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# Rhodoferax ferrireducens DSM 15236, DSM 15236

>Rfer_3906 CRISPR-associated protein Cas4
MDEPEKIPLSALQHWRYCPRQCGLIHLEQVFDDNVHTLRGQAVHAKVDQP
GVETAKGVRVERALPLWHDELGLVGKSDVVEFLAGGVPYPVEYKHGSRNK
AADIAACDDLQLAAQGMCLQAMTGKTVNEGALYYATSKRRRVVAITEQLR
ADVAQTADAIRQMLASGELPPPLVGEQATKRCKACSLLERCQPQATHAGL
IAARSALFDPDA
>Rfer_2511 Chromosomal replication initiator, DnaA
MKQIALDIGLATGPTLSSFFAGPNEAALRHLQIWVAGGANAAARSPVPTY
FFGSAGSGKTHLLKAVQEAFREQGASVGWLDASVQQPPEFDERWAAVLMD
DVHFYNVVQQQAAFNWFINAQTWQRGVLAAGELPPADLKLRDDLRTRLGW
GHVFQLQLLSEPERRAVLRQAADARGLFLSDEVMDFMLTRFSRDLGNLME
LLNLIDGYALQTKRAITIPLIKSMMDNT
>Rfer_0779 putative RNA methylase
MNQLQLFLPCAAGVEDYLAPEVLRITGLPPGCVTKQRGGVAVRTSFAHAM
LLNLYSRLAQRVLVLLSFTEYRNEQDLYRAASEVAWERWFTPRESIKVEV
TAQHSPLTSLNFAALKIKDAVCDRFRVTAGGVRPDVNTQWPDVRIYTHLT
TDSCSLYIDTSGEPLFKRGWREDKGDAPLKETLAAAMLAASGWADGDEDL
LPLYDPCCGSGTIVIEAAQIACNIAAGSLRRFAFEKYLPFQRPVWDAIKK
EAKESEVTRAPGQKPIIFGSDVAHRMVDFAQRNAQRAGVADVIEFRGGDA
LQRLPPIDIPGVMLLNPPYGERIEVAGVAKGARHAASQFEDEEAEVGRFG
ARELPQTQEGGEFFSQLASHWKKNYPGWSAWILTPDLKLPGKMRLKESRR
VPMWNGPIECRLFRFDMVAGKMGSARAT
>Rfer_2983 exodeoxyribonuclease III
MGWGLQPRLTRKILTMKFATWNVNSLTVRLPQVLDWLQANPVDVLALQEL
KLTDDKFPVDAFRQAGYHAECFGQKTYNGVALLSREPALNVVRNVPGFAD
DMARSISAEVNGVRVIGAYFPNGQEPGSDKFEYKMAWLKGLRDWVRGELL
THPRLVLMGDYNITFDDADVWDPVGLKDTIHCTEEERYHLRALIALGLHD
SFRLFAQPEKSYSWWDYRDFAFRRNHGLRIDHILVSDALKPLVTACVIDK
APRKNERPSDHAPVVVTLADTNKV
>Rfer_3077 DNA-cytosine methyltransferase
MLQRGEIPVIDLFAGPGGLCEGFSSIFDETGARRFAVKVSIEKDPVAHRT
LLLRAIFRKFAKGKVPDCYYEYLRGNITREQFFAHPDIKDAAEHAAKEAK
CAELGLTPHAEIDSWISEALGDKTDWVLIGGPPCQAYSLAGRSRLSGMKR
EEFESDKRHFLYTEYLRIIQQFEPSVFVMENVKGMLNSTHGGSRIFDRIL
ADLKAPKEGLSYEIRSLVVGGDELEPKDYVIQAENYGIPQNRHRVILFGI
RSDVAESTTALKTSPRQFLLRKSFPQVGVDEALAGLPAIRSRLSKEDDSH
KKWLSALRKAPTTLLTWHMPVREKIEVLMKSAAKKAKNHESAGEKFTAMK
VEPGEKMPQPLRAWLLDERVGGVVQHESRSHMRSDLHRYMFASCFLKSEK
YAPTLRNFPPRLLPAHLNVDAETVPFVDRFRVQVGNAPSSTVVAHIKKDG
HYYIHPDSSQCRSLTVREAARLQTFPDNYFFEGNRTEQYGQIGNAVPPLL
AKKIAKVIYKFLSSPRE
>Rfer_4202 IstB-like ATP-binding protein
MRDAKRDIQSELKALRLNGMATAWADLTAQGGDSTLDSSRWLIEHLLQAE
DVDRALRSIAHQMKSARFPVHRDIAGFDFEASIVDRILMGKLANLSFTED
AQNVVLIGGPGTGKTHLATALGISGLTHHSKRVRFYSTVDLVNALEQEKA
QGKAGRIAMSLLRMDLIILDELGYLPFSQAGGALLFHLLSKLYEHTSVLI
TTNLTFAEWSSVFGDAKMTTALLDRLTHHCHILETGNESYRFRHSSNEAK
GRIKSREQSRKAEARQGSEPKEDVDQL
>Rfer_2040 DNA polymerase III, alpha subunit
MFIHLRLHTEFSVVDGTNRIGDSVKAAAADGQPALAITDLSNLFGAIKFY
KAARKCGVKPLIGAEIWLEGLGQDASALSRLLLLVQNKQGYLNLSELLAR
AWTQQGNKAQASVKLDWLKELGEGLIVLSGAQAGPVGQALLQGDVARALD
AALQLAGVFTHRFYLELQRAGRPDDEAHVVATVQLAARAGLPVVATHPIQ
FAGPDDFEAHEARVCIADGEILSNPRRVRRFTREQYFKSSAQMQALFADV
PSALANTLEIARRCNLTLVLDKPQLPDFPTPEVNGQRMTPDDYFRYASHE
GLKERMAHLYPDAAQRGQEMPRYLARLEFELNTIVKMGFPGYFLIVGDFI
NWAKNNGCPVGPGRGSGAGSLVAYSLKITDLDPLRYNLLFERFLNPERVS
MPDFDIDFCQTNRNLVIDYVKSKYGKDAVSQIVTFGTMAARAAVRDVGRV
LDMSYTFCDGISKLIPNKPGVSVSLQLPPPDRKKDDKTVYAVEAEPLLAE
REAKEEDVKTLLELARKLEGLTRNVGMHAGGVLIAPGKLTDFCPLYQQPG
SDSAVSQFDKYDVEAIGLVKFDFLGLATLTILEIARDFIIERHRGQENFA
FENLPLDDMRVYKLFQEGKTEAVFQFESRGMQGMLKDAKPTRLEDLIALN
ALYRPGPMDLIPSFVARKHGREVVEYPHPLVAEMLSETYGIMVYQEQVMQ
TAQILGGYSLGGADMLRRAMGKKDADEMARQRQIFRDGAAKNNINQAKAD
EVFDLMEKFAGYGFNKSHAAAYSLLAYHTAWLKVHYTAEFFCANMTVEMD
DTDKLKVLYEDALKMGLTFEPPDVNRGGSRFEPISDKVIRYGLSAIKGSG
QQAIEAIVAAREGRGVGPSGDVAGPFKSLFDFCVRVDRSRVNKRTVEALI
KAGAFDAIQLNRASLLASTDLAFEFGAAALANANQGGLFDMDDDAQGSST
QEPELVQAVPWGVKERLTFEKTAVGFYLSGHLFDEVALEVRRFAKRQIDD
LIDIREPQLLAGIITDFRVINGQRGKLALFKLDDKSGVIEARADEALINA
HKNLLKDDELVIVMGQLKPDRFSGGMQLTVTQIWDLEQARCRFGKFLRLV
VSTQPGQAPDIARMARDYPPLREVTEQGELLRGLGVRLSVTCQGEGVRAA
AELQLGERAKFYPSNAALAGWRVQAGAGKSDIVYE
>Rfer_1819 restriction endonuclease
MARSKSNKRQKRAVNTLQEKGIGLCALGLGFLIIPWFIGSSPMLKVVAAG
LRTPGWLALAAGVVLLGIHHVTQAKIAKTNPLPQLTPRAPTPTERTVLQG
TKDDIAAHRRAPSAAAPPTRQVATRWSPAVFAAIEWRRFEAVCEALFAQA
GFETRSQSHGADGGVDIWLHSANAQGPVAVVQCKHWQGKAVGVKEIREFF
GVMASHQLKRGTYATTSTYTADAQQFAKANGINAMDGPALLALIAKRTPE
QQQALLAVAHEGEYWRPTCASCGIKLVERTPAKGGPAFWGCSNYPRCKSR
LPMVAAMR
>Rfer_2248 histone-like DNA-binding protein
MTSANFFKETIRLTLLPYQGFFVNKTELIEHIALNADISKAAATRALESA
IGAVKITLKKGGSVSLVGFGTFAVGKRAARVGRNPRTGDAIKIKAAKVPK
FRPGKALKDALN
>Rfer_2256 DNA-directed DNA polymerase
MSTTTVAPWIAAQTQTLLAQNGHAWLLLGPSGLGQYRLALALVCAWLCEQ
PTEQGACGVCGSCHAIEVRTHADLCVLMPETVALELGWPLSEKAQGEIDA
KTRKPSKEIRVDAMRDAVEFSQRTSARGRGKAVLVFPAERMNHVTANALL
KTLEEPPGDVKFVLASDAAHQLLPTIRSRCLAHTMVWPALDTSLAWLQQQ
GLDGRQAAVMLRACGGRPDDALLLAQAGPSGPTPASWVKLPNAMARGDVG
GLKDWTPTQAVDALQKLCHDLLAVKTGATPRFFDALDLPAGSSLATLTAW
GKALAAAVRTVEHPFNSGLMLEALVSQAQNAINAKN
>Rfer_1062 type III restriction enzyme, res subunit
MSNFAFLQSEWSTLYGAAIKAEGMANTDARTSCFYARRTLELAVDWLYKH
DPALRLPYQDHLSALIHEPSFKATAGDAVFTKAKLIKDLGNLAVHSTRKI
LPVDAVTATRELFHFCYWLARTYGQRARPAPDLRFVPALIPSASATATVP
DPAPQSVDQLQKLEAELQARDEKLTVLLSNKAALDDELKQLREQVAAAKK
ANTAQPDTHDYCETETRDKFIDLLLKEAGWQLNAKNFEIEVSGMPNNQGV
GYVDYVLWGDDGRPLGLVEAKRTRRDAKVGQQQAKLYADCLQAQYDQRPI
IFYSNGYEHWIWDDASYPPRPVQGFFKKQELELLIQRRTNRKKLADAVIN
DDIVNRYYQHRAVRRIGETFELENQRKALLVMATGGGKTRVVVALSDVLT
RCNWAKRILFLADRVALVKQAVNAFKTHLPDSSPVNLVSERHADGRVFVS
TYPTMMGLIDDAADGQRRFGVGHFDLIIIDEAHRSVYQKYRAIFDYFDAM
LVGLTATPKDEIDHNTYSLFDLESGVPTDVYGLDEAVAEGYLVPPRSISV
PLKFQREGIKYKDLSEEEKEQWDALEWDEDGNVPDAVDSAALNKWLFNTD
TVDKVLENLMSQGEKVAGGDRLGKTIIFAKNNAHADFIADRFNVNYPHYK
GAFARVVTYKTEYAQSLIDEFSMKEGMPHIAISVDMLDTGIDVPEVVNLV
FFKIIRSKTKFWQMIGRGTRLCLDLYGPGQNKQFFNVFDYCQNLEFFSLE
LPPDEGKNPVPLSTRLFRARLEMIAELDKRMAAGDHGATAQDAGSDDLTD
GQLRGELAGFLHQQVAAMNLDNFVVRPRRKSVERFAKRDSWHSLDADAHT
ELSHEVADLPTALLDNDEEAKRFDMLVLRTQLSILKASTDFATLRERMQA
IASALEEQEAIPAIKAQMVLIQSVASDEWWEDVTVAMLEAARKKLRALVK
LIEKGKKNIVYTDFEDELGTGTTIMLPGVSTGMNLAKFKDKARQFLRAHE
SHLSLQRLRRNQPLTPSDLIELERMLVEAGGSTEVIEQAKEQSHGLGIFI
RSLVGLDRETAKLAFSQFVVGTTATASQLEFINLIVEELTENGVMDPARL
YDSPFTDINPQGPEALFLPARVTEMVRVLEEIRERAVA
>Rfer_3252 DNA repair protein RadC
MPLKDLPPDARPREKLLARGPGALSDVELLAVLLRTGIKGKGVLQMAREL
LELKKSGSDDNDGFDGIAGLLHATSDDLKRIKGLGPAKRAELVAVLELSR
RALAQQLKERTIFATPDAVKHYLQLHLAAKPHEVFAVLFLDVQNRLLALE
ELFRGTLTQTSVYPREVVLRALHHQASSVVLAHNHPSGTVQPSRADEMLT
QTLKTTLALIDVRVLDHVIVAPGEALSMAERGLL
>Rfer_1822 DNA adenine methylase
MAFRNNISNQMTPILRWAGSKRYLAKYLLPQFPQVMHRYIEPFCGSASLF
FLSEPASSVLSDINSELINALDLIKSRNKSVMEKYESLPDDREIYYLVRS
LEPQALTKVERAARFLYLNRLCFNGLYRTNKSGQFNVPYSGQRNSKLLSR
EEVSDASRLLNNCELRNDDFKTTISRTKRGDFLYVDPPYASKEHNEFCEY
DASSFGLRDIQNLWVELNAADRRGVKFMLSYTECAEISRFSKRWNSTTIQ
VRRNIAGFAGHRKMAAEVVVKNY
>Rfer_2261 phage integrase
MRLPVLQKVPALQPAELSELTQHAVEDLLREGESQNTLASYRSALRYWAA
WYGIRYGRQIDLPVPTACVLQFIVDHAQRTTDKGLVSELPAEIDQALVQA
GYKGKPGALAHNTLVHRIAVLSKAHQMREFKNPCHDPKVRELLSRTRKAY
AKRGALPQKKDALTKDPLQAILATCDDSLRGKRDRALLLFAWSSGGRRRS
EVAGADMQFLKRVGPTAFIFTLAHSKTNQAGTDQPENGKPVLGAAGTALN
DWLQAGPITSGAIFRRIRKGGHLGDALSPAAVRTIVKDRCALAGIEGDFS
AHSLRSGFVTEAGRQNVPLAETMAMTGHHSLATVLGYFRSESALSSAAAR
LYE
>Rfer_1464 ribonuclease H
MNAVEIYTDGACKGNPGPGGWGAFLKSADSQKELFGGELGTTNNRMEMTA
VIEALAALKRPCQVTLHVDSQYVLKGMTEWLAGWKARGWKTAAKQPVKNV
DLWQRLDELVSTSGHRIDWRWVRGHNGDPGNEHADMLANRGVELALRQR
>Rfer_2175 excinuclease ABC, B subunit
MTVPTPAALVTSSDAEPVRSGTFVRYPDSPFELYQPYPPAGDQPEAINQL
VEGVNDGEVFQILLGVTGSGKTFTMANVIARLGRPAIVFAPNKTLAAQLY
SEFREFFPKNAVEYFVSYYDYYQPEAYVPQRDLFIEKDSAINEHIEQMRL
SCTKSVLERRDVVIVATVSAIYGIGQPEAYHKMVMTLRVGDKLGQRDMIA
QLVRMQYQRNDVDFSRGAFRVRGDTIDIFPAEHSEMAIRVELFDDEIESL
QLFDPLTGRIRQKIPRFTVYPSSHYVTPREQVLSAVEAIKIELAERIKEF
VGQGKLVEAQRIEQRTRFDLEMLSEVGHCKGIENYSRHLSGAAPGEPPAT
LTDYLPKDALMFLDESHVLIGQFGAMYNGDRSRKTTLVEYGFRLPSALDN
RPLKFEEFETRMRQAIFVSATPAQWEKDHAGKIVEQLVRPTGLVDPEVEV
RPAVNQVDDVLQEIRIRVEKHERVLITTLTKRMAEQLTDYLSDNGVKVRY
LHSDIDTVERVEILRDLRLGTFDVLVGINLLREGLDIPEVSLVAILDADK
EGFLRSERSLIQTIGRAARNLEGRAILYADKVTESMRKAIGETERRRVKQ
VTHNLAMGITPRSIVKQVKDLIDGVYSEKAGQEAEKLERDAMQRAQVEDM
SEKDISREIKRLEKLMMEHARNLEFEKAARVRDQLGILKEQAFGAAGRDN
VVVIAAGTKD
>Rfer_3216 conserved hypothetical protein
MVKDQQSAAISPQTPRLFGLPPLVSENTRLLVLGSFPSITSLARQQYYAH
PQNQFWRILQAIFPSSPRGISAASYQERSAWLLAQGLGIWDVYASCEREG
SLDTAIRQPQVNDFSGLRLRCPQLQLIAHNGGESFRHAKYTATLGLPVLK
LPSTSPANASWSFERKLAAWRKAVAAAGLL
>Rfer_0030 restriction modification system DNA specificity domain
MSEWIETTVGEIAASSRNALVGGPFGSNLVSKDYVDQGVPVIRGQNMGGR
WVAGDFACVSTEKAAALSANTARPGDIVFTQRGTLGQVALVPDSPYETYV
VSQSQMKLTVDPEKADSLFLYYLFSSPIQQEYIRQNSIQVGVPHTNLGIL
RDTPVVLPKSVDVQKDIARQLGTLDDKIELNRRMNETLEAMARAIFQSWF
VDFDPVRAKASGESADSICQRLGLTPKLLALFPDSFEDSELGEIPSGWMI
GSIGTLANVTGGSTPNTKEPKYWDDGVHCWATPKDLSRLSSPVLLETERK
VSDDGLAQIGSGLLKPGAVLLSSRAPIGYRVINEVPVAVNQGFIAMTPNS
GVSKYFLLYWAEWAHDEIVSRANGSTFLEISKANFRPIPVVRPTDALFEK
FDQYVGPLYKRIVSNEQEKQLLVAQRDSLLPKLLSGEVMVAAEEEAS
>Rfer_3152 exodeoxyribonuclease VII, large subunit
MATNKACHCGAFPCHSPTPAVVFFMFETDNPAMTPRVWQIGALCRAIAAA
