TABLE 3.

Selected genes showing synteny between SPI-7 and X. axonopodis pv. citri (accession number AE011859) or R. metallidurans (accession number NZ_AAA101000352)

Gene(s)Location (coordinates)Product size (amino acids)Function% Amino acid identity(ies) (range)a
tRNApheU (truncated)4409519-4409574
STY45214409652-4410686344parB-like partition protein41 (286 aa to XAC2205), 39 (289 aa to Reut4191)
STY45234412040-4413839599Hypothetical31 (580 aa to XAC2206), 30 (600 aa to Reut4193)
STY45264415107-4415664185Hypothetical32 (173 aa to Reut4194), 28 (165 aa to XAC2207)
STY45284415909-4417252447Hypothetical32 (405 aa to Reut4195), 29 (399 aa to XAC2208)
STY45294417838-4418617259Hypothetical30 (163 aa to XAC2209), 29 (227 aa to Reut4196)
STY45304418728-4420722664topB topoisomerase B50 (675 aa to XAC2212), 49 (677 aa to Reut4199)
STY45344421390-4421839149Hypothetical38 (136 aa to Reut4221), 33 (128 aa to XAC2236)
STY45354421920-442213872Hypothetical56 (65 aa to XAC2217)
STY45364422151-4422687178ssb single-stranded DNA-binding protein60 (174 aa to pWWO Ssb), 68 (162 aa to P1 phage Ssb-p1)
STY45394423868-4425112414pilL membrane-located open reading frame46 (126 aa to XAC2253), 38 (165 aa to Reut4232)
STY45544437266-4438141291traE (putative)23 (219 aa to R64 plasmid open reading frame TraE)
STY45574438648-4439562304Hypothetical membrane protein25 (170 aa to Reut4233)
STY45584439581-4440321246Hypothetical40 (227 aa to XAC2255), 37 (237 aa to Reut4234)
STY45594440435-4440986183Hypothetical44 (141 aa to XAC2256), 42 (148 aa to Reut4235)
STY45604441022-4441522166Hypothetical41 (160 aa to XAC2257), 39 (153 aa to Reut4236)
STY45614441532-4442101189Hypothetical51 (213 aa to NP_511181 [R46 plasmid])
STY45624442121-4444211696traG-like (DNA transfer region-associated gene)65 (541 aa to XAC2259), 61 (709 aa to Reut4237), 26 (630 aa to TraG-like open reading frame in R27 plasmid)
STY45634444208-4444966252Hypothetical42 (234 aa to XAC2260), 42 (228 aa to Reut4238)
STY45644445185-444545790Hypothetical42 (82 aa to Reut4247), 39 (81 aa to XAC2269)
STY45654445457-444569679Hypothetical membrane-spanning domains29 (77 aa to Reut4248)
STY45664445726-4446088120Hypothetical membrane-spanning domains37 (107 aa to XAC2270), 35 (89 aa to Reut4249)
STY45674446098-4446472124Hypothetical30 (90 aa to XAC2271)
STY45684446469-4447122217Hypothetical exported protein54 (219 aa to Reut4250)
STY45694447122-4448021299Hypothetical50 (255 aa to Reut4252), 44 (292 aa to XAC2272)
STY45704448011-4449489492Hypothetical exported protein38 (513 aa to XAC2273)
STY45714449482-4449925147Hypothetical lipoprotein47 (127 aa to Reut4254)
STY45724449922-4450341139Hypothetical50 (70 aa to XAC2274), 45 (108 aa to Reut4255 [all N-terminal end only])
STY45734450338-4452761807traC-like (putative Dtr protein)52 (817 aa to XAC2274), 51 (815 aa to Reut4255), 20 (354 aa to Virb4 Dtr protein from Helicobacter pylori)
STY45754453457-4453849392Hypothetical36 (113 aa to XAC2282), 36 (125 aa to Reut4258)
STY45764453846-4454814323Hypothetical49 (320 aa to XAC2283), 48 (320 aa to Reut4259)
STY45774454829-4456259476Hypothetical41 (402 aa to XAC2284), 40 (439 aa to Reut4260)
STY45794456592-4458097501Hypothetical membrane protein45 (499 aa to XAC2286), 42 (510 aa to Reut4262)
STY45834459393-4460640415ibrA regulatory protein (previously ybdN)85 (40 aa to IbrA from EcoR-9), 84 (415 aa to IbrA [Z1203 and Z1643] from O157:H7 EDL933)
STY45844460652-4461266204IbrB regulatory protein (previously designated ybdM)78 (203 aa to IbrB from EcoR-9), 78 (204 aa to IbrB [Z1204 and Z1644] from O157:H7 EDL933)
STY45854461477-4462019180Hypothetical74 (178 aa to STY4858), 74 (178 aa to STM4502)
STY45924467675-4469624649ardC (DNA escorting protein anti- restriction)34 (282 aa to ArdC from Mesorhizobium loti symbiosis island)
STY45934469696-4470604302Hypothetical33 (279 aa to STY4594)
STY45944470678-4471577299Hypothetical33 (279 aa to STY4593)
STY45954471619-4471978119Hypothetical41 (105 aa to XAC2221), 36 (74 aa to Reut4219), 38 (76 aa to Orf23 of plasmid pCTX-M3)
STY4599-STY46454473830-4507389SopE phage (S. enterica serovar typhi only)
STY46304496774-4497838354Hypothetical within A-T-rich region of SopE phage35 (363 aa to S060 of SXT element from Vibrio cholerae)
STY46314497835-4498899354Hypothetical within A-T-rich region of SopE phage40 (356 aa to S061 of SXT element from Vibrio cholerae)
STY46494508645-4509535296Putative 3-methyltransferase75 (288 aa to STY4856)
STY4651-STY46624510583-4524679ViaB operon
STY46644525533-4527044503helD DNA helicase39 (472 aa to Orf193 of plasmid Rts1)
STY46654527028-4528617529Hypothetical29 (451 aa to XAC2196), 28 (449 aa to Reut2852)
STY46664528781-4529794337int2 integrase35 (265 aa to integrase from Actinobacillus actinomycetemcomitans)
Truncated tRNApheU4529973-4529988
STY46674530221-453051497Similar open reading frames often associated with transposon elements98 (97 aa to STY4517), 98 (97 aa to STM4317), 26 (96 aa to Rv0918 of Mycobacterium tuberculosis)
STY46684530511-4530999162As for STY466792 (162 aa to STY4518), 92 (162 aa to STM4318), 50 (156 aa to Rv0919)
STY46734537312-453753373ner-like Mu DNA binding66 (68 aa to Ner open reading frame of Mu phage)
STY46804541654-4542913     (complement)419int integrase54 (416 aa to P4-like prophage integrase from Escherichia coli CFT073)
tRNApheU (full length, 75 bp)4543148-4543073
  • a aa, amino acids. The designations of the CDSs of X. axonopodis pv. citri begin with XAC, and the designations of the CDSs of R. metallidurans begin with Reut.