# TF - NsrR: Pnap_1327
>Pnap_1327(nsrR) Score=4.7 Pos=-128 [Polaromonas naphthalenivorans CJ2]
CATGCCAATAAAATACATT
>Pnap_1025(PF01152) Score=5.3 Pos=-78 [Polaromonas naphthalenivorans CJ2]
GATTCATTTAAAATACATC
>Pnap_1328(norB) Score=4.7 Pos=-104 [Polaromonas naphthalenivorans CJ2]
AATGTATTTTATTGGCATG
>Pnap_3969(PF10006) Score=5.3 Pos=-62 [Polaromonas naphthalenivorans CJ2]
GGTGTATTATAAATGCATC
>Pnap_3969(PF10006) Score=4.5 Pos=-51 [Polaromonas naphthalenivorans CJ2]
AATGCATCTTTTAAGCACC
>Pnap_1326(nirK) Score=5 Pos=-155 [Polaromonas naphthalenivorans CJ2]
CATGCATTTAATATGTACA
# TF - HexR: Pnap_0652
>Pnap_3873(pykA) Score=5.5 Pos=-30 [Polaromonas naphthalenivorans CJ2]
CGGAAACTAAATTACAA
>Pnap_0653(zwf) Score=4.9 Pos=13 [Polaromonas naphthalenivorans CJ2]
ATGAAACTTTATTACCT
>Pnap_2986(edd) Score=4.7 Pos=-54 [Polaromonas naphthalenivorans CJ2]
CCGTAATAAAGTTACAT
# TF - NrtR: Pnap_3721
>Pnap_3720(pncA) Score=6.2 Pos=-48 [Polaromonas naphthalenivorans CJ2]
AAGGTTGTTCAGTACAACCTA
>Pnap_3720(pncA) Score=5.7 Pos=-73 [Polaromonas naphthalenivorans CJ2]
AAGGTTGTATTATGCAACCCA
>Pnap_3721(nrtR) Score=5.9 Pos=-104 [Polaromonas naphthalenivorans CJ2]
TAGGTTGTACTGAACAACCTT
>Pnap_3721(nrtR) Score=5.8 Pos=-79 [Polaromonas naphthalenivorans CJ2]
TGGGTTGCATAATACAACCTT
# TF - NrdR: Pnap_2908
>Pnap_3385(nrdA) Score=5.3 Pos=-159 [Polaromonas naphthalenivorans CJ2]
GCACTAGCTGTAGTGC
>Pnap_3385(nrdA) Score=5.6 Pos=-190 [Polaromonas naphthalenivorans CJ2]
ACACTACCTGTAGTGG
# TF - Zur: Pnap_1145
>Pnap_1145(zur) Score=6.5 Pos=-77 [Polaromonas naphthalenivorans CJ2]
ATAATGCAACCTGATTGCGATAG
>Pnap_1145(zur) Score=6.6 Pos=-45 [Polaromonas naphthalenivorans CJ2]
GTAACGCAACTGAATTGCATTAA
>Pnap_1144(znuC) Score=6.5 Pos=-251 [Polaromonas naphthalenivorans CJ2]
TTAATGCAATTCAGTTGCGTTAC
>Pnap_1144(znuC) Score=6.1 Pos=-219 [Polaromonas naphthalenivorans CJ2]
CTATCGCAATCAGGTTGCATTAT
# TF - NorR: Pnap_1305
>Pnap_1305(norR) Score=4.4 Pos=-232 [Polaromonas naphthalenivorans CJ2]
GACGGTGGATTTGACGATG
>Pnap_1304(hmp) Score=4.4 Pos=23 [Polaromonas naphthalenivorans CJ2]
CATCGTCAAATCCACCGTC
# TF - IscR: Pnap_2291
>Pnap_2291(iscR) Score=6.3 Pos=-152 [Polaromonas naphthalenivorans CJ2]
ATACTTGACGAAATTAGTCAAGAAC
# TF - NtrC: Pnap_2777
>Pnap_2780(glnA) Score=4.6 Pos=-250 [Polaromonas naphthalenivorans CJ2]