LDSRFNPVVVRGELSGFSRASSGHCYFSLKDESAQVRCAMFRRAASSLDF
SPRDGELVEVRGRLGVYEPRGDLQLIVESMSRAGQGALFEQFLQLKAKLE
AQGLFAAERKRQLPVLPRGIGVVTSLGAAALHDVVTTLQRRVSHIPVVIA
PATVQGSNAPGELIQALLNLYRLTQEGRGLEPDFTKKTKKKGESAAPCID
VILLVRGGGSMEDLWAFNDEQLAHTLAQSPVPIVCGVGHETDFTIADFVA
DLRAPTPTAAAELVAQPRQLWLGALDAAARRLQDAVLRRLDQQSQRLDLT
TSRLGRPSALVGRQGLRLGASAQRLQLASTHFVQQRQQALLRQQAALPTA
AQRGLQRQDERLQRAALRLGLLDPHLVLARGYAWLSTPDGVGISSVQQTW
PGQAVRATLADGAVDLTVTPSI
>Rfer_3417 crossover junction endodeoxyribonuclease RuvC
MRILGIDPGLRTTGFGVIDVAGADLTYVASGTISTLHLDKGQLPARLKVL
FDGIREVVARYQPECASVEIVFVNVNPQSTLLLGQARGACITALVSGDLP
VAEYTALQMKQAVVGYGRADKSQVQEMVRRLLALPGLPGPDAADALGLAI
THAHAAKALARLAQADGVMGAGSGKYKAGRSR
>Rfer_3176 AAA ATPase
MTPVAHSTANSHVPLAERLRPRTLLEVIGQQQLLGEGMALRIAFESGQPH
SCILWGPPGTGKTTIARLMADAFDAQFITISAVLGGVKDIREAVEQAQVA
QGQGRRTIVFVDEVHRFNKSQQDAFLAHVESGLFTFIGATTENPSFEVNS
ALLSRAAVYVLQPLAPQDLEQIIARALALQALPAIEKIASERLVGFADGD
ARRLLNTLEMLSVAATQERVSEITDPWLQKVLGERMRRYDKGGEQFYDTI
SALHKSVRGSNPDAALYWLVRMLDGGAEPRYLARRLIRMASEDIGLADPR
ALRLALDAADVYERLGSPEGELALAQCVVYLAVAPKSNAVYKAFNAAKAF
VKQDGTRPVPMHLRNAPTRLMKELDYGKGYRYAHDEEGGFAAGERYLPDG
MAPPGFYRPVERGLEIRIAEKLKQLRALDLQHQKK
>Rfer_1225 conserved hypothetical protein
MLPSSLSVASLDFGAAVWRADALACAGGATVASGHGALDAELPGGGWPLG
AISEILQPPGVCQEWRLLLPALTRTCGPVVLVGPPQVPFGPGLAAQGLDA
RRLLWVGAAAPAARLWATEQALRCAEVAAVLAWLPQVRTEQLRRLQLAAQ
THSKLLFVLRPAAAQSESSPAVLRLLLVRASSAGVAPDALRVQILKRRGA
PLARTLVLSARPASLAVLLALRGDNPGPGQQLVAREEAGHALDCLAAGA
>Rfer_1202 UvrD/REP helicase
MNPFQRAREQAVALRRKLLDDRAGEAVHVSEFLTPDPIAAKLSLGVEYVP
KGAAELSNGDAILRRKEDYIYVRKDIGVAEQAYLVAHELGHFILDESQEE
VAIASLSSLTDAEGTPAVISVEAYGARERLELRANVFARELMLPREVARV
LHDAGVGPRKAARDLGIHLEIVRQQMLDAVMLPNVVLAPEARTQHPPSLD
QLLAIQAPERYVNVVAGPGSGKTSTLVHRIRYLIDEKAVDPSHILVLTFT
NKAAFELVDRLRDANIHRASDVWAGTFHAFGLDFLRKYHQCFGLESDLKV
ADRLNAITILNQELPKVELTHYRRVQDPYDWLPDVVNSIKRLKEEMVSPE
AYRLAIQGLPTAEPGRRECREDVASLYECYERALRERKMVDFVDLVAKPA
KAIEQDRPQYSELADKFQHVLVDEYQDVTHAMVELISQLAKNAKSLWVVG
DVRQAIHHWRGASVHSLTKFNERFEAQAGSGKIKTYPLAFNRRSSSEILE
LVKQAGKRHILETTSLKLENTTATSGPNGHPPTLVSCFPFVSMPDAIAAG
IHELHSEGVPFGKQAVLNRWNYELGMVAAGLRRVGIPVLHIGELAQRPEV
KTLLCLMQLMVERLPRALVGLMGDARLAVDFEDFQKLMELCEEDPLLQRG
AWLDDLPEDLSPQSRSVLVTIARLLNGQWRRSNPWGFVCDLLLEHRFGYP
PRADVSIEAHSLRIALWQFAYATRTGDGERKFPTLPRFLLRQQLRQRIGE
TYSERELPAEVAAIDAVRLLSIHGSKGLEFDSVHVNNVNTDDYGPKGRYW
ESPSEASRLVPPEVLRSSQETWNFEATVERNNLLYVALSRARKRLFMYQN
GEDTRKGAPQLSPPSAPVRALSFNGTVTAPAGQAPIPRPPLTEPLPFDEF
ETFVRCPLQHWYRFELRLAGEQGVDIAIKARWAVMAALKALAQKPGSSPK
EAFMAEWESRKLPSHTEDLQLWTHATAVFWDGLAIIKASAGAFVEPVTSI
NGLTIRLNWMLLNASAGRPALELIRFSGSDLTKAAQLLRPMLNDLQPVRA
RGVTIHSLLGAKKESFEPSGAIEKTAAFAAVQRFFAGNREPKVGRHCKRC
AYMTFCPTRPSM
>Rfer_2203 DNA primase
MSIPQTFIQELLARADVVEIVGRYVQLKKGGANFMGLCPFHGEKSPSFSV
SPSKQFYHCFGCGKNGDAISFLMEHAGMTFVEAVQDLAQQYGLQVPEDDA
SPQDRARALEQRQKQTTLTDVLERANDAYRKQLKESPRAVDYLKGRGVSG
EIAKQFGLGYAPEGWRSLASVFPSYDDPLLVESGLVILNVDENSGEEKRY
DRFRDRVMFPIRNVKGECIGFGGRVLGDDKPKYLNSPETPVFSKGRELYG
LFEARNALHEQGYALVTEGYMDVVALAQLGFSNAVATLGTACTAEHLHKL
FRFTDAVVFSFDGDAAGRRAARKALDGALPFATDVRSVKFLFLPPEHDPD
SFIREFGKEAFARYVSEAVPLSRFLIDAAREGCDLNTAEGRAHFASNAKP
LWLLLPDGALKLQLLSEIADLVQLSSRELTEVWNPSAAGKGNAKSKTYEK
HSASPNEYGGYSQKSSIKPPPRPRPGGRVRPTSRADYAARLLLGDMAALE
VLSAEDHTLLCDLPEPHGPLFVWLENQLHEHGPQAWVALREGLRGRQEEE
LAVRLMTGYELAGPLETDESSKELRDLLNRMLVEKLKVQETEAIQAAKAD
PGALQRYRELQARRFKLESVPTRSE
>Rfer_4005 conserved hypothetical protein
MATLIPALGACVSRMTGGERRLAERLEQKLDDDYLLWYDVPMGPKNAHPD
FCVMHPRRGILVLEVKDWKPSTIQQADKQTWTIIPDGIPKNVINPLEQAR
QYAHQVVNALERDPQLVQADGPHAGKLAFPWSYGVVLTNITRKQFEAAEL
QHAIEPHRVLCQDEMLESVGAEELQSRLWDMFPYMMRGVMSLPQLDRVRW
IMFPQVRVPHGSTGQTALFDDTDADADADAEMPSIMRVMDIQQEQLARSL
GDGHRVIHGVAGSGKTMILGYRAEYLAQARTASSKPILILCFNEPLGVKL
HSVMDAKGLSDKVHVRHFHKWCYDQLKYSGQAMPPQGPKFSEELVDRVIR
AVDRKQIPSGQYQAVLIDEGHDFAPEWLKLVTQMVDPTTNSLLLLYDDAQ
SIYERARSKQFSFKSVGVQAQGRTTILKINYRNTKQILQTANLIAADLLT
ADDRDDDGIPLVKPISCGREGQAPILIKLPSLREEAFAIADQLSHAHKDG
HAWGDMAILCADWKTMDLCADALHQRKLPFNVRKRTGEYNPAADAIQIMT
MKVSKGLEFPVVALPGVGHMPAKGEDEQEAARVFYVAATRATQRLVIGVG
GDGGFGVRLT
>Rfer_1751 DNA repair protein RecO
MATQRISDEPAYVLHRHDWSESSLILEVFTRHHGRIALVAKGVKRPSSSF
RPILLPLQLLHVAFGGDAEIRILKAAEWQGGHVMPTGDALMSGLYLNELL
LTLLARDDPHTRLFDVYTQVVQVIASGHGEVLQSALRAFELLLLREIGLL
PLLDAQTMTLLALDPESRYSLVPEGGLRQTNDADRASLSGAQWVALQQSL
VDSAPFTATLRACSEVMTQLKPQLRALLNYHCGVQTLRTRQMMIDLQSLS
L
>Rfer_2258 TatD-related deoxyribonuclease
MFTDSHCHLNFPELLSQLPAIRQAMSEARVDRALCISTTLEEFGTVHALA
TQYDNFWATVGVHPDSEDVQEPSLQDLLSRGQLPRVVGVGETGLDYYRLG
GRSVADMAWQRERFRTHIHAARQLAKPLVIHTRSASDDTLGILREEGENG
TLGSAGGVFHCFTETLDVARAALDLGFYISFSGILTFKNAQDLRDVAAFV
PSDRLLIETDSPYLAPVPYRGKTNNPSLVPFVAAQLAETRHRPVEHIAEI
TSRNFETLFKGVLL
>Rfer_1378 Holliday junction resolvase YqgF
MPLPLQPMPEPLIKPLADAAPGENPVHVAANLQTFLALDFGLKRTGFAVG
NRLLRTAQPQGTIAAEGDARFVKIALQLKEWQPDALVVGVPFHPDGAAHE
NTLRARRFARQLQGRFKLPVFEVDERYTTTEALGRGARDADAMAACIILE
QFLRSI
>Rfer_3221 TatD-related deoxyribonuclease
MTIWIDTHCHLDAQKSRPLAQAVRARAAINSVAHCVLPAVELGNFDVVRE
LAHTTGDSYALGIHPLCVKPALDAHLSRLDATLMQHRDDPRLVAVGEIGL
DFFLPELCVSPLRERQEYFFLAQLRLAQKYDLPVILHTRRSVDRVLKGLR
EVAGARGQWHGIAHAFNGSEQQAHAFMALGFKLGFGGALTYERALQLRRL
AISLPLDAIVMETDAPDMPPHWLYKTAEQRAAGAAQGRNEPGELPRIGAE
LAALRGISADELAEATTRNALVALPRLRALLPL
>Rfer_2572 DNA polymerase III, epsilon subunit
MLPCYVLLDLETTGGNPVHDRITEIAAVRIENGQEVARWSTLVNPGCSIS
PFIQHLTGISNAMVRGAPGFETVAQHLLALLDGAVLVAHNVRFDHGFLLN
ELARLDVALRVKTLCTVRLSRLLYPQHKGHGLDAIMQRHGIRTLERHRAM
GDVEVMQAWLQIARQEHGAELLGQQALALLQSSATLPPQLETRVADIPES
VGVYIFYGEGPLPLYIGKSIKLRSRVLAHFQAASRAPREMRMAQEIRRIE
WLETAGEIGALLLEARLVKERQPAYNRRLRRESTLCAWRLADDPLARPLL
SLVRGEALQPQEFGQMYGVYRSKNQALSSLRELADSQGLCLQALGLESGK
GRCFAHQIGRCQGVCCGEESPERHHLRLQLALAQQKLLVWPYPGKVGLRE
YNARSERTDIHIFDQWCHLATVHDETELTDALGSRSTLAFDLDTYRLLLK
HIAAPGKGKFELIDWTEKQQQTLNSL
>Rfer_3035 UvrD/REP helicase
MCGHWSAFYNRAMFSAITQQSPPDDLLLQHLNPEQRAAVTLPAEHALILA
GAGSGKTRVLTTRIAWLLQTGQVTPGGVLAVTFTNKAAKEMMTRLSSMLP
VNVRGMWIGTFHGLCNRFLRAHFKLANLPQSFQILDTQDQLSSIKRLYKQ
FGIDDERFPPKQMQWFIGGCKEDGLRPNMVEVRDEETRKKVEIYQLYEDQ
CQREGVVDFGELMLRSYEVLRDNDPIREHYQRRFRHILIDEFQDTNKLQY
AWIKMLAGTGAHSTADDASFNPTGCVLAVGDDDQSIYAFRGARVGNMADF
VREFKVKHQIKLEENFRSGSNILDSANELISYNTKRLGKNLRTAQGPGEP
VRVFEATSDFAEAQWMVEEMRQLVREGMERKEVAVLYRSNAQSRVIETAL
FNAGIPYKVYGGLRFFERAEIKNALAYLRLLENPRDDTSFLRAVNFPPRG
IGLRSLEQLQDVARASGCSLSDAVSGLGGKAGANIGAFLAGIDVLREQTS
GMKLSEIVERVLEHSGLIQHYKADREGADRVENLEELVNAAESFVSLENF
GRDAAALPVDEQGHALTQSPASQGLDLSQPVLDEPVPDLETGETQSPLAA
FLSHAALEAGDNQAQAGQDAIQLMTVHSSKGLEFDCVFITGIEEGLFPHE
NSMSDRDGLEEERRLMYVAITRARKRLYLSHSQTRMLHGQTRYNPKSRFF
DELPEAALKWITPKHQGFRADGATYSGANSQGYTGARGQFDINYSKFAAA
PAPIQKAAPAHGLRAGMKVFHAKFGEGTVQTLEGTGDDARAQINFPRHGV
KWLALSVAKLTPVP
>Rfer_1406 NUDIX hydrolase
MSINLPDRPLSSLPQFDPRQIPVIGVDSHLPAVPLASLQPAALRQRFASP
PVWVPELLAEKKFLDRAPMHASVLLPIVMREHPTVLLTERTMHLSTHSGQ
IAFPGGKADEDDADAAATALREAQEEVGLDPAFVQVLGVMPHYVTGSAFI
ITPVVALVQPGFSLTPNAYEVADIFEVPLEFLMNPAHHRRHAFEWEGVRR
EWFSMPYQDQLRQRFIWGATAGMLRNFYRLLSA
>Rfer_2654 Tyrosine recombinase XerD
MQDTALTPLGDASIDAFIDALWLEEGLSKNTLAAYRRDLTLYGAWLQPQH
KALPATLEHDLNGYFAAQHSATKASTANRRLTVFKRYFRWALREHLISAD
PTLKLQAAKQALRVPKTLSEFQVEALLAAPDEQTPLGVRDRTMLELMYAS
GLRVSELVTLKVFNVSLSDNVLRVFGKGNKERLVPFGEVASLWIKRYLAQ
ARPELLAGKQTEDLFVTHRGATPGTAMSRVMFWMIVKKYALSAGITAPLS
PHTLRHAFATHLLNHGVDLRAVQMLLGHVDISTTTIYTHVARERLKVLHA
QHHPRG
>Rfer_1656 formamidopyrimidine-DNA glycosylase
MPELPEVEVTRLSFAFEIAGARVISVRIGKPLRWPLGCSPTQLAGRSVQA
VRRRGKYLLIDLDQGLLLVHLGMSGSLSFARQLPPAGAHDHFEMTTTLGT
LRLTDPRRFGAVVYAKGEDAPEAHKLLGKLGMEPLSDDFDVDRFHDELKR
RRAAIKQVLLAGDTVVGVGNIYASEALFMAGIRPTLSAARLSRPRSARLH
AAIRDVLARAVATGGSTLRDFSSAKGENGHFQLEAMVYARQGQPCRVCAT
PIKSLRQGQRSTFYCPHCQKA
>Rfer_2183 DNA polymerase III, epsilon subunit
MRQIFLDTETTGLSADTGDRIIEIGCVELFKRKLTGNNKHFYLNPGRESH
EDALRVHGITSAFLKDKPKFEAVADELLAYVKDAEIIIHNAPFDLGFLNK
ELALLGRPRFKEFVGSVTDTLVMAKEMFPGKRNSLNALCDRLGVDNSGRA
LHGALLDAELLADVYINLTRGQDALLMEAGATESESLQVVQIDLGSIVLP
VLAANDQESAAHDDVLNQIDKASGNKTVWRKSA
>Rfer_0407 ATP-dependent DNA helicase, RecQ family
MQQTLESVFGYPQFRPGQEAVISAVLAGRSAAAIFPTGSGKSLCYQLPAL
LLPHLTLVVSPLLALMQDQLAYLTRHGIAAASIDSAQSREQTQSVMAQAR
TGQLKILMISVERLKNERFRNFIAQVPISLLVVDEAHCISEWGHNFRPDY
LKLPHYQRQFGIPQTLLLTATATPPVVADMQTRFAIAAHDVVTTGFYRPN
LHLLVEAVSGRDKLQRLLEWLSMRANQPTIVYVTLQKTAEQVARHLSQHG
LGAHAYHAGMPHEQRESIQKQFMAGRLNCIVAAIAFGMGIDKSDIRNVVH
FDLPKSIEGYSQEIGRAGRDGLPSDCLALANRDSLQVLENFVYGDTPEAG
GIRCVLDEILAVAPAKPWELSLNALSEQSNIRLLPLKTLLVQLELRGIIA
SRYAYFAEYRFKYLMEPEALLAHFKGERQQFVQAILRCARPARTWCTLDF
EALYQTCQAEHSRVVTALDYLAAQGWIELEAKQMTEVYAVLAPGFDAQTL
SLELLAYFQAKERSEIARIHAMLAFFAGEQCLSQHLAAYFGDSAAPLQCG
HCSVCHGQVAHLPAPAPRAALAGQNFPALCGDLMARHRALGPSPMSADSL
TRFLCGVAAPLLTQLKARSLAGFAALENHPYAEVRQWVGQQLANLEPGRP
PTD
