Distribution of Genes Encoding Nucleoid-Associated Protein Homologs in Plasmids

Table 3

Plasmids containing the gene encoding IHF homolog^a.

Plasmid name	Accession no.	Source organism	Length (nt)	G+C content (%)^b	Identity (%)^c	Query coverage (%)	Subject start	Subject end	Classification^d	MOB family^e
At	NC_003064	Agrobacterium tumefaciens str. C58	542868	57	36	82	112654	112412	−	MOBQ
Megaplasmid	NC_012811	Methylobacterium extorquens AM1	1261460	68	33	94	720582	720860	−
p2META1	NC_012809	Methylobacterium extorquens AM1	37858	65	44	95	28369	28635	−	MOBQ
pAACI01	NC_013206	Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446	91726	54	43	80	62668	62432	+
pACHL01	NC_011879	Arthrobacter chlorophenolicus A6	426858	64	32	92	408818	408546	+
pALVIN02	NC_013862	Allochromatium vinosum DSM 180	39929	53	60	98	10902	10627	−
pAph01	NC_013193	Candidatus Accumulibacter phosphatis clade IIA str. UW-1	167595	62	56	95	144197	144463	−	MOBP
pAph03	NC_013191	Candidatus Accumulibacter phosphatis clade IIA str. UW-1	37695	59	58	97	5412	5140	−
pAtK84b	NC_011990	Agrobacterium radiobacter K84	184668	59	38	86	54109	53855	−	MOBQ
pAtK84c	NC_011987	Agrobacterium radiobacter K84	388169	57	43	93	340807	340532	−
					46	93	10327	10052
pAtS4b	NC_011991	Agrobacterium vitis S4	130435	56	47	97	44880	45152	−	MOBQ
pBBta01	NC_009475	Bradyrhizobium sp. BTAi1	228826	61	39	86	6642	6388	−
pBFY46	NC_006297	Bacteroides fragilis YCH46	33716	34	35	89	25098	25343	−	MOBP
pBIND01	NC_010580	Beijerinckia indica subsp. indica ATCC 9039	181736	56	36	77	179816	179601	−	MOBF
pCHQ1	NC_014007	Sphingobium japonicum UT26S	190974	63	36	90	63111	63377	−
pGLOV01	NC_010815	Geobacter lovleyi SZ	77113	53	38	92	41196	41468	−
pM44601	NC_010373	Methylobacterium sp. 4-46	57951	65	35	97	7806	7534	−
pMPOP01	NC_010727	Methylobacterium populi BJ001	25164	65	49	93	10635	10375	−
pMRAD03	NC_010514	Methylobacterium radiotolerans JCM 2831	42985	63	38	94	26778	26515	−	MOBF
pMRAD04	NC_010517	Methylobacterium radiotolerans JCM 2831	37743	64	38	94	10763	10500	−
pPRO1	NC_008607	Pelobacter propionicus DSM 2379	202397	48	41	94	129679	129957	−
pRSPA01	NC_009429	Rhodobacter sphaeroides ATCC 17025	877879	68	49	97	783519	783791	−
pSWIT01	NC_009507	Sphingomonas wittichii RW1	310228	64	40	95	106554	106820	−	MOBF
					36	92	35341	35069
pTcM1	NC_010600	Acidithiobacillus caldus	65158	57	56	89	25186	25449	−	MOBP, MOBQ
pXCV183	NC_007507	Xanthomonas campestris pv. vesicatoria str. 85-10	182572	60	33	95	138753	138490	−
Ti	NC_002377	Agrobacterium tumefaciens	194140	55	43	97	180164	180436	−	MOBQ
Ti plasmid pTiBo542	NC_010929	Agrobacterium tumefaciens	244978	55	36	86	209743	209489	−	MOBQ
					45	98	187204	187479

^aThis list is the result of a TBLASTN analysis using the amino acid sequence of IHFα or IHFβ as a query under strict conditions (i.e., thresholds of 30% identity and 70% query coverage).
^bAverage G+C content of the plasmid.
^cReported TBLASTN identity to IHF.
^dPlasmid classification according to its source organism (−, Gram-negative plasmid; +, Gram-positive plasmid).
^ePlasmid classification according to its relaxase gene sequence as described by Garcillán-Barcia et al. [16].