Skip to main content

Table 1 Genes with two tandem Pho boxes found in their promoter regions by phylogenetic footprinting

From: Computational prediction of Pho regulons in cyanobacteria

Genome

Rank1

Tanscription unit

Names

Pho Boxes2

Positon3

Score4

ATCC29413

7

Ava_2541

phoA

GTTAATCTtcaGTTAACCT aaaTTTATATT

-111

9.07

 

11

Ava_4516 Ava_4515 Ava_4514 Ava_4513

pstS2 pstC2 pstA2 pstB2

TATTTGTAtatTTTAACTTgaaATTAACCA

-403

8.75

  

Ava_4512

-

   
 

17

Ava_2477

pstS1 pstC1 pstA1, pstB1'

TTTTTCCTtgtTTTAACCTttcGTTAACCT

-66

8.54

 

27

Ava_3716

sphX

CTTTACTGataCATCAACT tttTTTGATGA

-104

8.29

 

47

Ava_4728

nucH

TTTTACCTtttCCTATTATtctCTTAATCT

-174

8.04

Aprime

3

CYA_1552 CYA_1553 CYA_1554 CYA_1555

pstS pstC pstA pstB

AATAACCTgaaTTTAACCTcttGTTAACCA

-175

10.11

  

CYA_1556 CYA_1557

--

   

Bprime

10

CYB_2765 CYB_2766

nucH -

CTTAAGCGtacCTTAACTG cccCTTTACTC

-91

9.49

BF-1

2

tlr2164 tlr2165 tlr2166 tlr2167

sphX pstC pstA pstB

TTTAAACAaacTTTTACCTtctCTTAACTT

-23

9.91

IMS101

21

Tery_3534

pstS

TTTGATATtttTTTAACCTgttCTTAATCT

-164

8.18

PCC6301

1

syc0545_d

nucH

TTTAAAGTgctGTTAATCC ttcCTTTACCG

-276

9.76

 

2

syc1661_d syc1662_d syc1663_d syc1664_d

sphX pstS pstC pstA

CTTAGGGTcgcCTTAATAG gctGTTAAACT

-48

9.75

  

syc1665_d syc1666_d

pstB pnp

   
 

4

syc0163_d

phoA

TTTAACTAtttCATAATCTattCTCAATCT

-216

9.41

PCC6803

1

sll0679

sphX

TTTAACCAaac CTTTACTAgggCTTAACCT

-105

10.31

 

2

slr1247 slr1248 slr1249 slr1250

pstS2 pstC2 pstA2 pstB2

CTTAATTCtatCTTAATTTc gaCTTAATCA

-303

10.10

 

7

sll0654 sll0656

phoA nucH

CTTAACCTtttCATAGTCT aacCATAAGTT

-156

8.80

 

14

sll0680 sll0681 sll0682 sll0683 sll0684

pstS1 pstC1 pstA1 pstB1 pstB1'

ATTCCATAgacCTTAACCTtccCTTTACCA

-73

8.46

PCC7120

6

alr5291

phoA

ATTAATCTttaGTTAACCT gaaTTTATATT

-223

9.25

 

10

all4575 all4574 all4573 all4572

pstS1 pstC1 pstA1 pstB1

TTTTCTCTtgaTTTAACCTttcGTTAACCT

-64

8.97

 

38

alr1094 alr1095

sphX gap3

CTTTACTAataCATCAACT tttATTGATGA

-106

8.19

 

51

alr0276

nucH

TTTTACCTtctCCTATTAT tctCTTAATCT

-178

8.05

PCC7421

31

glr0445 glr0446 glr0447 glr0448

pstS pstC pstA pstB

GTTAACCTtgcCTTAATC GaatTTCGTTAC

-80

8.64

PCC7942

1

Synpcc7942_1000

nucH

TTTAAAGTgctGTTAATCCttcCTTTACCG

-310

9.72

 

2

Synpcc7942_2445

sphX

CTTAGGGTcgcCTTAATAG gctGTTAAACT

-46

9.71

 

4

Synpcc7942_1392

phoA

TTTAACTAtttCATAATCTattCTCAATCT

-214

9.37

  

Synpcc7942_2441

-

   

CCMP1375

18

Pro0598 Pro0597 Pro0596

pstC pstA pstB

CTTAACTCtctCTTAAACA tgcACTTGATA

-47

7.36

MED4

14

PMM0710

pstS

TTTAACTAgccCTTAATCAtttCTTATATT

-245

8.07

 

24

PMM0723 PMM0724 PMM0725

pstC pstA pstB

TTTATATAtacCTTTAACCcttCTTAAAGT

-48

7.67

MIT9312

8

PMT9312_0722

pstS

TTTAAAGAgaaCTTAAACTtccCTTAAATT

-231

8.49

NATL2A

13

PMN2A_0311 PMN2A_0310 PMN2A_0309

pstC pstA pstB

ATTAACCCtctCTTAGTGAaaaATTTGAAA

-47

7.52

  

PMN2A_0308 PMN2A_0307

--

   

WH8102

1

SYNW2391 SYNW2390

- phoA

TTTGATCAgatCTTAAACTattCCTAACTT

-59

11.18

  1. 1. The rank of three tandem Pho boxes recovered by our scanning algorithm.
  2. 2. Bold, the two tandem Pho boxes identified by phylogenetic footprinting; light, the additional Pho box found by our scanning algorithm; Italics, known Pho boxes.
  3. 3. Positions of the Pho boxes relative to the first codon in the operon.
  4. 4. The scores of the three tandem Pho boxes recovered by our scanning algorithm.