# STOCKHOLM 1.0 #=GF ID Sigma54_DBD #=GF AC PF04552.8 #=GF DE Sigma-54, DNA binding domain #=GF PI sigma54_DBD; #=GF AU Finn RD #=GF SE Prosite #=GF GA 20.80 20.80; #=GF TC 20.80 20.80; #=GF NC 20.70 20.70; #=GF BM hmmbuild HMM.ann SEED.ann #=GF SM hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq #=GF TP Domain #=GF RN [1] #=GF RM 10894718 #=GF RT The bacterial enhancer-dependent sigma(54) (sigma(N)) #=GF RT transcription factor. #=GF RA Buck M, Gallegos MT, Studholme DJ, Guo Y, Gralla JD; #=GF RL J Bacteriol 2000;182:4129-4136. #=GF DR INTERPRO; IPR007634; #=GF CC This DNA binding domain is based on peptide fragmentation data. #=GF CC This domain is proximal to DNA in the promoter/holoenzyme #=GF CC complex. Furthermore this region contains a putative #=GF CC helix-turn-helix motif. At the C-terminus, there is a highly #=GF CC conserved region known as the RpoN box and is the signature of #=GF CC the sigma-54 proteins [1]. #=GF SQ 29 #=GS Q9PJD0_CHLMU/264-419 AC Q9PJD0.1 #=GS Q9Z7D5_CHLPN/269-424 AC Q9Z7D5.1 #=GS O69080_PLALI/335-494 AC O69080.1 #=GS O51406_BORBU/263-415 AC O51406.1 #=GS RP54_HELPJ/253-408 AC Q9ZLC8.1 #=GS Q9F0Q3_ENTFL/280-441 AC Q9F0Q3.1 #=GS RP54_BACSU/274-434 AC P24219.1 #=GS O66858_AQUAE/244-398 AC O66858.1 #=GS O66858_AQUAE/244-398 DR PDB; 2AHQ A; 1-67; #=GS O66858_AQUAE/244-398 DR PDB; 2O9L A; 3-63; #=GS O66858_AQUAE/244-398 DR PDB; 2O8K A; 16-76; #=GS O54393_MYXXA/344-503 AC O54393.1 #=GS Q9K710_BACHD/282-443 AC Q9K710.1 #=GS Q9RII3_RHOSH/270-426 AC Q9RII3.1 #=GS RP54_RHOCB/263-423 AC D5ANH9.1 #=GS RP54_RHOSH/269-429 AC Q01194.1 #=GS Q9F1E7_GLUDI/298-457 AC Q9F1E7.1 #=GS RP55_BRAJA/353-513 AC P30333.1 #=GS RP54_RHIME/343-503 AC P17263.2 #=GS Q98AS6_RHILO/303-463 AC Q98AS6.1 #=GS O69778_RHIET/312-472 AC O69778.1 #=GS RP54_AZOC5/341-501 AC P33984.2 #=GS Q98GS5_RHILO/338-498 AC Q98GS5.1 #=GS RP54_CAUCR/330-491 AC Q03408.3 #=GS Q59085_AZOBR/359-519 AC Q59085.1 #=GS Q9PDH1_XYLFA/301-460 AC Q9PDH1.1 #=GS RP54_ACIGB/321-480 AC P33983.2 #=GS