Table 2.
Classification according to the function categories of absent ORFs in Shigella spp. strains
| Description | MG1655 total ORFs | Absent MG1655 ORFs in Shigella spp. strains* | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Total (%) # | C1 (%) # | C2 (%) # | C3 (%) # | SS (%) # | D1 (%) # | D8 (%) # | D10 (%) # | B13 (%) # | ||
| Information storage and processing | ||||||||||
| Translation, ribosomal structure and biogenesis | 171 | 22(12.9) | 16(9.4) | 6(3.5) | 8(4.7) | 4(2.3) | 5(2.9) | 2(1.2) | 3(1.8) | 4(2.3) |
| RNA processing and modification | 2 | 1(50.0) | 1(50.0) | 1(50.0) | 1(50.0) | 0 | 0 | 0 | 1(50.0) | 0 |
| Transcription | 280 | 173(61.8) | 126(45.0) | 91(32.5) | 108(38.6) | 46(16.4) | 70(25.0) | 38(13.6) | 52(18.6) | 83(29.6) |
| Replication, recombination and repair | 220 | 79(35.9) | 64(29.1) | 49(22.3) | 49(22.3) | 24(10.9) | 31(14.1) | 24(10.9) | 35(15.9) | 35(15.9) |
| Cellular processes | ||||||||||
| cell division and chromosome partitioning | 34 | 7(20.6) | 4(11.8) | 6(17.6) | 2(5.9) | 1(2.9) | 2(5.9) | 1(2.9) | 0 | 3(8.8) |
| Defense mechanisms | 48 | 22(45.8) | 12(25.0) | 12(25.0) | 13(27.1) | 7(14.6) | 13(27.1) | 7(14.6) | 9(18.8) | 12(25.0) |
| Signal transduction mechanisms | 134 | 67(50.0) | 54(40.3) | 29(21.6) | 37(27.6) | 8(6.0) | 27(20.1) | 13(9.7) | 10(7.5) | 19(14.2) |
| cell envelope biogenesis, outer membrane | 235 | 122(51.9) | 90(38.3) | 71(30.2) | 69(29.4) | 28(11.9) | 48(20.4) | 26(11.1) | 35(14.9) | 42(17.9) |
| cell motility and secretion | 107 | 89(83.2) | 79(73.8) | 45(42.1) | 70(65.4) | 29(27.1) | 65(60.7) | 35(32.7) | 36(33.6) | 51(41.7) |
| Intracellular trafficking, secretion, and vesicular transport | 37 | 14(37.8) | 7(18.9) | 9(24.3) | 10(27.0) | 7(18.9) | 6(16.2) | 4(10.8) | 5(13.5) | 5(13.5) |
| Posttranslational modification, protein turnover, chaperones | 128 | 30(23.4) | 15(11.7) | 8(6.3) | 8(6.3) | 1(0.8) | 6(4.7) | 4(3.1) | 2(1.6) | 7(5.5) |
| Metabolism | ||||||||||
| Energy production and conversion | 275 | 151(54.9) | 94(34.2) | 59(21.5) | 87(31.6) | 24(8.7) | 47(17.1) | 17(6.2) | 31(11.3) | 34(12.4) |
| Carbohydrate transport and metabolism | 368 | 249(67.7) | 182(49.4) | 109(29.6) | 133(36.1) | 69(18.8) | 116(31.5) | 58(15.8) | 58(15.8) | 97(26.4) |
| Amino acid transport and metabolism | 350 | 152(43.4) | 106(30.3) | 58(16.6) | 85(24.3) | 19(5.4) | 38(10.9) | 24(6.9) | 29(8.3) | 44(12.6) |
| Nucleotide transport and metabolism | 87 | 33(37.9) | 22(25.3) | 13(14.9) | 17(19.5) | 6(6.9) | 12(13.8) | 7(8.0) | 8(9.2) | 11(12.6) |
| Coenzyme transport and metabolism | 123 | 26(21.1) | 17(13.8) | 7(5.7) | 14(11.4) | 2(1.6) | 7(5.7) | 0 | 2(1.6) | 4(3.3) |
| Lipid transport and metabolism | 83 | 36(43.4) | 26(31.3) | 19(22.9) | 20(24.1) | 13(15.7) | 17(20.5) | 6(7.2) | 10(12.0) | 13(15.7) |
| Inorganic ion transport and metabolism | 191 | 98(51.3) | 64(33.5) | 55(28.8) | 59(30.9) | 11(5.8) | 25(13.1) | 21(11.0) | 19(9.9) | 39(20.4) |
| Secondary metabolites biosynthesis, transport and catabolism | 68 | 46(67.6) | 29(42.6) | 22(32.4) | 25(36.8) | 6(8.8) | 16(23.5) | 5(7.4) | 13(19.1) | 21(30.9) |
| Poorly characterized | ||||||||||
| General function prediction only | 338 | 178(52.7) | 135(39.9) | 95(28.1) | 90(26.6) | 31(9.2) | 59(17.5) | 37(10.9) | 43(12.7) | 63(18.6) |
| Function unknown | 308 | 154(50.0) | 101(32.8) | 64(20.8) | 85(27.6) | 29(9.4) | 49(15.9) | 16(5.2) | 33(10.7) | 43(14.0) |
| Not in COGs | 692 | 496(71.7) | 413(59.7) | 305(44.1) | 359(51.9) | 219(31.6) | 295(42.6) | 216(31.2) | 221(31.9) | 266(38.4) |
| Total | 4279 | 2245(52.5) | 1657(38.7) | 1133(26.5) | 1349(31.5) | 584(13.6) | 954(22.3) | 561(13.1) | 655(15.3) | 896(20.9) |
* C1 contains D strains (D3, D4, D5, D6, D7, D9, D11, D12, and D13) and B strains (B1, B2, B3, B4, B6, B8, B10, B14, and B18) with F6 as minorities. C2 is mainly composed of B strains (B5, B7, B9, B11, B15, B16, B17) and D2. C3 consists mostly of F strains (F1a, F1b, F2a, F2b, F3, F4a, F4b, F5, Fx, Fy) and B12. Shigella strains are labelled according to the designations in Table 1.
#The % indicated in parenthesis is relative to MG1655 total ORFs.