	0	100	0	24
*763	DUF1474 family	106	84	0	0	49	100	100	100	100	100	100	100	100	100	63	63	100	60	84
*764	Primase alpha helix C-terminal Domain-Containing	290	83	0	0	94	100	100	100	100	100	100	100	100	100	97	97	100	26	200
*765	DNA helicase	570	21	0	0	99	100	100	100	100	100	100	100	100	100	99	99	100	22	200
*766	Hypothetical in SaPI	127	30	0	0	99	100	100	100	100	100	100	100	100	100	98	98	100	0	199
*767	Hypothetical in SaPI	214	97	0	0	100	100	100	100	100	100	100	100	100	99	95	95	100	92	405
*768	Hypothetical in SaPI	114	97	0	0	100	100	100	100	100	100	100	100	100	100	99	99	100	98	353
*769	Hypothetical in SaPI	193	98	0	0	100	100	100	100	100	100	100	100	100	100	97	97	100	0	312
*770	Capsid morphogenesis B	43	97	0	0	100	100	100	100	100	100	100	100	100	100	97	97	100	0	312
*771	Spore coat	176	97	0	0	100	100	100	100	100	100	100	100	100	98	96	96	100	94	406
*772	Hypothetical in SaPI	114	86	36	36	100	100	100	100	100	100	100	100	100	100	85	85	100	85	405
*773	Terminase SaPI	190	97	46	46	96	100	100	100	100	100	100	100	100	100	99	99	100	96	839
*774	Hypothetical	59	0	0	0	87	100	100	100	100	100	100	100	100	100	100	100	100	0	42
*775	Hypothetical	130	0	0	0	95	100	100	100	100	100	100	100	100	100	100	100	100	0	48
*776	Hypothetical	403	0	0	0	89	100	100	100	100	100	100	100	100	100	91	91	100	0	48
*777	Hypothetical	109	44	44	44	52	100	100	100	100	100	99	100	100	100	58	58	100	55	10
*778	Hypothetical	164	0	0	0	100	100	100	100	100	100	100	100	100	100	0	0	100	0	37
779	CsbD stress response	65	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100	1011
1641	Hypothetical	121	45	60	60	64	100	100	96	64	64	84	84	64	84	60	60	38	38	7
*1642	Hypothetical	198	50	75	75	75	100	99	99	75	75	100	100	75	100	75	75	0	0	7
*1643	Secretory antigen SsaA-like transposon-related	343	61	79	79	79	100	100	99	79	79	99	99	79	99	79	79	46	46	7
*1644	Hypothetical	644	51	71	71	70	100	100	100	70	70	98	96	70	98	71	71	0	0	7
1645	Hypothetical	78	0	72	82	0	100	100	100	0	0	70	70	0	70	72	72	0	0	3
1646	Hypothetical	56	0	0	0	85	100	100	85	85	85	85	87	85	85	0	0	0	0	2
1647	Hypothetical	454	81	95	95	94	100	100	99	94	94	100	100	94	100	95	95	27	27	27
*1648	Hypothetical	111	0	69	69	0	100	100	94	0	0	94	94	0	94	69	69	0	0	7
*1649	Hypothetical	77	0	0	0	0	100	100	99	0	0	96	96	0	96	0	0	0	0	4
*1650	Hypothetical	73	0	0	0	0	100	100	100	0	0	94	94	0	94	0	0	0	0	7
1651	Hypothetical	832	85	91	91	90	100	90	100	90	90	100	97	90	100	91	91	0	0	387
*1652	Hypothetical transposon-related	130	62	78	78	78	100	100	100	78	78	98	93	78	98	78	78	0	0	7
1653	Hypothetical	87	60	72	72	72	100	100	100	72	72	97	82	72	97	72	72	0	0	7
1654	Hypothetical transposon-related	359	65	86	86	87	100	96	100	86	86	98	91	86	98	86	86	0	0	6
1655	Hypothetical	359	67	92	92	91	100	100	100	91	91	99	96	91	99	92	91	0	0	26
1656	Hypothetical	101	63	92	92	92	100	100	100	92	92	98	94	92	92	92	92	0	0	27
1657	Hypothetical	112	55	87	87	87	100	100	100	87	87	100	95	87	100	87	87	0	0	27
1658	Conserved hypothetical transposon-related	102	26	85	85	85	100	100	100	85	85	100	85	85	100	85	85	0	0	27
*1659	Hypothetical protein	95	71	78	80	87	100	100	100	87	87	99	91	87	99	78	78	0	0	22
1660	Acetyl-coenzyme A carboxyl Transferase alpha chain	315	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100	99	100	1014

PEG originally identified as possibly chicken pathogen specific are indicated (*). Annotations are derived from SEED augmented by BLASTp queries at NCBI. The 29 human isolates are from the clades surrounding the ED98 clade as described in the text and identified in Table S1. Avian isolates include 2 chicken commensals (ch3 and ch5); 10 chicken pathogens from the ED98 clade; a partridge (pa3), pheasant (ph3) and unknown host (X22) from the X22 clade; and chicken isolate ch24 (not in the ED98 or X22 clade). Count for NCBI S. aureus Desc is the number of descriptions returned (max 5000) with >80% identity for an NCBI tBLASTn search of S. aureus (Taxonomy ID: 1280), which roughly approximates the number of genome entries encoding a highly related polypeptide. Additional genome details are in the text and Table S1.