Prediction of transcriptional terminators in Bacillus subtilis and related species: Supplementary material

The full supplementary material for our paper "Prediction of transcriptional terminators in Bacillus subtilis and related species" (PLoS Computational Biology 1(3): e25 (2005)) is available from the PLoS website. For this paper, we predicted transcriptional terminators for 57 Firmicutes. Since publication, we have extended this list to include recently sequenced bacteria. The full set of predicted transcriptional terminators, as well as their statistical properties, is available below.

Predicted transcriptional terminators in bacterial species of the Firmicutes phylum and their properties

The files containing the predicted transcriptional terminators can be downloaded by clicking on the organism name. Each row in these files contains the following column: The file name corresponds to NCBI's accession number for each organism.

Terminator prediction in bacterial species in the Firmicutes phylum
NCBI accession Name Sensitivity (%) Stem length Loop size -ΔG [kcal/mole] ΔG / LSL [kcal/mole/nucleotide] Number of Ts in the T-stretch
Bacillales; Bacillaceae; Bacillus
NC_000964
 Bacillus subtilis subsp. subtilis str. 168
97.18
9.1
5.2
14.9
0.644
9.3
NC_006322
 Bacillus licheniformis ATCC 14580
95.14
9.9
5.3
15.8
0.637
9.1
NC_006270
 Bacillus licheniformis ATCC 14580
94.95
9.8
5.3
15.8
0.640
9.1
NC_003997
 Bacillus anthracis str. Ames
96.35
9.8
5.2
14.8
0.602
9.6
NC_007530
 Bacillus anthracis str. 'Ames Ancestor'
96.35
9.7
5.2
14.8
0.603
9.6
NC_005945
 Bacillus anthracis str. Sterne
97.33
9.7
5.2
14.8
0.603
9.6
NC_005957
 Bacillus thuringiensis serovar konkunian str. 97-27
96.88
9.9
5.2
14.9
0.602
9.6
NC_003909
 Bacillus cereus ATCC 10987
94.53
9.7
5.3
14.7
0.596
9.6
NC_004722
 Bacillus cereus ATCC 14579
95.85
9.9
5.1
15.1
0.609
9.6
NC_006274
 Bacillus cereus ZK
97.24
9.7
5.0
14.7
0.604
9.6
NC_002570
 Bacillus halodurans
84.34
10.4
5.6
14.9
0.563
9.1
NC_006582
 Bacillus clausii KSM-K16
87.15
10.3
5.5
15.7
0.608
8.8
Bacillales; Bacillaceae; Geobacillus
NC_006510
 Geobacillus kaustophilus HTA426
86.39
11.1
5.7
16.9
0.609
8.5
Bacillales; Bacillaceae; Oceanobacillus
NC_004193
 Oceanobacillus iheyensis HTE831
88.30
11.5
5.9
14.9
0.514
9.5
Bacillales; Listeriaceae; Listeria
NC_002973
 Listeria monocytogenes str. 4b F2365
97.47
11.1
5.2
16.8
0.613
10.0
NC_003210
 Listeria monocytogenes EG
97.16
11.2
5.3
17.2
0.625
10.0
NC_003212
 Listeria innocua Clip11262
98.16
10.9
5.3
16.7
0.617
10.0
NC_008555
 Listeria welshimeri serovar 6b str. SLCC5334
98.11
11.3
5.7
16.7
0.591
10.0
Bacillales; Staphylococcus
NC_007622
 Staphylococcus aureus RF122
93.09
13.5
6.1
16.8
0.494
9.7