>Rfer_3774 excinuclease ABC, A subunit
MNSPTDAALEPPPDGQYLARALQLQNISIRGARTHNLKNIDLDIPRNQLV
VITGLSGSGKSSLAFDTLYAEGQRRYVESLSTYARQFLQLMDKPDVDLIE
GLSPAISIEQKATSHNPRSTVGTVTEIHDYLRLLFARAGTPFCPEHDLPL
QSQTVSQMVDAVLALPLDTRLMILAPLAREKKGEFLDVFADMQAQGYVRF
RVNGQAFEFDELPALKKTEKHDIDVVIDRIKVRHPPAQQASAEADSDAAP
DPTPDASRSAAQADFENLRQRLAESFEAALRLAGGRAIAVEIDSVSRNND
GGYRPIEHIFNAKFACPVCSYSIAELEPRLFSFNSPVGACPACDGLGAND
FFDPARVVAFPSLSLAGGAIKGWDRRNAYYFAMLESLAAHYQFDIEQAFE
SLPPTVQHAVLFGSGEEDIKFSYVMDSGTQTGKKVSKKHPFEGIIPNMQR
RYAETDSAVVREDLARYRSTQPCPQCGGSRLRREARHVKIGEGEQARAIF
ELSHLTLRESYQYFNTLSMHGAKGEIASKVVREIGLRLKFLNDVGLNYLS
LDRSAESLSGGESQRIRLASQIGSGLTGVMYVLDEPSIGLHQRDNDRLIG
TLKHLRDIGNSVLVVEHDEDMMRAADHIIDMGPGAGLHGGRVMAQGTFEQ
VRANTESLTGQYLAHTLRIAVPRQRTPWLPTVQARAAADKPKAHRFAPSP
AALRRAEREALHLATQGKLQSLRVIGASGHNLQGVDVEFPVGLFTCVTGV
SGSGKSTLVNDTLYAAVARTLYRAHEEPAGHEAIEGIEHFDKVISVDQSP
IGRTPRSNPATYTGLFTPIRELMAEVPMARERGYGPGRFSFNVSQSSGGG
RCEACQGDGMVKVEMHFLPDVYVPCDVCVGHRYNRETLEVLYKGKNIAQI
LDLTVEVAHEFFKAVPTIARKLRTLLDVGLSYIRLGQSATTLSGGEAQRV
KLALELSKRDTGRTLYILDEPTTGLHFADIDLLLKVLHQLRDAGNTIVVI
EHNLDVIKTADWLIDMGPEGGAGGGQVVGIGTPEDLAANPASHTGHYLKR
LL
>Rfer_1173 transposase IS3/IS911
MLKEPDLARYSSRPTHRTYTRQFKAELVVACQQPGASIAAIALQHGMNAN
VLHRWLKEHERDGRHRLIGPDPLGVAVPATPVPAFIPLKLPTSMLEPTAC
DIKVELRKGAVSMILTWPASAAADLVHWTRAILK
>Rfer_2896 UvrD/REP helicase
MPDSQPAPAYEHNGQLISAEAFYAIACDPRRSVAVEACAGAGKTWMLVSR
IVRALLDGVDASSGELRVQPHEILAITFTKRAASEMRERLYQWLAEFAVA
DRATLLKELTLRGVLDKNELHPPSVLPEQLSKLYQNILRSGRQVQVRTFH
SWFAALLRSAPLAVLQQMELPANYQLLEDDTPAKALVWRRFYAALLRPKP
AQVGGAELRGDAPDESCGFTLQFDYEAVVFDYGRAQTDKALQTALDKRTE
FTLADAQGVVLRSVLPFGTQFPEFAGLGTPDDFLRDQPQRWQILLDAAAA
LGRASAKTFAAKGVELEMALSSGDLSAAFAALLTDKDAPRKFSEKIAGIE
AVREAQDLVLRVVAARLQHAAWTYQQRMARLTRALLKEFAALKREHGWVD
MNDVERAALVMLSDPVLCGWVQERLDARIKHLLIDEFQDTNPLQWQALKS
WLSGYAGTGGGASGGAGATAPRVFIVGDPKQSIYRFRRAEPQVFKAAKAF
VRDGLNGDLLSCDHTRRNATGVIAVVNAVMTQAVQADGYEGFRAHTTSAS
ELGLVCKLPPIARPERLAGAASSGDETEGGGTASAGWRDSLDTPRELPEE
TLRTLEARQAAHWIAQQLASAETPDTEGRGLQAADVMVLSRKRAGLLPLQ
LELRKLHIAAQIGEKTNLIDCCEVQDLVALLDVLVSPRHDLSLARVLKSP
LFDMTDAALVQLAQAVRAQSQPPADGSWFDVLQKSELSTQDGRGLAACLM
RWKGWLDQWPPHDALQAIYFDGDVLARFAAAAPASQRDAVLANLTALLGM
SLQLDGGRFSTPYAFVRALKGGGVLAPAAVNPQAVRLLTVHGAKGLEAQV
VLLLDTDTPERNADTMGVLIDWPGEAAWPSKFVFLASESQPPACAVPTLE
AERLERQREELNALYVALTRARRTLAISSIAPYRSAERSWWQRLSDLAQP
AVPAGAAALAAPLPDAVTVADAVFYIKELPLAPVEYRQVAIKSEANLGGS
RGGDDANADADALSARLGKAMHRLLEWGDATPANTAACAREFALTPEQGA
QAAAMAARILQGEGAWAWDNTRLAWQGNEIELLYQGQCLRLDRLVQRTDA
QHAGHWWVLDYKSAPAPHEQAELLAQLRDYRAAVQAIYPDAVVKAAFLTA
HGALIEVNEVNWNSA
>Rfer_0331 Protocatechuate 4,5-dioxygenase
MALDKPYKDIPGTIIFDADQSRKGYHLNQFCMSLMKAENRERFKRDQRAY
LDEWPMSEEQKQAVLDMDLNRAMALGGNIYFLAKIGATHGKSFQQMAGSM
TGMSEEEYRAMMLAGGRSIEGNRHLGEDGDAQPQHQPQGQAGRKASV
>Rfer_4006 N-6 DNA methylase
MARAPTAKPDKEEPLEKQLWKAADKLRKNIDAAEYKHVVLGLIFLKYISD
SFEELFTKLQGGAGDYAGADPEDKDEYKAENVFFVPPQARWSFLLGKAKQ
PDVGSHVDAAMDAIEKENPSLKGVLPKVFARQNLDPASLGGLIDLVGNIA
LGDAKARSADVLGHVFEYFLGEFALAEGKQGGQFYTPRSIVELLVVMLEP
YKGRVFDPCCGSGGMFVQSEKFVTEHQGRINDISIFGQESNQTTWRLAKM
NLAIRGIDASQVKWNNEGSFLNDAHKDVKADFIIANPPFNVSDWNGELLR
KDGRWQYGVPPTGNANFAWLQHFNHHLAPNGRAGVVLAKGALTSKSSGEG
DIRKAMVVDGNLIDCIVNLPAKLFLNTQIPAGLWFMNRARNNGHPRKGEI
LFIDARNLGHLINRRTRELSDEDIQKVASVYHAWRTGESEYADEKGFCAS
VPLARVAELDYVLTPGRYVGLPDEEDDFDFAERFASLKAELEAQLLEEAE
LNQAIAENLAKVKV
>Rfer_1413 DEAD/DEAH box helicase-like
MTDAIQATGDISLVENFSNDTVEVTQNPAQVAAVIQIAQVPAAVEAIAEV
PNGFVTLGLAPELIQAVKDLGFTQPTTVQLKTIPLAMQGHSASDDAARFI
DLMVSSQTGSGKTAAFLLPVLHTLLTQMAQAEAKERSDFERAVADAAAKG
EAPPKRAKRKDPTNPRHFAPAAPGALIVCPTRELAQQVAHDAIDLVQHCR
GLRVANIVGGMPYQLQIAKLQNANLVVATPGRLLDLQRSMQIKLDQVQFL
VVDEADRMLDLGFSDDLAEINQLTIERKQTMMFSATFAPRIQQLASRVMR
EPQRLQIDSPQEKHANISQKLFWADNAQHKRKLLDHWLRDTTINQALVFA
STQIECDGLANDLQQEGFSAVALHGALSQGLRNRRLMALRQGQVQILVAT
DVAARGIDVPTVTHVFNFGLPMKAEDYTHRIGRTGRAGRDGIAVTFAEFR
DRRKIMDIEHYTHQQLKGETIPGMEPQQRFPDSRPTSNFGGRESRGGGGD
YHSRERGFGGGGRPGGFGANRGGFADRNAGAPRDSGNNGYQNASNNGFGQ
RDARSGGAPEGFNYERKGGFNDRFAGARNDGAAPRGDFGARKPAFGKPMG
AKPGNGGKVFVPRDAKKRPARSA
>Rfer_1668 conserved hypothetical protein 95
MAQEFPPYSSSLMKQDKSAAPQKPAQPIRPRSPQTHEVRIIGGLWKRTKL
AVVEHPGLRPTPDRVRETLFNWLGQDLTGWRCIDAFAGTGALGFEAASRG
AKEVLLVEQDTALVAQLKRVQIQLQASTTQIVRGDGLAALKHLDPASMDA
VFLDPPFDSVLFEAALQAAGRAVAAGGFVYLEAPIPWTDAQLESAGLQVH
RHLKAGAVHAHLLKRIGSDA
>Rfer_3688 ATP-dependent DNA helicase RecG
MQNRRMSLPTVPQLPKPLTGPQKALRKLGLERAIDLALHLPLRYEDETRI
ERLSEVREGEVAQVEGVVTHCEVKLSGHRQLLVTLDDGTDTCLLRFFTFY
PSSQKALAVGNRIRVRGEVKGGFGGLTMMHPAFKSAGGELAVALTPIYPT
VAGLPQAYLRRAVQGGVARAELSDTVPLENLCEIGLQPSWNMRNALLFLH
NPTPEVALATLQDHSHPAWQRLKAEELLAQQLSQLQAKRERARLRAPVLH
SQALDDLVDDAHAAGRRDARLKPGLPGSLRNRLLATLPFQLTAAQHRVSA
EIARDLARPVPMHRLLQGDVGSGKTVVAALAAAICIDAGWQCALMAPTEI
LATQHFAKLVSWLEPLGIRVAWLTGSQKAKERREMLALIASGEAGLVIGT
HAVIQDKVQFKNLALAIIDEQHRFGVAQRLALRSKLSAQTDHPELVEGPA
AASSLRQAQDQPSSVRTVGLEPHLLMMTATPIPRTLAMSYYADLDVSTID
ELPPGRTPIITKVVNDARREEVIARIRAQLDAGRQIYWVCPLIEESEALD
LSNATETHAQLSAALPGAMVGLLHSRMPVAEKKAVMSLFTSGRMGLLVST
TVIEVGVDVPNASLMVIEHAERFGLSQLHQLRGRVGRGAAASACVLLYST
GDAPRLSETARARLKAMAETHDGFEIARRDLEIRGPGEFLGARQSGAAML
RFADLATDTALLQWARQLAPVMLDQHPALAERHVLRWLGGKAEFLKA
>Rfer_2433 transposase, IS4
MTRYIQGSDRSQVTLLPECLDDYIDENNPVRVVDVLVDELDLTGLGFERV
VPAITGRPGYHPAVLLKLYLYGYFNRIQSSRRLEREAQRNVELMWLTGRL
APDFKTIADFRRDNGVGIRNVCRRFVAMCRQLKLLSQVVCTNGESQRNHL
>Rfer_1365 N-6 DNA methylase
MTQKIGAGLLEYAGKIWDTADTLRGAGIKESEWPTYMMPFFALMMLESRL
RRFKQERIAEYEEETGAAFDPEDATHAKWLDDTAKAVGKGYHKDLLLHDK
GLRETCLVPGGNFLNRLLSHLNSYDPDTKKLLGIDYAQGSAKFLDMQGKA
SDLNARDNNPLYPFAQKWASIDLTPFDNSEITTIEEHIKRKWADISAETA
GEQYTPSDVIDLATAIIIELRREGKGGTGIADVYDMACGGGNFLFATEDA
LRDAFPKLSVRTRGQELNDPLFALASIEARFREDAQIEWGNTLTNDLFLL
DKFDAIVANPPYGVDWKDFKQSLGMDASGRFAKDRMPPTSDGQLLFLQHA
AFHLSEVGVAAIVHSGSTLFSGDAGGGESETRRWLIQQQDIVEAIIQLPK
NEFFNTGISTYLWILNRAKPQARKGKVLLINAEDQFVKLKKNLNKKNCKI
DEANCAAIVKAFRACKDGPISKVLTVDQLLYNKVEIILHRHDAEGRAIQE
ETALNGEVITVTIGGQSHIIKNGPLIKPDHLTTKEAAAAFNEAIKAAETL
TVQSGKLTYTRDNETGAIRLDDGTTLSELGLGVLAVKAKVAKARGAEVLK
VEVTLGPLKEKDTETTAFSFDPAGNDAIIRDFLATWVKEPFERVPDAVTV
GCEINFNKQFPKKSEVGTVKDLLEKLHRLNAKGAEQEADFTASISGA
>Rfer_1060 restriction modification system DNA specificity domain
MSGAATVTLSEFCATGSGGTPSRAQMERYYEGGTIPWIKSGELRETVING
AEEHVTDVALKESSIKLVPAGAILLAMYGATVGRLGILGIEATTNQAVCH
IIPDPRIAVTRYVYHALSSQVPSLISMGVGGAQPNINQGIIKNLAIPLPA
KPEQRRIAAILDQADALRAKRREALAQLDSLTQSIFIQMFGDPVSNPKGW
PDATTLGQVANIASGVTKGRNLTGKVTRTIPYLAVANVQDKSLNLSAVKE
IDATEDEIERYLLKWNDLLLTEGGDPDKLGRGTLWKNELPECIHQNHIFR
VRVTSQAVTPLFLNWLVGSQRGKKYFLRSAKQTTGIASINMTQLRSFPLL
LPPVELQRDFETIAEVVAEQHAIHSVSLAELEALFVSLQHRAFRGEL
>Rfer_0459 ATP-dependent DNA helicase RecQ
MILSIHLILQEVFGYDAFRGPQQAIIEHVVAGGDALVLMPTGGGKSLCYQ
IPAIAREQAGQGITVVISPLIALMHDQVGALHEAGIKAEFLNSTLSGEQA
TQVERRLLRGDITLLYAAPERVTTPRFLAQLDSLYERGKLSLFAIDEAHC
VSQWGHDFRPEYRALTVLHERYGSVPRIALTATADALTRADIVERLQLQD
ARLFISSFDRPNISYTIVEKRDATQQLLRFITSEHMGDAGIVYCQSRKRV
EDIANLLCDEGIAALPYHAGLEAKVRQANQDQFLRSEGIVMVATIAFGMG
IDKPDVRFVAHLDMPKNIEGYYQETGRAGRDGQAAQAWMCYGLQDVVNQR
RMIDESPAGEEFKQGLRGKLDALLGLAEATDCRRVRLLHYFDEESKACGN
CDNCLHPPAVWDGTDAARKLLSTIYRVQQMGGSYGAVHIMDILRGKSTEK
VTQRGHETLSTFGIGADLSEVQLRGVLRQLIAIGAVAVDAQAFNTLQLTD
ASRAVLRGEVPVQLRASVSSPAERKAKRSSAVHAGSVGKTPIALDAAAQT
RYTALKAWRGEVAKEHNLPAYVIFHDATLAAIAERAPLSLDDLQGISGIG
AKKLEAYGEEVLRVMVSV
>Rfer_3043 metallophosphoesterase
MALKLLHSADWQIGRIYAQFEPDDAAALFEARFLSVERLATLATEHKVDA
VLVAGDVFDAQTVSDKSIRRLFNAMMGYPGAWVMLPGNHDAALAESVWTR
AHRLGVVPPNAVICLEPSVRIVGERFAVLPAPLTQRHTYGDLTEWFSFAS
TPEGLHRIGLAHGCVQGVLSDDVDSANPIAANRAATAGLDYLALGDWHGS
KRIDERTWYAGTPETDRFRANDSGQALLVDIAAPGAVPDVQTLQIGRYRW
QQMEPRLAVPSDLDETLQTLAETRSDDVLQIRVYGVCDLNGQRRLQQAVE
AARARLRALVYESHALRLEPTEEDFASLRADGYVGEVLQQLRTEQDGPQA
DRARDALVVLARMLDELGSRPAATGTEARA
>Rfer_1654 A/G-specific adenine glycosylase
MVTDFATQVVRWQKTHGRHDLPWQNTRDPYRVWLSEIMLQQTQVATVLDY
FPRFLERFPSVESLAAAALDDVLGLWSGLGYYTRARNLHLCAGAVMRLHG
GLFPPTAQLLQTLPGIGRSTAAAIASLCFGERVAILDGNVKRVLTRVLGF
DSDLASVANERRLWDEASRMLPLRDLTHAMPRYTQGLMDLGATVCTAKKP
DCAVCPLARSCVARGLGRPESYPMKTRKLKRSSQAIWLLWAQGEDNSVWL
SQRPTPGVWAGLYCLPWFDQREALEAAVPARYRTALHDTPSFVHVLTHKD
LYLHPVQVQMPGSALASSQGRWMSADEWPRLGLPAPVKKLLLQG
>Rfer_3579 DEAD/DEAH box helicase-like
MPFSSLGLSPALLRAISDQAWSAPTPIQAVAMGPALQGRDLLASAQTGSG
KTAAFALPLLQQFEAAVPQSPRRLRALILVPTRELSTQVGEEIRFLGQHL
PRALKVSIVFGGVSINPQMLRLRGGADIVVATPGRLLDLIDHNALSLSGV
ATLVLDEADRLLDLGFAEELNRILALLPVQRQNLFFSATFPPAVQTLAQV
LLRDPVRIEVAPEPQTQPDIEQRVIEVDAAQRTQLLRHLMAQHHWSRVLV
FVATKHAAEMVADKLRKARINAEPFHGELSQGKRTQVLADFKASRLKVVV
ATDVAARGLDIAQLPVVVNFDLPRSALDYIHRIGRTGRAGEKGVALSFVS
AATDAHWRLIEKRQGLSLPREQVPGFEPTAVSPATDSDATADLPATGGIK
GQRPSKKDKLRAAAARIAAEK
>Rfer_3308 DNA mismatch repair protein MutL
MNATLHLAAPAPRRPILELPDELISQIAAGEVVERPASVVRELVDNALDA
