From / Froma / Toa / Size
(AA) / Startingcodon and RBSb / Froma / Toa / Size (AA) / AA identity
(%)
0.1 / 1600 / 1755 / 51 / gccgattGAAcAAGGccATG / not present
1 / 1765 / 2049 / 94 / aaacctAGGAGGcgccgATG / 1746 / 2030 / 94 / 81
2 / 2049 / 2276 / 75 / cAAGGGAGGGGcttgtaATG / 2030 / 2257 / 75 / 57
3 / 2286 / 2825 / 179 / ccatctGAGGtgacaccATG / 2268 / 2801 / 177 / 80
4 / 3313 / 3681 / 122 / caagcGAGAActgaaccATG / 2805 / 3173 / 122 / 77
5 / 3668 / 3886 / 72 / cgcAGGGAGcagctaccATG / 3160 / 3387 / 75 / 67
6 / 4233 / 4412 / 59 / gagaatcaggcAGGAGGGTG / 3434 / 3745 / 103 / 50
7 / 4412 / 4684 / 90 / gtggcGGAGGGtgagtgATG / 3745 / 4032 / 95 / 40
8 / 4681 / 4923 / 80 / cagctcgtgcAGGGAGAATG / 4029 / 4265 / 78 / 57
9 / not present / 4281 / 4574 / 97
10 / 5003 / 5413 / 136 / ccttcAGGAGctacatcATG / 4653 / 5072 / 139 / 90
11 / 5482 / 5841 / 119 / ccatAGGAGGAGtcaccATG / 5141 / 5500 / 119 / 100
12 / 5883 / 6653 / 256 / ctAAGctcgcatcgtccATG / 5503 / 6312 / 269 / 83
12.1 / 6734 / 7153 / 139 / tctGGAGGAtcacgaacATG / 6392 / 6811 / 139 / 95
13 / 6924 / 7466 / 180 / gttGAGGGAtatggaagATG / 6582 / 7124 / 180 / 88
13.1 / 7456 / 7584 / 42 / catGAGGGcgcccggtcATG / 7114 / 7242 / 42 / 100
14 / 7652 / 8476 / 274 / tGGGAGGAAtggtaccaATG / 7310 / 8134 / 274 / 99
15 / 8520 / 9716 / 398 / gtgtggtgcctGAAGGGATG / 8178 / 9371 / 397 / 99
16 / 9703 / 10302 / 199 / cttcGAGAGtaccgaccATG / 9361 / 9978 / 205 / 36
17 / 10302 / 11246 / 314 / ggatGGGAGAAcaagtaATG / 9978 / 10925 / 315 / 58
17.1 / 11243 / 11506 / 87 / tacAAGGGGGtaaaggtATG / not present
18 / 11490 / 11834 / 114 / acAGGAGGctaaacgccGTG / 10922 / 11257 / 111 / 50
19 / 11831 / 14257 / 808 / AAGAActggtattccctATG / 11254 / 13677 / 807 / 94
20 / 14254 / 14565 / 103 / aatatGGAGGtgattcaGTG / 13674 / 13985 / 103 / 78
21 / 14620 / 15675 / 351 / cacAAGAGAGAccacgtATG / 14042 / 15091 / 349 / 93
22 / 15675 / 16616 / 313 / gcggtgccgcAGGtctaATG / 15091 / 16032 / 313 / 97
23 / 16606 / 17046 / 146 / gcGGAGGGAAAGcgactATG / 16022 / 16462 / 146 / 94
24 / 17043 / 18089 / 348 / cacaacgcGAGGAAcgtATG / 16459 / 17505 / 348 / 96
25 / 18099 / 18467 / 122 / gcaactAAGGAGGtcctATG / 17515 / 17883 / 122 / 94
25.1 / 18464 / 18610 / 48 / AAGGAGGctggtccgcgATG / 17880 / 18029 / 49 / 98