RP54_AZOVI/341-500 AC P08623.1 #=GS Q9KP49_VIBCH/326-485 AC Q9KP49.1 #=GS RP54_ECOLI/316-475 AC P24255.2 #=GS RP54_THIFE/315-474 AC P24695.1 #=GS RP54_CUPNH/333-492 AC P28615.2 Q9PJD0_CHLMU/264-419 KDHLSQQIRAAKQLLRNIKKREETLLAVLRVLIPYQEEFLLKKRSVPKAFSVKQLARELSLHETTICRAINNKTLATPIGLISMRSLFPQAV.GACPDQS..KATILH.WIHQWISTE...KNPLSDEAISQKIIAKG.IPCARRTVAKYRSQLNIPPAHQRKH Q9Z7D5_CHLPN/269-424 QKNLSQQILSAKWLIKNLRKREQTLLQVMETLLPKQEDFLLGKIPAPYPLGIKDLAEDLSFHESTIFRAIENKAVAAPIGIFPLKHLFPRGI.HQDSSHS..KENVLQ.WIRQWIATE...QTPLSDSVISDRITAKG.IPCARRTVAKYRAQLKILPANKRKK O69080_PLALI/335-494 REYIKRKVESAKWLIESIEQRHNTLKRVAQAIVDHQIEFLEKGPEFISPLKMQQIADIVKVHVTTVSRAVDDKWIQTPRGLFPLKRFFGGGT.TTAEGEE.VAWHIIRLKLKEIVDGEN.KDDPLSDDALVEELAKHG.FNLARRTVTKYRKALNIPSSRQRRS O51406_BORBU/263-415 TSENPQKQKKAKWLIESLRYRDEILAKIGIAIYTLQKEFLRRGFKSLRPMNLSILSEKISVSKSTISRAIKNKYLKCEWGTILIKELFSS.V.GGAKTNE.FSKLSIKITVKKLLEA.N.KKM..SDKEISVILKSKG.ISISRRTVNKYRNELK...SEKGRT RP54_HELPJ/253-408 SDYLKEKLKEAKDLIDALNLRKATIYKIGLMLLEYQYDFFK..GKELRPLKLLDLANEFNHSVSTISRAISNKYLACERGVFPIKHFFSIAL.DNSETSN....AVIKDYLLELIKNED.KKEPLSDAKILELIEEKFHLKMVRRTITKYRQLLNIASSSERKR Q9F0Q3_ENTFL/280-441 QEYIKDKKNEFEWLERAVNQRGDTILRVGQEIVRRQEAFFLEADRPLKPMTLKEIADALSIHESTVSRAVNGKYLETTFGVFELRSFFSTSILSSEEDGEDVSTTMVKKQLQKLIDQEV.KSKPLSDQKLVERLKDSG.MEISRRTVAKYREALGIPSSSKRKR RP54_BACSU/274-434 VSYLSAKYQEWRWLSRALRQRKQTITRIINELITRQKDFFLKGRSAMKPLTLREVADCLSLHESTVSRAIKGKTIQTPYGLFEMKLFFSAKA.EASGDGD.ASNYAVKTHLENLINQED.KTKPLSDQKLVDLLYEQHGIQISRRTVAKYRDQMNIPSSAARKR O66858_AQUAE/244-398 QKELKEAFERYESIRKVLDIRRRNLRKVLEKIVERQKDFLT.GKGSLKPLTLREVSSEIGIHESTLSRIVNSKYVKTPVGTYSLRTFFVRES.AEGLTQG....ELMK.LIKEIVENED.KRKPYSDQEIANILKEKG.FKVARRTVAKYREMLGIPSSRERRI #=GR O66858_AQUAE/244-398 SS XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSXXXXXSS.XXSS-SS....TTHH.HHHHHHTTS-.TTS---HHHHHHHHTTTT.S---HHHHHHHHHHHT-S-SHHHH- O54393_MYXXA/344-503 KDFIQDKLRSAMWLIRSIHQRQRTIYKVTESIVKFQRDFLDKGIAYLKPLILRDVAEDIGMHESTVSRVTTSKYVHTPQGIFELKYFFNSSI.ARVSGED.TASEAVKHHIKQLVAQED.ARNPYSDQKIVELLRSQG.TEIARRTVAKYREVLGILPSSKRKR