TABLE 5.
Primary active transporters other than ABC transportersa
| Family and transporterb | TC no. | ORF | No. of TMSs | Putative substrate | Occurrence | Comments | E value | PRSS P value | Xylella annotation | COG |
|---|---|---|---|---|---|---|---|---|---|---|
| Phosphate bond-driven active transporters— F-type ATPases | ||||||||||
| F-ATPase | 3.A.2.1.1 | XF1149 | 5 | H+ | BO | ATP synthase, A chain | 2e-68 | 4.2235e-37 | ATP synthase, A chain | COG0356 (29 proteins), F0F1-type ATP synthase a subunit |
| F-ATPase | 3.A.2.1.1 | XF1148 | 1 | H+ | BO | ATP synthase, C chain | 6e-17 | 3.018e-12 | ATP synthase, C chain | COG0636 (53 proteins), F0F1-type ATP synthase c subunit/archaeal/vacuolar-type H+-ATPase subunit K |
| F-ATPase | 3.A.2.1.1 | XF1142 | 0 | H+ | BO | ATP synthase, epsilon chain | 2e-27 | 1.2088e-22 | ATP synthase, epsilon chain | COG0355 (30 proteins), F0F1-type ATP synthase epsilon subunit (mitochondrial delta subunit) |
| F-ATPase | 3.A.2.1.1 | XF1143 | 0 | H+ | BO | ATP synthase, beta chain | 0.0 | 3.4964e-128 | ATP synthase, beta chain | COG0055 (31 proteins), F0F1-type ATP synthase beta subunit |
| F-ATPase | 3.A.2.1.1 | XF1144 | 0 | H+ | BO | ATP synthase, gamma chain | 2e-95 | 3.282e-72 | ATP synthase, gamma chain | COG0224 (32 proteins), F0F1-type ATP synthase gamma subunit |
| F-ATPase | 3.A.2.1.1 | XF1145 | 0 | H+ | BO | ATP synthase, alpha chain | 0.0 | 1.2431e-115 | ATP synthase, alpha chain | COG0056 (31 proteins), F0F1-type ATP synthase alpha subunit |
| F-ATPase | 3.A.2.1.1 | XF1146 | 0 | H+ | BO | ATP synthase, delta chain | 3e-21 | 2.6852e-18 | ATP synthase, delta chain | COG0712 (31 proteins), F0F1-type ATP synthase delta subunit (mitochondrial oligomycin sensitivity protein) |
| F-ATPase | 3.A.2.1.1 | XF1147 | 0 | H+ | BO | ATP synthase, B chain | 4e-33 | 1.5018e-19 | ATP synthase, B chain | COG0711 (38 proteins), F0F1-type ATP synthase b subunit |
| Additional phosphate bond-driven active transporters | ||||||||||
| IISP | 3.A.5.1.1 | XF1172 | 10 | Protein | B | SecY subunit | e-141 | 8.9569e-70 | Preprotein translocase SecY subunit | COG0201 (46 proteins), preprotein translocase subunit SecY |
| IISP | 3.A.5.1.1 | XF0225 | 7 | Protein | B | SecD protein | e-136 | 3.8605e-83 | Protein export membrane protein | COG0342 (35 proteins), preprotein translocase subunit SecD |
| IISP | 3.A.5.1.1 | XF0226 | 6 | Protein | B | SecF protein | 2e-53 | 1.2289e-41 | Protein export membrane protein | COG0341 (32 proteins), preprotein translocase subunit SecF |
| IISP | 3.A.5.1.1 | XF2639 | 2 | Protein | B | SecE protein | 6e-13 | 1.4354e-11 | Preprotein translocase subunit | COG0690 (33 proteins), preprotein translocase subunit SecE |
| IISP | 3.A.5.1.1 | XF0073 | 1 | Protein | B | Ffh (signal recognition particle protein homologue) | e-154 | 7.5182e-76 | Signal recognition particle protein | COG0541 (44 proteins), signal recognition particle GTPase |
