# STOCKHOLM 1.0 #=GF ID MEDS #=GF AC PF14417.1 #=GF DE MEDS: MEthanogen/methylotroph, DcmR Sensory domain #=GF AU Anantharaman V #=GF SE Manual #=GF GA 28.70 28.70; #=GF TC 29.50 28.70; #=GF NC 28.00 27.80; #=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 1938878 #=GF RT Identification of dcmR, the regulatory gene governing expression #=GF RT of dichloromethane dehalogenase in Methylobacterium sp. strain #=GF RT DM4. #=GF RA La Roche SD, Leisinger T; #=GF RL J Bacteriol. 1991;173:6714-6721. #=GF RN [2] #=GF RM 15814558 #=GF RT MEDS and PocR are novel domains with a predicted role in sensing #=GF RT simple hydrocarbon derivatives in prokaryotic signal #=GF RT transduction systems. #=GF RA Anantharaman V, Aravind L; #=GF RL Bioinformatics. 2005;21:2805-2811. #=GF DR INTERPRO; IPR025847; #=GF CC MEDS is prototyped by DcmR and is likely to function with the #=GF CC PocR domain in certain organisms in sensing hydrocarbon #=GF CC derivatives [1][2] The MEDS domain occurs fused to Histidine #=GF CC Kinase and as standalone version [2]. Sequence analysis shows #=GF CC that it is a catalytically inactive version of the P-loop #=GF CC NTPase domain of the RecA superfamily [3]. #=GF SQ 30 #=GS Q8TRA6_METAC/1-191 AC Q8TRA6.1 #=GS Q8PUQ7_METMA/1-191 AC Q8PUQ7.1 #=GS Q8PUQ6_METMA/1-191 AC Q8PUQ6.1 #=GS Q8TP40_METAC/1-191 AC Q8TP40.1 #=GS Q46B59_METBF/1-191 AC Q46B59.1 #=GS Q8TT86_METAC/1-191 AC Q8TT86.1 #=GS Q8TR62_METAC/1-191 AC Q8TR62.1 #=GS Q8TT85_METAC/61-251 AC Q8TT85.1 #=GS Q8TSN6_METAC/1-191 AC Q8TSN6.1 #=GS Q466R1_METBF/1-191 AC Q466R1.1 #=GS Q8TRB0_METAC/1-191 AC Q8TRB0.1 #=GS Q8TKN3_METAC/226-416 AC Q8TKN3.1 #=GS Q8TU70_METAC/11-201 AC Q8TU70.1 #=GS Q8TPC2_METAC/13-203 AC Q8TPC2.1 #=GS Q46CF4_METBF/1-181 AC Q46CF4.1 #=GS Q46EN4_METBF/2-191 AC Q46EN4.1 #=GS Q8TRM6_METAC/2-200 AC Q8TRM6.1 #=GS D8JTG8_HYPDA/80-265 AC D8JTG8.1 #=GS Q606E7_METCA/4-191 AC Q606E7.1 #=GS A4JRB5_BURVG/13-188 AC A4JRB5.1 #=GS Q826M4_STRAW/1-168 AC Q826M4.1 #=GS Q5YYL0_NOCFA/12-186 AC Q5YYL0.1 #=GS Q7BU48_STRAM/1-167 AC Q7BU48.1 #=GS Q9R422_STRCO/1-167 AC Q9R422.1 #=GS Q9RIS9_STRCO/1-167 AC Q9RIS9.1 #=GS Q73VA3_MYCPA/1-171 AC Q73VA3.1 #=GS B2HHE9_MYCMM/1-169 AC B2HHE9.1 #=GS Q8PUQ5_METMA/1-191 AC Q8PUQ5.1 #=GS Q8TIW4_METAC/3-196 AC Q8TIW4.1 #=GS Q46AI0_METBF/1-191 AC Q46AI0.1 Q8TRA6_METAC/1-191 