BIMEs in Salmonellaand close bacterial species

Species Flanking genes Accession number Structure Comments
S. typhimurium aceA - aceK U43345 Z1> 5 <D In E. coli, BIME-2 with 3 PUs.
S. typhimurium aceK - orf U43345 Y< 6 >Z1 -
S. typhimurium orf  - adk L26246 'Y> 12 <D First PU incompletely sequenced.
S. typhimurium adk  - hemH L26246 Z1< 1 >Y In E. coli, boxC at the same location.
S. typhimurium alr  - orf M12847 D> 12 < PU' The second PU is not completely sequenced. In E. coli, Y L.
S. typhimurium apaH - folA U24176 Z2 In E. coli, Z2.
S. typhimurium araA - araD M11047 Z1> 4 <Y< 8 <Z1 In E. coli, BIME-2 with 6 PUs.
S. typhimurium argA - recD - Z1> 14 <Y/2 In E. coli, Y.
S. typhimurium asd  - orf AF015781 (Z1> 8 <)Z2 -
S. typhimurium barA - orf AF171069 Y In E. coli, BIME-1 (with repeats).
S. typhi bigB - trpS AF133185 Z1 -
S. typhimurium caiE - caiD U81260 Y> 13 <Z1 -
S. typhimurium cheW - orf J02656 PU -
S. typhimurium cheZ - flhB M16691 Z1> 7 <PU In E. coli, atypical BIME with 2 PUs.
S. typhimurium cobA - yciL L08890 Y -
S. typhimurium cpsB - cpsG X59886 D -
S. typhimurium crr  - orf287 U11243 D> 10 <Z1 -
S. typhimurium cysI - cysH M23007 Z1 In E. coli, Z2.
S. typhimurium deoB - orf AF003833 Z1 An IRU is distant from 21 bp.
S. typhimurium envZ - pckA X12374 Z2 -
S. typhimurium eutG - eutH AF093749 Y< 11 >Z2 In E. coli, BIME-2 with 4 PUs.
S. typhimurium eutM - eutN AF093749 Z2< 10 >Z1 genes previously called cchA-cchB
S. typhimurium eutR - hemF AF093749 D> 21 <Y -
S. typhimurium glyA - orf X15816 Z1 -
S. typhimurium hemL - orf M60064 D In E. coli and S. typhi, BIME-2 with 2 PUs.
S. typhimurium hemM - hemA J04243 Z1 -
S. typhimurium hemN - orf U06779 Z1> 13 <D In E. coli, BIME-2 with 2 PUs.
S. typhimurium hisG - hisD J01804 Z1> 23 <D -
S. typhimurium hisJ - hisQ V01373 Z1> 8 <D -
S. dublin hpaH - hpaF AF144422 Z2> 29 <Z1 In E. coliW, Y> 18 <Z1. The whole region is absent from K-12
S. dublin hpaX - hpaI AF144422 Z1 In E. coliW, Y> Y>S<Z1. The whole region is absent from K-12
S. typhimurium hsdR - orf X99719 Z1 -
S. typhimurium ilvC - ppiC AF233324 Z1> 15 <D In E. coli, boxC.
S. typhimurium ilvH - fruR X55456 Z2> 13 <Z1 -
S. typhimurium infB - rbfA AJ002552 Z1 An IRU is distant from 6 bp. In K. oxytoca, PU, in E. coli, BIME.
S. typhimurium lamB - malM X54292 D In E. coli, BIME-2 with 3 PUs.
S. typhimurium leuD - orf X02528 Z1 -
S. typhimurium lexA - orf X63002 Y/2< 3 >Z1> 27 <Y -
S. typhimurium livJ - livK D00478 Z1 An IRU is distant from 30 bp.
S. typhimurium malE - malF X54292 Y> 6 <Z1 In E. coli, BIME-2 with 3 PUs. In K. pneumoniae, BIME-2 with 2 PUs.
S. typhimurium melB - fumB S41630 Z1 In E. coli, BIME-1.
S. typhimurium miaB - ybeZ AJ249116 Z1 -
S. typhimurium mviM - mviN Z26133 Z2< 5 >Y An IRU is distant from 59 bp.
S. typhimurium mviN - flgN Z26133 Z1> 5 <Y -
S. typhimurium nadR - yjjK M85181 Z2> 29 <Y In E. coli, BIME-2 with 3 PUs.
S. typhimurium nagD - asnB AF029564 D> 13 <Z1 BIME-1 in E. coli
S. typhimurium nrdA - nrdB X72948 Z1> 11 <Y In E. coli, BIME-2 with 3 PUs.