26 / 18619 / 21069 / 816 / aagcgatAGGAGAcggaATG / 18035 / 20485 / 816 / 96
27 / 21224 / 21478 / 84 / cataGGAGAtatgatagATG / 20646 / 20897 / 83 / 86
28 / 21475 / 21948 / 157 / gcagtGGAGcttaaaggATG / 20897 / 21370 / 157 / 96
29 / 21893 / 22189 / 98 / ccGGAGAGccaagccttATG / 21315 / 21611 / 98 / 97
30 / 22201 / 23733 / 510 / tactGACGAGGtacgccATG / 21623 / 23155 / 510 / 97
31 / 23737 / 24720 / 327 / tcgcAGGAGtctgatagATG / 23159 / 24127 / 322 / 91
32 / 24775 / 25782 / 335 / AAGAGAGAGAGGAtcgcATG / 24180 / 25187 / 335 / 98
33 / 25879 / 26433 / 184 / gctttAGGAGAAAccctATG / 25284 / 25838 / 184 / 96
34 / 26435 / 28915 / 826 / tagcttGAGGAcctgatATG / 25841 / 28321 / 826 / 94
35 / 28915 / 29460 / 181 / acctacAGGAGGGtgtgATG / 28321 / 28866 / 181 / 92
36 / 29460 / 32156 / 898 / cctAAAGGAGGcaactgATG / 28866 / 31562 / 898 / 99
37 / 32160 / 36173 / 1337 / caacagcGGAGtaagacATG / 31566 / 35579 / 1337 / 98
38 / 36175 / 36930 / 251 / catcAAAGGGGAAtaacGTG / 35581 / 36336 / 251 / 94
39 / 36930 / 37388 / 152 / gctatGGAGGAcgaataATG / 36336 / 36776 / 146 / 50
40 / 37381 / 38289 / 302 / gagcgcGGAGcttaccaATG / 36766 / 37644 / 292 / 25
41 / 38292 / 38897 / 201 / gtggcGAGGGCGtaagtATG / 37641 / 38231 / 196 / 50
42 / 38897 / 39202 / 101 / ttcAGAGGGcacatgtaATG / 38231 / 38536 / 101 / 99
43 / 39212 / 41017 / 601 / cccactAAGGAGGcagcATG / 38546 / 40351 / 601 / 96
44 / 41014 / 41214 / 66 / ccAAAAGGAcgaagactATG / 40351 / 40548 / 65 / 100
45 / 41211 / 41693 / 160 / cgccGGAGGttgaagaaGTG / 40545 / 41027 / 160 / 95
46 / 41651 / 41980 / 109 / aacgcGGAGAtcaagaaATG / 40985 / 41314 / 109 / 96
46.1 / 41868 / 42068 / 66 / gcgccAGGAGGtggaccGTG / 41202 / 41401 / 66 / 99
47 / 42071 / 42385 / 104 / catcAAGGAGActgaccATG / 41404 / 41718 / 104 / 99
48 / 42435 / 42629 / 64 / gcgtacAAGGAActgccATG / 41768 / 41962 / 64 / 100
a Nucleotide positions correspond to the first nucleotide of the initiation codon and the last nucleotide of the termination codon.
b Ribosomal Binding Site, defined as a GA-rich region upstream the initiation codon and indicated with capital letters.
c As defined in (24). Newly annotated or extended ORFs are indicated in bold.
d Percentage homology between the corresponding ORFs of LKD16 and KMV.
Table S1B. Putative genes of LKA1 and their closest phage homologue.