GATQVTVRLLAGGVRLIAVEDDGAGILREELPMAFKRHATSKISSLTDLE
SVGTMGFRGEALAAINSIADCVIRSRATGQNNAYLLDGGSGELQPVARST
GTTVEVKELFFSTPARRKFLKTDATELAHCVEAVRRHALARPDVGFAIWH
EGKLVEQWRRCEGRGPALAALEQRLADVLGAEFVARSVWVDFQSSTSPGR
SDNTPSIRVWGRAGIPDAARARADQQFAYVNGRFVRDKVLSHAARSAYDD
VLHGQRQPVFALYVEIDPTRVDVNVHPTKIEVRFRDSREVHQAVRHALED
ALAAPRVGSATSLGTTGRQSVAAANAGLAPEPSAPVVYIQNQSLAPVISE
QAAINFGVQTGHRVSDLGALWQPDGAAPVGLHNKPALAAPLTAPPAAPLP
GGDWPLGRALAQLQGIYILAENAQGLIIVDMHAAHERIVYERLKAQWRER
GSAVNATSGWIGSSATRPGLASQPLLIPATFAATPSEVTTAEAHVDTLQT
LGLEITAFSAKTLAVRAVPTTLAQGDAVELARGVLAELAQHEASTVIERA
QNELLSSMACHGAVRANRRLTLEEMNALLRQMEATERSDQCNHGRPTWRQ
FKLSELDALFLRGR
>Rfer_2353 DNA-directed DNA polymerase
MSEKIRRIAHLDMDAFYASVELLRYPQLQGLPVVIGGARRAEDETLRQLQ
EHNSLARIALDAFPRLQGYTGRGVVTTATYAARQFGVGSALGLMKAAKLC
PQAILLPVDFAEYRKYSRAFKTIVTDIAPLMEDRGVDEVYIDFTDVPGGQ
REGGRVLARLIQKTIFEQTGLTCSIGVAPNKLLAKMASEFNKPKGIAVVF
EEDLQSKIWPLACRKINGIGPKTDVKLQGMGIQTIGELAQKTVDWLIDHF
GQKTGAWLFDAAHGRDQRPVVLESEPVSISRETTFERDLHAVRDKAALGA
IFTRLCQQVASDLAAKGYVGKTIGIKLRYEDFKSVTRDQTLDDYTADFAV
IRQTAGLCLKRVPLAQRLRLLGVRVATLVKAEQVQEFITNQPLAPVKQTQ
SAIDIEARNNQLF
>Rfer_1507 NUDIX hydrolase
MDDRHLVEEKLSSEELVKGHFLHAYRDIVRLPNGTTTSREYIVHPGAVMI
VPLLEDAEGGVRLVLERQFRYPVGQVMIEFPAGKVDSGEDLQLCAQRELL
EETGYTASQWSHAGVLHPVISYSTEFIDIWFARGMTPGQRQLDHGEFLDV
FTATPTELLQWCRDGLITDGKTLTAALWLQNFLSGAWLLNWHPAATPGQA
G
>Rfer_1459 recombination protein RecR
MADLNSLDVLIQALRRLPGVGVKSASRMAFHLLQHDRPGALALSRALQVA
ADQMRHCERCHTFTQADICATCLDPRRDASKLCVVETPADQSALERTGAY
HGLYFVLMGKLSPLDGIGPKDIGLKGLFDRACDGTVQEVILATNFTAEGE
ATAHVISEGLKSRGLRLTRLARGVPVGSELEYVDLGTIAHALLDRR
>Rfer_2908 NUDIX hydrolase
MSSAMLVADAALPREGGANRPVVDVAVGVLIRPDGGFLLTSRPVGKVYAG
YWEFPGGKLEAGEGVAQALHRELHEELGITIGPVMPWRVEMVDYPHALVR
LNFCKVFNWMGDLQMREAQLFAWQQLPVQVAPVLPGTVPVLQWLADERGF
KNATYLVAT
>Rfer_1171 transposase IS116/IS110/IS902
MSTPLQTVVQVQDAAIQVELYMSIELSDKKWQLTLSDGRRGPSRYSVEAG
DTGAVAQCIAKAKERCKLQPQAKVHSCYEAGRDGWWLHRWLVEQGIDNIV
IDSASIEVNRHARRAKTDRLDGDKLLTMLLRHRTGERVWSVLHEPSAEDE
DARRTHRELARLAKERTAHTNRISSLLVLHNVRPRIIIGGRDWGRWWDNH
CEQVPPALRAEIERESARLALVKQQVKALEVARLQELADGKQPLVAQLIR
LRAIGPKGAWILVKELFGWRRFSNRRELAGCLGLAPTPYASGDSQIEQGI
SKAGNKRARALLVELSWSWLRLQPASDLSQWFNKRFAAGGKRMRRVGIVA
LARRLVIALWRYLEHGEIPNGAVLKPTTA
>Rfer_2169 DEAD/DEAH box helicase-like
MKFEELNLAPAIIKAVLEQGYETPTPIQAQAIPAVLDGHDLLGGAQTGTG
KTAAFVLPMLHKLSQSEAARNKFGGIGIRALVLTPTRELAAQVEESVQTY
GKYVELTSTVIFGGVGMNPQISRVKKGVDILVATPGRLLDLLQQGVLDLS
QVQILVLDEADRMLDMGFIHDVKKVLAVVPKDKQSLLFSATFSEEIRELA
ATLLKSPLTIQVTPRNTTVQRITQLIHPVGRGKKKALLAHIVQERNWSQV
LVFTRTKFGANNVAEFLTKSGINAMALHGNKSQAARTQALAGFKSGDIRA
LVATDIAARGIDIDDLPHVVNYDIPNVCEDYVHRIGRTGRAGADGAAVNL
VCLDEEGFMQAIERFTKQDIEVQIVEGFMPEPGEQAEPIAMGRQTIWGGA
GKPPSRDVMQAAARTARTEMLQRVRENKGPQGERGGRAGAGRGGNGGGQR
SAAPRSHASAGEQAARGPGQRPAQGRAGNAGGYPGGNGGGNSGAYGGGNS
APSRSPSSQPDPMRTSVDMMAERGARRGGGGFGGGNRTGGSYAGSGGRSG
GAGGFGGGGNGSRGPGSSRGSFNR
>Rfer_2642 DNA topoisomerase (ATP-hydrolyzing)
MALKPTNEYSEASIRVLKGLEPVKQRPGMYTTTDTPLHVIQEALDNAADE
ALAGHGKKIRVVLHLDGSVSIEDDGRGIPFGLHPTENAPVIELVFTQLHA
GGKFDKGKGGAYSFSGGLHGVGVSVTNALATRLEATTYREGKVASLVFAG
GDVIEPLRVREPAPGERKSGTTVRVWPDAKYFETLALPMAQLVHLLRSKA
VLMPGVTVTLVNEKTKETQNWLFKGGLLDYLMQTLAGELVIPVFEGDGFA
DAQHDNFAEGEGASWCVAFTEDGPLVRESYVNLIPTTAGGTHEAGLRDGL
FTAVKSFIELHSLLPKGVKLMPEDVFARASYVLSAKVLDPQFQGQIKERL
NSRDAVRLVSNYVRPALELWLNQHVEYGKKLAELAIKAAQTRQKAGQKVE
KRKGSGVAVLPGKLTDCESRDLAYNEVFLVEGDSAGGSAKMGRDKESQAI
LPLRGKVLNTWEVERDRLFANNEIHDISVAIGIDPHGPNDTPDLSGLRYG
KVCILSDADVDGSHIQVLLLTLFFKHFPKLIETGRIFVARPPLFRVDAPA
RGKKQASKAYALDEGELTAILDKLRKEGVREGAWSISRFKGLGEMNAEQL
WDTTLNPDTRRLLPVHLGSIDFLQTQGLFTQLMGKGEAAARRELMELHGD
AVEIDI
>Rfer_1325 DNA polymerase I
MNDSFTDSPAKPKTLLLVDGSSYLYRAFHAMPDLRAVPGDPSSAPTGAIR
GMINMLQSLRKEVPADYAACIFDDKGPTFRDALYPEYKAHRSPMPDDLRS
QIEPIHEVVRLMGWKVLAVPGVEADDVIGTLAVTAARQGIEVIVSSGDKD
LAQLVNSHITIIDTMNGRRRDVAGVEAEFGVPPQLMVDFQTLVGDVIDNV
PGVPKVGPKTAAKWLQEYGSLDAVVANADQIKGVVGENLKKSLDWLPLGR
QLLTIKTDCDLDGWMPDLPALDSIATGTMDTGALAIFYEKYGFKGLARTL
GGGAASVASKASSGFGVGPKERSDAGSDPNSVRQLTREPGLFDEPEAASD
PIPSSVTNLHYDTILTWEAFDRWLAKVQAADLVALDTETTSLDEMRAQIV
GISFSVTPGEAAYIPLAHAYPDAPAQLPLADVLAKLKPWLQDASHKKLGQ
HVKYDRHVFANHGIEVQGYAHDTMLQSYVLEVTKPHGLASLAERHLGRSG
ISFEDLCGKGANQICFDQVDIAQAAQYSCEDSDMTLDVHRALWPLLQAND
KLRFIYELEIASSEALYRIERNGVLIDGPTLAVQSHELGQRILQLEKEAH
ELAGQPFNLSSPKQIAEIFFTKLGLPVVKKTPTGSPSTDDEVLQKLAEDY
PLPAKILEHRGLAKLKGTYTDKLAQLAHPRTGRVHTHYAQAIAVTGRLSS
LEPNLQNIPVRTPEGRRVREAFVAPPGSVIASADYSQIELRIMAHISGDA
ALLLAFHDGIDVHRATASEIFGVDRAQVTSEQRRYAKVINFGLIYGMSAY
GLAKALSIDNTAAKNYIERYFDRYPGVKNYMEHTRALAKRQGYVETVFGR
RLYLPEINSPNGPRRSGAERAAINAPMQGTAADLIKLSMVKVQQVIDEEK
RATKMIMQVHDELVFEVPESEIDWVRHEVPRLMAGVAHLKVPLLAEVGVG
ANWDKAH
>Rfer_1196 phage integrase
MESSSQAVSPLRQRMIEDMRLRKLAPKTQSAYVRAVRKLAGFIGRSPDTA
SAEDLRRFQLHMVDSGASPITLNATIVGLNFFFSITLGREEVMAKMQSVR
VPHRLPVVLSKEEVARLLAAVGHIKHQTALSLAYGTGLRVGEVVALKVSD
IDSQRMTLRVEQGKGRKDRYAMLSPVLLERLRCWWRVARAQGKMLDGGWL
FPGLNPIESLGTRQLNRAIHEAALVARIDKRVSMHTLRHSFATHLLEQKV
DIRVIQVLLGHNRLDTTAQYVQVATDILREVISPLETLEPA
>Rfer_2033 Helicase c2
MSTDDLAGLSLAAFDQMVDATAGFRSRPGQRDMAQQIASALSGVTLGEHA
EPNKSIAVIQAGTGVGKSAAYLATTVALALARKTRVVISTATVALQEQLM
TKDLPALAAVLESPFVFALAKGRGRYVCKFKLERLAGPGGDELNEELFGV
DEDTPPTRAAFAAQLQGVDPEERRMKLYDALATALSQGKWDGDRDKLAEQ
PDARDWSAVAAERHSCTARHCPRFRDCSYYQARTQLAEANVIVANHDLVL
ASLGMNALPELEKCLVVFDEGHHLPAVALDQFSSSMDLSSLRWLDKLPKI
LLEVSEKISRTPDQDVNTLAQQLKTALLDVSRIAMDLLRTGGTGYDGTQR
FKNGVLPVVLLEPMTLIQGHARGLSGVLEALGAELKRRAKEDPALALSSS
LLYAKLGPMAPRLGSVLATSGMLLQQGPQPLAKWLKSDTSSGLVFMSAHA
CPIVPGELLQQSLWRQVRGAVITSATLTSCGSFDFFLQEAGLDNDETVST
LEVASPFNYTAQGRLIVVETVADPKNVEAYTRELVAELLLDLSQIEHGAL
ALFTSRVQMKAAVDALSPTLQDVVLVQGQMARTRLLATHQARVEAGRPSV
IFGLQSFGEGLDLPGRLCETVLIAKLPFSPPSDPVEEARSEWLKSVGRDP
FSELVVPATGIRLLQWTGRAIRTEEDVATVICYDRRLLTMAFGRRMLQGL
PAYAVLRRSAGVLRAM
>Rfer_0829 PHP-like
MPITNADVVAVFSEIADLLEIEGANPFRVRAYRNAARMLGELGRSVRTMV
DRPEELDALPGIGPDLAGKIVEVVTTGSCALLQRLRKELPPVITELLKIP
GLGPKRVRTLHRELGIETLAQLRQAAEQGRVQSVHGFGAKSERQILEATG
RLLQQERRYKWADMEPVAQALLADLHATPGVHRAVAAGSLRRGRETVGDL
DLLVTAENPGTVMDRLTASEDIQRVLEQGVTRSSVVLKSGLQVDLRAVAP
ASFGAAWLYFTGSKAHNIALRKLAQDKDLKLNEYGLYRGKQRIAGDTETA
VYKALGLPFIEPELREDRGEIEAARSGALPRLLQLTDLRGDLHAHTKDSD
GHDPIEAMAEAARAHRLHYLAITDHSKRLALVHGLDADGLSRQIDRIDEI
NASLRDFVLLKGVEVDILEDGSLDLPDAILGRLDLVVGAVHSGFDLSRDK
QTDRLLRAMDHRCFSILAHPTGRLINERPPCDIDLPRVVRKARERGCFLE
LNAHPARLDLSDAACRIAKSEGVLVSINSDAHSRLQFDSLRFGVSQARRG
WLETGDVLNTRTLGQLRSLLAATMARGVGQ
>Rfer_1565 histone-like DNA-binding protein
MTRSDLIEELAARFGQLTRRDAEFAVKAILDAINDALVRGHRIEIRGFGS
FAINHRPPRIGRNPRNGESVAIPEKRVLHFKPGKALREAVDQRTAEAASQ
HKA
>Rfer_3931 SNF2-related
MQNDSAAVGPWFSTQSLANSIDRATWDRGLTLYLAQKVLSLEIKPMGDYW
QLLATVQGSQRWPYQVSIELTFKPNGEVANWDSDCSCPVGYQCKHGVAVL
LKAAQQGRRLMDPSAALSACAPAAPTPEQIEAAQQVARERAAEQARREAE
APLLHWLQELNQAARQGAQAGIDTDARSVHEQYLYLLSVAGAKGRTPELQ
MDVVVSCPKVHGGWAKPKALRIAPARGQTTFDQATQVDQELLQLMRALPS
GSSGYYSYGYKAKVTLYGKIGVMVLQQAASTGRLLFESGKGLPGAPVQWG
APQDLRWEWHEVASPNDAEPAWALRARLGNARAQLCLNTPTLYLDAASGL
CGLVQADGVPAAQLSVLLKAPPLKPSALKTHQLALLQQLGPVPPPPVLEQ
LPTLSGITPHACLHIAPLPVSDTLLKGLLQAQLQFDYAGRRGWWAGLGTT
VLVDDAQGRVLLHRDPEAEFEAVAQLTGMGLRSTEPGRFGLPGDASQQSW
LQWADSGFAAFKAAGFEVTLDDALIDWISHADDLDVKLQGRGDDEDGAHD
PHAGHAGVNGKEDEDGDAGVTSPWFDLSLGMEINGVRHNILPWLPTLIAQ
AATSPLDPATGLPNIPPFIFLPNTAGQGFIRLPTDALKPWMAALLELVGD
RSHDFTGDCLKLSRLDAMRTTASLGEGAVWDGAQALRKLVKQLSGQTELP
TVPVPTSVQASLRPYQQQGLNWLQFLRQYSLGGILADDMGLGKTLQTLVH
IQVEKDAGRLKYPALIVAPVSLMGNWQREAARFCPNLRSLVLHGKDRHEL
ADSLHDHDIVITPYSLLERDRERWLKTRWHLVVLDEAQNIKNASTQAAQV
ASQMRARQRLCLSGTPMENHLGEIWSLFHFLMPGFLGSQKKFQDLFRTPI
EKLGNPERLEQLRSRVTPFMLRRTKALVAGELPPKIETAMRVELTGKQAD
LYETIRLGMEKSVREALDTKGMAKSQITILDALLKLRQVCCDPHLVTLAA
AKKVSNSAKLERLMEMLPEMLAEGRRILLFSQFTSMLKLIEAELQKRNIP
WIKLTGQSQKRDALIEQFTSGAVPLFLISLKAGGVGLNLPQADTVIHYDP
WWNPAVENQATDRAHRIGQTQSVWVVKLVAQGTIEERILGLQERKAALAE
SMYSGAVGRKQPLFSESDLAELLKPLSV
>Rfer_4129 Uracil-DNA glycosylase superfamily
MAEPEAAYPNLDALLTAVRNCRACESHLPLGPRPVLRAGEAARILIVGQA
PGVRVHTTGIPWDDPSGERLRAWMGVDKALFYDESRIAIIPMGYCYPGRA
RGGDLPPRRECAALWLDQLLSRMPRIELTLLVGQYAQHHFLGSRRKPSLT
ETTMAWREYAPRFIPLPHPSPRNQPWFKQHAWFEEDVVPALQARINAMIA
R
>Rfer_2641 DNA gyrase/topoisomerase IV, subunit A
MSDQTTLDFPAGPDAGAGADDDALNLATYAQRAYLEYALSVVKGRALPDV
CDGQKPVQRRILYSMSRMGLGFGGPNGNTGAKPVKSARIVGDVLGRFHPH
GDSSVYDAAVRMAQDFSQRYPLIDGHGNFGSRDGDGAAAMRYTEARLAKI
TGLLLDEIDEGTVDFMPNYDGSTQEPSQLPARLPFNLLNGASGIAVGLAT
EIPSHNLREVADACIALIKSPQLSESDLFALIPGPDYPGGGQIISSAEDI
AEAYRSGRGSLKCRARWKIEDLARGQWRLVLTELPPGVSTQRVLEEIEEL
SNPKVKAGKKALSLEQNQLKATLLSVLDGVRDESSKDAAVRLVCEPKTSR
ISQQELITTLLAHTSLETSSPINLTMIGLDGRPTQKSLRQMLTEWIAFRQ
KTIERRSQHRLGKVLDRIHILEGRALVLLNIDEVIAIIRQADEPKAALIA
RFHLSDRQAEDILEIRLRQLARLEAIKIEQELAGLRGEQQKLEEILGSPS