NC_002951
 Staphylococcus aureus subsp. aureus COL
91.36
13.9
6.0
17.2
0.503
9.7
NC_002952
 Staphylococcus aureus subsp. aureus MRSA252
92.15
13.9
6.0
17.5
0.512
9.7
NC_002953
 Staphylococcus aureus subsp. aureus MSSA476
90.40
13.6
6.2
17.0
0.503
9.7
NC_003923
 Staphylococcus aureus subsp. aureus MW2
91.73
13.5
6.2
16.8
0.502
9.7
NC_002758
 Staphylococcus aureus subsp. aureus Mu50
93.45
13.3
6.3
16.7
0.501
9.7
NC_002745
 Staphylococcus aureus subsp. aureus N315
93.75
13.3
6.3
16.9
0.505
9.7
NC_007795
 Staphylococcus aureus subsp. aureus NCTC 8325
89.12
13.4
6.2
16.5
0.489
9.8
NC_007793
 Staphylococcus aureus subsp. aureus USA300
92.16
13.7
6.0
17.5
0.515
9.7
NC_004461
 Staphylococcus epidermidis ATCC 12228
92.43
12.7
6.3
16.5
0.513
9.6
NC_002976
 Staphylococcus epidermidis RP62A
91.40
12.6
6.1
16.4
0.513
9.6
NC_007168
 Staphylococcus haemolyticus JCSC1435
92.51
13.1
6.2
17.3
0.526
9.6
NC_007350
 Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305
96.43
13.0
5.7
18.7
0.585
9.4
Clostridia; Clostridiales; Clostridiaceae; Clostridium
NC_003366
 Clostridium perfringens str. 13
94.15
12.0
5.5
13.9
0.472
10.0
NC_008261
 Clostridium perfringens ATCC 13124
91.53
12.7
5.4
13.3
0.445
10.3
NC_008262
 Clostridium perfringens SM101
95.29
12.2
5.7
13.6
0.450
10.1
NC_004557
 Clostridium tetani E88
93.91
10.6
5.0
13.5
0.504
9.9
NC_003030
 Clostridium acetobutylicum ATCC 824
94.30
10.8
6.0
13.3
0.478
9.8
NC_008593
 Clostridium novyi NT
95.02
10.9
5.1
13.9
0.523
9.9
Clostridia; Clostridiales; Peptococcaceae; Carboxythermus
NC_007503
 Carboxydothermus hydrogenoformans Z-2901
90.16
9.2
5.5
13.4
0.560
9.4
Clostridia; Clostridiales; Peptococcaceae; Desulfitobacterium
NC_007907
 Desulfitobacterium hafniense Y51
79.19
12.3
5.3
18.3
0.596
8.7
Clostridia; Clostridiales; Syntrophomonadaceae; Syntrophomonas
NC_008346
 Syntrophomonas wolfei subsp. wolfei str. Göttingen
73.63
10.6
5.8
14.4
0.522
8.9
Clostridia; Thermoanaerobacteriales; Thermoanaerobacteriaceae; Thermoanaerobacter
NC_003869
 Thermoanaerobacter tengcongensis MB4
87.55
9.7
5.9
13.5
0.545
9.5
Clostridia; Thermoanaerobacteriales; Thermoanaerobacteriaceae; Moorella group; Moorella
NC_007644
 Moorella thermoacetica ATCC 39073
78.46
9.9
5.3
16.2
0.648
8.3
Lactobacillales; Lactobacillaceae; Lactobacillus
NC_004567
 Lactobacillus plantarum WCFS1
90.65
9.1
5.9
13.5
0.545
9.5
NC_005362
 Lactobacillus johnsonii NCC 533
97.18
11.1
5.5
15.6
0.569
9.8
NC_006814
 Lactobacillus acidophilus NCFM
96.15
10.2
5.2
13.8
0.547
9.9
NC_007576
 Lactobacillus sakei subsp. sakei 23K
94.35
12.3
4.8
19.9
0.677
9.4
NC_007929
 Lactobacillus salivarius subsp. salivarius UCC118
97.33
12.7
5.6
16.4
0.522
9.7
NC_008054
 Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842