MKGQLRKSGIDVVG.DVPWGTHFCQFYQTKEDLIEILVPYFRAGLENSEYSVWITSE..PLETGEAKEALRKAVPDI...DVYLEKGQIEIISCTHWC...LKNGVFDKESLLNRWVEK.IGQALK.....NGYEGLRTATNISWLEKK..DWNDFVDYEEQGDGVVSNC...PVLSLCTYSLDRCNAGEIIDVVANHQFALIKREGKWDP Q8PUQ7_METMA/1-191 MKGQNRESGIDAIG.DIPWGTHFCQFYQTKEDLIEIFIPYFKAGLENNELCLWITSE..PLGIEEAKKFLKKAVPDI...EIYLEKGQIEIIPETFFY...LENGAFDSSRALNKGTER.FNRAID.....NGYCGLRSGGNISWLKKA..DWDNFTGYEEKIDSAIGNC...KIISMCAYSLDNCNATDIIDVVANHQFTLIKKGRRWEK Q8PUQ6_METMA/1-191 MKGQLRKSGIDAIG.DIPWGTHFCQFYQTKEDLIEIIVPYLKAGLENNELCLWITSD..TPGVEDAKEALKKSVPHI...DTYLNREQVEIIPETLFY...LEKGAFDQKKALNMGTEK.FLRAAE.....EGYCGLRTIGNLSWLKKS..DWDNFADYEEKVDSAIGNC...RIISMCAYSLDKCNATDIIDVVANHQFTLIKREGNWER Q8TP40_METAC/1-191 MEGKLRNSGIEIIG.NVPWGTHFCQFYQTKEDLMEILVPYFKAGLENNENCIWITSQ..PLEVEEAKEALRRAVPDF...EIYLKKGQIDIFPYIHGY...INEGVFDSERAVNGLKEK.LNQALE.....SGYEGLRVTGDACWLEKE..GWTDFVNYENKVDSVIEKH...QMISLCSYHLEMCNATEILDIAFNHQFSLIKREERWDR Q46B59_METBF/1-191 MKKNTRDSGIDIVG.EVSWGTHFCQFYQTKEDLMDILIPYFKTGLENNELCVWITSQ..PLEMEEAKAAMKRAIPDF...DVYLEKGQIEIISYNSGY...LKDDIFDPDRVVNSCVEK.INQALA.....RGYDGLRAAGDNHGLGKE..SWNEFVEYENKVDAVIAKN...HVIALCPYYLDMCNTAEIIDVVSSHQFALIKRKGIWKR Q8TT86_METAC/1-191 MKESLRKSGIDIIG.EVPWGTHFCQFYHTEEDLMDTLVPYFKAGLENNELCVWIISQ..PLEVEDAKEAMKRVVPDI...DVYLEKGQIEIIPYAHGY...LKGGIFDPDGIVNSWVEK.IDQALA.....RGYDGLRAAGDNRWLEKE..GWNGFVDYENKMDAIIDKH...QVIALCPYYLDMCSTAEIVDVVSNHQFALIKREGKWER Q8TR62_METAC/1-191 MRKKLRNSGIDIVG.DVPWGTHFCQFYHTEEDLIDILVPYFKAGLENNELCVWIISQ..PLEVEEAKAAMKRAIPDI...DVYLEKGQIEIVPYTHGY...LKGGIFDPDGVVNSWVEK.IDKALA.....RGYDGLRAAGDNRWLEKE..GWSGFIDYENKVDAIIGKS...HVIALCPYYLDMCSTTEVIDVVSNHQFALIKREEKWER Q8TT85_METAC/61-251 MKESLRKSGIDIIG.DVPWGTHFCQFYQTKEELVEILVPYFKSGLENNELCVWIISK..PLEVREAKEALRRVIPDF...DVYLEKGQIEIIPCTHEH...INEGVFGSEKVIKGRVKK.SDPFLA.....GGYDGLRTAGDTPWSKKG..ELDDFVDYESEVDANIGKY...QTISLFPYFLDMCSTVDILKIAFNHQFALIKKEGKWER Q8TSN6_METAC/1-191 MREKLRKSGIDIIG.DVPWGTHFCQFYQTKEDLTDILIPYFKSGLENNEFCFWVTSQ..PLVVEEAKEALRTAIPDI...DVYLAKGQIEIVPYTQGY...VNGEVFDSKQVINAWAKK.FDQALS.....RGYDGLRVAGATPWLKKE..EWKDFAAYEKRGDANTGKQ...HMISLCPYSFDVCSAADIIDVAFNHQFALIKREGKWER Q466R1_METBF/1-191 MEKSLRNSGIDIIG.EVPWGTHFCQFYQTKQDLIDILVPYFKAGLENNEFCMWVTSE..PLEVEEAKGALRKAIPEI...DVYLEKGQIEIIPYTYWY...VKEGIFDSQKVLNGWIEK.LNRALA.....DGYDGLRLSGNTFWLEKN..DWNSFVDYEKEIDSIIGNY...SMIALCTYCLERCSATEIIDVVINHQFALVKKEEKWTQ Q8TRB0_METAC/1-191 MEEKLRTSGIDIIG.DIPWGTHFCQFYQTKEDLMDVLVPYLKAGLENNEFCMWVTSQ..PLDVKDAKEALRRAVPDL...DTYLEKGQIEIIPYTHWY...VQEGSFDSERVLNGWIEK.LNKALA.....NGYDGLRLTGNTFWLEKK..DWNDFVDYEEEVDRVIGNY...RMIALCTYCLEKCNSTEIVDVVINHQFALIKREEKWEQ Q8TKN3_METAC/226-416 GKGKLRTSGIDIIG.DIPWGTHFCQFYQTKEDLMDVLVPYLKAGLENNEFCMWVTSQ..PLDMKDAKEALRRAVPDL...DTYLGKGQIEIIPYTHWY...VQEGSFDSERVLNGWIEK.LNKALA.....NGYDGLRLTGNTFWLEKK..DWNDFVDYEEEVDRVIGNY...RMIALCTYCLEKCNSTEIVDVVINHQFALIKREEKWEQ Q8TU70_METAC/11-201 MRKYLRNSGIDIVG.NVSFGTHFCQFYQTKEDLMDMLVPYFKAGLESNEFCMWVTSQ..PLEVEKAKKALRKSVPDL...DIYLEKGQIEIIPCTCWY...LNEGIFDSRRILNGYVEK.LDQALA.....NGYDGLRLSESTFWGGKK..DWNNFVNYEKEIDRVIGNY...HMLALSTCPLDRCSATEIIEVVSSHQFSLIKKEGKWER Q8TPC2_METAC/13-203 MRKKLRSSGVDIIG.DVPWGTHFCQFYHTKKDLMDVLASYFKAGLENNEFCMWVTSQ..PSETEEAKEALRKAVHDF...DVYLEKGQIEIVSSTHWY...VQEGSFDSERVLNCWIEK.LNKALA.....SGYDGLRLRENPFWQEKK..DWSSFDNYEKELDRIIGNY...RMISLCTYSLDRCDATEIIDVVSKHQFALIKRNGKWEQ Q46CF4_METBF/1-181 MKSGNRISGIDIIG.NVPWGIHFCQFYRTKEDLMDILVPYFKAGLEDNEYCLWVISE..PVDEEEAKEALKIAIPDI...GAYIENGQIDIVPYPYWH...VEEDVLDPQTVLNRLTEK.TSKALA.....NGYDGLRYSGN............NFSGHEKLLDSVIGRY...PIIALYTYPIDKYSAVEILDIVANHQFALTKKEGKWEH Q46EN4_METBF/2-191 RKNIAEDSGPSL...KVPQSHQISAVYEDTKGLIELLVTYFKEGLEGGEYCLWVSPD..KLAAEEAKNELMKVGVDV...EPYLTSSQLEFLPANP.....LPEDLTLLASTVTELAEKGYRKTLS.....GGFSGFRTNFEIKNAGNS..LKPCLETCGKAIEIMALEKN.KSITFLYTIPLEELSGRVLLELMEESNVFTKRKGKLESL Q8TRM6_METAC/2-200 LGILKKKVKSEFCFCSTIPANGLTAIYKETEERTDLIAAYIKAGLQQNEHCIWIVPD..PESAELAKELLSNSELDI...ENYIEKSRLKIIPLQGTE..AISAEQTEGSGSYFDWNAGVFQKEILKFIHTGNWQYLRINLEVKPLGKS..IPGSLKELKRILDENRPEK...KIWPLFTIKEEDLSPGEVFDIIEAGGKLLIYRDGRWKH D8JTG8_HYPDA/80-265 PDSVKNAAKTQVAGMDIAYHDHICAIYGRPAGRLKLSVPLLREGLKAGDICFLNATQ..PGKA.HILKVLREVYPDV..H.KAIKDGQL.IFPA..........LKRNKAEMLDQLEEM.FLKATY.....SGEQKLRLVGDMEWALSV..DWSEQEVYEYELEYNNTLGHRFPIISLCQYDVRVFSSKGILDALKSHEDTYKYPLRDCCI Q606E7_METCA/4-191 SARATVSLGFTAEL..FPPGTHMCYIYNDERERLEIMSEFVRSGIESGEKIAYFV.......EEMSPQALRDYLAGL..GIVPTEEAQLEIAPSVDVY...CPEGRFSPDRMLGRLRSA.YEDGIR.....EGFNGVRLTGEMHWALRGLPGSERLAEYESRINLLVVDC...PLTVICQYDANHFDGATLFKILNAHPMMIVRGQVVHNP A4JRB5_BURVG/13-188 .................MRTDHFVQFYDSDEQLVSEVASFSADALRDGGSAIVIARPERLAAVYARLGTLERANGSAARDRVFMSSAQALLDSCM.......DGGLPDPARFRRSIGTI.VEAAVR.....AGR.PVHAFGEMVALLCAQHRYAGALRLEALWNELIERY...RFSLYCGYPHDAFPSAEQSEM.FRHVCALHRRILPSAS Q826M4_STRAW/1-168 .......MMSTAAP.ADPF.VHPALFYRGDRQYVAGTVPFVLDGLSAGEPVAVAVP...GPQLKLMKTEL............GADADQVHFLDM........TQAGRNPGRIIPGVLRA.FADAR.......STARVRIIGEPIWPGRTSAEYPACVQHEALINAAFRGR...EVTILCPYDADGLDEKVLADAYATHPLVIDEGRELASA