ALRRLMIKEIEADAKTFADPRRTLIQAEKKAVLEVKVVDEPVTVVVSQKG
WVRAQKGWASERAANGVLPAEYSFKAGDALYDTFECRTVDTLLAFGSNGR
VYSVAVALLPGARGDGQPMTSLLELEAGTQLLYYFAGPAPATLLLSSSGG
YGFLASVENMTSRLKAGKAFVTCNAGEILCRPSPVAGGSGATPWPAATHV
ACASAGGRILTFEISQLKTMATGGRGLMLIDLEDKDRLAGACAYTRSVKI
EGLGRGGKPRDETLEIRSLNNARALRGRKGKVADLGFKPATITRVA
>Rfer_1043 hypothetical protein
MPEADSPAVAASWRALEAMYACLEAGQSFRLEAGAGAGKTYSLIKALQFL
IERDHQSLPKRSQQIACITFTNVASSAAGADVRGEPGISVEFSRPVIATA
GPVWAFVGP
>Rfer_1298 NUDIX hydrolase
MKGRLNGARFFMPKVYKIPQSVLVVIYTPALDVLLIKRADAADFWQSVTG
SKDTLDETFEQTAVREVLEETGIECAPGTPLAAHLRDWRLENVYDIYPRW
RHRYEPGVTRNTEHLFGLQVPAATPVRLSPREHTSYLWLPYLEAAAACFS
PSNAEACLMLPRMAAAKASI
>Rfer_3039 phage integrase
MATITERGPYQFQAIVRQKGYPSRTKTFETRNDAKKWVSVIESEMHRGIF
ADRAECERTTLGEALGRYQKEKTIHKRSPQQEIHRIRAWQKHPLAMRSLA
SLRTADFAEYRDERLDVVGRNTVRLELALIGHLCTVAISEWSLPIERSWI
VKGLLPKPGDARSRRLVGDEETRLLAAAEQSYALNLTLAIKLGILTGMRN
GELTHLEWSQIDLEQHTISLSMTKNGDARVVPLFKAAVELLRAIPRPKDG
GRLFEFHDSNGLSAAFRRACERANIVDLHFHDLRHEAASRLAPHVPATAL
CKLMGWRSFQMSLRYYNQLASEAVNLLHEIEHKVVRLPA
>Rfer_1704 methylated-DNA--protein-cysteinemethyltransferase
MPTQAYALFPTPIGHCGIAWSERGLTGVQLPEQDEAATRARMDRRFPQCS
EAIAPPQVQEAIDAVMALLSGALQAPVDLMNVVLDMDGVPPFHQRVYELA
RRLLPGETVTYGDIARQLGDPGAARAVGQALGANPFAPVVPCHRVLAADG
RAGGFSAHGNVTTKLRLLLIEHAQFNGPGLFDDPVDAQLS
>Rfer_2607 endonuclease III
MTPAAIESFFATLKAANPHPQTELAYASVFELLVAVLLSAQATDVSVNKV
TRRLFLVANTPQKMLDLGLEGLEEHIKTIGLYHAKARHLMQTCRMLVDQY
GGAVPRTLEALQTLPGVGRKTANVILNVAFGEPTMAVDTHLFRVANRTGL
APGKTPYEVEMKLLKRIPAEYLVDAHHWLILHGRYVCQARKPLCWQCAVS
AFCDFKPKTPPDKARAR
>Rfer_3001 methylated-DNA--protein-cysteinemethyltransferase
MKFAPSTVQASYDSPLGRIILAAAHDRLTGVWFDGQSHQPDTARWPVDRD
LPVLQQAKTQLSAYFAGRRQAFELALDLSAGTDFQQSVWRALLQIPFGAT
LSYGALSASIGKPAAVRAVAGAVARNPLSIIVPCHRVLGAGASLTGYAGG
LPRKTALLQLEGASFKPEPNQPQEATP
>Rfer_2316 Helicase c2
MNLQNLTRETFAPGGLLSRMVEEFTPRVGQTDMAVAVARTIEDGGVLVVE
AGTGIGKTFSYLVPALLSGTRVLLSTATKTLQDQLFGRDLPRLMKALSLP
VRTALLKGRGSYLCLHRLAVARQDADPSDRVLGRTLAKIEAWAQLTRSGD
LAELPGLDERSPAIAVVTSTRDNCLGSQCPEFRDCHVNQARREALAADVV
VINHHLFFADLAIRESGMAELLPSVQTVIFDEAHQLNETGVQFLGQQLTT
GQLLDFVRDLLFHGLQHARGLQDWQTLAFDAEHAARDLRLVVGQASPGAK
LRWVGAAPDQVDESAWHDALGALQAACARVMLALDTVSAVAPDLMRLRER
ASVFIERLAFFSDDCASESVRWLDVGVQLRLVESPLDIANAVQTRLIKST
AADASQRAWIFTSATLGADAQLRWFTEPCGLADAEILKIDSPFNYAEQAA
LYVPRHLPRPSDPGHSAQVAEFVARAACVIGGRTLVLTTTLRALQAVSES
LQRHFAESRSLEILVQGQQPKRELMQRFRQGDQGDRQGCILVASASFWEG
VDVPGDALQMVVIDKLPFAPPTDPLVEARSRRLVAAGRSVFKDYALPEAA
IALKQGAGRLIRRESDRGILVVCDTRLALMGYGKKLLSALPSMRQISSEE
ELTEVLQALTRPSTRDQCSF
>Rfer_0001 chromosomal replication initiator protein DnaA
MTEGQYANHPDFKGTGDGQSLWQTCVDQLAQELPEQQFNTWIKPLSAQVT
DDLAQITIFVANRFKLDWIRAQYSKRITSLLEMFSGQTIHLELALAPREI
FVRSQLTHRSMEPIPMDGVAELGEDRNPSSLKNRLNTALTFDTLIEGTAN
RMARAAAMHVAGMPGHLYNPLFIYGGVGLGKTHLMHAVGNRLLADQPNAK
VLYIHAEQFVSDVVKAYQRKTFDEFKERYHSLDLLLIDDVQFFANKERTQ
EEFFNAFEALLAKKSHIVMTSDTYPKGLTDIHERLVSRFDSGLTVAIEPP
ELEMRVAILINKARVEGIVMPEEVAFFVAKNVRSNVRELEGALRKILAYS
RFNQKDISILLAREALRDLLSIQNRQISVENIQKTVADYYKIKIADMYSK
KRPASIARPRQIAMYLAKELTQKSLPEIGELFGGRDHTTVLHAVRKIGGE
RQQMTELNQQLHVLEQTLKG
>Rfer_2932 protein of unknown function DUF1568
MARLPRLTLPGYPHHIIQRGNNRQAIFATKADYQTMLDLLAENARKFDVA
IHAYVLMSNHFHLLATPHTADGLPQMMQAVGRRYVRYFNDSQKRSGTLWE
GRYKSTLIQTERYLLACMVYIDLNPVRAGLVGQAGDYPWSSYGHYTGLRS
DKLITPHPLVWELGNTPFAREAAYAELVQGGLNPVQQAALTDSVLRGWAL
GEPDFVAELQKRTQRRLAKISAGRPVSIQKNTQN
>Rfer_1053 hypothetical protein
MSRYISRYQLTAGQAAKRFSDIEQLAIPLNLTGRHLLPEFELLCGGLKKI
FLCSTQDKEILLQFLALGEAHAAIHYPSTLAHVKGINAKLPWGDTTCPAT
MLTGLAGTGKSELLKALNRLLGNESFLDLPGHDRVPLVPGWFMNVKEGSS
PNSLLLPWIEQKKVVSKCNKVDSTEEYQRKDLNLPRLAELSRRVAFRDGV
CIISIDEFQFISKSTSANSLATNLLLRLLAIGPRLIFGANYSLAHRLDAR
GQEDRQRLLARRIYLKPENLCSPDGIRLLKEYFKILPMDFTLDAIAVAQQ
VQDYTFGIKRLVVDLLAISWVHAKKSGGVKANVTTDDLRCAFLSRDFCAN
RVDVEILQRQEIEKRQIRRDLWDPFFSEQQDNVFEVVPAISAFEKRVEER
RLDSFLTPNERLGFDAIKKLVGATPKEANVVPMNPLKRSKQGLADALRLL
ND
>Rfer_2002 Ribonuclease H
MLHTPSIKQASLLWDVAGLVAGVDEAGRGPLAGPVVAAAVILDDLQPIKG
LADSKILSARRREQLFDEIRAKALCCCIAQASVEEIERLNILQATLLAMR
RAVEGLRLKPALVLVDGNRLPVLTMRAEAIVKGDALVAAISAASILAKVH
RDRWCAEVDVQYPQYGFARHKGYGTVQHLAALTKHGACPQHRKTFGPVAE
VLREALP
>Rfer_3071 conserved hypothetical protein
MTQKTRNAPPRANAMLEALRGLGYSTAAALADIIDNSISAGASEARLDFA
WNGATSRISVLDDGRGMTDAELESAMTLGDKNPLDARASHDLGRFGMGMK
TASFSQCRRLTVATVKDGDTSCLRWDLTELAAHPDSGWLMHEGAANGSEQ
FLAPLHGKAYGTLVLWETLDRIVSTGYTVDDYLALIDEVQAHLAMVFHRL
IQGPRPKLRLFIQERAIAPWDPFMAGHLATWSSPVARKPTPDGVVEVECH
VLPHKDKLSDDEWKRCAGPNGWTAQQGFYVYRNERLLLAGGWLGLGPSKA
WNREEAHRLARIRLDIPNTADAAWKIDIKKSTARPPVALRPWLTTLAEDT
RDRARKVFAYRGSPTPSPTGTLLEQAWRVDHTATGARYRIDDKHPAVSAV
LEGAGPLLPMVKAMLRVIQETVPVQRIWLDTAENKETPRTAFAGEAPEAV
MGVMRTIYNDMVGRRGMTPDLAKRALLSTEPFQNFPVLVANLSASDTFNN
PQ
>Rfer_3772 single-strand binding protein
MASVNKVILVGNLGRDPEIRYLPSGDPVANITIATSSKYKSKTGEMVEET
EWHRVTFFGKLAEIVGQYLKKGRSVYVEGRIKTRKYTDKDGIEKYATDII
ANEMQMLGGREGMGGPSDDDEGASGGYSRPAPASRPAASAPAARPAPAPA
QAKPSSGFDDMDDDIPF
>Rfer_1436 ATP dependent DNA ligase
MAHPFISRPFSCLTLLLGSVFSPGAFAVADTTAVDTQDVSVSPPALMLAK
YWQSGVDPAAFLVSEKLDGVRAFWDGHTLRSRSGRRIAAPDWFTSALPAT
ALDGELWLGRGSFDRLSGMARRNTPVDAEWRELRYMIFDLPGASDTFALR
VQRLNQVVANARQPWLQVVVQQRVPDAAALQALLQQTVQNGGEGLVLHRT
NALWSPGRSDVLLKLKPMPDEEARVVAHLPGRGRNQGRMGALLLEMSNGQ
RFALGTGFADAQRADPPPVGSLVTYRYRDRTPKGLPRFASFLRVRAPE
>Rfer_2106 ATP-dependent helicase HrpA
MPLQIEFPESLPVSGKRDEIMAALEQHQVIIVCGETGSGKTTQLPKIALA
MGRGKLNYPPGRGKLIGHTQPRRIAASSVAKRIAEELKTTLGDVVGFKVR
FQDRLSRDTSVKLMTDGILLAETQTDPLLKAYDTIIIDEAHERSLNIDFL
LGYLRQILPRRPDLKIVVTSATIDAQRFADHFASRNGPAPVIMVSGRMFP
VEQRYRPFEESRDYDLNSAIADAVDELWRDVHNSGDILVFLPGEREIREA
ADHLRGHLSHQPVFRNAEVLPLFARLSQAEQDRIFDGHTGRRIILATNVA
ETSLTVPGIRYVIDAGTARMKRYSFRSKVEQLLVEPISQSSANQRAGRCG
RVANGICIRLYDEKDFNGRPRFTDPEILRSSLAGVILRMKSLRMGLVEEF
PFIERPSGRAIADGYQLLNELGAVDDANELTTMGQELAKLPLDPRVGRMI
LEARERGALDEVLVIASALSVQDVRDRPMEAQQQADQAHAKFDDEKSEFS
GYLRLWKWINDGKGGEGQHKLSNRQYEQLLRQNFVNIRRVREWRDIHSQL
HTVVAEHKWRLNTLPANYEQLHLSMLSGLLGNIGCKLETEGDKPGGGGEY
LGARGIKFYPHPGAHLVKKPGRWIVAAELVETTRLFGRGIAAIEPQWLEQ
VGGHLLKKQLLDPHWEKKVAEVTALERATLYGIVIYSGRRVNFGRVDMVA
AREIFIRQALVDGQWETKLPFLESNQKLIKQVEDLEHKARRQDVLVDEEL
IFAFYDQQLPADVCSGHSFENWYREEIKKNPKLLLLTREELMRHEAAGIT
TQSFPKTIRLGGVDCAAAYLHEPGDAKDGLTVTVPLFVLNQVNEERCEWL
VPGMLKDKIQALIKTLHQRPRSRLVPLPDTASKMAETLNAPEVFGHGSLL
DAVMKLVRLATSIDIVRADIKVDMLSPHFFMNFRVVDEHGRQLGTGRNLG
ALKAELGAKARGAFQALAGLKMAKDAAALPVFKENKPIARVHSTKEAIKN
IVTPVAPAGQRHTAWTFGELPELLEIQKGGQTLIGYPALIDAGDAVMIEV
FDEPDVAAAKHRAGLRRLFSLAVKDALKYLEKNIPDLQKMAVTFMQVGKG
ADGSGGGTIEELREQILAVALDRAFLLDPLPTDEFAFKRRVEEGRGRLTL
IANEVARLAATILLEYSVAARKIKDTKNAPEATADAAQQLARLMPKRFLI
LSPWGPLQHFARYQKAITARLEKYRADPARDAARLAELRPLEQRYWRLVA
ERKGVLDERLQEFRWLLEELRVSFFAQELRTPQPVSVKRLEKAWGQLQ
>Rfer_4078 conserved hypothetical protein
MKFSIAKTTLISLTLLLSASVCTAADTKAVAPQQAASKAQATTKSVKSGA
DAKPKVAPKIKLVDINSASAAELKKLPGISDAQAAKIIAGRPYGSKAWLV
SHNIIDAAVYEGLRQQVIAKQPNKDAVKNAELYIKKK
>Rfer_0820 Holliday junction DNA helicase RuvB
MSIQTDDFAAPPPKRILSGAPASPNEEAVERALRPKLLDEYVGQAKVREQ
LEIFISAARMRDEALDHVLLFGPPGLGKTTLSHIIAHELGVNLRQTSGPV
LEKPKDLAALLTNLEKNDVLFIDEIHRLSPVVEEILYPALEDYKIDIMIG
EGPAARSIKLDLQPFTLIGATTRAGMLTNPLRDRFGIVARLEFYSPEELA
SIVRRSAGLLKVPTDEKGGFEIARRSRGTPRIANRLLRRVRDYADVKGAG
EITLDIAHRALVMLDVDPQGFDLMDRKLLEAVIHRFDGGPVGLDNIAASI
GEERETIEDVIEPYLIQQGYLQRTPRGRIATLAAYKHLGVTPPAAQSGGD
MFGAMRPE
>Rfer_1581 helix-turn-helix, Fis-type
MSHMPIEECVRSNLEGYLRDLGGTEPDGMYNMLVNVVERPLLEVVMRHAD
HNQSKAAQWLGLNRNTLRKKLLDHKLIK
>Rfer_3450 hypothetical protein
MAVTTVLSLKFLSTILGAAGAPLFAGLMVYKIEIDFDQLRANEAQQRALN
DPAKATPALWTITKPNLDVIEQAGAKLLHQHPCFQRLLSDLGVPADFIDV
TFAQTGCPQAADHSQL
>Rfer_2709 transposase IS3/IS911
MLKESDLARYSSRPTHRTYTRQFKAELVAACQQPGASIAAIALQHGMNAN
VLHRWLKEHERDGRHRLIGPDPLGVAVPTSPGPAFIPLKLPTGMLEPTAC
DIKVELRKGALSMIVTWPASAAADLARWTRAILK
>Rfer_2519 Transposase and inactivated derivatives-like
MNGAFPSRASRAFAATGNKVPRWEVQLLINSFAKGKFMTIVTVGIDLAKN
VFAVHGVDATGKPVLIRPSLARTRLAKLMVSLPPCLIGMEACSGAHHWAR
LFATYGHTVRLMAPKFVTPYRLSGKRGKNDAADAAAICEAVTRPNMRFVS
VKSASSSSPVCSCTERARATVQELLGHSDASTTMISTHVPKVAAGGLASP
LDLRSGMAA
>Rfer_3040 DNA helicase related protein
MTRESSQSTEAGTPENSAVSEVPPPIVRLQISAAKKLNLAAFQNAVPALL
ELAVVNDTASQLTELTIHLTSEPAFVKPRTWNLDAVGPGESYHLPDLDVR
LDGALFSRLTEAEPAVLRFELRSAMQPDLVLAAHESNVELLARNQWGGIG
RLPEMVAAFVQPNDPAVDRLLKGAALSLQAADKSGSIDGYTHGPKRAWEL
TSAIWAAVLQRKLNYSLPPASFEHTGQKVRSPSQIMDSGIATCFDSTLLF
AACLEQANLNPLLVFTKGHSFVGFWLRNEEFSTAVVDDITALRKRLKLQE
LVVFETTLATQGQPVNFSQAIDNANRQLAEEEEDKFELVIDVKRARMSRI
KPLAQAQAVADVVPHTLEPETTITIEEAPDLPDEVVIDTPTAELDPKDRL
ARWQRKLLDLSLRNALLNFKQGKKALLLDVAAPSLEDTLAEGHTIKLLPS
PELMQGQDPRSQQLHEARSLEDLRKTHAADALQRREVFIRLEQQELESRL
VELYRGARNAMQEGGANTLFVALGFLVWSRSDKPEHRVKAPLILLPITLN
RKSARSGFTLQAHEDEALFNPTLVEMLRQDFQLELGIPAGDLPRDESGLD
