Distribution of Genes Encoding Nucleoid-Associated Protein Homologs in Plasmids

Table 2

Plasmids containing the gene encoding HU 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
1	NC_006823	Aromatoleum aromaticum EbN1	207355	58	55	99	186175	185909	−
1	NC_007949	Polaromonas sp. JS666	360405	57	52	99	61052	60786	−	MOBH
1	NC_008010	Deinococcus geothermalis DSM 11300	574127	66	38	97	550805	550545	+
1	NC_008503	Lactococcus lactis subsp. cremoris SK11	14041	34	37	94	9732	10007	+	MOBP
1	NC_008242	Chelativorans sp. BNC1	343931	62	41	94	133932	133678	−	MOBQ
2	NC_012529	Deinococcus deserti VCD115	314317	64	38	93	269648	269899	+
3	NC_012528	Deinococcus deserti VCD115	396459	61	40	96	8700	8957	+
Megaplasmid	NC_007974	Cupriavidus metallidurans CH34	2580084	64	51	99	1393415	1393149	−	MOBV
Megaplasmid	NC_005863	Desulfovibrio vulgaris str. Hildenborough	202301	66	31	98	5502	5765	−
Megaplasmid pDF308	NC_013940	Deferribacter desulfuricans SSM1	308544	24	41	100	253817	253548	−
Megaplasmid pHG1	NC_005241	Ralstonia eutropha H16	452156	62	48	99	343060	342791	−
p49879.1	NC_006907	Leptospirillum ferrooxidans	28878	58	47	99	3281	3015	−	MOBQ
p49879.2	NC_006909	Leptospirillum ferrooxidans	28012	55	48	99	15858	15592	−	MOBQ
pAH187_270	NC_011655	Bacillus cereus AH187	270082	34	59	100	113139	112870	+
pAH820_272	NC_011777	Bacillus cereus AH820	272145	34	58	100	153060	152791	+
pAM04528	NC_012693	Salmonella enterica	158213	52	57	99	14067	14333	−	MOBH
pAOVO01	NC_008765	Acidovorax sp. JS42	72689	62	46	100	65140	64871	−	MOBF
pAPA01-011	NC_013210	Acetobacter pasteurianus IFO 3283-01	191799	53	47	100	154736	154467	−
					46	99	38442	38708
pAR060302	NC_012692	Escherichia coli	166530	53	57	99	15755	16021	−	MOBH
pAsa4	NC_009349	Aeromonas salmonicida subsp. salmonicida A449	166749	53	60	99	26844	26578	−	MOBH
pAtS4c	NC_011984	Agrobacterium vitis S4	211620	59	45	94	141245	140991	−	MOBQ
pAtS4e	NC_011981	Agrobacterium vitis S4	631775	57	41	94	40476	40222	−	MOBQ
pBc239	NC_011973	Bacillus cereus Q1	239246	33	52	100	191895	192164	+
pBF9343	NC_006873	Bacteroides fragilis NCTC 9343	36560	32	35	92	15803	15558	−	MOBP
pBPHY01	NC_010625	Burkholderia phymatum STM815	1904893	62	43	99	826527	826252	−
pBPHY02	NC_010627	Burkholderia phymatum STM815	595108	59	45	99	98625	98359	−
pBtoxis	NC_010076	Bacillus thuringiensis serovar israelensis	127923	32	52	99	77382	77648	+
pBWB401	NC_010180	Bacillus weihenstephanensis KBAB4	417054	34	59	100	338347	338078	+
pCAR1	NC_004444	Pseudomonas resinovorans	199035	56	42	99	97809	98075	−	MOBH
pCAUL01	NC_010335	Caulobacter sp. K31	233649	67	44	99	97598	97329	−	MOBQ
pCER270	NC_010924	Bacillus cereus	270082	34	59	100	169548	169279	+
pDBORO	NC_009137	Lactococcus lactis subsp. lactis bv. diacetylactis	16404	35	37	94	16387	16112	+
pDVUL01	NC_008741	Desulfovibrio vulgaris DP4	198504	66	31	98	198317	198054	−
peH4H	NC_012690	Escherichia coli	148105	53	57	99	14067	14333	−	MOBH