90.83
10.2
4.8
16.3
0.660
9.6
NC_008529
 Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
90.51
10.0
4.9
16.1
0.659
9.5
NC_008497
 Lactobacillus brevis ATCC 367
94.74
12.9
5.1
20.4
0.658
8.7
NC_008526
 Lactobacillus casei ATCC 334
87.06
12.8
5.5
19.2
0.611
8.9
NC_008530
 Lactobacillus gasseri ATCC 33323
97.08
11.2
5.4
15.8
0.578
9.8
Lactobacillales; Lactobacillaceae; Pediococcus
NC_008525
 Pediococcus pentosaceus ATCC 25745
96.00
12.1
5.4
16.6
0.558
9.8
Lactobacillales; Leuconostocaceae; Leuconostoc
NC_008531
 Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
95.00
9.6
5.3
13.01
0.536
10.0
Lactobacillales; Leuconostocaceae; Oenococcus
NC_008525
 Oenococcus oeni PSU-1
90.48
8.8
5.5
9.6
0.424
9.6
Lactobacillales; Streptococcaceae; Streptococcus
NC_004116
 Streptococcus agalactiae 2603V/R
96.93
9.1
4.8
12.4
0.541
9.8
NC_007432
 Streptococcus agalactiae A909
97.13
8.9
4.8
12.2
0.539
9.9
NC_004368
 Streptococcus agalactiae NEM316
98.77
8.9
4.9
12.6
0.554
9.8
NC_004350
 Streptococcus mutans UA159
95.00
11.1
6.3
13.3
0.459
9.6
NC_008533
 Streptococcus pneumoniae D39
94.30
10.9
5.5
14.7
0.543
9.2
NC_003098
 Streptococcus pneumoniae R6
94.76
10.6
5.3
13.8
0.525
9.3
NC_003028
 Streptococcus pneumoniae TIGR4
92.48
10.8
5.5
14.3
0.530
9.2
NC_002737
 Streptococcus pyogenes M1 GAS
95.77
10.5
5.4
14.2
0.530
9.6
NC_008021
 Streptococcus pyogenes MGAS9429
91.89
10.5
5.6
13.8
0.517
9.7
NC_008022
 Streptococcus pyogenes MGAS10270
92.42
10.6
5.4
14.4
0.541
9.7
NC_006086
 Streptococcus pyogenes MGAS10394
94.47
10.5
5.4
14.2
0.536
9.6
NC_008024
 Streptococcus pyogenes MGAS10750
96.24
10.7
5.5
14.4
0.530
9.7
NC_008023
 Streptococcus pyogenes MGAS2096
92.31
10.7
5.6
14.3
0.529
9.6
NC_004070
 Streptococcus pyogenes MGAS315
95.63
10.4
5.5
13.9
0.527
9.6
NC_007297
 Streptococcus pyogenes MGAS5005
95.95
10.5
5.6
14.0
0.523
9.6
NC_007296
 Streptococcus pyogenes MGAS6180
95.56
10.6
5.6
14.1
0.525
9.6
NC_003485
 Streptococcus pyogenes strain MGAS8232
93.33
11.2
5.3
14.8
0.539
9.6
NC_004606
 Streptococcus pyogenes SSI-1
94.37
10.7
5.3
13.8
0.520
9.6
NC_006449
 Streptococcus thermophilus CNRZ1066
94.76
9.7
5.2
12.4
0.520
9.6
NC_008532
 Streptococcus thermophilus LMD-9
95.26
9.5
5.1
13.0
0.541
9.5
NC_006448
 Streptococcus thermophilus LMG 18311
94.35
9.6
5.2
12.3
0.519
9.5
Lactobacillales; Streptococcaceae; Lactococcus
NC_002662
 Lactococcus lactis subsp. lactis Il1403
99.30
8.3
5.1
10.9
0.511
10.5
NC_008527
 Lactococcus lactis subsp. cremoris SK11
95.03
8.5
4.9
10.9
0.512
10.4
NC_009004
 Lactococcus lactis subsp. cremoris MG1363
96.79
8.4
4.9
10.9
0.515
10.5
Lactobacillales; Enterococcaceae; Enterococcus
NC_004668
 Enterococcus faecalis V583
96.93
11.9
5.5
