TABLE 3.
Electrochemical potential-driven transportera
| Family and transporterb | TC no. | ORF | No. of TMSs | Putative substrate | Occurrence | Comments | E value | PRSS P value | Xylella annotation | COG |
|---|---|---|---|---|---|---|---|---|---|---|
| Major facilitator superfamily | ||||||||||
| DHA1 | 2.A.1.2.4 | XF0268 | 8 | Tetracycline:H+ antiporter | B | TetA antiporter; Blast with filter E value, 0.010 | 2e-05 | 1.2286e-07 | Conserved hypothetical protein | COG0477 (925 proteins), permeases of the major facilitator superfamily |
| DHA1 | 2.A.1.2.18 | XF1749 | 11 | Drug:H+ antiporter 1 (sugar efflux) | BE | Lactose and melibiose (and IPTG) efflux | 3e-40 | 2.0382e-18 | Transcriptional regulator | COG2814 (42 proteins), arabinose efflux permease |
| DHA1 | 2.A.1.2.18 | XF1728 | 10 | Drug:H+ antiporter 1 (sugar efflux) | BE | Lactose and melibiose (and IPTG) efflux | 1e-34 | 7.5481e-15 | Transport protein | COG2814 (42 proteins), arabinose efflux permease |
| DHA2 | 2.A.1.3.10 | XF1765 | 14 | Drug-H+ antiporter 2 | BE | Also similar to 8.A.1 | 3e-66 | 2.0866e-25 | Drug: proton antiporter | COG0477 (925 proteins), permeases of the major facilitator superfamily |
| MHS | 2.A.1.6.2 | XF0087 | 8 | Metabolite | B | α-Ketoglutarate:H+ symporter | e-157 | 4.0568e-83 | α-Ketoglutarate permease symporter | COG0477 (925 proteins), permeases of the major facilitator superfamily |
| FHS | 2.A.1.7.2 | XF1609 | 10 | Glucose/galactose | B | Glucose/galactose permease | e-109 | 2.3545e-56 | Glucose/galactose transporter | COG0738 (16 proteins), fucose permease |
| FHS | 2.A.1.7.2 | XF1462 | 9 | Glucose/galactose | B | Glucose/galactose permease | 2e-44 | 3.732e-25 | Glucose/galactose transporter | COG0738 (16 proteins), fucose permease |
| DHA3 | 2.A.1.21.3 | XF0993 | 8 | Drug | B | Tetracycline resistance determinant TetV | 2e-21 | 1.1218e-11 | Drug:proton antiporter | COG0477 (925 proteins), permeases of the major facilitator superfamily |
| PAT | 2.A.1.25.2 | XF0165 | 11 | Drug, glycopeptide | BE | AmpG penicillin derivative uptake permease | 1e-46 | 6.2703e-36 | β-Lactamase induction signal transducer protein | COG0477 (925 proteins) permeases of the major facilitator superfamily |
| Other secondary porters | ||||||||||
| CAT | 2.A.3.3.1 | XF2208 | 11 | Cationic a.a. | BAE | High-affinity basic a.a. transporter CAT1 of Musmusculus | 6e-64 | 7.6968e-36 | Cationic amino acid transporter | COG0531 (170 proteins), amino acid transporters |
| CAT | 2.A.3.3.1 | XF2207 | 9 | Cationic a.a. | BAE | High-affinity basic a.a. transporter CAT1 of Mus musculus | 2e-74 | 1.1345e-43 | Cationic amino acid transporter | COG0531 (170 proteins), amino acid transporters |
| CAT | 2.A.3.3.3 | XF0408 | 12 | Cationic a.a. | BAE | Similar to amino acid transporter AAT1 of Arabidopsis thaliana | 2e-58 | 3.6814e-27 | Amino acid transporter | COG0531 (170 proteins), amino acid transporters |