GGCCCTGAATTGGTGCG
>Pnap_2780(glnA) Score=5 Pos=-200 [Polaromonas naphthalenivorans CJ2]
CGCACTTTTTTGGTGCT
>Pnap_0120(glnK) Score=4.7 Pos=-319 [Polaromonas naphthalenivorans CJ2]
TGCATCAAAGTTGTGCA
>Pnap_0120(glnK) Score=4.5 Pos=-295 [Polaromonas naphthalenivorans CJ2]
TGCATCATGATGGTGCG
>Pnap_1414(nrtA) Score=4.7 Pos=-334 [Polaromonas naphthalenivorans CJ2]
GGCGCCGAAATGGTGCA
# TF - LexA: Pnap_1918
>Pnap_1918(lexA) Score=5.9 Pos=-84 [Polaromonas naphthalenivorans CJ2]
TACTGGATATTCATACAGTC
>Pnap_1918(lexA) Score=5.5 Pos=-103 [Polaromonas naphthalenivorans CJ2]
AGCTGTATAAAAATGCAGTT
>Pnap_4894(imuA) Score=6 Pos=-33 [Polaromonas naphthalenivorans CJ2]
TACTGGTTATTCATACAGTA
>Pnap_1199(parE) Score=5.4 Pos=-64 [Polaromonas naphthalenivorans CJ2]
AACTGTATGTTTGTACAGGT
>Pnap_3956(recA) Score=4.4 Pos=-102 [Polaromonas naphthalenivorans CJ2]
TACTGTTCATGCACCCAGTA
# TF - LiuR: Pnap_0453
>Pnap_0454(paaI) Score=5.1 Pos=-68 [Polaromonas naphthalenivorans CJ2]
GTTTACGTAAACGTCAAG
>Pnap_0454(paaI) Score=6.6 Pos=-74 [Polaromonas naphthalenivorans CJ2]
ATTGACGTTTACGTAAAC
>Pnap_0453(liuR) Score=5.1 Pos=-80 [Polaromonas naphthalenivorans CJ2]
GTTTACGTAAACGTAAGA
>Pnap_0453(liuR) Score=6.3 Pos=-86 [Polaromonas naphthalenivorans CJ2]
TTTGACGTTTACGTAAAC
>Pnap_3524(mcm) Score=4.8 Pos=-75 [Polaromonas naphthalenivorans CJ2]
GTTTACGTAAACGTAATA
>Pnap_3524(mcm) Score=6.6 Pos=-81 [Polaromonas naphthalenivorans CJ2]
GTTGACGTTTACGTAAAC
>Pnap_1223(etfB) Score=5.1 Pos=-44 [Polaromonas naphthalenivorans CJ2]
GTTTACGTCAACGTCAAT
>Pnap_1223(etfB) Score=5.6 Pos=-50 [Polaromonas naphthalenivorans CJ2]
GCTTACGTTTACGTCAAC
>Pnap_1609(paaH) Score=5.5 Pos=-80 [Polaromonas naphthalenivorans CJ2]
GTTGACGTAAACGTCAAA
>Pnap_1609(paaH) Score=6.1 Pos=-86 [Polaromonas naphthalenivorans CJ2]
ATTGACGTTGACGTAAAC
# TF - FadP: Pnap_3478
>Pnap_1842(fadB) Score=4.9 Pos=-106 [Polaromonas naphthalenivorans CJ2]
AAGAACGGTCGTACTA
>Pnap_1223(etfB) Score=5.7 Pos=-147 [Polaromonas naphthalenivorans CJ2]
TAGAACGACCGTTCTT
>Pnap_3478(fadP) Score=5.7 Pos=-31 [Polaromonas naphthalenivorans CJ2]
TAGAACGACCGTTCTT
>Pnap_3655 Score=5.5 Pos=-41 [Polaromonas naphthalenivorans CJ2]
AAGAACGACCGTTCTA
# TF - VanR: Pnap_2731
>Pnap_2731(vanR) Score=4.9 Pos=-137 [Polaromonas naphthalenivorans CJ2]