ORF / Froma / Toa / Size (AA) / Starting codon andRBSb / Best phage homologue / e-value
1 / 990 / 1142 / 51 / taaccGGAGttaccactATG / none
2 / 1571 / 1843 / 91 / gaatAGGAGGcgcagccATG / ORF70 [pap3] / 5x 10-3
3 / 1840 / 2025 / 62 / ttctGGAAtccgcaagcATG / none
4 / 2036 / 2515 / 160 / gcagtAGGAGAcccaccATG / ORF71 [pap3] / 2 x10-28
5 / 2986 / 3306 / 107 / ccgcAAGGtggcctagtATG / none
6 / 3308 / 3616 / 103 / acGAAGGGGGAAAtagcATG / none
7 / 3662 / 4228 / 189 / tcgaatAGGAGAGAccaATG / none
8 / 4225 / 4419 / 65 / ctgttcccGGAGtcggtATG / none
9 / 4412 / 4696 / 95 / catcctGGAGtacatcaATG / none
10 / 4620 / 4853 / 78 / tctGGAGGAAcccagccATG / none
11 / 4863 / 5168 / 102 / ccctgtAAGGAGtcgttATG / none
12 / 5155 / 5412 / 86 / gcgcctGGAGGAActcgATG / none
13 / 5409 / 5792 / 128 / cacggctGGGAGGtcgtATG / none
14 / 5792 / 6055 / 88 / atcgtGGAGAAActgtaATG / none
15 / 6055 / 6234 / 60 / gaactGGAGAAActgtaATG / none
16 / 6231 / 6434 / 68 / aagaccAAGGAGGccgtATG / none
17 / 6521 / 6874 / 118 / cgtacAGGAGCAAcatcATG / none
18 / 6979 / 7428 / 150 / aacgacGAGGtgagaccATG / none
19 / 7454 / 8368 / 305 / gcgggctGGAGGtcaagATG / none
20 / 8175 / 8978 / 268 / cgccAGGCGcaatcgtaATG / gp14 [KMV] / 2 x 10-44
21 / 8959 / 9141 / 61 / gatacAGGAGAtgataaATG / none
22 / 9138 / 9347 / 70 / gacttccGGGAGGAGcaATG / none
23 / 9340 / 10605 / 422 / gggcgacGAGGAtgattATG / gp15 [KMV] / 2x 10-97
24 / 10616 / 10801 / 62 / ttcttaaacagtGGGGAGTG / none
25 / 10798 / 10995 / 66 / ctcGGGAGGAttccgcgATG / none
26 / 10985 / 11407 / 141 / accacGGGAGcaaacgaATG / none
27 / 11397 / 12413 / 339 / gtaccAGGAGttcttgaATG / ORF6 [VP4] / 6 x 10-38
28 / 12410 / 12589 / 60 / gctGAGGGtctgaaagcATG / none
29 / 12586 / 14961 / 792 / ttctactGGTGGcgtaaATG / gp19 [KMV] / 0
30 / 15152 / 15376 / 75 / ctactGGAAtacacgccATG / none
31 / 15373 / 16317 / 315 / ccagtaccGGAGAAAGtATG / gp21 [KMV] / 1x 10-66
32 / 16314 / 17270 / 319 / ccGGGGGtagcccaggcATG / gp22 [KMV] / 1x 10-71
33 / 17254 / 17679 / 142 / gaagctGGAGGAGcgtgATG / gp23 [KMV] / 2x 10-35
34 / 17679 / 18710 / 344 / ccgcgtAAGGAGAcctgATG / gp24 [KMV] / 4x 10-100
35 / 18691 / 19197 / 169 / ctcGAAGGAGGtgcgttATG / gp25 [KMV] / 2 x 10-4
36 / 19190 / 19381 / 64 / tccGAAGGAGAAGActgATG / none
37 / 19391 / 21826 / 812 / agctgtAAGGAcctgtgATG / gp26 [KMV] / 4x 10-139
38 / 21857 / 22087 / 77 / atgaccAGGAGAAAAccGTG / gp27 [KMV] / 0.11
39 / 22101 / 22478 / 126 / ctgacGGAcgctggttcATG / gp28 [KMV] / 2x 10-14
40 / 22447 / 22746 / 100 / aagctacAGGAGGGtctATG / gp29 [KMV] / 2x 10-8
41 / 22749 / 24293 / 515 / attaacgtGGGGtaagcATG / gp30 [KMV] / 1x 10-121
42 / 24290 / 25066 / 259 / gcAGGAGtcctgacctcATG / gp31[KMV] / 9 x 10-29
43 / 25079 / 26083 / 335 / tgtAAGGAGActgattcATG / gp32 [KMV] / 6x 10-88
44 / 26173 / 26808 / 212 / aacAAAAGGAGAttcctATG / gp33 [KMV] / 2x 10-38
45 / 26735 / 29068 / 778 / caagcGAGGtacaatcaATG / gp34 [KMV] / 4 x 10-142
46 / 29068 / 29697 / 210 / cgctatAGGAGGcagtaATG / gp35 [KMV] / 4 x 10-15
47 / 29707 / 32271 / 855 / ggcgatAGGAGAGtaatATG / gp36 [KMV] / 3 x 10-114
48 / 32282 / 35293 / 1004 / aaactaacGGAGGctacATG / gp37 [KMV] / 1 x 10-158
49 / 35299 / 37608 / 770 / ttGAAGGAGtaacaaccATG / ORF27 [D3] / 3 x 10-68
50 / 37611 / 37904 / 98 / atttatGAGGtgtaattGTG / gp42 [KMV] / 7 x 10-9
51 / 37908 / 39695 / 596 / tgtacGGAGcataacctATG / gp43 [KMV] / 0
52 / 39692 / 39895 / 68 / cGAAAGAGGttcgggagATG / gp17.5 [K1-5] / 6.5
53 / 39888 / 40439 / 184 / ggagcGGGGtaagaccgATG / gp58 [JL06] / 1x 10-8
54 / 40436 / 40726 / 97 / tgcatGGAGGAcgtgcgATG / gp46 [KMV] / 6x 10-4
55 / 40650 / 40847 / 66 / ggtgcGAGGtgcgctgaATG / gp46.1 [KMV] / 8 x 10-7
56 / 40859 / 41182 / 108 / gactGAAGGAGAAAcacATG / none
a,b As defined in Table S1A.