pG9842_209	NC_011775	Bacillus cereus G9842	209488	30	60	100	88828	88559	+
pH308197_258	NC_011339	Bacillus cereus H3081.97	258484	34	59	100	83033	83302	+
pHD5AT	NC_012752	Candidatus Hamiltonella defensa 5AT (Acyrthosiphon pisum)	59032	45	45	99	14981	15247	−	MOBP
pIP1202	NC_009141	Yersinia pestis bv. Orientalis str. IP275	182913	53	57	99	14067	14333	−	MOBH
plasmid 2	NC_007972	Cupriavidus metallidurans CH34	171459	61	46	99	125530	125261	−
pMOL28	NC_006525	Cupriavidus metallidurans CH34	171461	61	46	99	51529	51798	−
pMP118	NC_007930	Lactobacillus salivarius UCC118	242436	32	54	99	56763	56497	+	MOBV
pNPUN02	NC_010632	Nostoc punctiforme PCC 73102	254918	41	44	99	74804	74538	−	MOBV
pOANT02	NC_009670	Ochrobactrum anthropi ATCC 49188	101491	59	49	94	32700	32446	−
pP91278	NC_008613	Photobacterium damselae subsp. piscicida	131520	52	57	99	125918	126184	−	MOBH
pP99-018	NC_008612	Photobacterium damselae subsp. piscicida	150157	51	57	99	133314	133580	−	MOBH
pPER272	NC_010921	Bacillus cereus	272145	34	58	100	153060	152791	+
pPMA4326A	NC_005918	Pseudomonas syringae pv. maculicola	46697	55	42	99	1520	1786	−
pPMA4326B	NC_005919	Pseudomonas syringae pv. maculicola	40110	55	45	99	1457	1723	−
pQBR103	NC_009444	Pseudomonas fluorescens SBW25	425094	53	51	99	182862	183128	−
pR132503	NC_012853	Rhizobium leguminosarum bv. trifolii WSM1325	516088	59	47	94	300662	300916	−	MOBQ
pRA1	NC_012885	Aeromonas hydrophila	143963	51	58	99	15573	15839	−	MOBH
pRALTA	NC_010529	Cupriavidus taiwanensis	557200	60	46	98	153542	153276	−
pREB1	NC_009926	Acaryochloris marina MBIC11017	374161	47	46	100	339743	340012	−	MOBF
pREB2	NC_009927	Acaryochloris marina MBIC11017	356087	45	48	100	57583	57852	−	MOBF
pREB3	NC_009928	Acaryochloris marina MBIC11017	273121	45	46	100	234682	234951	−	MOBF
					42	100	243339	243608
pRL7	NC_008382	Rhizobium leguminosarum bv. viciae 3841	151564	58	48	94	20484	20230	−	MOBQ
pRLG203	NC_011370	Rhizobium leguminosarum bv. trifolii WSM2304	308747	58	49	94	141121	140867	−
pRp12D01	NC_012855	Ralstonia pickettii 12D	389779	58	37	99	321346	321080	−	MOBH
pSG2	NC_007184	Sodalis glossinidius	27240	45	45	86	10072	9845	−
pSG3	NC_007186	Sodalis glossinidius	19201	51	51	100	13812	13543	−
pSN254	NC_009140	Salmonella enterica subsp. enterica serovar Newport str. SL254	176473	53	57	99	14067	14333	−	MOBH
pTiS4	NC_011982	Agrobacterium vitis S4	258824	57	41	94	27356	27102	−	MOBQ
					40	94	83408	83154
pTi-SAKURA	NC_002147	Agrobacterium tumefaciens	206479	56	44	94	95763	95509	−	MOBQ
pVSAL840	NC_011311	Aliivibrio salmonicida LFI1238	83540	40	60	99	31361	31627	−	MOBF
					58	99	77350	77084
pYR1	NC_009139	Yersinia ruckeri	158038	51	57	99	15070	15336	−	MOBH
Ti	NC_003065	Agrobacterium tumefaciens str. C58	214233	57	44	94	139735	139481	−	MOBQ

^aThis list is the result of a TBLASTN analysis using the amino acid sequence of HUα or HUβ 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 HU.
^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].