TGTATACA
>Pnap_2731(vanR) Score=4.1 Pos=-201 [Polaromonas naphthalenivorans CJ2]
TGAATACA
# RNA - TPP
>Pnap_0019(thiC) Score=75.9 Pos=-204 [Polaromonas naphthalenivorans CJ2]
GCAGCTTGTCGGGGTGCCCGGGATGTTCACATCCGGGGCTGAGATCGCAAAAATGCGAGACCCGCTGAACCTGATCGGGATCATGCCCGCGTAGGAAACAAGGCACTTTGGCTCCG
# TF - HrcA: Pnap_0909
>Pnap_0658(groS) Score=6.8 Pos=-134 [Polaromonas naphthalenivorans CJ2]
TTAGCACTCGATGAGGTGGAGTGCTAA
>Pnap_0889(rpoH) Score=6 Pos=-57 [Polaromonas naphthalenivorans CJ2]
CTGGCACTCTCTCTGATGGAGTGCTAA
# TF - GntR: Pnap_0047
>Pnap_0047(gntR) Score=6.1 Pos=-128 [Polaromonas naphthalenivorans CJ2]
CTTGGATAGCGCTATCCGTT
>Pnap_0046(gntK) Score=6.5 Pos=-140 [Polaromonas naphthalenivorans CJ2]
ATAGGATAGCGCTATCCCAA
>Pnap_0046(gntK) Score=6.1 Pos=-30 [Polaromonas naphthalenivorans CJ2]
AACGGATAGCGCTATCCAAG
# TF - NmlR: Pnap_2189
>Pnap_2189(nmlR) Score=4.8 Pos=-35 [Polaromonas naphthalenivorans CJ2]
CTTGGAGCGCGCTCTAAC
# TF - CadR-PbrR: Pnap_4002
>Pnap_4001(cadA) Score=4.9 Pos=-50 [Polaromonas naphthalenivorans CJ2]
ACCTTCAAGTGGGTTCAGGGT
# RNA - SAH_riboswitch
>Pnap_0117(metH) Score=50 Pos=-106 [Polaromonas naphthalenivorans CJ2]
AACTCAAGGAGCGTTGCAGCAAAACATCCGTTTTGTCAGGCTTGGGTAAACAGGGCCGCATCATCCCCTTTTAGCAACGACGCTCACCTTTATT
>Pnap_0489(ahcY) Score=50.2 Pos=-176 [Polaromonas naphthalenivorans CJ2]
CTCCTGAGGAGCGTTGCAACCCACGGCATGTGGTCTAGGCTCAGGACTTCTATTTGCAACCACGCTCACCCGCATG
# TF - CueR: Pnap_4091
>Pnap_4089(copZ2) Score=5.5 Pos=-67 [Polaromonas naphthalenivorans CJ2]
ACTTTGCCACCGTGGGAAGGT
>Pnap_4090(copA) Score=5.7 Pos=-82 [Polaromonas naphthalenivorans CJ2]
ACCCTGCCATGATGGCAAGGT
# TF - YrdX: Pnap_2106
>Pnap_2105(PF02635) Score=5.1 Pos=-320 [Polaromonas naphthalenivorans CJ2]
ATTGCATG----ATTGCATT
>Pnap_2105(PF02635) Score=6.1 Pos=-224 [Polaromonas naphthalenivorans CJ2]
GTTTATCG----ATTGATTG
>Pnap_2105(PF02635) Score=6.6 Pos=-105 [Polaromonas naphthalenivorans CJ2]
ATTGATTG----CTTGATTG
>Pnap_2105(PF02635) Score=6.6 Pos=-324 [Polaromonas naphthalenivorans CJ2]
CTTGATTG----CTTGATTG
# TF - ModE3: Pnap_1508
>Pnap_1509(tupA) Score=5.8 Pos=-84 [Polaromonas naphthalenivorans CJ2]
CTATGCAAACAGCTTCATAA
>Pnap_0048(Ajs_3943) Score=5.9 Pos=-60 [Polaromonas naphthalenivorans CJ2]
CTATGCAAATCAATTCATAG