| CDF | 2.A.4.1.1 | XF0866 | 6 | Heavy metal | BAE | Cd2+, Zn2+, Co2+ efflux permease | 1e-84 | 3.4023e-58 | Cobalt-zinc-cadmium resistance protein | COG1230 (28 proteins), Co/Zn/Cd efflux system component |
| RND (HME) | 2.A.6.1.2 | XF0243 | 12 | Heavy metal | BAE | Heavy-metal efflux pump (Co2+, Zn2+, Cd2+) | 3e-73 | 1.25e-45 | Acriflavin resistance protein | COG0841 (73 proteins), cation/multidrug efflux pump |
| RND (HME) | 2.A.6.1.2 | XF2083 | 11 | Heavy metal | BAE | Heavy-metal efflux pump (Co2+, Zn2+, Cd2+) | 3e-71 | 7.6213e-42 | Cation efflux system protein | COG0841 (73 proteins), cation/multidrug efflux pump |
| RND (HAE1) | 2.A.6.2.1 | XF2094 | 12 | Multidrug | BAE | Multidrug (acriflavin) resistance pump | 0.0 | 4.0016e-167 | Multidrug-efflux transporter | COG0841 (73 proteins), cation/multidrug efflux pump |
| RND (HAE1) | 2.A.6.2.6 | XF2385 | 12 | Multidrug | BAE | Multiple drug; N-(3-oxododecanoyl)-l-homoserine lactone autoinducer efflux pump | e-115 | 1.1486e-70 | Acriflavin resistance protein D | COG0841 (73 proteins) cation/multidrug efflux pump |
| RND (HAE1) | 2.A.6.2.7 | XF2386 | 12 | Multidrug, aminoglycosides | BAE | Multidrug efflux pump AcrD; exports aminoglycosides | e-108 | 9.7384e-69 | Acriflavin resistance protein | COG0841 (73 proteins), cation/multidrug efflux pump |
| RND (SecDF) | 2.A.6.4.1 | XF0225 | 7 | Protein | B | SecD protein | e-136 | 3.8605e-83 | Protein export membrane protein | COG0342 (35 proteins), preprotein translocase subunit SecD |
| RND (SecDF) | 2.A.6.4.1 | XF0226 | 6 | Protein | B | SecF protein | 2e-53 | 1.2289e-41 | Protein export membrane protein | COG0341 (32 proteins), preprotein translocase subunit SecF |
| RND (HAE2) | 2.A.6.5.1 | XF0777 | 12 | Drug, antibiotic | BAE | Antibiotic actinorhodin transport-associated protein ActI13; Blast with filter E value, 0.32 | 3e-13 | 2.6152e-08 | Membrane protein | No COG |
| CitMHS | 2.A.11.1.2 | XF0320 | 9 | Citrate | BE | Citrate:H+ symporter | e-157 | 3.1147e-74 | Mg2+/citrate complex transporter | COG2851 (10 proteins), H+/citrate symporter |
| AAA | 2.A.12.1.2 | XF1738 | 10 | ATP:ADP antiporter | BE | Similar to Npt1 of Chlamydia trachomatis | 1e-16 | 3.5714e-13 | Hypothetical protein | COG3202 (15 proteins), ATP/ADP translocase |
| POT | 2.A.17.1.1 | XF1891 | 10 | Oligopeptide: H+ symporter | BAE | Di- or tripeptide:H+ symporter | 7e-55 | 2.0679e-25 | Di-tripeptide ABC transporter membrane protein | COG3104 (18 proteins), dipeptide/tripeptide permease |
| SSS | 2.A.21.7.1 | XF2251 | 13 | Phenylacetate | BAE | Phenylacetate permease | e-178 | 9.1145e-62 | Solute:Na+ symporter | COG0591 (79 proteins), Na+/proline, Na+/panthothenate symporters and related permeases |
| DAACS | 2.A.23.1.2 | XF1937 | 9 | a.a., dicarb. | BE | Glutamate, aspartate:Na+, H+ symporter | 6e-59 | 3.4059e-32 | Proton glutamate symport protein | COG1301 (39 proteins), Na+/H+-dicarboxylate symporters |