Q5YYL0_NOCFA/12-186 ARSEPVPPHDDRAH.DDPF.HHPAFFYRDSEEYLAGTLAFIGAGLSRGEPVAVSVP...GPNLALIRAAL............GADAADVRLMDM........TVEGRNPGRIIPGVLRA.FADEH.......PEGRVRIIGEPIWASRSATEYPACAQHEALINAAFTGR...EVSILCPYDVSRLAPAVVEDALATHPVVLDGHGERVSP Q7BU48_STRAM/1-167 ........MSTVTT.EESF.SHPALFYRSAGEYTDRTVTFVREGLAAGEPVAVAVP...APNLELIRGGL............GPDARGVTFLDM........TEAGRNPGRIIPGVLRA.FADTH.......ARERVRIIGKPIWAGRSAAEYPACAQHEALINAAFTGR...AATILCPYDETRLAPDVLADALVTHPTVITAGRERVSE Q9R422_STRCO/1-167 ........MSTATA.DEAF.IHPALFYRSETEYTDRTAAFVREGLAAGEPVAVAVP...GPNLELVRAGL............GSDARDVTFLDM........TEAGRNPGRIIPGVLRA.FADAH.......PRVRVRIVGEPVWAGRSAAEYPACAQHEALINAAFAGR...RATILCPYDETRLAADVLADALVTHPTVITEGSERISE Q9RIS9_STRCO/1-167 ........MSTATA.DEAF.IHPALFYRSDTEYTDRTAAFVREGLAAGEPVAVAVP...GPNLELVRAGL............GSDARDVTFLDM........TEAGRNPGRIIPGVLRA.FADAH.......PRVRVRIVGEPVWAGRSAAEYPACAQHEALINAAFAGR...GATILCPYDETRLAADVLADALVTHPTVITEGSERISE Q73VA3_MYCPA/1-171 ......MTADDETR.QYGF.VHAALIYRSQQEFLDVVAGFVGDGLAGNEAVLLAVP...PALMALLRDELYAG.........GEPPAGVRMADI........TESARNPSRFMAMQGA..FVDEH.......PDRRVRIVSQLAWPGRSREEFVACIEHEALVNEAMDGY...PATALCLYDASTLDDGVLADARATHPLLCKSGALQRSP B2HHE9_MYCMM/1-169 ......MTTSTVTG.QRNF.VHSALLYHSQHEYLESVQRFVREAMVLDEPVLVAVP...TDRLALLGSRLR...........GGATAELQMIDI........TEAARNPSRLLALQNA..FVARH.......RGRRVHIVSQLVWPGRTVDECLACMQHEALVNAALEND...SVTALCLYDAERMEEEVLADARATHPLLWKCGSPQRSA Q8PUQ5_METMA/1-191 MDEKLRTSGVQVIG.DIAWGTHFCQFYRTQEELVNVVCPYLKAGLEGNELCIWALPR.DFETKKEAEGPLRRTIPKL...DIYLEKGQMEIISYKDRY...AEKEIPDSKKALENLIKK.ADYALL.....NGYSGLRLVQDTSWL.KN..DWKNLTGYEEELDIAIENR...RITALCTYSSGKFDTDETIYAALSHRFVLVKKEGNWEK Q8TIW4_METAC/3-196 MGTKIRSSGINIIG.DIPWGTHLCQFYQTKEDLMDILVPYFKAGLKDHEFCIWITSQ..PSDVEEAKEALRKSIPDI...DIYLEKGQIEIISYMHWNSKGSKEGIFDPERLINRWIEK.LNNALA.....DGYDGLRLTENISWLEKE..NRSDFLKFEEKIDSVIGNH...RIAALFTYSLDMFDTIEIIDIVANHRFSLIKRKGAWQQ Q46AI0_METBF/1-191 MKDSLRKSGIDIIG.YVPWGTHICQFYQTKEDFMNTLVPYFKTGLENNEFCMWIMSE..PSEVGDAKESLRMTVPNI...DSYLDKGQIQIIPYSRFY...AEEGVFDSNRVLNILVEK.LNQALS.....SGYDGLRLSGNALWLEKQ..DWSDFVNYEVKLDSDIGNC...QMIALCTYSLDRFDATKIIEAAVNHQFVLIKREGKLEQ #=GC seq_cons hctthRpSGl-llG.-lPaGTHhCQFYpTcE-Lh-lllPYhKuGLEsNEhChWlsop..P.plE-AKpuL+cslP-l...-hYL-+GQl-Ilsh..hh...hp-ushDspRllsshlcK.hscAlt.....pGYcGLRlsGsshWhtKp..-asshssYEpclDuslssp...phhuLCsYsl-chsus-llDllssHpFsLlK+ct+Wpp //