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. 2003 Nov;69(11):6888–6898. doi: 10.1128/AEM.69.11.6888-6898.2003

TABLE 2.

Plasmid pBM400-carried genes

ORF Start site (bp) Stop site (bp) Strand Size (aa) Molecular mass (kDa) Fickett valuea (%) Shine-Dalgarno sequenceb Gene product or homolog Originc Organism No. positives total (%)d E value
1 2142 3428 + 428 106.6 92 ttAAAGGAGAAGAtgaacaaATG Clone I replication protein P Bacillus megaterium 393/419 (94) 0.0
2 2962 3225 + 87 22.1 98 agccattGttGGtttAGAtaaatATG No significant homology NA
3 3421 3041 − 126 32.4 100 tttcttcactttttgattacgaaATG Ultrahigh-sulfur keratin-1 G Homo sapiens 41/103 (38) 6e-07
4 3536 4291 + 251 61.2 92 gtAGGAGGAGAtcacgATG RNA polymerase sigma factor 70 G Helicobacter pylori 67/150 (44) 3e-05
Plasmid stability Bacillus megaterium
5 4275 5183 + 302 75.4 98 atGGAcAAcGttcGGttgtctATG No significant homology NA
6 5490 6122 + 210 50.8 92 tcAGGAGGAAGaatATG OrfC215 (pTA1015), DNA binding P Bacillus subtilis 74/154 (47) 3e-07
Ptr (p1414) P Bacillus subtilis 73/154 (46) 5e-07
Hypothetical DNA binding (pX02-68) P Bacillus anthracis 93/180 (51) 2e-07
7 7325 6993 − 110 28.6 40 tcAGAAGGGGtgcaatATG Hypothetical protein G Bacillus anthracis 50/100 (50) 3e-06
8 7634 9238 + 534 134.5 77 ttgagatatatAGGtGAaaaatgtATG Copper export protein G Listeria innocua 255/556 (45) 3e-35
9 8395 8676 + 93 30.6 98 ctAAAGAAtAAGtGGcttgatttttatATG No significant homology NA
10 8910 8545 − 121 30.8 92 acgtttttacGAGAAActctATG No significant homology NA
11 9263 9898 + 211 52 98 ttAGAAAGAAGGAAGGAaaagaaATG YcnI G Bacillus subtilis 120/205 (57) 2e-38
12 10891 10040 − 283 71.1 77 ttAAAAAGGAGGGAcattaATG YcgQ G Bacillus subtilis 199/285 (69) 5e-83
13 11427 11678 + 83 21.1 100 aGGcAAcAAcAccAcGttcaatcATG No significant homology NA
14 11776 10907 − 289 74.1 98 ttGGAGtGAGtataATG YcgR G Bacillus subtilis 229/288 (78) 1e-96
15 13256 12294 − 320 80.1 77 atAGGAGAAGtggtATG BH1517, unknown conserved protein G Bacillus halodurans 185/315 (58) 1e-57
16 13945 13730 − 72 18.8 92 tttAccGGtttgtgaATG No significant homology NA
17 14253 13267 − 328 85.1 77 ttGGAGGtGAAAcGAtagattATG BH1518, unknown conserved protein G Bacillus halodurans 246/331 (73) e-100
18 15591 16772 + 393 98.8 77 tcAAAGAAAGAAGGtcctcctATG Transposase G Enterococcus faecalis 313/390 (79) e-154
19 16945 17253 + 102 25.4 92 tgattGGtGGtAtctAGAtattaATG Cation transporting ATPase G Nostoc sp. PCC 7120 38/72 (52) 1e-02
20 17272 17679 + 135 33.8 92 ttaAGGAAAGGGAGGGAtgagcATG Hypothetical protein G Fusobacterium nucleatum 59/111 (53) 8e-02
21 17768 17550 − 72 18.5 77 ccttAtccttAAtGAtGttgtATG No significant homology NA
22 17806 19920 + 704 174.4 92 atAAGGGGGAAAAGAAtaggtgATG Cation (cadmium) transporting ATPase G Fusobacterium nucleatum 448/736 (60) e-134
23 20547 20771 + 74 18.3 98 ttAtGGGGGAGttttataATG No significant homology NA
24 21389 21874 + 161 40.6 77 ttAGtGAAGAGttcAttGGcatggGTG Zinc-binding dehydrogenase G Bacillus anthracis 120/159 (74) 4e-53
25 23325 22237 − 362 89.6 92 ttGAAAAAGAGActctgtattaTTG Styrene monooxygenase subunit A G Pseudomonas putida 142/289 (48) 5e-28
26 24475 24735 + 86 20.7 77 ttGGGGGtGAAtaaATG Cell wall hydrolase CwlJ G Bacillus subtilis 60/84 (70) 2e-17
27 26242 27039 + 265 64.6 98 atcctcatatAGAGAaaATG DNA segregation ATPase FtsK/SpoIIIE G Thermoanaerobacter tengcongensis 143/276 (50) 1e-21
