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Table 2 Classification according to the function categories of absent ORFs in Shigella spp. strains

From: The use of comparative genomic hybridization to characterize genome dynamics and diversity among the serotypes of Shigella

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)
  1. * 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.
  2. #The % indicated in parenthesis is relative to MG1655 total ORFs.