| DAACS | 2.A.23.1.2 | XF0656 | 7 | a.a., dicarb. | BE | Glutamate, aspartate:Na+, H+ symporter | 1e-56 | 2.4966e-28 | Glutamate symport protein | COG1301 (39 proteins), Na+/H+-dicarboxylate symporters |
| DAACS | 2.A.23.1.3 | XF0976 | 8 | a.a., dicarb. | BE | C4-dicarboxylate transporter | e-164 | 1.1088e-67 | C4-dicarboxylate transport protein | COG1301 (39 proteins), Na+/H+-dicarboxylate symporters |
| CPA1 | 2.A.36.3.1 | XF2019 | 12 | Na+? | BE | Putative antiporter (function unknown) | e-114 | 6.1394e-66 | Na+:H+ antiporter | COG0025 (39 proteins), NhaP-type Na+/H+ and K+/H+ antiporters |
| CPA2 | 2.A.37.1.1 | XF2140 | 12 | K+ mostly | BAE | Glutathione-regulated K+ efflux protein C | 2e-56 | 1.7293e-30 | Cation:proton antiporter | 2 domains: 1 XF2140_1, COG0475 (60 proteins), Kef-type K+ transport systems, membrane components; 2, XF2140_2, COG1226 (79 proteins), Kef-type K+ transport systems, predicted NAD-binding component |
| CPA2 | 2.A.37.2.1 | XF1398 | 11 | Na+/H+ | BAE | Na+:H+ antiporter | 9e-11 | 1.6718e-08 | Na+/H+ exchange protein | COG0475 (60 proteins), Kef-type K+ transport systems, membrane components |
| DASS | 2.A.47.4.1 | XF0785 | 11 | Divalent anion | BAE | Sulfur deprivation response | 3e-73 | 6.3827e-45 | Sulfur deprivation response regulator | COG0471 (50 proteins), di- and tricarboxylate transporters |
| Amt | 2.A.49.1.1 | XF1844 | 11 | Ammonium | BAE | Ammonium transporter | e-138 | 1.8823e-49 | Ammonium transporter | COG0004 (38 proteins), ammonia permeases |
| Nramp | 2.A.55.1.2 | XF1015 | 9 | Metal | BAE | Putative low-affinity Mn2+ uptake | 2e-73 | 1.0721e-48 | Manganese transport protein | COG1914 (25 proteins), Mn2+ and Fe2+ transporters of the NRAMP family |
| Tat | 2.A.64.1.1 | XF0562 | 6 | Protein | BA? | TatC channel | 8e-61 | 1.0933e-37 | Sec-independent protein translocase | COG0805 (31 proteins), Sec-independent protein secretion pathway component TatC |
| Tat | 2.A.64.1.1 | XF0177 | 0 | Protein | BA? | TatC protein; exports proteins with leading sequence TRRXFLK | 9e-24 | 6.1298e-22 | Conserved hypothetical protein | COG0084 (58 proteins), Mg-dependent DNase |
| Tat | 2.A.64.1.1 | XF0563 | 0 | Protein | BA? | TatB protein; Blast with filter E value, 0.024 | 7e-11 | 2.0218e-12 | Hypothetical protein | COG1826 (51 proteins), Sec-independent protein secretion pathway components |
| Tat | 2.A.64.1.1 | XF0564 | 0 | Protein | BA? | TatA protein | 2e-09 | 1.0113e-09 | Conserved hypothetical protein | COG1826 (51 proteins), Sec-independent protein secretion pathway components |
| Tat | 2.A.64.1.1 | XF1913 | 0 | Protein | BA? | TatD protein | 1e-64 | 2.857e-54 | Type V secretory pathway protein | COG0084 (58 proteins), Mg-dependent DNase |