Name / Start / In front of genea / SequenceA HOST PROMOTERS -35 -10
LKD16 / A1 / 779 / 1 / GTTGACAGGGTAGGAGTGTGTCTGTAGAGTGCGCCCTGTCTCCAC
A2 / 857 / 1 / GTTGACACACTGCCAGGGTATCGGTAGAGTGCGCAGCCAGAGGGA
A3 / 1009 / 1 / ATTGACAAGGTAGTAAGATGCGG-TAAGATGTGCGGCGTCAAGTG
A4 / 1111 / 1 / CTTGACACTGCAAGGCTCAGTCGGTAAGATGGGCACCCATAGCGG
A5 / 1260 / 1 / GTTGACACGACAAGGCCAAGTCGATAACATGGCCACCACAAAGGG
LKA1 / A1 / 475 / 1 / GTTTGAATATAAGTACCACTCAGGTTATATAACGAATTGGTATTGA
A2 / 513 / 1 / TATTGACGGGGCTTCAGCAGGTCTGTAGAGTTCGCAGCCATGGTTA
A3 / 685 / 1 / GCTTGACAAGCCAA-GCGGATGCTGTAAGATGCGAGTCGTAACTCA
A4 / 1170 / 2 / ACTTGACAAGCGAACGCCCAGTCTGTACGATGGGCACCAAGCAAGA
consensus / TTGACA TATAAT
B PHAGE PROMOTERS
LKD16 / P1 / 3254 / 4 / GGGCGACCATCGCCTACTCCGGGGCCA
P2 / 6653 / 12.1 / GGGCGACCAGGGCCTACTCCGGGGTCA
P3 / 14563 / 20 / TGACGACCCTTCCCTACTCCGGCCTTA
P4 / 24718 / 32 / TAACGACCCTGCCCTACTCCGGCCTTA
conserved nucleotides / ---CGACC----CCTACTCCGG----
conserved nucleotides KMVb / ---CGACC----CCTACTCCGG----
LKA1 / P1 / 275 / 5 / GCCGCGTGCCGGCTGCACTCGCGGCTCGAA
P2 / 3608 / 7 / ATGCCGTAACCGCTGCACTCGCAGCCCGAA
P3 / 6926 / 18 / TACCCGTAACCGCTGCACTCGCAGCTCAAT
P4 / 15011 / 30 / TACGCGGTACCGCTGGACGCTCGGCATCCT
conserved nucleotides / --SSCG---CCGCTGCACTCGCRGC-----
C TERMINATORSc / dG (kcal.mol-1)
LKD16 / T1 / 25782 / 33 / CCCGCGCAGATTCCCTGCGTGGGTTTTT -25,2
T2 / 42628 / DTR / AGTAGTTCAAGCCGAGCACCTGCATAGTCGGGTGCTCCACT -27.2
GGAACTACTGAATTTTTATT
LKA1 / T1 / 6893 / 18 / ggggctggccgcataaccggccccttct -16.8
T2 / 26102 / 44 / GGACCTATCCTTCGGGGTAGGTCCTTTTTTTGGTT -21.2
T3 / 41296 / DTR / cgcgcccccatgcccctgcgtgcgcgtttctt -10.0
Table S2. Predicted regulatory sequences in the LKD16 and LKA1 genomes.
a DTR = Direct Terminal Repeat
b As defined in (26).
c Stem structures are underlined.