TABLE 3.

Prophages and genomic islands of C. rodentium ICC168

Name	Start position	End position	Length (bp)	Insertion site	Flanking repeat (bp)a	Type	Virulence-related and other notable factors encoded
Prophages
CRP28	285,573	325,997	40,425	lfiG-lfiI	ND	Mu-like prophage; intact	Dam
CRP99	990,424	1,027,608	37,185	ROD_08971	ND	Mu-like prophage; intact	Dam
CRPr11	1,143,137	1,151,111	7,975	ROD_t18 (tRNASer)	70 DR	Putative lambdoid prophage; remnant
CRPr13	1,304,879	1,315,433	10,555	potC-potB	12 DR	Putative lambdoid prophage; remnant	Three T3SS effectors (EspX7, EspN1c, EspK)
CRPr17	1,762,632	1,769,107	6,476	uspF-ttcA	25 DR (2 MM)	putative lambdoid prophage; remnant	Three T3SS effectors (NleC, NleB2c, NleG1)
CRPr20	2,096,166	2,115,165	19,000	fliC	8 DR	P2-like prophage; remnant	Dam
phiNP	2,730,430	2,775,336	44,907	ssrA (tmRNA)	25 DR	Untypeable prophage; intact	Five DNA methyltransferases (3 Dam, 1 Dcm, 1 unknown), DinI
CRPr33	1,304,879	1,315,433	3,912	ROD_31701-ROD_31781	ND	Putative lambdoid prophage; remnant	Three T3SS effectors (NleG2c, NleGc, EspM3)
CRP38	3,838,308	3,875,066	36,759	ROD_36451	ND	P2-like prophage; intact	HokA
CRP49	4,945,776	4,986,231	40,460	gatD	28 IR (8 MM) 4 DR	Mu-like prophage; intact	tRNAArg
Genomic islands
GI1	363,963	378,377	14,415	ROD_t04(tRNAThr)-ROD_03491	40 IR (2 MM)	Genomic island; no integrase; previously IS flanked	Two T3SS effectors (EspS, NleA/EspI), Aap-like protein, tRNAThr
GI2	981,787	1,036,635	17,664	ROD_t17(tRNASer)	ND	Putative genomic island; no integrase	T1SS and large repetitive proteinc
GI3	1,151,112	1,154,180	3,069	ROD_t18(tRNASer)	70 DR (1 D, 3 MM)	Genomic island; integrasec
GI4	1,185,005	1,194,883	9,879	ROD_t19(tRNASer)	18 DR (1 MM)	Genomic island; integrasec	Three T3SS effectors (EspL2, NleB1 and NleE)
GI5	2,147,048	2,164,244	17,197	ROD_t28(tRNASer)	19 DR (1 MM)	Genomic island; integrase	Two H-NS
GI6	2,712,024	2,730,042	18,019	smpB_ssrA	ND	Putative genomic island; no integrase	T1SS and large repetitive protein
GI7	2,775,891	2,794,475	18,585	ROD_26351-ROD_26491	ND	Genomic island; no integrase; IS flanked	LifA
GI8	3,124,334	3,142,596	18,263	ROD_29461-ROD_29651	ND	Genomic island; no integrase; IS flanked	CroR/I, T1SS, and large repetitive protein
LEE	3,142,637	3,183,242	40,606	ROD_29641-ROD_30191	ND	Genomic island; no integrase; IS flanked	T3SS, intimin, seven T3SS effectors (EspG, EspF, EspB, Tir, Map, EspH, EspZ)
GI9	3,340,622	3,370,076	29,455	ROD_t53(tRNAPhe)	ND	Genomic island; integrasec	LifA-like protein, one T3SS effector (EspN2-1c)
GI10	3,517,032	3,557,418	40,387	ROD_t56(tRNALeu)	51 DR (1MM)	Degenerate ICE element (ICECr1); integrasec	T1 RM system (M+,S+,R−)
GI11	4,316,630	4,333,192	16,563	ROD_40761-ROD_41011	ND	Genomic island; no integrase; IS flanked	Intimin-like proteinc, five T3SS effectors (EspM1c, EspO, EspT, NleG8. and EspM2)
GI12	5,017,131	5,037,202	20,072	ROD_47721-ROD_47851	ND	Genomic island; no integrase; IS flanked	LifA-like protein, one T3SS effector (EspN2-2)
GI13	5,064,524	5,087,409	22,886	ROD_48131-ROD_48201	ND	Putative genomic island, no integrase	T1SS and large repetitive proteinc
GI14	5,146,469	5,158,968	12,500	yjjG-prfC	22 DR (4 MM)	Genomic island; integrasec	Four T3SS effectors (NleH, NleF, NleG7, and EspJ)
GI15	5,207,322	5,212,668	5,347	ROD_t85(tRNA-gly)	21 DR	Genomic island; integrase
GI16	5,218,554	5,271,734	53,181	ROD_t86(tRNAPhe)	17 DR	Genomic islandb; integrase	AIDA-like protein, hemolysin, PagC-like protein

^aND, none detected; DR, direct repeat; IR, inverted repeat; MM, mismatch; D, deletion.

^bAlso known as GIpheV-CR_ICC168 (32).

^cPseudogene.