IAGIWKRVRSVIKDIRGWEVSEDVVLSMFSFAKYLMWKDLADRTDDLRKS
PVVAHLIDTPREPYPSTTPFPDARRLDTDYAPQQVFCPLPADSSQLSAVM
AAANGKDFVLIGPPGTGKSQTIANLIAQCLAEGKRVLFVAEKIAALDVVF
RRLREVGLGEFCLELHSNKSRKLDVLSQLQKSWESKGEVDAATWEAKARK
LGQVREQLSTYVERLHQRHGNGWTIYKAIGCVVGGDALPDLRFSWATPRA
HDEVALTALRNLAGRLQANAAAVGPEQLLTGALVPVHVTDWSAKWQQEMV
RSAQTLQTTSHGFLAAAQDLGQMIGMEWPALHRQTRSSIGVLAKVLPQAS
TQDWSFCALPDSDTVCAALKAGNDLLGQHRVLSSKMSTPWPTELQTRLAQ
ALDLLDKRRNLYTELGSPWPPTVSDEIERGVQWIEEMGQLRASLSVKYGA
GVGQLNVAQLQRDWAKADKSFWPMSWLGKRKVRGVLEAVIEGTGEPRVAD
DLSALVRIRSLREEVQQLNPGAAAEGLWVGVKTRTDHASSALKANAALHA
ARMHKPFSLEGLEGASEGYCGERWTREAQRLKALLDLDHRLSECAPLSES
SQGLWQGHDTGSAILRAALAFERERLGLPQRGSLQTPHPNVAEGRCGPAL
QQQHALLQTRGAVETRLLSMSGLAAECPGVWNALDTDREGIERALKFHAS
LKAGLSGLGLEPSSIVEARQSLHQVLGTRRAELSDTALIGQACHQVLAQL
AEINAATDQFCQTATQPENVHRAFADLAPAELAEAAVRLEGGHLGLHAWC
AWRHAQTDARDAGLPALVSAIEAGDLTPAQVPTAFEVNYARWWLAEAVDE
DEVLKRFVSAEHELRIKEFRALDDEFTKVSREWIRAKLCANLPATDSIQR
NSEWGILRHEITKKKQHKPLRQLLQEIPSVVLRLTPCLLMSPLSIAQYLS
AEASNFDLVVFDEASQIPVWDAIGAMARGKQVVMVGDPKQLPPTNFFGRS
DSTDGDDDVVEGDLESILDECLGASLPTRNLSWHYRSRHESLIAFSNHRY
YGGGLVTFPSPVTDDRAVSFHLGKGCYEKGGARINQPEAKALVVDLVSRL
KRPGFRESGLTIGVVTFNSEQQGLIEDLLDEARRKDPGLEPYFSEMELEP
VFVKNLESVQGDERDIMYFSITYGPDMAGAVSMNFGPLNRDGGERRLNVA
VTRARHELRVFSSLRGEQMDLSRTKAAGVRDLKHFLEFAEFGPRALAEAH
HGSQGDFESPFEASVATALGRKGWQVHTQIGASSFRLDLGVVHPDFAGRY
LAGVECDGATYHRSATARDRDKLREQVLRGLGWEIVRIWSTDWWVNPGGT
LERVHAALTELLEKDRERRANEAEVPPDEALSEPSDDEATPSLHAINEAE
AAITRAAAGLPPAAVEPHQETADAPTEAVYARSASTPSTPVLGGADTQRD
RRFQASQPTDAVPPGAISTDLFYEPTYDAVLQPMVEWVVQREGPVLDAVL
ARRIARAHGFQRTGSRIQERVEQSARRLFKTTEEAGDTFYWPREVEPCSE
VAFRWPTDDDSTRGVEEICEAELLSLARLVLRRGHSGQEALIAMARELGL
QRLREASRDRLEGVLLKGCESK
>Rfer_2276 transposase, IS4
MLKQQTLAMAADQSFENYRKPTRRDEFLKTMEAIVPWVALCEVIEPFYPK
AGNGRPPIGLERMLRIHFIQHWFNLADLSCEEALYDSVSLRRFVGIDLGR
EPVPDATTMLKFRKLLHDNQLGEALFAQVGAVLQSKGFKVNTGTIVDATI
IGAPSSTKNAGKARDPDMHQTRKGQQWYFGMKLHIGVDSQTGLAHSAVVT
SANVLDKHPLPDLLHGNEQRVYGDSAYASQKDLIHSAAPNVRDFTNQRTR
RNGVVNETLKSRNRNKSRIRARVEHVFGVVKRLWGFGKVRYRGLQKNATR
AFTALALTNIYLSRQRLRAQVRP
>Rfer_1571 DNA gyrase, A subunit
MTQFAKETLPVSLEEEMRRSYLDYAMSVIVGRALPDARDGLKPVHRRVLF
AMHELNNDWNRPYKKSARIVGDVIGKYHPHGDQSVYDTIVRMAQDFSMRH
MLVDGQGNFGSVDGDNAAAMRYTEIRLSKIAHELLADLDKETVDFGPNYD
GSEKEPLVLPTRLPNLLVNGSGGIAVGMATNIPPHNLNEVVDACLHLLRN
PEASIDELMEIIPAPDFPTAGIIYGIQGVKDGYRTGRGRVVMRAKVHFED
IDKGQRQSIIVDELPYQVNKKTLQERMAELVHEKKIEGISHIQDESDKSG
MRLVIELKRGEVPEVVLNNLYKQTQLQDTFGMNMVALIDGQPKLCNLKDL
IKVFLQHRREVVTRRTVFNLRKARERGHVLEGLAVALANIDEFIAIIRNA
PTPPVAKVELMAKPWDSKLVREMLTRTRADGGVINADDYRPDGLEKMYGM
GSDGLYRLSDTQAQEILQMRLQRLTGLEQDKIVAEYKEVMGEIEDLLDIL
AKSERVSTIIYEELTAIKTEFGQTKLGARRSLVEHSSFDLSTEDLITPTD
MVVTLSHSGYIKSQPLSEYRAQKRGGRGKQATATKEDDWVDQLFIANTHD
YILCFSNRGRLYWLKVWEVPQGSRGSRGRPIVNMFPLQEGEKINVVLALT
GEKRSFPADQYVFMATSMGTVKKTPLDEFSNPRKGGIIAVGLDEGDYLIG
AALTDGKHDVMLFSDGGKAVRFDENDVRPMGRNARGVRGMMLEDGQGVIA
MLVAEDELQSVLTATVNGYGKRTSITEYTRHGRGTKGMIAITQSERNGKV
VAATLVHADDEIMLITDKGVLVRTRVSEIRELGRATQGVTLIGLDEGSKL
SGLQRIVENDANPVADETPGDDQDDTSSTD
>Rfer_3814 excinuclease ABC, A subunit
MPQGIIRIRGARQHNLKNLDLDIRTGELTVVTGPSGSGKSSLVFDTLFAE
GQRRYVETFSAYARQFLDRMDKPAVDKVEGVPPAIAIDQTNPVRSSRSTV
GTMTELNDHLKLLFARAGALFDRVTAQPVRHDSPETIYAQLLERSAQANT
RLAITFPVELPASATPEEVAQWLSVSGFTKVQAERDLEVEASPAVGHKKP
GKAAPEPASRRKVLDVVADRFRLAHAERARVLEAIEVALKHGSGRINVYV
LNEPQAPDIQGSLATDSIVNSVPEIWRFSTGLHCPESNLRYTDPIASMFS
FNSAVGACDACRGFGRVIGVDYGLVIPNDKLTLRAGAIKPMQTPAWQEAQ
DDLMRHAEGAGIPRDTPWYKLTPEQQHWVIDGSPNWNGKWNQHWFGIRRF
FEYLETKSYKMHIRVLLSKYRSYTPCPTCGGARLKTESLLWRMGSKADAD
KVLDPAKRFMPAGVKWSREQLEALPGLCLHDLMLLPLDRVRRFFDSMQAR
LGVSERAAPETAGEPGLSVAVVTSEADAKTLKLLFEEISTRLKYLCEVGI
GYLTLDRQSRTLSGGEVQRINLTTALGTSLVNTLFVLDEPSIGLHPRDMH
RIIVAMQRLRDAGNTLVVVEHDPAVMLAADRMIDMGPGPGERGGQIVFDG
STADLRHADTLTGAYLGGRKQVGLGFQRLVAANTPRLILEGAREHNLKNV
GVEFPLQRLVCITGVSGSGKSTLIQDILAPALKRHFGKPSEAPGAFERLL
GAEQLSDVVFVDQSPIGKTARSNPVSYVGAWDAIREIFANAPLSRQRGYT
ASKFSFNNGDGRCATCGGSGFEHVEMQFLSDVYLRCPDCDGKRYRPEILE
ITIERPLRIKSAGPAPSVRHINVADVLNLTVSEAAMLFEHDREVIRGLQP
IIDVGLEYVKLGQPVPTLSGGEAQRLKLAGFLADAAKSASASRQAIARRG
TLFMFDEPTTGLHFDDIAKLMRALRKLLDVGHSLIVIEHNLDVIRASDWL
IDLGPEGGDAGGEVVAFGTPDDVRQHPASHTGKALRDYATAMGGVHGVNE
FTAPYLVHATAAGVTPGASDAGSTSLPGATPAAADHGVHAAENAIQIINA
REHNLKSLSVNIPRGKFTVVTGVSGSGKSTLAFDILFNEGQRRYLESLNA
YARSIVQPAGRPEVDAVYGIPPTVAIEQRLSRGGRKSTVGTTTEVWHFLR
LLFVKLGTQHCIHDGTPVAPQTPDSIAAQLMKNFRGQHIGLLSPLVMNRK
GVYTELADWARPRGFTHLRVDGNFLPTTAFPRIDRFKEHTIELPVASLDV
LPEQEAALRAALAQALMHGKGVVHVLSNLSGLRAAMLAGTPTAQIGTLQA
FSTLRACPVCSTSYAELDPRLFSYNSKHGWCPDCVGTGVRLTKEQRKVFD
DSVVDNDNKGREQTFAEPEVEDLVDAVCPACQGTRLNATARAVKFGLQLA
SPATASIRARQAIEGVAITELARLSVTDLRQWVETLQTQGRMSQRETDIA
RDLVPEIKGRLEFLEQVGLGYLTLDRGAPTLSGGEAQRIRLAAQLGSNLQ
GVCYVLDEPTIGLHPRDNQILLGALQSLSDQGNTLVVVEHDEDTIRYADH
IIDIGPSAGKRGGQLVAEGSVADIQGAAESQTGRYLLHAMKHPLKPRRPV
LMLADVGVGIGTGAVLAASRAGSPGASDAGSTSLPGKPAPAAKPLTLSAN
LSVAASNVTTTVNLGSNSIFIPAPPKKKKAASKLESDPNFTTPEVQRWLT
VTNATMHNLQHVTAQVPLSRLVAITGVSGSGKSTLARDVLLANVHTAVQK
RSTKAGRDALDAGEQISWTGCTSVTGFESVDRVLEVDQTPIGKTPRSCPA
TYIGFWDIIRKLFADTLEAKARGYAANRFSFNTGEGRCAGCEGQGIRTIA
MSFLPDVKVLCETCKGARFNPETLAVTWRGKNIGDVLQMEVDEAVQFFAA
MPNISHPLQLLKDVGLGYLTLGQPSPTLSGGEAQRLKLVTELSKVRDDIT
RRGQKAPHTLYVLDEPTVGLHMADVEKLIKVLHRLVDGGHSVVVIEHDLD
VIAEADWVIDLGPDGGNAGGRVVAATTPEGVVTLGTPTGVALAAVLAR
>Rfer_1376 Deoxyribodipyrimidine photolyase
MNKQFDSGLMWFRRDLRVIDNAALCLALAACRQLHCVFVFDRDILDTLPR
ADRRVEFIRASLCELDVALGQLSGKAGVGLIVRHAVASEEIVTLAKTLQV
QAVFAAHDYEPQALARDARVRGALAHVGIVLHTCKDHVIFENREILSKTG
TPYGVFTPYKNTWLATVTPQHLRHHDATPVAQALVPRPEGLQQPVPTLAA
IGFEKTNLSQLKIPTGASGGARLFEDFFERMDSYHETRDLPAVKGPSYLG
VHLRFGTVSVRQLAATALQRQIQGSRGAAVWLGELIWRDFYFSILANFPH
VAQGAFKPEYDAIKWEHGKHADSLFQAWCEGRTGYPLVDAAMAQINQTGY
MHNRLRMVAGSFLVKDLGIDWRWGEKYFARHLNDFDLAANNGGWQWVSSS
GCDAQPYFRIFNPVTQSEKFDADGKFIRRYLPQLARLPSKVIHAPWTAQA
LELQMEGVTLGQNYPAPIVAHAAARALTLQRYAVVKKHQAAT
>Rfer_1749 RelB antitoxin
MYDDVYGRGDTVEAVIKSRIDAGLKAEVEQVLSALGLTVSDVMRMTFAQI
AARKGLPFDVKLPNAQTMDVLKESDAALNRLRAGAAPRFDSLDNYFAAMD
GKVARSDGKN
>Rfer_0003 DNA gyrase, B subunit
MTEENKPVQPPENEVNGEDAVHTGEGASDSSNFQPTIDAHQIGASEAYGE
GSIQILEGLEAVRKRPGMYIGDTSDGTGLHHLVFEVVDNSIDESLAGHCD
DILVTIHSDNSVSVVDNGRGIPTGVKMDDKHEPKRSAAEIALTELHAGGK
FNQNSYKVSGGLHGVGVSCVNALSKMLRLTIRRDGKVHVMEFSRGFVQNR
VTEVVNGVEVSPMKVIGTTEKRGTEVHFLPDSEIFQQNSDFHYEILSKRL
RELSFLNNGVRIRLKDERSGKEDDFSGAGGVRGFVNFINKGKTVLNPNIF
HALGDRQSDQDTNIGVEVAMQWNSGYNEQVLCFTNNIPQRDGGTHLTGLR
AAMTRVINKYIDDSELAKKAKVEVTGDDMREGLTCVLSVKVPEPKFSSQT
KDKLVSSEVRGPVEDIVSKLLYDYLQERPADAKIIVGKIIEAARAREAAR
KARDMTRRKGVLDGMGLPGKLADCQEKDPALCEIYIVEGDSAGGSAKQGR
DRKFQAILPLRGKILNVEKARYEKLLTSNEILTLITALGTGIGNAGGSTG
SDDFNVAKLRYHRIIIMTDADVDGAHICTLLLTFFYRQMPELVERGHIYI
AQPPLYKVKAGKEELYLKDGDELDRFLLRIALVNASVFTGGENGTTLKGE
TLAELARKHQTTQAVIARLRNFLDAEALRSVADGVALNLDTVADAEISAA
ALQARLPDAEVAGEFDVASDKPILRISRRHHGNIKSSVLTQDFVHGADYA
VLADAASTFKDLLSPGAIVMRGEGERQKEEKVSDFRQAMTWLLAQAEHAT
SRQRYKGLGEMNPAQLWETTMDPTVRRLLRVQIDDAIETDRVFTMLMGDE
VEPRREFIEANALRAGNIDV
>Rfer_0002 DNA polymerase III, beta subunit
MIVLKATQDKVLSVLQSVAGIVERRHTLPILANVLIRKTGTSLQLTTSDL
EIQIRTTAELDGDTGDFTTVGARKLIDILRTMPADQTVSLESSAAKLILK
GGKSRFTLQTMAAEDFPLVQEAASFGPVFSVPQKTLKDLLSQVSFAMAVH
DIRYYLNGILFVAEGSQLSLVATDGHRLAFASATLDVEVPKQEVILPRKT
VIELQRLLSDTQGAIEMQFANNQAKFSFDGMEFVTKLVEGKFPDYNRVIP
KNHQNSITLGRSALLATLQRTAILTSEKFKGVRLNIDPGTLRVASNNAEQ
EEAVDELDIDYGGDSIEIGFNVTYLIDALANMSQDMVRLELSDGNSSALF
TIPDNATFKYVVMPMRI
>Rfer_0187 phage SPO1 DNA polymerase-related protein
MSLALDPRQRAMLQEMGVRVWLPAAAADLAAPALPAAVQAAPEAPSNAIE
NVATNITTTGATAQKILKTSAPPETRGTATGSGVPATDVAGLDWPALTQA
IATCQACPLCIGRRTAVQAAPDAPRLADWLLVGEPPDDADEQAGAPFAGA
AGQLLDNMLKALGLSRHAGSGVAAPAAQATTAAYVTPIVKCRPAQTRNPT
QAELASCENYLRREVALVQPKVILALGRFAAQGLLQGSLPGLAGTPLGQL
RGQIYRYQGIPVIVSYPPSYLLRSPQHKARAWVDLCQAQEALRRGG
>Rfer_0942 transposase, IS4
MKQQTLAMAADQTFENYRKPTRRDEFLKTMEAIVPWVALCEVIEPHYPKA
GNGRPPIGLERMLRIHFIQHWFNLADLACEEAPYDSASLRRFVGIDLGRE
PVPDSTTITKFRKLLNDNKLGEELFAKVGKELQARGFKVNTGTIVDATII
GAPSSTKNTDKARDPEMHQTRKGQQWYFGMKLHIGVDSQSGLAHSAVVTP
ANVHDKHPLPDLLHGNEQRVYGDSAYASQKDLIASKAPKAKDFTNQRTRY
AGIIDKAVRAKNRNKSRIRSRVEHVFGVVKRLWGFGKVRYRGLQKNATRA
FTALALANIYLSRQRLMAQVRP
>Rfer_3640 Integrase
MKSEPHYSQLDYQDRQTIAIGLEQGLSIRAIGRVLNRSASTISREIARNS
GGNGYSCRYAQQRRVRRRRHARPAPKLVAGNHLFESITELLRQRWSPQQI
AAHLAKLHPSDAAQRASHETIYNVIYAQPRGELRKELIACLRMARAKRWP
RSKGEDRRGQMANLLSIHVRPPEIEDRQFPGHWEGDLIKGALNQSAVGTL
VERNTRLLILVKLPHPNPATAAHVLQAFTDKLSAVAQPMRKTLTYDRGTE
MAYHQQLSANTGIAVYFCDPHSPWQRGTNENTNGLIRQFLPKGTDLSGYS
QEQLDAIADLMNGRPRKTLDWCTPHEVYSAWLAKLENSVQTIQ
>Rfer_3755 NUDIX hydrolase
MTTRWKPNVTVAAVIEHDGRFLLVEEHTLDGLRLNNPAGHLDCGETPAQA
CTRETLEETSYAFSPRALVGVYLSRQPQSNAEAITYLRFAFCGELGAPDP
TRKLDVGIVRTLWMTLEEIRASTARLRSPMVLCCIEDYLAGKRYPLQLVV
ADASIAG
