TABLE 2.

Location and possible gene products of NBU1 ORFs

ORF or region	Locationa (5′ to 3′)	No. of bp	No. of amino acidsb	%G + C	Search results (accession no.) and comments
attN1 region (14 bp and IRs)	2697–3216c (2960–3027)	500c
intN1	3232–4569	1,338	445	40.6	C-terminal similarity to lambda family of site-specific integrases
orf2	4577–5518	942	313	43.2
orf −1	5487–4905	582	194	43.2
orf2x	5688–6002	316	104	41	62% similarity to C-terminal 53 aa of tnpA of Tn4555 (U75371)
orf3	6007–7197 (Y5 bp 7003)	1,191	396	46.6	Helicase-like protein in Sulfolobus islandicus sequence (U93082).
prmN1	7429–8385 (Y11 bp 7726)	957	318	47.2	>80% sequence identity to prmN2 of NBU2 and a sequence contained on Tn4399 (10, 16); N-terminal amino acid similarity to bacterial DNA primases, e.g., Listeria monocytogenes (55% [U13165]), Legionella pneumophila (60% [U63641]), and dnaG of E. coli (38% [U28379])
oriTd	8213–8433 (nic at 8385)d	220			>90% sequence identity to NBU2 and Tn4555 (16, 31)
mobN1	8592–9995 (Y17 bp 9381)	1,404	467	44.3	83% identity to NBU2 mobN2 (L42370) (16), 73% identity to mobATn Tn4555 (U38243), and 27–31% identity to Bacteroides plasmids pBI143 and pIP421, respectively (30, 33, 40)
orf6	36–755	720	239	31.7
orf7	811–1254	444	147	28.3
orf8	1264–2004	741	246	34.6	67% identity and 83% similarity to C-terminal 160 aa of DNA topoisomerase I (topA) from Methanococcus jannaschii (U67605) and lower but significant similarities to DNA topoisomerases from Helicobacter pylori (Y10747) and Methanobacterium thermoautotrophicum (AE000921)
orf −2	2839–2030	810	269	40.1	None

^aLocation of ORFs relative to PvuII site of the circular excised form of NBU1 in Fig. 1. 

^bNumber of amino acids in the translated ORF with the first possible start codon. 

^cSmallest region tested that could integrate when integrase was provided in trans (27). 

^dRegion determined by Li et al. (15) and nick site determined for Tn4555 (31).