| IISP | 3.A.5.1.1 | XF0224 | 1 | Protein | B | YajC subunit | 6e-17 | 4.8984e-21 | Preprotein translocase YajC subunit | COG1862 (27 proteins), preprotein translocase subunit YajC |
| IISP | 3.A.5.1.1 | XF0304 | 1 | Protein | B | SecG protein | 1e-14 | 1.9945e-14 | Protein export membrane protein | COG1314 (24 proteins), preprotein translocase subunit |
| IISP | 3.A.5.1.1 | XF1910 | 1 | Protein | B | FtsY (signal recognition particle receptor homologue) | 1e-83 | 1.5495e-61 | Cell division protein | COG0552 (46 proteins), signal recognition particle GTPase |
| IISP | 3.A.5.1.1 | XF0806 | 0 | Protein | B | SecA subunit | 0.0 | 2.2789e-172 | Preprotein translocase SecA subunit | COG0653 (35 proteins), preprotein translocase subunit SecA (ATPase, RNA helicase) |
| IVSP | 3.A.7.1.1 | XFa0011 | 7 | DNA-protein complex | B-p | VirB6 | 4e-06 | 1.5005e-07 | Conjugal transfer protein<@0300>> | COG3704 (8 proteins), predicted membrane protein involved in conjugal plasmid transfer |
| IVSP | 3.A.7.1.1 | XFa0006 | 2 | DNA-protein complex | B-p | VirB3 | 2e-07 | 1.0811e-08 | Conjugal transfer protein | COG3702 (3 proteins), uncharacterized membrane protein |
| IVSP | 3.A.7.1.1 | XF2049 | 1 | DNA-protein complex | B-p | VirB10 | 5e-16 | 1.2192e-11 | Conjugal transfer protein | COG2948 (15 proteins), VirB10 component of type IV secretion system a0040 a0014 |
| IVSP | 3.A.7.1.1 | XFa0012 | 1 | DNA-protein complex | B-p | VirB8 | 3e-17 | 4.9039e-18 | Conjugal transfer protein | No COG |
| IVSP | 3.A.7.1.1 | XFa0014 | 1 | DNA-protein complex | B-p | VirB10 | 6e-51 | 5.1851e-28 | Conjugal transfer protein | COG2948 (15 proteins), VirB10 component of type IV secretion system a0040 |
| IVSP | 3.A.7.1.1 | XFa0040 | 1 | DNA-protein complex | B-p | VirB10 | 2e-15 | 1.2046e-11 | Conjugal transfer protein | COG2948 (15 proteins), VirB10 component of type IV secretion system a0014 |
| IVSP | 3.A.7.1.1 | XFa0007 | 0 | DNA-protein complex | B-p | VirB4—ATPase | e-135 | 2.8766e-100 | Conjugal transfer protein | COG3451 (15 proteins), predicted ATPase |
| IVSP | 3.A.7.1.1 | XFa0013 | 0 | DNA-protein complex | B-p | VirB9 | 3e-30 | 5.3519e-27 | Conjugal transfer protein | COG3504 (13 proteins), component of conjugal plasmid transfer system a0042 |
| IVSP | 3.A.7.1.1 | XFa0015 | 0 | DNA-protein complex | B-p | VirB11—ATPase | 1e-45 | 5.2895e-38 | Conjugal transfer protein | COG0630 (48 proteins), predicted ATPases involved in pilus and flagellum biosynthesis, VirB11 family |
| DNA-T | 3.A.11.1.1 | XF1078 | 10 | ssDNA | B | DNA translocase | 1e-45 | 1.0811e-42 | DNA uptake protein | 2 domains: 1, XF1078_1, COG0658 (30 proteins), predicted multitransmembrane, metal-binding protein; 2, XF1078_2, COG2333 (17 proteins), predicted hydrolases of metallo-β-lactamase fold |
| DNA-T | 3.A.11.1.1 | XF0252 | 0 | ssDNA | B | DNA translocase | 1e-06 | 1.2545e-11 | ATP-dependent RNA helicase | COG0513 (165 proteins), superfamily II DNA and RNA helicases |
