International Journal of Evolutionary Biology

Research Article

Distribution of Genes Encoding Nucleoid-Associated Protein Homologs in Plasmids

Table 4

Plasmids containing the gene encoding Lrp 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_008688	Paracoccus denitrificans PD1222	653815	67	41	92	252075	251623	−
					42	93	464218	464673
					36	96	639341	639811
					37	85	110140	109724
A	NC_009007	Rhodobacter sphaeroides 2.4.1	114045	69	39	93	30241	29789	−	MOB_F
B	NC_007488	Rhodobacter sphaeroides 2.4.1	114178	70	43	96	81861	81385	−
bglu_1p	NC_012723	Burkholderia glumae BGR1	133591	61	36	90	124017	123577	−
Megaplasmid	NC_008043	Ruegeria sp. TM1040	821788	59	41	84	143820	144233	−
					41	91	687257	687706
					36	91	734136	733690
Megaplasmid	NC_007974	Cupriavidus metallidurans CH34	2580084	64	44	88	1171245	1170814	−	MOB_V
					40	91	1169702	1169256
					38	97	1586726	1586250
Megaplasmid	NC_006569	Ruegeria pomeroyi DSS-3	491611	63	36	88	356303	355869	−	MOB_C
Megaplasmid	NC_007336	Ralstonia eutropha JMP134	634917	61	35	93	377503	377045	−
p42e	NC_007765	Rhizobium etli CFN 42	505334	62	34	71	255037	255384	−
p42f	NC_007766	Rhizobium etli CFN 42	642517	61	45	88	436907	437341	−
					43	91	406350	405901
					41	85	491383	491799
					39	95	210634	211098
					39	96	199426	199899
pAB510a	NC_013855	Azospirillum sp. B510	1455109	68	57	88	274908	275342	−
					44	95	979549	980013
					32	94	1180335	1179874
pAB510b	NC_013856	Azospirillum sp. B510	723779	67	44	84	471830	472243	−
					32	94	318139	318600
pAB510c	NC_013857	Azospirillum sp. B510	681723	67	45	85	408064	407645	−
					34	91	36385	36834
pAB510d	NC_013858	Azospirillum sp. B510	628837	68	44	79	472768	472379	−
					40	90	323184	322741
					37	87	281438	281866
					30	85	619027	618623
pAtS4e	NC_011981	Agrobacterium vitis S4	631775	57	30	87	460443	460871	−	MOB_Q
					34	74	425247	424888
pBPHY01	NC_010625	Burkholderia phymatum STM815	1904893	62	46	85	1153608	1154027	−
pBPHY02	NC_010627	Burkholderia phymatum STM815	595108	59	41	91	271795	271346	−
pC	NC_010997	Rhizobium etli CIAT 652	1091523	61	46	88	617696	618130	−	MOB_Q
					42	90	609059	608619
					39	95	417738	418202
					42	79	714804	715193
					39	93	406570	407025
pCAUL01	NC_010335	Caulobacter sp. K31	233649	67	34	89	182479	182042	−	MOB_Q
pEST4011	NC_005793	Achromobacter denitrificans	76958	62	58	88	41224	40793	−	MOB_P
					58	88	34233	33802
pGMI1000MP	NC_003296	Ralstonia solanacearum GMI1000	2094509	67	43	98	1737958	1738437	−
					46	93	822030	821572
pHV4	NC_013966	Haloferax volcanii DS2	635786	62	33	71	401763	401410	Archaea
pIJB1	NC_013666	Burkholderia cepacia	99448	63	58	88	74907	75338	−	MOB_P
pK2044	NC_006625	Klebsiella pneumoniae NTUH-K2044	224152	50	33	90	194643	195086	−
pLVPK	NC_005249	Klebsiella pneumoniae	219385	50	33	90	46236	46679	−
pMLa	NC_002679	Mesorhizobium loti MAFF303099	351911	59	32	93	185603	185148	−
					30	89	207314	206877
pMLb	NC_002682	Mesorhizobium loti MAFF303099	208315	60	37	93	24632	24177	−
pNGR234a	NC_000914	Rhizobium sp. NGR234	536165	58	41	70	197189	196845	−	MOB_Q
					30	89	188867	188430
pNGR234b	NC_012586	Rhizobium sp. NGR234	2430033	62	46	90	656547	656107	−	MOB_Q
					45	85	667494	667913
					43	90	1038020	1038463
					44	85	682796	683215
					38	96	2400849	2401319
					44	79	709104	708715
					41	89	28336	28761
					33	89	1108900	1109337
					36	90	703213	702764
					32	77	1112953	1112582
pPNAP04	NC_008760	Polaromonas naphthalenivorans CJ2	143747	59	35	90	142511	142068	−
pR132501	NC_012848	Rhizobium leguminosarum bv. trifolii WSM1325	828924	60	47	88	234905	234471	−	MOB_Q
					44	86	386338	386760
					39	93	645542	645087
					42	79	147165	146776
pRALTA	NC_010529	Cupriavidus taiwanensis	557200	60	38	91	465839	465393	−
pRHL1	NC_008269	Rhodococcus jostii RHA1	1123075	65	36	91	854207	854656	+
					33	84	783666	783253
pRL12	NC_008378	Rhizobium leguminosarum bv. viciae 3841	870021	61	46	88	599116	598682	−	MOB_Q
					43	88	658287	658718
					39	93	45601	45146
					42	79	450080	449691
pRL8	NC_008383	Rhizobium leguminosarum bv. viciae 3841	147463	59	33	87	70763	70344	−	MOB_Q
pRLG201	NC_011368	Rhizobium leguminosarum bv. trifolii WSM2304	1266105	60	45	89	917573	917136	−	MOB_Q
					44	85	41998	42417
					44	79	473039	472650
					40	93	1162146	1161691
					40	93	1150939	1150484
					32	88	707587	707162
pRSKD131A	NC_011962	Rhodobacter sphaeroides KD131	157345	70	42	96	148295	147819	−
pRSKD131B	NC_011960	Rhodobacter sphaeroides KD131	103355	70	39	93	98400	97948	−
pRSPA01	NC_009429	Rhodobacter sphaeroides ATCC 17025	877879	68	40	90	31309	30866	−
					39	88	659383	658952
pRSPH01	NC_009040	Rhodobacter sphaeroides ATCC 17029	122606	70	39	93	118088	118540	−
pSMED01	NC_009620	Sinorhizobium medicae WSM419	1570951	61	40	77	143180	143557	−	MOB_Q
					34	89	574284	573847
pSMED02	NC_009621	Sinorhizobium medicae WSM419	1245408	60	42	91	556486	556932	−	MOB_Q
					40	91	842324	842758
					31	87	22345	21917
pSMED03	NC_009622	Sinorhizobium medicae WSM419	219313	60	46	95	105044	105508	−
pSmeSM11a	NC_013545	Sinorhizobium meliloti	144170	60	46	96	70449	70922	−	MOB_Q
pSymA	NC_003037	Sinorhizobium meliloti 1021	1354226	60	43	89	1060699	1060262	−	MOB_Q
pSymB	NC_003078	Sinorhizobium meliloti 1021	1683333	62	38	90	440778	440335	−	MOB_Q
					36	89	29555	29992
pTiS4	NC_011982	Agrobacterium vitis S4	258824	57	42	79	96920	97309	−	MOB_Q
Unnamed	NC_011961	Thermomicrobium roseum DSM 5159	917738	66	30	85	736739	737146	−	MOB_P

^aThis list is the result of a TBLASTN analysis using the amino acid sequence of Lrp 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 Lrp.
^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].