>Rfer_1366 putative type I site-specific restriction-modification system, S subunit
MKDSGAAWIGEIPQGWEIKRMKDCFISNSRAQPNKTVLSLSYGKVIVKDM
EEKKGVTPESFDSYQGVHPGDVVLRLTDLQNDQKSLRVGRATTKGIITSA
YLCVSSRSLNDRYSAYLLHDVGDIQKLFYGLGGGVRQSMKFADLAELLFS
LPTPAEQRAIADYLDRQTALIDQRLTTLAEKKAVLAELRKATIHEAVTKG
LNKNAPMKDSGVAWIGEIPQGWEIKRMKDCFISNSRAQPNKTVLSLSYGK
VIVKDMEEKKGVTPESFDSYQGVHPGDVVLRLTDLQNDQKSLRVGRATTK
GIITSAYLCVSSRSLNDRYSAYLLHDVGDIQKLFYGLGGGVRQSMKFADL
AELLFSLPTPAEQRAIADYLDRQTALIDTQLATLDEQAQVLKVLRKAIIH
EAVTGKIDLSGYVPQTSEAQAA
>Rfer_1434 HNH endonuclease
MKVLKLSAQGLPQSWISLEQAVIHYAAAEVRWEMGAQIAVFHGGHNALTG
AQSIITVNSIIGTKGVPSINPFHLKPGLTNAKLFARDRQLCAYCGEQFDE
ETLTREHIIPFAQNGIDTWMNVVTACRPCNHRKSHRTPEQAGMPLLYAPY
VPSLWEDFILRNRRILADQMEFLMAHVPRSSRLLD
>Rfer_1190 Integrase
MKQRPRIYYSDSQKALMWERWKKGESLQQIAQLFDRNHSSISRILGETGG
IRPAQRCRSQFALSLAEREEISRALAAGRSIRSIACLLGRAPSTVSREIQ
RNGGQGCYRATLADQAAWDRACRPKTCKLVEKRKLASLVAGKLQLQWSPQ
QIAGWLKQAYADDENYQVSHETIYRSLFIRARGALKKELLQHLRRTRAMR
RSRQHIQKTDNHGKITNAVSISERPASVQDRAVPGHWEGDLLFGSLNNQI
ATLVERQTRYVMLVKVAHKDTQTVINALIKNARKLPQELYKSLTWDRGHE
MADHKRFTLATDISVYFCDPQSPWQRGSNENTNGLLRQYFPKGIDISNYS
QAQLNAVARKLNERPRKTLNYETPAERFSQLVASTD
>Rfer_2117 DNA polymerase III chi subunit, HolC
MTEVAFHFNAPDRVAYACRLLRKAAASGAKLVVIGSPDVLQQLDRALWTF
SAVDFVPHCFLESESHVVAASPVILSTSTHAVPHQQVLLNLGQLVPEGFE
RFERVIEVVGQEDEDRQSARSRWKSYADRGYVITRHDLALKTSY
>Rfer_3777 DNA polymerase III, epsilon subunit
MKINRRLLLATAAVGLGLALWLVLTLALVWSTLEPSQRESMGALLAPRLA
LLGMSWGVALLLVASLLRLLYRRYVSAPARLLEATRVLLTATEPQSLRPN
GTTETRALALAINELAAQRDHLRADMTQQVAQASLSVKQEKNRLAALMAE
LTQSVVVCNLDGRILLYNNRARLQLPQFSQARGLADGAGSIGIGRSIYAV
FDRQLVVHALENIHRRLVRGAASPSTQFVTTTPSGQLLRVQMAPVRPGEI
DASNVDAFTGFVLVLDNITRNFEQESLRDQLLHGLTEGSRSSLANMQAAL
DMLGYPDLEPAMHERFMGVLREELVAMSARITDLVQHSTLGLKTRWPLEE
MLGTDLMTAAQRQIGNYCQRPVTLDTLDESLWLKVESFTLLQALTYLASR
LVEEFEVKFLRLRLQAVGERAQLDLIWTGHAMSTETVMTWEMDAMRFGTE
STPLTVRDVVERHGGEMWFERERIRHEAFFRFLLPVASAQEQLEAMQVMQ
IESRPEYFDFDLFQVTEEGRALDERALSDLSYTVFDTETTGLNPAEGDEI
IQIGAARIVNKKILRQESFEQLVNPDRLISAASVQIHGITQDRVIGQPRI
GEVLPAFHAFAQDTVLVAHNAAFDMKFLQLKEAATGLAFHQPVLDTLLLS
AVVHPNQESHRLEAIAERFNITVLGRHTALGDAMVTAEVWLRLIPLLNAM
GIYTLRQAREAAQKTYYARLKY
>Rfer_2072 Exodeoxyribonuclease I
MTPSPSHHTFLWHDYETFGTNTRRDRPAQFAAIRTDAELNVIGAPLMLYC
QPAGDFLPDPQACLITGITPQLCLEKGIPEYQFAAQIEQAFSLPGTVGVG
YNTIRFDDEITRFMFWRNLIDPYAREWQNDCGRWDLLDVVRTAYALRPDG
MEWPLNAEGKPSFKLTDLSAANGLLHEAAHDALSDVRATIALARLIKTAQ
PKLFDFCFGLHKKDRVMAELGLPTTLTQARPFLHISGMFAPERGCLALMW
PLAMHPANKNELLAWDLAFDPRELAQMNAEQIRLRLFTKTADLPEGVQRL
PVKSIHLNKSPTVIGNYKTLSSAMAQRWGLNLDAQLANAAHAQALPDMSG
IWPAVFKRPAAATPDVDEDLYGGFVGNADRRRLNDLRQLKAQELASARPA
FDDARLTELLWRYRARNFPQSLSADELARWEAHRSARLFDGEGGALTIEQ
LFEELDSLAESADERGEAILGALYDYAELIAPQRV
>Rfer_2244 excinuclease ABC, C subunit
MPHLPDSMSPEAPAGPAPATLPAHPAQLLSDVAGLPPLPGVYRYFDFDGA
VLYVGKAINLKKRVSSYFQKNHGGTRIGHMVSKIVRLETTVVRSEAEALL
LENNLIKTLNPKYNILFRDDKSYPYLKMTGASSSSNPGTSFPRVSYYRGA
VEKKHQYFGPYPSAWAVKEAILLMQKVFHLRTCEDPVFNNRTRPCLLYQI
KRCSAPCVGHISAADYAQDVANAERFLRGDARQVMEALEARMMAHAEKLE
FEQAAELRNQVAALSNVLHQQSVDNVADRDVDILAVKVQGGRACVNLAMV
RGGRHLGDRPYFPAHVEDATEIYNAGGFEEAVEDSTTAPPVPSVETQVLE
AFVAQHYLNVPVPPTLIVSAPVNKQLLEALAIQSGVKVTAVHQPREQRRV
WLEMAQTNAGLQLARLLSEEGSQQARTRALAEALDLALDDLDALRVECFD
ISHTAGEATQASCVVFAHHKMQNAEYRRYNINDITPGDDYAAMRQVLLRR
YGKLAETLREAQQTGQMPAGTGRLPDLVLVDGGRGQVSMAREVFEQLGLD
LSLIVGVEKGEGRKVGLEELVFADGREKVYLGKDSAALMLVAQIRDEAHR
FAITGMRAKRAKVRVDGGKLEEIPGIGPKRRSKLLQRFGGVRGVALAGAE
DIATVAGISRELAEEIYRALH
>Rfer_0739 Holliday junction DNA helicase RuvA
MIGKLSGTLDDKNPPQVIVDCHGVGYEVLVPMSTFYNLPELGARVSLLTH
FVVREDAQILYGFATSQERAAFRELIKISGVGPRTALSVLSGMSVAELAQ
AVTLQEGGRLIKVPGIGKKTAERLLLELKGKLGPDIGVAASVANDSQADI
LQALLALGYSDKEAAAALKALPSDVGVSEGIRLALRALGK
>Rfer_3477 5'-3' exonuclease
MSLLIIDALNIIRRIHEAIAEPDSEEKVADTIKSSLGSFKRALKTHRPTH
AVAVFDHGGRTWKHDLYDGYQANRKPMPQPLRDGLLTLKRELHDMGLHWI
AIEGIEADDAIAALVEKWCKYSAKQAIILSTDKDFLQLLNDQVCIYDHFK
EVWRDSAYVQEKFGVTPSQMGDLLALMGDAVDGVPGVDKVGRKTAATLLR
INGNLDRLISNADKVGGQVGANLRKGIEIARLSRQLVSFKTDRPLGLTWK
MLAQVRIPTPPSHTMADSSP
>Rfer_3442 phage integrase
MTRAPSGASTAHEVTAVGTDLVERYLEHVRVEKRLAQRTVELYALDLQKL
SQQAAQAGVELLQVQNSHIRRWVAQMNAGGRSGRGIALILSGWRGFYVWL
GREGLISSNPVQDVRAPKAGKPLPKALSVDQAVQLASFASGSNDPWLEAR
DAAMVELLYGAGLRVGELTGLDTVASSSARGWIDLQGGEAHVLGKGGKRR
SVPVGAKAVLAITHWLALRDQALAQAKPGLQGPGGNAQAALFMGRNGTRL
SAQSIWQRLRQRSLQAGLTTPVHPHMLRHSFASHLLQSSSDLRAVQELLG
HASITTTQAYTRLDFQHLAKAYDAAHPRAKIKGATPK
>Rfer_3948 recA protein
MRQIYADSTGSYFKEIFMDAPVVALKAPTPAPTPINSEKAKALQVALAQI
EKQFGKGTIMRLGEGEVIEDIQVVSTGSLGLDIALGVGGLPRGRVVEIYG
PESSGKTTLTLQVIAEMQKTGGQCAFIDAEHALDIQYAQNLGVNLQDLLI
SQPDTGEQALEIVDSLVRSGAVDLIVVDSVAALTPKAELEGEMGDSLPGL
QARLMSQALRKLTAHIKKTNCMVIFINQIRMKIGVMFGSPETTTGGNALK
FYASVRLDIRRTGTIKKGDVAIGNETKVKVVKNKVAPPFKTAEFDILFGE
GISRQGEIIDMGVNANILDKSGAWYAYNGEKIGQGRDNARDFLRENPALS
QEIENKVRASLGIPLLPGAPEPDVKAKAASKKAA
>Rfer_3862 DNA processing protein DprA, putative
MERDELAAWLRLTLSSGVGNEAARKLLVAFGLPAKVFEQSSSTLQQVVSA
RQATALRAEPPELAPLLEQTWAWLRDTGVGSGRRQIVVLGDANYPQSLLN
IEDPPLMLYLLGAGEFMSNQAVATANKGQAATTSVVNKLALRLANSIAVV
GSRNPTPQGAVNARQFAKALGLAGLTVVSGLALGVDGAAHEGALDSLAPG
SDRLATVAVVGTGLDRVYPKRHLALAHRIAQNGLLISEYPLGTPPLPANF
PKRNRLIAGLAQATLVIEAALKSGSLITARLSAEQGKDVFAIPGSIHSTQ
ARGCHALIKQGAKLVESAQDVLEEMRIDSGLTHALDSIAVDACSTGATGS
FGTQAVLLDAIGFDPVGLDALQARCGIDTAGLQAQLMTLELDGLLVRLPG
GLFQRMSRG
>Rfer_3929 exodeoxyribonuclease III
MFKLTSLNLNGIRSATAKGLEAWLTKTQPDCICVQEVKAQALDVQDRFEH
LAGLRGHFHFAEKKGYSGVGLYSRHEPSDVRVGYGSSQFDAEGRYVELRF
DTPSAKRSIISCYFPSGSSGEERQQAKFRFLEEFYLHLAQLKNGREFILC
GDVNIAHQEIDLKNWKGNRKNSGFLPEERAWMTKLLTEAGLVDVYRQLQP
TATDEAYTWWSNRGQAYAKNVGWRLDYHLATPAMAALARSETIYKAEKFS
DHAPLTIEYDWTL
>Rfer_2201 DNA ligase, NAD-dependent
MATNDLFPPEPPLPDPAHVAQLRRALHEHAHHYYVEDAPTIPDAEYDRMF
QELQAIEAQHPELITPDSPTQRVGGRALEQFASVRHAVPMLSIRTETDTE
ASGARNFDTRVRRELGLDEAAPAVAYVAEPKFDGLAMNLRYESGILVQAA
TRGDGEVGEDVTQNVRTIGQIPLRLPADAPSILEVRGEVYMRRDDFEKLN
EQQRARGQKTFVNPRNAAAGAVRQLDPAIAAQRPLSFFAYGLGEVTPEQA
GGPAFGTHYELLQALKTWGFPVSALVGLAQGATELVAYYESIARQRDALP
FDIDGVVYKVNSLALQRRMGFVTREPRWAVAHKFPAQEQFTTVLDIDVQV
GRTGKLTPVAKLAPVFVGGVTVTNATLHNEDEARRKDVRVGDTVIVRRAG
DVIPEVVSVLLDKRQPGATEFTMPRQCPVCGSAAVREEGEVDYRCTGGLF
CSAQRKQAILHFAQRRAVEVEGLGEKLVDQLVDGHVIRILPDLYRLGLTA
LASLDRMADKSAQNILQALEKSKQTTLPRFLFGLGIRHVGEATAKELARH
FGSLDAVMDASLEQLLQVNDIGPIVAQSLRTFFDQPHNREVVEQLRACGV
TWQEGPPAPVTPTPLSGKTFVITGTLPSMSRDEAKDLIEAAGGKVAGSVS
KKTTFVVAGTEAGSKLTKAQELGVAVLDEAGLKELLDGHS
>Rfer_3061 transposase IS3/IS911
MLKEPDLARYSSRPTHRTYTRQFKAELVVACQQPGASIAAIALQHGMNAN
VLHRWLKEHERDGRHRLIGPDPLGVAVPATPVPAFIPLKLPTSMLEPTAC
DIKVELRKGAVSMILTWPASAAADLVHWTRAILK
>Rfer_0822 primosomal protein N'
MTHQLAVLVHTPVHSAVAGTLSYVSELPLTVGSLVRVPLGQRELLGVVWD
APLDSPAASFDPQKLRPISSALDGIAPLSASWRQLVTFAAHYYQRSVGEV
ALAALPPQLRDLSTQQWGRRLKRHAKAGAVGEPALVDASELVALSPEQTG
AIAQFNTNSGPFLLFGATGSGKTEVYLQCVEQLLVREPDAQAMVMVPEIN
LTPQLEARFMARFAPMYGDGAVVSMHSGMTPAQRLKSWLAAHSGAARIVL
GTRMAIFASLPKLKLIIVDEEHDPSYKSGEGARYSARDLAVYRGRLDGAK
VMLGSATPSLESWHHSRPAAEGGRYLRLVMPSRIGSITALPTAQGDTTRL
VNDAAAASAGLPVVRRVDMNHQPKHCVFSPPLLAAIMERIARGEQSMVFL
NRRGYAPVLHCADCDWKSECPHCSAYRVFHKIDRTLRCHHCGYAERVPRA
CPACGNPDIAPMGRGTERLEEHLAELLLEVRRPNSVSDQWPEGEPVRIVR
IDADSTKLKGELQAQLARVHSGEVDVLVGTQMIAKGHDFRRITLVAAINP
DNALFSSDFRAPERLFSLLMQAAGRAGRDADISGQSEMWVQTFHPQHPLF
EALKRHDYPAFAAEQLKEREQAGMPPFSFQALVRAEARTQEVAQGFLSAA
SAAATRMAQADQLLAHLTLYPAVPMSIQRVANVERAQMLIESPSRAALQR
FLAAWQVVLHATRKQPEGRGLLRWAIDVDPLAI
>Rfer_3873 protein of unknown function UPF0102
MAIPQIKTQVGTSKQAGDAAEESALRHLQQAGLRLLQRNYRTPGRGGGEI
DLIMRAPDGTTVFVEVRQRANASHGGAAASISVTKQRRIIFAARHYLMRL
REPPPCRFDVVTLECGVIQWLQAAFEAC
>Rfer_3234 single-stranded-DNA-specific exonuclease RecJ
MKILVREIPPRSAWALEQAGIHPLLAQLYAARGVQSVQELDDGLTRLIAP
TEMLGLSAAATLLADAIAADQTLCIVADYDCDGATACAVGIRGLRLLGAK
HVSYIVPDRVVDGYGLTSPISERVKASGADVLITVDNGIASFEGVATARA
LGLQVLVTDHHLPASRDGQIVLPEADVIVNPNQPGCTFASKSIAGVGVMF
YVLLALRAELRQRGVFHAATQPKLDALLPLVALGTVADVVKLDANNRRLV
AQGLKRVRALMLPTGLASLFVAAGRDAQVATTFDFGFALGPRINAAGRLS
DMTLGIECLLTDDAARGLELAKALDGINRERREIEGSMREQALAVAESLF
DDNEEAPPAICVFDPDFHEGVVGIVASRIKDKLHRPTFVFAQSKAPGREH
ELKGSGRSIPGFHLRDALDLVAKRHPGVLLRFGGHAMAAGCTIAVEDFDA
FEQSLSQVAREWLDAATLMRRLDTDGPLKPEYRRVELVDALHKEVWGQGF
APPTFSEEVEVLSQRLVGEKHLALKLKHQGQPVDGIWFGHTEPLPARVKL
AFRLDADAWNGVRRVRFLVEAAQAEL
>Rfer_1920 conserved hypothetical protein
MHDEPLIQFNPNFEEFFMFKKLLAFFAAMFLVAAFAAVDVNKATEAELDG
IKGIGPVTTKLIISERKKGEFKSWDDFVTRVKGVGDKNAAKFSAEGLTVS
GATYQGPSAAPAKKANKPLTEKAKDAAVTTKDAVKGAAISTKDAVKGAAV
GTKDAVKETAKDVKTAVTPKADAAKPAASAAKK
>Rfer_1652 DNA repair protein RecN
MSLKRIVLRDFVIVRELDLDLADGFTVLTGETGAGKSILIDALQLVTGGR
ADVGVIREGSSRTDVSAEFDATADLALWLETAGFELGDSLLLRRTVDAQG
KSRAWINGSPATATQLRAVGEQLLDIHGQHAWQSLTRPEAVRGLLDAYAQ