| DNA-T | 3.A.11.1.1 | XF0593 | 0 | ssDNA | B | DNA translocase | 3e-11 | 5.4989e-12 | Conserved hypothetical protein | COG1555 (24 proteins), DNA uptake protein and related DNA-binding proteins |
| FPE | 3.A.12.2.1 | XF1518 | 3 | Protein | B | Pilin (PilA) secretion/fimbrial assembly system; membrane component | 9e-60 | 8.6426e-52 | General secretory pathway protein F | COG1459 (31 proteins), general secretory pathway protein F |
| FPE | 3.A.12.2.1 | XF2538 | 3 | Protein | B | Pilin (PilA) secretion/fimbrial assembly system; membrane component | e-131 | 2.6194e-83 | Fimbrial assembly protein | COG1459 (31 proteins), general secretory pathway protein F |
| FPE | 3.A.12.2.1 | XF1517 | 0 | Protein | B | Pilin (PilA) secretion/fimbrial assembly system; cytoplasmic ATPase component | e-100 | 2.8292e-70 | General secretory pathway protein E | COG2804 (33 proteins), predicted ATPases involved in pilus biogenesis, PilB homologs |
| FPE | 3.A.12.2.1 | XF2544 | 0 | Protein | B | Pilin (PilA) secretion/fimbrial assembly system; cytoplasmic ATPase component | 0.0 | 7.1114e-11 | Pilus biogenesis protein | COG2804 (33 proteins), predicted ATPases involved in pilus biogenesis, PilB homologs |
| Oxidoreduction-driven activetransporters | ||||||||||
| NDH | 3.D.1.1.1 | XF0318 | 13 | H+ | BO | NuoN subunit | 3e-64 | 3.4453e-26 | NADH-ubiquinone oxidoreductase, NQO14 subunit | COG1007 (23 proteins) NADH:ubiquinone oxidoreductase subunit 2 (chain N) |
| NDH | 3.D.1.1.1 | XF0316 | 12 | H+ | BO | NuoL subunit | 1e-27 | 2.1006e-15 | NADH-ubiquinone oxidoreductase, NQO12 subunit | COG1009 (38 proteins), NADH:ubiquinone oxidoreductase subunit 5 (chain L)/Multisubunit Na+/H+ antiporter, MnhA subunit |
| NDH | 3.D.1.1.1 | XF0317 | 10 | H+ | BO | NuoM subunit | 1e-93 | 3.061e-38 | NADH-ubiquinone oxidoreductase, NQO13 subunit | COG1008 (24 proteins), NADH:ubiquinone oxidoreductase subunit 4 (chain M) |
| NDH | 3.D.1.1.1 | XF0312 | 6 | H+ | BO | NuoH subunit | 1e-64 | 4.6176e-31 | NADH-ubiquinone oxidoreductase, NQO8 subunit | COG1005 (24 proteins), NADH:ubiquinone oxidoreductase subunit 1 (chain H) |
| NDH | 3.D.1.1.1 | XF0314 | 4 | H+ | BO | NuoJ subunit | 3e-16 | 2.647e-13 | NADH-ubiquinone oxidoreductase, NQO10 subunit | COG0839 (26 proteins), NADH:ubiquinone oxidoreductase subunit 6 (chain J) |
| NDH | 3.D.1.1.1 | XF0305 | 3 | H+ | BO | NuoA subunit | 3e-13 | 1.7523e-13 | NADH-ubiquinone oxidoreductase, NQ07 subunit | COG0838 (22 proteins), NADH:ubiquinone oxidoreductase subunit 3 (chain A) |
| NDH | 3.D.1.1.1 | XF0313 | 2 | H+ | BO | NuoI subunit | 3e-21 | 1.2041e-23 | NADH-ubiquinone oxidoreductase, NQO9 subunit | COG1143 (36 proteins), formate hydrogenlyase subunit 6/NADH:ubiquinone oxidoreductase 23-kDa subunit (chain I) |
| NDH | 3.D.1.1.1 | XF0311 | 1 | H+ | BO | NuoG subunit | 3e-51 | 6.7891e-40 | NADH-ubiquinone oxidoreductase, NQO3 subunit | COG1034 (21 proteins), NADH dehydrogenase/NADH:ubiquinone oxidoreductase 75-kDa subunit (chain G) |
