Table 1 Genetic repertoire of loci characterized by atypical tetranucleotide usage patterns and extreme OUV (section III in Fig. 4) identified in bacterial chromosomes
From: Differentiation of regions with atypical oligonucleotide composition in bacterial genomes
Genome | Genes and the encoded protein | Start* | Length (bp) | ΔD† | ΔOUV‡ |
|---|---|---|---|---|---|
Acinetobacter sp. | putative hemagglutinin/hemolysin-related protein | 923,008 | 11,136 | 3.11 | 4.13 |
non-coding multiple repeats TTTAGAAA | 2,448,000 | 5.600 | 2.24 | 17.33 | |
Bordetella bronchiseptica RB50 | BB1186: putative hemolysin | 1,268,967 | 10,041 | 5.13 | 4.12 |
Bradyrhizobium japonicum USDA110 | blr325: unknown | 3,592,327 | 17,058 | 3.17 | 4.65 |
bll356: unknown | 3,930,196 | 10,326 | 6.23 | 5.02 | |
bll371: unknown | 4,106,955 | 12,387 | 4.39 | 4.95 | |
bll547: unknown | 6,017,600 | 12,633 | 5.04 | 6.16 | |
Corynebacterium efficiens YS-314 | fasA: fatty-acid synthase I | 962,711 | 8,919 | 2.85 | 3.85 |
fasB: fatty-acid synthase II | 2,541,750 | 9,069 | 2.88 | 5.42 | |
Deinococcus radiodurans R1 chromosome 1 | DR1461-1462: hypothetical proteins | 1,465,188 | 10,000 | 2.19 | 8.27 |
non-coding tandem repeats CCCGCCC | 519,833 | 8,415 | 7.06 | 8.42 | |
E. coli O157:H7 | Z0609, Z0615: RTX family exoproteins | 581,356 | 20,160 | 1.82 | 9.43 |
Mycobacterium tuberculosis H37Rv | Rv0272c-Rv0279c hypothetical Gly-, Ala-rich proteins | 328.573 | 10,499 | 1.52 | 9.15 |
Rv0297-Rv0304c: hypothetical Gly-, Ala-, Asn-rich proteins | 361,332 | 11,431 | 8.79 | 7.91 | |
Rv0355c: Asn-rich protein | 424,775 | 9,903 | 8.31 | 10.91 | |
Rv0573c-Rv0578c: hypothetical Gly-rich proteins | 665,849 | 10,066 | 0.60 | 4.72 | |
Rv0742-Rv0747: hypothetical Gly-rich proteins | 832,979 | 7,876 | 1.24 | 3.97 | |
Rv1060-Rv1068c: hypothetical Gly-, Ala-rich proteins | 1,183,506 | 8,641 | 1.04 | 5.54 | |
Rv1084-Rv1092c: hypothetical proteins | 1,207,634 | 11.395 | 2.19 | 6.44 | |
multiple repeats CCGCCGCCA | 1,630,636 | 7,592 | 2.33 | 8.84 | |
Rv2490c-Rv2494: hypothetical Gly-rich proteins | 2,801,252 | 7,482 | 2.60 | 5.50 | |
Pseudomonas aeruginosa PAO1 | PA1874: hypothetical protein | 2,036,441 | 7,407 | 2.61 | 5.61 |
P. putida KT2440 | PP0168: Thr-rich surface adhesion protein | 194,494 | 26,046 | 2.58 | 6.97 |
PP0806: surface adhesion protein | 926,690 | 18,930 | 1.17 | 4.39 | |
P. syringae DC3000 | PSPTO3229: filamentous hemagglutinin | 3,629,677 | 18,825 | 2.34 | 7.87 |
Rhodopirellula baltika 1 | RB3077: putative cyclic nucleotide binding protein | 1,588,083 | 18,024 | 1.62 | 6.19 |
RB4375: large polymorphic membrane protein, probable extracellular nuclease; | 2,242,933 | 9,171 | 3.23 | 7.09 | |
RB11769: probable aggregation factor core protein MAFp3 | 6,335,006 | 24,522 | 5.25 | 6.31 | |
Rhodopseudomonas palustris CGA009 | conserved hypothetical protein | 1,459,664 | 9,891 | 2.61 | 3.38 |
conserved hypothetical protein | 1,475,303 | 13,008 | 2.89 | 4.18 | |
Sulfolobus solfataricus P2 | non-coding tandem repeats GAATTGAAAG | 1,228,221 | 12,238 | 1.94 | 15.25 |
1,253,000 | 5,000 | 1.50 | 8.67 | ||
1,305,242 | 5,000 | 1.89 | 12.39 | ||
Staphylococcus aureus N315 | ebhA – ebhB: large surface anchored proteins | 1,437,928 | 20,142 | 4.04 | 10.07 |
SA2447: similar to streptococcal hemagglutinin | 2,755,253 | 6,816 | 3.03 | 9.29 | |
Streptomyces coelicolor A3(2) | SC8F4.01c: Ala/Glu-rich protein | 586,509 | 3.981 | 2.16 | 5.40 |
SC2H4.02: hypothetical protein | 6,836,057 | 6,552 | 2.86 | 4.80 | |
Xanthomonas campestris ATCC33913 | yapH: putative autotransporter adhesin | 2,374,740 | 11,886 | 3.22 | 6.61 |
Xylella fastidiosa Temecula 1 | non-coding sequence, multiple | 1,183,606 | 11,095 | 1.31 | 9.81 |
repeats (GGT)n | 1,447,312 | 11,139 | 1.37 | 10.91 | |
pspA1: hemagglutinin | 2,082,143 | 10,134 | 1.06 | 9.78 | |
pspA2: hemagglutinin | 2,501,956 | 10,374 | 1.41 | 11.79 | |
Yersinia pestis KIM | irp1-2: yersiniabactin peptide/polyketide synthetase; | 2,654,642 | 15,867 | 4.27 | 6.05 |
yapH: putative autotransporter adhesin | 3,747,888 | 11,133 | 2.66 | 8.60 | |
y3579: putative filamentous hemagglutinin | 3,961,333 | 9,888 | 3.31 | 4.32 |