| MATE | 2.A.66.1.1 | XF2686 | 10 | Antimicrobials | BE | Multidrug efflux system | 1e-71 | 1.1291e-37 | Multidrug efflux protein | COG0534 (83 proteins), Na+-driven multidrug efflux pump |
| OPT | 2.A.67.2.1 | XF2261 | 15 | Oligopeptide: H+ symporter | BE | Similar to ORF HI0561/560 of Haemophilus influenzae | e-117 | 6.1557e-43 | Oligopeptide transporter | COG1297 (14 proteins), uncharacterized membrane protein |
| KUP | 2.A.72.1.1 | XF1903 | 11 | K+ | BE | K+ uptake permease | e-169 | 2.7402e-91 | Potassium uptake protein | COG3158 (13 proteins), K+ transporter |
| ICT | 2.A.73.1.1 | XF0103 | 7 | HCO3− | C | Putative HCO3−:Na+ symporter; Blast with filter E value, = 6e-04 | 1e-08 | 1.7299e-06 | Membrane protein | COG3307 (22 proteins), lipid A core-O-antigen ligase and related enzymes |
| RhtB | 2.A.76.1.1 | XF2730 | 5 | Amino acid | B | Homoserine/homoserine actone/β-hydroxynorvaline efflux permease | 5e-21 | 5.0767e-16 | Amino acid transporter | COG1280 (67 proteins), putative threonine efflux protein |
| Energizers | ||||||||||
| TonB | 2.C.1.1.1 | XF0010 | 2 | Siderophore, B colicin | B | ExbB protein | 9e-17 | 1.0079e-13 | Biopolymer transport ExbB protein | COG0811 (45 proteins), biopolymer transport proteins |
| TonB | 2.C.1.1.1 | XF1079 | 2 | Siderophore, B colicin | B | ExbB protein | 4e-12 | 6.5391e-12 | Conserved hypothetical protein | COG0811 (45 proteins), Biopolymer transport proteins |
| TonB | 2.C.1.1.1 | XF0009 | 1 | Siderophore, B colicin | B | TonB protein | 5e-16 | 4.7175e-07 | TonB protein | COG0810 (32 proteins), periplasmic protein TonB, links inner and outer membranes |
| TonB | 2.C.1.1.1 | XF0011 | 1 | Siderophore, B colicin | B | ExbD1 protein | 7e-17 | 4.87e-19 | Biopolymer transport ExbD1 protein | COG0848 (45 proteins), biopolymer transport protein |
| TonB | 2.C.1.1.1 | XF1080 | 1 | Siderophore, B colicin | B | ExbD protein | 1e-10 | 4.9777e-13 | Conserved hypothetical protein | COG0848 (45 proteins), biopolymer transport protein |
| TonB | 2.C.1.1.1 | XF2287 | 1 | Siderophore, B colicin | B | TonB protein: Blast with filter E value, 0.001 | 9e-10 | 7.0449e-06 | TonB protein | COG0810 (32 proteins), periplasmic protein TonB, links inner and outer membranes |
| TonB | 2.C.1.1.1 | XF2327 | 1 | Siderophore, B colicin | B | TonB protein | 5e-13 | 1.8723e-07 | TonB protein | COG0810 (32 proteins), periplasmic protein TonB, links inner and outer membranes |
| TonB | 2.C.1.1.1 | XF0012 | 0 | Siderophore, B colicin | B | ExbD2 protein | 4e-15 | 1.4428e-16 | Biopolymer transport ExbD2 protein | COG0848 (45 proteins), biopolymer transport protein |
| TonB | 2.C.1.2.1 | XF1900 | 3 | Colicin A, DNA | TolQ protein | 8e-56 | 1.9298e-42 | TolQ protein | COG0811 (45 proteins), biopolymer transport proteins | |
| TonB | 2.C.1.2.1 | XF1899 | 0 | Colicin A, DNA | B | TolR protein | 2e-19 | 2.517e-15 | TolR protein | COG0848 (45 proteins), biopolymer transport protein |
a
See Table 2, footnote a.