| NDH | 3.D.1.1.1 | XF0306 | 0 | H+ | BO | NuoB subunit | 4e-41 | 1.1315e-38 | NADH-ubiquinone oxidoreductase, NQO6 subunit | COG0377 (26 proteins), NADH:ubiquinone oxidoreductase 20-kDa subunit and related Fe-S oxidoreductases |
| NDH | 3.D.1.1.1 | XF0307 | 0 | H+ | BO | NuoC subunit | 3e-17 | 1.5812e-18 | NADH-ubiquinone oxidoreductase, NQO5 subunit | COG0852 (27 proteins), NADH:ubiquinone oxidoreductase 27-kDa subunit |
| NDH | 3.D.1.1.1 | XF0308 | 0 | H+ | BO | NuoD subunit | 1e-81 | 2.4758e-66 | NADH-ubiquinone oxidoreductase, NQ04 subunit | COG0649 (27 proteins), NADH:ubiquinone oxidoreductase 49-kDa subunit 7 |
| NDH | 3.D.1.1.1 | XF0309 | 0 | H+ | BO | NuoE subunit | 5e-20 | 7.2428e-24 | NADH-ubiquinone oxidoreductase, NQO2 subunit | COG1905 (21 proteins), NADH:ubiquinone oxidoreductase 24-kDa subunit |
| NDH | 3.D.1.1.1 | XF0310 | 0 | H+ | BO | NuoF subunit | 2e-92 | 1.8278e-69 | NADH-ubiquinone oxidoreductase, NQO1 subunit | COG1894 (21 proteins), NADH:ubiquinone oxidoreductase NADH binding (51 kDa) subunit |
| NDH | 3.D.1.1.1 | XF0315 | 1 | H+ | BO | NuoK subunit | 4e-34 | 4.5288e-27 | NADH-ubiquinone oxidoreductase, NQO11 subunit | COG0713 (22 proteins), NADH:ubiquinone oxidoreductase subunit 11 or 4L (chain K) |
| QCR | 3.D.3.1.1 | XF0909 | 8 | H+ | BO | Ubiquinol cytochrome c oxidoreductase, cytochrome b subunit, also hit 3.E.2-PRC | 5e-90 | 2.3737e-43 | Ubiquinol cytochrome c oxidoreductase, cytochrome b subunit | COG1290 (30 proteins), cytochrome b subunit of the bc complex |
| QCR | 3.D.3.1.1 | XF0908 | 1 | H+ | BO | Ubiquinol cytochrome c oxidoreductase, iron-sulfur subunit; also hit 3.E.2-PRC | 1e-24 | 1.6097e-25 | Ubiquinol cytochrome c oxidoreductase, iron-sulfur subunit | COG0723 (35 proteins), Rieske Fe-S protein |
| QCR | 3.D.3.2.1 | XF0910 | 1 | H+ | BO | Ubiquinol cytochrome c oxidoreductase, cytochrome c1 subunit | 2e-11 | 1.4333e-14 | Ubiquinol cytochrome c oxidoreductase, cytochrome c1 subunit | COG2857 (18 proteins), cytochrome c1 |
| COX | 3.D.4.5.1 | XF1389 | 14 | H+ | BO | Cytochrome o ubiquinol oxidase, subunit I | 0.0 | 6.6568e-104 | Cytochrome o ubiquinol oxidase, subunit I | COG0843 (30 proteins), heme/copper-type cytochrome/quinol oxidases, subunit 1 |
| COX | 3.D.4.5.1 | XF1388 | 5 | H+ | BO | Cytochrome o ubiquinol oxidase, subunit III | 2e-77 | 1.1358e-44 | Cytochrome o ubiquinol oxidase, subunit III | COG1845 (27 proteins), heme/copper-type cytochrome/quinol oxidase, subunit 3 |
| COX | 3.D.4.5.1 | XF1390 | 2 | H+ | BO | Cytochrome o ubiquinol oxidase, subunit II | 1e-91 | 1.5195e-64 | Cytochrome o ubiquinol oxidase, subunit II | COG1622 (33 proteins), heme/copper-type cytochrome/quinol oxidases, subunit 2 |
a
See Table 2, footnote a.
b
IISP and IVSP, type II and type IV general secretory pathway, respectively; DNA-T, DNA transformation; FPE, fimbrillin/protein exporter; NDH, NADH dehydrogenase I; QCR, quinol:cytochrome c reductase; COX, cytochrome oxidase; ssDNA, single-stranded DNA.