28 27036 27731 + 231 58.1 77 ttAGAGAAGGAGGAGcagcgATG Hypothetical protein G Bacillus thuringiensis 115/207 (55) 3e-28
29 28196 28744 + 182 46.4 7 ctcactatatAAGAAAAtattcATG ORF14 G Actinobacillus actinomycetemcomitans 59/138 (42) 1e-01
30 30074 29634 − 146 36.1 92 acGGGGAGAGctaaagATG Hypothetical protein G Oceanobacillus iheyensis 116/146 (79) 5e-54
31 31675 31815 + 46 11.2 - aAGGAGGtAGGAGGtatctgaaaTTG Hypothetical protein G Methanosarcina mazei 23/40 (57) 2e-03
32 32224 32991 + 255 63.7 77 atAAGGGGGAtttaaaaGTG YqhA G Bacillus subtilis 112/209 (53) 4e-21
33 33363 33659 + 98 24.1 77 atAGGAGGtGGAtttttATG Hypothetical protein G Methanosarcina barkeri 70/93 (74) 2e-24
34 34647 36296 + 549 134.8 29 acGAAAAGGAGcgtgctgttATG Reverse transcriptase-endonuclease (pXO1-07) P Bacillus anthracis 380/558 (68) 1e-163
35 36652 37098 + 148 36.8 92 acAAAGGGAGAGAaaatcATG YjgB/Putative lipoprotein G Bacillus subtilis 38/79 (47) 1e-03
36 38155 37943 − 70 17.4 92 ataaaAAAGGGGGGAtttaaATG Chromosome segregation ATPase G Thermoanaerobacter tengcongensis 37/66 (55) 1e-01
37 38684 38487 − 65 16.1 aaAGAtAAAGGGGttGAtgttttATG YpiB G Bacillus subtilis 34/51 (66) 8e-04
38 40007 40360 + 117 30.5 77 ttaacttAtcGAtAtGtGctaaatATG No significant homology NA
39 40760 39651 − 369 90.9 77 tcAAcAGAAGttcAActtaaaaATG Uncharacterized protein G Clostridium acetobutylicum 227/368 (61) 1e-71
40 42303 41155 − 382 93.7 29 ttGAAAGGAGAGGttttATG Integrase-recombinase (pXO1-103) P Bacillus anthracis 156/321 (48) 5e-37
41 42781 43167 + 128 31.3 77 atAGAAGGAGtgtgcttaATG Hypothetical protein (pXO1-101) P Bacillus anthracis 64/109 (58) 5e-07
42 43278 43766 + 162 39.9 40 ccGtAGAAGAtccgattATG No significant homology NA
43 44407 44712 + 101 24.4 92 ttAGGGAAAGGAGtatctatATG No significant homology NA
44 44709 45833 + 374 10 92 aaatGAGGAGGttgaggaaatATG FtsZ, cell division G Pyrococcus horikashi 167/363 (45) 8e-19
45 46850 46641 − 69 17.1 29 atGAAcGGGAAGtAGctcagcTTG Hypothetical protein G Streptococcus pyogenes 24/31 (76) 8e-04
46 48178 48495 + 105 26.8 40 ttGAGGGGGcttcatgcttagATG Hypothetical protein G Chlamydia muridarum 83/104 (78) 2e-36
47 48524 48736 + 70 18.3 92 ttGAGcGAtGGcccttccATG Hypothetical protein G Chlamydia pneumoniae 44/60 (73) 9e-14
48 48589 48302 − 95 23.4 29 gtaAAGGcAcAAGGGAgcTTG Hypothetical protein G Sulfolobus tokodaii 37/61 (60) 1e-10
49 50691 50930 + 79 20.9 40 ccAAGAGGcAAGcctcTTG No significant homology NA
50 51548 51267 − 93 23.3 92 ccGGAGGAAGGtggggATG Hypothetical protein G Magnetospirillum magnetotacticum 46/59 (77) 5e-16
rrn operon
    5S 48710 48033 − 5S rRNA G Bacillus halodurans 639/678 (94) 0.0
     G Bacillus subtilis 158/174 (90) 2e-50
     G Staphylococcus aureus 76/76 (100) 4e-33
    23S 50876 48732 − 23S rRNA G Bacillus halodurans 1967/2149 (91) 0.0
     G Bacillus cereus 1466/1577 (92) 0.0
     G Bacillus anthracis 1465/1577 (92) 0.0
     G Bacillus subtilis 1140/1210 (94) 0.0
    16S 52720 51234 − 16S rRNA G Bacillus megaterium 1477/1486 (99) 0.0
     G Bacillus flexus 1508/1529 (98) 0.0
a

Fickett score (PCgene) is the percent probability that an ORF codes for a protein based on context, codon usage, and %GC content.

b

Possible ribosomal binding site. Bacillus consensus, AGGAGGAGA. ATG, possible start codon; uppercase, similar to consensus; lowercase, not similar to consensus.

c

P, plasmid origin; G, genomic origin; NA, not applicable.

d

No. of positives are the totals of identical and similar amino acids.