18.2
0.610
9.9
Mollicutes; Acholeplasmatales; Acholeplasmataceae; Candidatus Phytoplasma; Candidatus Phytoplasma asteris
NC_005303
 Onion yellows phytoplasma OY-M
97.37
9.1
5.0
9.7
0.454
10.5
NC_007716
 Aster yellows witches'-broom phytoplasma AYWB
97.40
9.4
5.3
8.5
0.373
10.6
Mollicutes; Entomoplasmatales; Entomoplasmataceae
NC_006055
 Mesoplasma florum L1
100
7.4
5.3
8.0
0.407
10.9
Mollicutes; Mycoplasmataceae; Mycoplasma
NC_007633
 Mycoplasma capricolum subsp. capricolum ATCC 27343
100
8.7
5.4
9.5
0.443
10.9
NC_004829
 Mycoplasma gallisepticum R
94.94
10.3
5.6
12.7
0.497
10.3
NC_000908
 Mycoplasma genitalium G-37
90.20
9.3
5.8
7.1
0.307
10.1
NC_006360
 Mycoplasma hyopneumoniae 232
99.13
9.4
6.5
6.8
0.276
10.7
NC_007332
 Mycoplasma hyopneumoniae 7448
98.20
9.2
6.4
6.9
0.282
11.0
NC_007295
 Mycoplasma hyopneumoniae J
97.35
9.0
6.1
6.5
0.269
10.9
NC_006908
 Mycoplasma mobile 163K
98.13
7.7
5.0
7.3
0.377
10.7
NC_005364
 Mycoplasma mycoides subsp. mycoides SC str. PG1
94.56
10.2
5.2
9.6
0.395
10.7
NC_004432
 Mycoplasma penetrans HF-2
99.25
10.4
6.0
10.6
0.408
10.7
NC_000912
 Mycoplasma pneumoniae M129
82.89
9.5
5.7
10.0
0.424
9.4
NC_002771
 Mycoplasma pulmonis UAB CTIP
100
9.5
6.3
8.6
0.352
10.8
NC_007294
 Mycoplasma synoviae 53
100
7.7
5.1
8.4
0.423
10.7
Mollicutes; Mycoplasmataceae, Ureaplasma
NC_002162
 Ureaplasma parvum serovar 3 str. ATCC 700970
96.55
9.6
5.7
9.3
0.380
10.7

Terminator prediction in Gram-positive bacteria other than Firmicutes
NCBI identifier Name Sensitivity (%) Stem length Loop size -ΔG [kcal/mole] ΔG / LSL [kcal/mole/nucleotide] Number of Ts in the T-stretch
Actinobacteria; Actinobacteridae; Actinomycetales; Corynebacterineae; Corynebacteriaceae; Corynebacterium
NC_002935
 Corynebacterium diphteriae NCTC 13129
60.76
13.1
5.3
20.9
0.645
8.3
NC_004369
 Corynebacterium efficiens YS-314
37.58
14.1
4.7
25.6
0.770
7.2
NC_003450
 Corynebacterium glutamicum ATCC 13032
63.61
12.9
5.4
21.4
0.681
8.1
Actinobacteria; Actinobacteridae; Actinomycetales; Corynebacterineae; Mycobacteriaceae; Mycobacterium
NC_002944
 Mycobacterium avium subsp. paratuberculosis str. k10
11.82
12.5
5.1
19.3
0.653
7.1
NC_002945
 Mycobacterium bovis AF2122/97
15.18
11.9
4.6
18.1
0.655
6.9
NC_000962
 Mycobacterium tuberculosis H37Rv
15.02
11.9
4.6
18.3
0.660
6.9
NC_002755
 Mycobacterium tuberculosis CDC1551
14.51
11.7
4.6
18.0
0.659
6.9
NC_002677
 Mycobacterium leprae TN
30.46
11.9
4.8
14.8
0.540
8.0
Actinobacteria; Actinobacteridae; Actinomycetales; Corynebacterineae; Nocardiaceae; Nocardia
NC_006361
 Nocardia farcinica IFM 10152
13.36
14.4
4.7
29.0
0.874
6.0
Actinobacteria; Actinobacteridae; Actinomycetales; Streptomycineae; Streptomycetaceae; Streptomyces
NC_003155
