Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake

Table 2 Bacteria outside of the Firmicutes with many high-confidence terminators

Organism	F _TT	N _TT
Neisseria (β-proteobacteria)
Neisseria meningitidis Z2491	79	360
Neisseria meningitidis MC58	77	357
Neisseria gonorrhoeae FA 1090	77	356
Vibrio (γ-proteobacteria)
Vibrio fischeri ES114	76	714
Vibrio parahaemolyticus	74	955
Vibrio vulnificus CMCP6	72	866
Vibrio vulnificus YJ016	65	919
Vibrio cholerae	64	739
Pasteurellaceae (γ-proteobacteria)
Pasteurella multocida	80	360
Haemophilus influenzae 86 028NP	75	322
Haemophilus influenzae	76	292
Mannheimia succiniciproducens MBEL55E	71	445
Haemophilus ducreyi 35000HP	63	310
Other γ-proteobacteria
Psychrobacter cryohalolentis K5	69	485
Psychrobacter arcticum 273-4	65	417
Pseudoalteromonas haloplanktis TAC125	64	667
δ-Proteobacteria
Desulfovibrio desulfuricans G20	62	661
Fusobacteria
Fusobacterium nucleatum	66	267

Bacteria from outside the Firmicutes division for which TransTermHP finds a high-confidence terminator following > 60% of the genes that were followed by at least two convergently transcribed genes (that is, robust tail-to-tail regions). A tail-to-tail region extends from 25 nt upstream of the stop codon to 500 nt downstream of it, or until the stop codon of the convergently transcribed gene is found, whichever is longer. The region between two convergently transcribed genes counts as two robust tail-to-tail regions (one for each strand) if both genes are preceded by a co-directed gene. F_TTis the percentage of robust tail-to-tail regions containing a terminator, and N_TTis the number of robust tail-to-tail regions in each organism.

ISSN: 1474-760X