Q9K710_BACHD/282-443 AQYAKEKYHQMQWLVKSIQQRQQTLLKVTEAILRKQRAFFEEKEGALQPLTLREVAEEIGVHESTVSRATTNKYAQTPRGLLELKSFFVSSI.SSRFGEKGPSSDSVKKLVRKLVEEEN.KAKPLSDQKIAHLLKDQYNVEASRRVIAKYRDELGIPSSTKRKR Q9RII3_RHOSH/270-426 TPAARAAWTQAQAVGRMIENRNATLLRVAREILARQEAALDEGPSALVALTMTEVAEALGIHESTVSRVVAGTCVDTPRGTWWLRRMFSGRL.AEGGPSA....AAIRAAIARLVAQED.PAAPLSDGALVEALAAED.MQLARRTVAKYREMLNIPPGHRRRR RP54_RHOCB/263-423 RAERRKALAEARALAQALERRGDTLLRTAAVLVARQSAFLDKGPAHLVPLTLEDVASELGLHASTISRAVSGRMIQTQTRALPLRAFFSRAV.STQGGGEAVSRDSALDFVQRTVGGED.PQNPLSDDAIVTLAERAG.LRIARRTVAKYRSTLGLASSYERRR RP54_RHOSH/269-429 DAWLARARSQARWLERAVERRQATLLRTAVCLVRHQADFLDQGPRALRPLSMEEVALELDLHPSTISRATATRLIETPRGLIPLRAFFSRSV.SSDGPEAPQSQDALMALVREIIARED.RTKPFSDDAIVKQAKLAG.AVLARRTVTKYRETLGIPSSYDRKR Q9F1E7_GLUDI/298-457 RTYLNDTLTSANWLIRALQQRSMTILRVSTEILRRQEDFLQHGPQALQPLNLRTVAEALNIHESTVSRVTANKYVATPRGVLPLKFFFVAAM.TGNDGEI.RSNIAIQSVIRRMIQGER.PDAVLSDEAISLTLRRQG.IDIARRTVAKYREAMGFPNSLQRLQ RP55_BRAJA/353-513 KSYFTDALQNATWLVRALDQRARTILKVATEIVRQQDGFFTHGVAHLRPLNLKAVADAIQMHESTVSRVTANKYMATNRGTFELKYFFTASI.ASADGGEAHSAEAVRHHIKQLIDSEA.PAAILSDDTIVERLRASG.IDIARRTVAKYREAMRIPSSVQRRR RP54_RHIME/343-503 QAFLNECLQNANWLTRSLDQRARTIMKVASEIVRQQDAFLIHGVGHLRPLNLRIVADAIKMHESTVSRVTSNKYMLTPRGLFELKYFFTVSI.GSAENGDAHSAESVRHRIRTMINQES.ADAVLSDDDIVDVLKQAG.VDIARRTVAKYREAMSIPSSVQRRR Q98AS6_RHILO/303-463 QSFLNECLQNANWLIRSLDQRAKTILKVAAEIIRQQDAFFEHGVAHLRPLNLRTVADAINVHQSTVSRVTSNKYMLTPRGVFELKYFFTVAI.GSSEGGDAYSAEAVRHQIKAMVAVES.PNEVLSDDDIATRLKETG.IDIARRTVAKYREALNIPSSARRRR O69778_RHIET/312-472 QSFLNECFQSASWLVRSLDQRATTILKVATEIVRHQDVFLEDGIAHLRPLNLKTIADAIDMHESTVSRVTSNKYILTPRGVFELKYFFTVAI.PSSQGGDAHSAEAVRHQIRALIAAET.LHDVLSDDGIVAKLKETG.VDIARRTVAKYREAMRIPSSTQRRR RP54_AZOC5/341-501 KTFLADCLQSASWLTRSLDQRARTILKVASEIVRQQDAFLVHGVRHLRPLNLRTVADAIGMHESTVSRVTSNKYISTPRGVLEMKFFFSSSI.ASSGGGEAHAAEAVRHRIKSLIEAES.ADDVLSDDTLVQKLKDDG.IDIARRTVAKYRESMNIPSSVQRRR Q98GS5_RHILO/338-498 KDFLAECLQNANWLTRSLDQRAKTILKVASEIVRQQDAFLVHGVRQLKPLNLRTVADAIGMHESTVSRVTANKYMLTPRGVFELRYFFTASI.AASGGGDAHSSEAVRDRIKQLIDEEK.PVDVLSDDAIVDMLKESG.VDIARRTVAKYREGMNIPSSVQRRR