Table 2.
The potential H-NS binding sites on the promoter region of SPATEs as predicted by Virtual Footprint Software a.
| SPATEs | Potential H-NS Binding Sites |
|---|---|
| boa | −97GCAATAAACC−88 (−), −96GCAATAAAAT−87 (−),−80GCTATAAAAA−71 (−) |
| sigA | −179TGGTTAGATA−170 (−),−170GTGATTGATT−161 (−), −19CCGATATTTC−10 (−) |
| pic | −159CAGATAAAAC−150 (+), −109TGCATTAATG−100 (−), −35GGGATATAAA−26 (−) |
| sepA | −176ATGATAAAAA−167(+), −35AAGATTAATT−26 (−) |
| tsh/hbp | −164CACATAAAGT−155 (−), −28AAAATAAAAT−19 (−), −10GTAATTAAAA−1 (+) |
| espC | −300ACCATTAAAA−291 (+), −299CCATTAAAAT−290 (+), −111GCCACAAACT−102 (−) |
| espP | −280TCGATTGTTA−271 (−), −96CAGATAAATG−87 (−), −46CTGATACATT−37 (+) |
| pet | −177ATGATTAATT−168 (+),−42AGGATTAAGA−33 (−),−24TCAATAAATG−15 (+) |
| sat | −177ACGATCAATT−168 (+),−166ACGATCAATT−157 (+),−24TCAATAAATG−15 (+) |
| eatA | −88GCTATCTATT−79 (+),−71ACAATAAATG−62 (+),−40TCCACACAAC−31 (−) |
| eaaA | −314ACCATACAGC−305 (−),−124GCGGTAAAAA−115 (−) |
| tagB | −304ACGAAAAAAA−295 (−),−161CTGATAAATA−152 (−),−128TCGATAAATG−119 (+) |
| tagC | −256GCAATTAATA−247 (+),−62TCGCTATATT−53 (+),−56ACTATAAATA−47 (−) |
| sha | −187CCCACAAATC−178 (−),−48TCCTTATATT−39 (+),−32TCAATAGATA−23 (−) |
| vat | −296TCCATATATC−287 (+),−295TGGATATATG−286 (−),−107GCTATATAAT−98 (−) |
a Virtual Footprint software [140] was used for in silico analysis of different SPATEs promoter region for putative regulatory H-NS binding sites and additional experimentation is required to confirm a role for H-NS in regulation of SPATE gene regulation. Pattern matching tool Virtual Footprint used specific position weight matrices (PWMs) to generate the top three potential binding sites upstream to the start codon with high scoring matches. (+/− strand).