S. typhimurium nrdD - nrdG AF242390 Z2< 5 >Y In E. coli, BIME-2 with 2 PUs.
S. typhimurium omp  - sfbA A102556 Z2 -
S. typhimurium orf  - abrR AF029554 Y -
S. typhimurium orf  - ampE AF029440 Z1> 11 <Y -
S. typhimurium orf  - corC AF085347 Y> 11 < Z1 -
S. typhimurium orf  - fhuA Y14025 PU> 24 <Y First PU not completely sequenced
S. typhimurium orf  - livJ D00478 Y< 3 >Z1 In E. coli, BIME-1.
S. typhimurium orf  - orf AF029422 Z1> 10 <Y -
S. typhimurium orf  - orf AF029578 D -
S. typhimurium orf  - orf AF029580 D> 8 <Z1 -
S. typhimurium orf  - orf AF029586 Y> 5 <Z1 -
S. typhimurium orf  - orfA X73226 'Y PU not completely sequenced
S. typhimurium parC - parF M68936 Y< 5 >Z2 -
S. typhimurium pepB - orf AF201078 Z1< >Z2 -
S. typhimurium pepM - ORF1 X55778 Z2> 137 <Y An IRU is inserted between the 2 PUs.
S. typhimurium pfkA - sbp * Z1 > 13 < D In E. coli, BIME-1.
S. typhimurium phnR - phnS U69493 Y > 17 < Z1 -
S. typhimurium phnV - thiI U69493 D -
S. typhimurium phnX - thiJ U69493 Y> 13 <Z1 -
S. typhimurium proM - hemY AF233324 < Z1 -
S. typhimurium prpB - prpC U51879 <D Z1> In E. coli, BIME-2 with 8 PUs.
S. typhimurium purG - orf U68728 Y -
S. typhimurium purN - ppk AF085682 Y -
S. typhimurium radA - nadR M85181 Z2> 19 <Z1 -
S. typhi rcsB - rcsC X87830 Z1> 15 <D In E. coli, BIME with 4 PUs
S. typhimurium rep - gppA AF233324 < Z1 In E. coli, Z2
S. typhimurium rrfB - murB J14816 D -
S. typhimurium tpiA - orf * Z1> 12 < D In Enterobacter cloacae, BOCE.
S. typhimurium trpR - orf L13768 Z2 In E. coli, BIME with 3 PUs.
S. typhimurium ushAo - orf X04651 Z1> 12 <Y In E. coli, Y*.
S. typhimurium uvrD - corA L11043 Z1> 20 <D In E. coli, BIME with 2 PUs.
S. typhimurium wzc - wcaA AF285084S1 Z1 In E. coli, Y.
S. typhimurium yahO - prpR U51879 Z1 In E. coli, Y
S. typhimurium yfgJ - yfgK AF140550 Z1 -
S. typhimurium yhiQ - orf AF137028 Z1> 13 <D -
S. typhimurium yigB - uvrD AF233324 Z1 > 3 < Z1 -
S. typhimurium yihW - orf AF220439 Y -
S. typhimurium yjbH - mig7 AF020807 Y -
S. typhimurium yjdE - yjdB L13395 Z1 ORF1 is in the 5' region of pmrA.
Citrobacter freundii cfa  - dhaK U09771 Z1 -
Citrobacter freundii hrpB - ponB Z49960 D In E. coli, BOCE. (ponB=mrcB)
Enterobacter aerogenes ampC - orf AF211348 D < 22 >Z1 -
Enterobacter aerogenes lsp  - orf M26713 Z2> 15 <Z1 In K. pneumoniae and E. coli, BIME.
Enterobacter cloacae fadA - ubiB AF191029 <Z1 Z1> In E. coli, BIME-2.
Enterobacter cloacae pfkA - sbp AF098509 Z1> 10 <D In E. coli, BIME-1.
Enterobacter cloacae pstS - pstC D89963 Z1> 8 <D In E. coli, PU.
Enterobacter aerogenes ushA - orf AF068226 PU PU not completely sequenced. In E. coli and S. typhimurium, PU.

* : the sequences were obtained in the lab by C. Wilde. The BIME regions were the targets of IS1397 that integrates specifically into E. coli BIMEs (Bachellier et al.,1997 ; Clément et al., 1999.)

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Please send questions and comments to Sophie.Bachellier@pasteur.fr.