# TF - Daci_0595: Pnap_0403
>Pnap_0402(PF00892) Score=16.4 Pos=-197 [Polaromonas naphthalenivorans CJ2]
GCCGTGTGCTG-(10)-CAATACAGTTT-(15)-AAACTGTATTG-(0)-GTGGTGTGCTG
# TF - YdcR: Pnap_2093
>Pnap_2096(COG0348) Score=7.9 Pos=-98 [Polaromonas naphthalenivorans CJ2]
AACTGATATGGTTTT---------AACTGCATCTTACGC
# TF - GabR: Pnap_2866
>Pnap_2865(puuD) Score=12.8 Pos=-153 [Polaromonas naphthalenivorans CJ2]
AGTGGCAC-(15)-AATGGCAC-(7)-GACCCAAT
# TF - GabR2: Pnap_2629
>Pnap_2630(gabT) Score=15.3 Pos=-149 [Polaromonas naphthalenivorans CJ2]
GTGTGTAGAGGT-(6)-GGCAGCACAGTA-(18)-ATCTGTATATGG
# TF - Aave_3430: Pnap_3431
>Pnap_3431(Aave_3430) Score=16.2 Pos=-118 [Polaromonas naphthalenivorans CJ2]
ACAGCCACAGCCCG-(11)-ACCGGAACAGGCGT-(9)-GCATCTGTTATGGT-(11)-TCGGCTGTATCTGT
>Pnap_3430 Score=20.9 Pos=-148 [Polaromonas naphthalenivorans CJ2]
ACAGATACAGCCGA-(11)-ACCATAACAGATGC-(9)-ACGCCTGTTCCGGT-(11)-CGGGCTGTGGCTGT
# TF - UxuR2: Pnap_2075
>Pnap_2074 Score=4.9 Pos=-262 [Polaromonas naphthalenivorans CJ2]
TATTTGGTCAGGCCACATT
>Pnap_2074 Score=4.3 Pos=-248 [Polaromonas naphthalenivorans CJ2]
ACATTGGCCTGACCGAAAG
>Pnap_2074 Score=3.9 Pos=-107 [Polaromonas naphthalenivorans CJ2]
TATACGGTAAGGCCAATCT
>Pnap_2074 Score=5.1 Pos=-75 [Polaromonas naphthalenivorans CJ2]
AAATTGGCCTTACCAAATA
>Pnap_2075(uxuR2-2) Score=5.1 Pos=-188 [Polaromonas naphthalenivorans CJ2]
TATTTGGTAAGGCCAATTT
>Pnap_2075(uxuR2-2) Score=3.9 Pos=-156 [Polaromonas naphthalenivorans CJ2]
AGATTGGCCTTACCGTATA
>Pnap_2075(uxuR2-2) Score=4.3 Pos=-15 [Polaromonas naphthalenivorans CJ2]
CTTTCGGTCAGGCCAATGT
>Pnap_2075(uxuR2-2) Score=4.9 Pos=-1 [Polaromonas naphthalenivorans CJ2]
AATGTGGCCTGACCAAATA
# TF - SdhR: Pnap_3031
>Pnap_3031(sdhR) Score=7.4 Pos=-38 [Polaromonas naphthalenivorans CJ2]
TCTTATGTCTTATATAAGATATGATT
>Pnap_3030(mdh) Score=7.4 Pos=-202 [Polaromonas naphthalenivorans CJ2]
AATCATATCTTATATAAGACATAAGA
>Pnap_2855(aceA) Score=6.5 Pos=-91 [Polaromonas naphthalenivorans CJ2]
TAAATAGTCTTATATAAGACATAAGA
# TF - GudR: Pnap_1131
>Pnap_1130(gudD) Score=5.7 Pos=-93 [Polaromonas naphthalenivorans CJ2]
AAATGTTACCGATAACATTG
# TF - GguR: Pnap_1590
>Pnap_1590(gguR) Score=4.7 Pos=-58 [Polaromonas naphthalenivorans CJ2]
ACGTTGTCTGATGACTC
>Pnap_1591(udh) Score=4.7 Pos=-98 [Polaromonas naphthalenivorans CJ2]
GAGTCATCAGACAACGT