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 G [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 G [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 G [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