 Streptomyces avermitilis MA-4680
14.19
14.5
4.4
29.8
0.888
6.0
NC_003888
 Streptomyces coelicolor A3(2)
11.70
14.3
4.6
28.0
0.842
6.2
Actinobacteria; Actinobacteridae; Actinomycetales; Micrococcineae; Cellulomonadaceae; Tropheryma
NC_004551
 Tropheryma whipplei TW08/27
55.36
8.8
5.6
10.3
0.447
8.8
NC_004572
 Tropheryma whipplei str. Twist
51.24
9.5
5.9
10.8
0.447
8.7
Actinobacteria; Actinobacteridae; Actinomycetales; Propionibacterineae; Propionibacteriaceae; Propionibacterium
NC_006085
 Propionibacterium acnes KPA171202
21.45
13.3
5.0
22.2
0.692
7.1
Actinobacteria; Actinobacteridae; Bifidobacteriales; Bifidobacteriaceae; Bifidobacterium
NC_004307
 Bifidobacterium longum NCC2705
49.23
12.4
5.0
22.3
0.748
7.5
Actinobacteria; Symbiobacterium
NC_006177
 Symbiobacterium thermophilum IAM 14863
46.39
13.5
4.7
28.6
0.902
6.3
Chloroflexi; Dehalococcoidetes; Dehalococcoides
NC_002936
 Dehalococcoides ethenogenes 195
76.12
9.1
5.5
13.3
0.578
8.8
Deinococcus-Thermus; Deinococci; Deinococcales; Deinococcaceae; Deinococcus
NC_002944
 Deinococcus radiodurans R1
58.74
11.5
5.4
20.8
0.731
8.0
Bacteroidetes; Bacteroides (class); Bacteroidales; Bacteroidaceae; Bacteroides
NC_004663
 Bacteroides thetaiotaomicron VPI-5482
80.21
12.5
5.7
16.2
0.521
9.3

Table S3: Terminator prediction in Gram-negative bacteria outside of the Firmicutes phylum
NCBI identifier Name Sensitivity (%) Stem length Loop size -ΔG [kcal/mole] ΔG / LSL [kcal/mole/nucleotide] Number of Ts in the T-stretch
Proteobacteria; Alphaproteobacteria; Caulobacterales; Caulobacteraceae; Caulobacter
NC_002696
 Caulobacter crescentus CB15
32.09
11.3
4.5
21.3
0.802
7.1
Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Escherichia
NC_000913
 Escherichia coli K12
67.47
10.2
5.2
15.1
0.611
8.4
Proteobacteria; Epsilonproteobacteria; Campylobacterales; Helicobacteraceae; Helicobacter
NC_000915
 Helicobacter pylori 26695
84.55
9.5
6.1
9.3
0.390
9.6
NC_000921
 Helicobacter pylori J99
85.71
9.4
6.0
8.9
0.382
9.6
Aquificae; Aquificales; Aquificaceae; Aquifex
NC_000918
 Aquifex aeolicus VF5
75.72
9.4
5.8
9.3
0.394
9.5
Cyanobacteria; Chroococcales; Synechocystis
NC_000911
 Synechocystis sp. PCC 6803
60.55
9.4
5.5
10.3
0.431
9.0
Spirochaetes; Spirochaetales; Spirochaetaceae; Borrelia and Treponema
NC_001318
 Borrelia burgdorferi B31
60.55
9.9
6.0
8.0
0.331
10.2
NC_000919
 Treponema pallidum subsp. pallidum str. Nichols
51.91
10.4
5.3
11.9
0.466
8.4
Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae; Pyrococcus
NC_000961
 Pyrococcus horikoshii OT3
55.94
8.9
5.9
8.7
0.382
9.5
Archaea; Euryarchaeota; Archaeoglobi; Archaeoglobales; Archaeoglobaceae; Archaeoglobus
NC_000917
 Archaeoglobus fulgidus DSM 4304
47.36
10.1
5.9
10.3
0.396
9.2