RP54_CAUCR/330-491 KTFVADCMASANWLVKSLDQRAKTILKVASEIVRQQDGFLAFGVEHLRPLNLKTVADAIGMHESTVSRVTSNKYIATPRGVFELKFFFTSAI.QSSEGGEAHSAASVRHKIKGLVDAEKCEADVHSDDRIVEILKAAG.VDIARRTVAKYREAMRIPSSVERRR Q59085_AZOBR/359-519 KEYITERFQSANWLVKSLHQRATTILKVASEIIRQQDAFFIHGVSHLKPLILRDIAEAIGMHESTVSRVTTNKFMATPRGVFELKYFFTSAI.QGADGQAAHSAEAVRYRIKAMIDAEK.PDDVLSDDKIVEILRGEG.IDIARRTVAKYREAMRIPSSVQRRR Q9PDH1_XYLFA/301-460 ASYLRNQLQEARWLLKGLEARGETLLKVVNSLIRHQTGFLEFGQHALRPLTIRELATELALHESTVSRAIAGKYVRTPRGTLPLRTFFASGI.STDSGGE.TSNSAIQAIIRRLIETEN.PRKPLSDAKLAELLKTSG.IPVARRTIAKYRDAMNISASHERVR RP54_ACIGB/321-480 NQYLRNQMLEAKNFIKSVDERHKTLLKVASCIVQHQREFLEIGAEGMKPLVLRDVAEEVELHESTVSRVTTNKFLLTPRGLFELKYFFSSHV.GTTSGGE.ASSTAIRAKIKKLVADEN.PRKPLSDNTIANLLKEEG.IDVARRTVAKYRESLHIPSSSDRKV RP54_AZOVI/341-500 NTFMRNQLQEARWFIKSLQSRNETLMKVSTQIVEHQRGFLDYGEEAMKPLVLHDIAEAVGMHESTISRVTTQKYMHTPRGIYELKYFFSSHV.STAEGGE.CSSTAIRAIIKKLIAAEN.PKKPLSDSKIAGLLEEQG.IQVARRTVAKYRESLSIAPSSERKR Q9KP49_VIBCH/326-485 SNYIRTNLQEAKWLIKSLESRNETLLKVAKCIVEHQHDFFEYGEEAMKPMVLNDVAMAVEMHESTISRVTTQKYMHTPRGIFELKYFFSSHV.STDNGGE.CSSTAIRALIKKLVAAEN.PAKPLSDSKIATLLADQG.IQVARRTIAKYRESLGIAPSSQRKR RP54_ECOLI/316-475 SQFIRSNLQDAKWLIKSLESRNDTLLRVSRCIVEQQQAFFEQGEEYMKPMVLADIAQAVEMHESTISRVTTQKYLHSPRGIFELKYFFSSHV.NTEGGGE.ASSTAIRALVKKLIAAEN.PAKPLSDSKLTSLLSEQG.IMVARRTVAKYRESLSIPPSNQRKQ RP54_THIFE/315-474 HKYIQDQLNEARWFIKSLQSRQDTILKVARAIVERQKDFFANGPESMRPMVLRHIADAVEMHESTVSRVTNQKYMITPRGLYEFKYFFSSHV.GTDSGGS.ASATAIRALLIKMTQAED.AQHPLSDAEIARVLADQG.IQIARRTVAKYREAANVPPASQRRR RP54_CUPNH/333-492 TAGLQQKLQEARWLIKNIQQRFDKILRVSQAIVERQKNFFSHGEIAMRPLVLREIADTLGLHESTISRVTTNKYMATPMGTFELKYFFGSHV.STETGGA.ASSTAIRALIKQLIGAED.PRNPLSDSRIAELLGEQG.FVVARRTVAKYREALKIPAVNLRKS #=GC SS_cons XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSXXXXXSS.XXSS-SS....TTHH.HHHHHHTTS-.TTS---HHHHHHHHTTTT.S---HHHHHHHHHHHT-S-SHHHH- #=GC seq_cons psalpcplppApWLl+uLcpRtcTlLKVuppIVcpQcsFLpcG.ptL+PLsL+clA-slshHESTVSRlTssKYltTPRGlaELKaFFouul.uossGu-.tSspAl+thI+pLlssEs..pcPLSDspIsphLccpG.lplARRTVAKYREuLsIPuSspR+R //