VSSAALATLWQQWRQAQSDLAQAHGAQESLERERERLAWQIGEVEKLAPQ
PHEWLELNTEHGRLSHAQALLDAAQGALQTLGSDDDGGALVALHDACQLL
QQQEHLEPYFKGLTEVLTSSLAQVEDTVHCLRGYLRKTELDPQRLGELDE
RMALWLSLARRYRRDPAELPDLLLSWKQELQKLDAAGDLAGLEAACAAAL
GAYMQQARQLSKARTKAAPRLAAAITQAMQGLGMQGGRFEVALQASAQPT
QSGLEEVSFLVAGHAGSTPRPVNKVASGGELSRMALAIAVTTSRLGTAQT
LIFDEVDAGVGGAVAETVGRLMQQLGVDRQVLAVTHLPQVAACADHHWVV
AKQLLGKSTVSSVLAVQGEQRVAEVARMLGGERLSGTTLAHAREMLQTGE
SFDEVRGR
>Rfer_1367 type III restriction enzyme, res subunit
MAHGFKESDFQNGIFIPYLTAPQPGGLDWIQGKPTDIDAARWIVPGDLLH
FLRDGCPLNVAAFAKASKGYGSDMDFLQAFLLDALLPKIEAKANAAFVLR
ESITFAGQSFVLWNEAPRTGADSGAADLFKKNYLRVIPEAPFERVFPHSN
KRIKRRPDVVFFVNGLYLSYAELKTAQTGQTAAGHGRKKIAHDCIEAGSA
ALQEARERYAAQGGKWPGFRHRDLREKERQEIRQSICLYEKAAHISCVDM
GAMMILSDIEWLLPEIDDAIEANDTQALVETLPGKVMDAFMRAAEMRDKP
ASEALADHLASFFSAADGVDREIYFFNQIRPSRTTTGTEILRPRPAQRAM
LHQSVKRVCALYADESKSKINEPDIRAALAESLPDLDPKKVNEIVAKTLL
HRNGQESHSILLQGAAGLGKTNVIVWLAQALSDMPDPRSKAASPLFDLCI
LLTDRTELRQNVAEEAARLGATKNIVAEAETFKGLYDSLQDGARVVVVNI
QKFPSIKRLAQDDAALSKLLTGKRVAFIIDEVHRSQGGVLHDATIEIFDE
WGSLRPAGAKRNLIIGLTATPRDEVLARFGEWRAPRAAGDDIRWAPYFAY
TMTQAIRERVILNPIQNVIRFEDHLQYRITDTVQKLRPGDELRPPSSDEI
YQNPDRQSMVAKNAALVFVAKTMMAIRPPGGRALGDGKAMFAAHSIKAAI
AYQPLLRAELDKLADDPRFVEHAQAIKATPVLLLYTDKQGEASCASLNGG
RNQDAIIDEFRRKGEGAKQGAKVHNALIVVVDKLLTGFDEPTLHTLFIDR
GMDDVLLFQAACRVNRWRKWKNDCLLVDFSHDGVVSKNLPKVFAKYGGLT
VSSLDAMELKDKMDAAFKVFFDEKDINAHWRAWKATSSGGKDQESATGLS
DFLDGLVKNEVERAKTIRKAGSAWLSSRERLSGILDFTKPALAKHADEKR
AAFAEQVVKHLASKLRDDDDRVGAVFDIDLVEDAVGWGLDELPEAEEKKK
KPKGEAGLPHSVGGLMSSLDAIELLAALQLTEQQKLQLIEKLKSFLIALF
QVIDNEGAKRNNDIHRKMIQAMANEGADFPWDERFTKFKGLLDTTATNLK
ILTHPDRKALLLPLLKRPELMMADYEEWVVSEGASIAMGDQPVEREVVKT
SASKVLDELRSIKQRSAEFLRLQLGVDSKWSQINDAFWSVIVKSDRRVLC
LADLSPIADAGGWQQSELLAVLGLLGAPKAALLRMELRAPDGTEVPAEEV
SQKLAAWWKSKTMTDAEWKAWASQYAVSWSPVVAQGAAK
>Rfer_3600 uracil-DNA glycosylase
MFASDVPRLTGWAPERWPVAADWRPVVDRFLTSETGRALERFVRARLAGG
AVIYPQQPLRALALTPLAQVKVVILGQDPYHGPGQAEGLAFSVAPGVRPP
PSLCNIFREIARDPLLSPGNLIPHGDGSLVAWARQGVLLLNSCLTVEEGQ
PASHAGRGWEALTDEVVKAVASIDNPVVFLLWGAHAQAKQRLIAATARQG
GRAAADHLVLTANHPSPLSARRPPLPFLGCGHFGLANAYLLQHGCAPIAW
>Rfer_1227 DNA polymerase III, alpha subunit
MACSLETVVPATEPASVPAYCELHCLSNFSFGRGASHPEELVARAAALGY
AALALTDECSVAGVVRAHTEAKKLGLKLLPGAEFAVTQADGAGGGALEAG
FRLVALPHDLQAWGDLCEFITQARRAAPKGQYRLLWQDAPWALLGGCEVL
LGLPSALHFEAACAITTRARALFGSNLWLLVELLLAPDDTLQGQRLQQLA
RLTGVPLVAAGNVHMHVRSRKPLQDVLSAVRLGQPVFDCGRALQPNAEAH
LRSRQRLAAIYSPDVLANTLTVAARCTFSLDELRYQYPLETVLEGLSAAQ
TLRRYAAEGALNRYPQGTPASVQQQLDHELALITELHFEMYFLTVHDIVR
FARSRHILCQGRGSAANSAVCYCLGVTEVDPSRMNMLFERFISRERNEPP
DIDVDFEHQRREEVIQYIYAKYGRERAALSAVVISYRPRSALRDVGRALA
VPEALISALAKEHPGMYSRTVLVERLQSALALLAADVAPPAECLQLWLDL
STQLQRFPRHLSQHPGGFVLTRGKLTRLVPVENAAMPERSIIQWDKDDLD
AMGLLKVDVLALGMLSAIRRCLDLISVQRGTPFSMQDIPPEDLATYDMIC
QADTVGVFQIESRAQMSMLPRLKPRCFYDLVVEVAIVRPGPIQGGMVHPY
LKAREHPEQVPYPSPALQEVLKRTLGVPIFQEQVMQIAMAAADFSAGESD
SLRRSMAAWKRQGGVHKFYDRLVGGMLKNGYSLEFAEQIFKQIEGFGEYG
FPESHAASFALLVYVSSWLKRHQPACFLAALLNSQPLGFYSPSQLVQDAQ
RHGVGVRPVDVTRSDWDCTLEPAKSTKLLGSDPNSGAAQLPDVCRSPFVR
LGLRQVSGLSESAAQRIVAARVEAPFTSTEDLALRCALEAGDLKALASAD
ALASLSGHRRQQVWDAAAQQNAPGLLRAVPVAEAALQLPAASEGEEVIFD
YAALGLTLRSHPLLLLREQLSKMRLMTAAQLRDLPNGRLARACGIVTMRQ
QPQTAKGVIFVTLEDETGQVNVIVWKSLKERQRPALLRSRLLAVYGTWQR
DVESGGDVCHLIAGHLQDLTPLLGGLTTQSREFC
>Rfer_2266 transposase IS116/IS110/IS902
MGQVIARMVHAEPGEFPCLLVSPTSPIPSARTALPAPFPFRPNMRFVPIR
DVEQQSVLALHTVRQGFVKARTAQANQIRGLLSEFGLIIPQGIWYIQSGV
PELIEDASNELPGSFRLLIQRLLDHFKILDTRVDELESQIVKWHRQSSAS
SNLAQVPGIGPITASALVASLGDTKNFDSGRQVAAWMGLVPRQHSSGGKQ
NLLGISKRGNSYLRSLLIHGARSVIYNGKDKTDSTCRWINEIVSRRNNNV
AAVALANKNARIVWSLLTHDREFRPDYTREAVGV
>Rfer_2877 Exonuclease VII, small subunit
MTKSLKSRFFLRNFPDCMASTPKTVSTTPASFEAAQEELEQLVARLESGD
LPLDQLLSQYQRGAELLKFCRDRLEAVESQIKVLDQGTLKTWTPE
>Rfer_1059 N-6 DNA methylase
MLTGELRSQIDAIWNSFWTGGISNPLEVMEQITYLLFLRRLDDLHTLEEN
KSVRLGKPMERRTFPEGPDTKGRDYNDLRWSRFKNFAPAEMYTVVGEHVF
PFLRSMGGDGSTYAHHMKDARFTIPTPALLAKVVDLLDHVPMEDRDTKGD
LYEYMLSNIASAGQNGQFRTPRHIIRLMVEMTAPTAKDVICDPASGTCGF
LVATGEYLREKHPEILRNPASREHFHHGMFHGFDFDNTMLRIGSMNMALH
GVDNPDIRYQDSLAQDHAGDEGRYSLILANPPFAGSLDYENTAKDLLAIV
KTKKTELLFLALFLRLLKPGGRAAVIVPDGVLFGSSKAHKELRRMIVEEQ
KLDAVISLPSGAFKPYAGVSTAILLFTKTNSGGTDNVWFYDMKADGWSLD
DKRQPLLSDDKLSLQPFQDGHSQLSEAEHTKNNLPDVLARWGQRASSELE
RDRTEQSFCVPKGDIVGNDYDLSINRYKEVVHAVSEHLPPKEILARLAVL
EAEIQAGMKELAGMLG
>Rfer_1273 NUDIX hydrolase
MLDREGFRPNVGIVLLNQKNQVFWGKRIRTHSWQFPQGGIDRGETPEQAM
IRELHEEVGLLREHIRIVARTRDWLRYEVPDRYIRRDARGFYKGQKQIWF
LLQLVGHDWDLNLRATDHPEFDAWRWNDYWVPLDAVVEFKRGVYEIALTE
LARYLPRNELRNRFLRQGVRPHEQETTFDAVPGANFELPPGGSFEPNPQT
SYGLDASGKPHET
>Rfer_1832 DNA mismatch repair protein MutS
MQNEKTQSKKPSPVPAEHSPMMAQYFGLKADYPDTLLFYRMGDFYELFFA
DAEKAARLLNITLTQRGQSAGQPVVMAGVPFHSVDTYLARLIKLGESVAI
CEQVGEVTGKGPVERKVVRVVTPGTLTDLELLSDKSESMLLAVHQGPRNT
CGLAWLSVTQGEVHLAECAVDDLAQWVLRIAPGEIIFSAGTTPTFEARLR
GAPLAGAVSVSVRPDWQFDAGLGEKKLLAQLQAASLAPWQAQDLPQAHAA
AAALLGYAEHTQGQALTHIQSVRVQRSDELIDLPPTTRRNLELTQTLRGE
DQPTLFSLLDTCMTGMGSRLLKNWLLEPRRDRGEAQQRLNAIAALQSGDA
HTSRAGVWRQLREQLKGSTDVERITARIALRQVRPRELVALQLTLQKTEL
LTHTTRGLEVYLTQISGHLLAPEACADLLARAIDPEPAVLVRDGGVIASG
FDAELDELRAIQTNCDGFLLDLEVREKARTGIANLRVQFNKVHGFFIEVT
QGQVDKVPDDYRRRQTLKNAERFITPELKAFEDKALSAQERALAREKWLY
EQVLDQLQVFVPALTRVARALATLDALCALTERSLTLDWCAPQFVKEPCL
DITQGRHPVVQARLAETSSGAFIANDTRMGPKQRMQIITGPNMGGKSTYM
RQIAVIVLLASMGSYVPASACRLGPIDAIHTRIGAADDLANAQSTFMLEM
LEAAQILIAATPNSLVLMDEIGRGTSTFDGLALASSIATQLHDKTQAYTL
FATHYFELTEFPAQHHAAINVHVSAAEAGRDIVFLHEIQPGPASKSYGIQ
VARLAGMPAAVLNQARQTLAALESQATQNQAQVDLFAAPPATETAADSAI
ETAVAALNPDNLSPREALEALYQLKKLASGKA
>Rfer_1350 HhH-GPD
MSATSTTAAVAAAPAYWSDACKHLMKKDRVMKRLIPQFGDACLQTRGDAF
VTLARSVVGQQISVKAAQTVWNRFALLPKKITAANVLKLKVDDMRAAGLS
VRKVEYLVDLALHFDSGTVHVETWETMDDEAIIAELIAIRGIGRWTAEMF
LIFHLMRPNVLPLDDVGLINGISKNYFSGDVVSRSDAREVAAAWAPYCSV
ATWYIWRSLDPLPVDY
>Rfer_1457 DNA polymerase III, subunits gamma and tau
MSYLVLARKYRPRNFTEMVGQDHVVQALTNALTTQRLHHAYLFTGTRGVG
KTTVSRILAKSLNCQGPDGQGGITATPCGVCQACIDIDSGRFVDYTELDA
ASNRGVDEVQALLEQAVYKPVQGRFKVFMIDEVHMLTGHAFNAMLKTLEE
PPEYLKFVLATTDPQKVPVTVLSRCLQFNLRPIAPETIREHLQTVLQAEK
VAADVPSLRLLARAAHGSMRDALSLADQAISFGAGQIEEATVRQMLGSVD
RSYVFRLLEALAQGDGKTVVETSEALRLNGLSAASTLEEMSMVLQRMAVV
QAVPSAVESDETDPQALDVARLAALMPADETQLLYSICLHGRAELGLAPD
EYAALTMVLLRLLAFKPRAGNLPVAEKKTLTDAPRGLAAAAPRPVPALGQ
VVTEVPVFEKKETPAPVEYSQSAIKIVANAEAQINTEEKVESEVHAEAEA
LQPPPTGQHLHVVQLPVAAGQSLTSEQNRPLAPVEYAQDAAKIVAIPVRV
QADSRAEAVAGQSAASLLLPTEEGEFWHGIVRQLIAREAINAMVRELALQ
SQLVARDTDQWLLRVERESLNQSGSRDRLATALQAAGYAVRLVVEIGRVT
DSPARRNAALVAERQLAAEKIIFDDPFVQAMMRDFGAKIVPGSITPG
>Rfer_4010 type I site-specific deoxyribonuclease, HsdR family
MLTESAIETFAIKLFERLGYVYLHGPDIAPDSDGPERSSYAEVLLPGRLA
QAAGRINHKLPRDVVEMALKEVQRAHSPDLLASNEAFHRLLTEGVPVSMQ
KDGDTRGERVWLIDFARPENNEFVVANQFTVIENHQKKRPDLVLFVNGIP
LVVIELKNAADENATLKSAYQQIETYKQAIPSLFTANALVVISDGLEAKA
GSISASLSRFMAWKSADGKAEASHLVSQLEALILGMLNQGTLLDLVRHFI
VFEKGSKEDPNTGQITISTIKKLAAYHQYYAVNAAVASTLRAADMGGPLS
VRENPASYGLPGIADQPKSDMKAGVVWHTQGSGKSLSMVFYTGKIVLTLD
NPTVLVITDRNDLDDQLFNTFAASKQLLRQEPVQAKDREHLKALLKVAAG
GVVFSTIQKFQPDEGNVYDQLSNRPNIVVIVDEAHRTQYGFAAKTVDEKN
ADGMVIGKKVVYGFAKYLRDALPRATYLGFTGTPIEKTDVNTPAVFGNYV
DIYDIAQAVEDGATVRIYYESRLAKVSLSEEGKKLIAELDEELEQDELTE
TQKPKAKWTKMEALIGSEQRVKNIARDIVGHFEARQEVFAGKGMVVSMSR
RIAADLYDEIIKLRPDWHADELSKGVIKVVMTAASSDGPKLAKHHTTKEQ
RKLLAERMKAEDDPLKLVIVRDMWLTGFDAPSMHTLYIDKPMKGHNLMQA
IARVNRVYKDKPGGLVVDYLGIAADLKEALSFYSDAGGKGDPTLLQEQAV
GLMLEKLEVISALYHGFAYEHYFGANTAQKLSLILAAEEHILGLDDGRKR
YINEVTALSQAFAIAIPHEQAMDVKDEVGFFQAVKARLVKYDSVEGERSN
EEIETTIRQVIDQALVSEKVIDVFDAAGIKKTDISILSDEFLAELKGYEH
KNVALEVLKKLLNDELKIRAKRNLVQSRSLMEMLEASIKKYHNKILTAAE
VMDELIKVSKEIVAADDEARHMGLSDFEYAFYTAVANNDSARELMQQDKL
RELAVVLTQRVRENASIDWTIKENVRAKLKVIVKRTLRQFGYPPNMELLA
TETVLKQAEMIANELTQ
>Rfer_3028 DEAD/DEAH box helicase-like
MTDLMTELTPDTLPMAFAQLQLAAPLARAVADMGYETMTPIQAQAIPVVL
QGRDVMGAAQTGTGKTAAFALPLLQRMLKHENSSTSPARHPVRALVLLPT
RELADQVAQAIKDYAVHTNLRSAVVFGGMDMKPQTLELKKGVEVLVATPG
RLLDHIEAKNCVLNQVEYVVLDEADRMLDIGFLPDLQRILSYLPKQRITL
LFSATFSSEIKRLASSYLQDPVTIEVARSNAAASTVEQHFYSVDADDKRH
ALHQILKSRGMKQAFVFVNSKLGCARLARSLEHEGLKTTALHGDKSQDER
LKALEAFKSGEVDLLVCTDVAARGLDIKDVPAVFNFDIPFNAEDYVHRIG
RTGRAGAAGLAVSFVAKSDIRLVADIEKLLNTKIELEAVEYDEDVPDIRK
QGRINDGHRMYAEGAQNDSRHGAHRSGSLRDVAHEGQYARPERPPRRDFT
RPLSAPRDPFFDKPYEPAVVAAEAPSWEAAATRQGGRSASANIKPKRRVA
ALFKSA
>Rfer_0032 N-6 DNA methylase
MNDEEQQYLNNLDKQLWAAADRLRAAVNPSEYMHVVLGLVFLKYISDAFK
ERRLELQAAFQDPANDYYLGTDADELIAQELEARDYYTETNVFWVPALAR
WDFLKDNAKVAIDTVLTVKNGKTFEYKFKGIGRLLDDALEAVEKDNPKLK
GVLDKSYARWRVDEALPGLIDEFSKIPFNHGALKAKDILGHIYEYFLGEF
SIAAGKRGGEFYTPKSIVSVIVEMLEPFEGRVYDPCCGSGGFFVQSERFV
LEHGGKIGQLSIYGQEFNPTTWRLASMNMAIRGLDFDFGKEPASTYTRPQ
HPDLRADFIMANPPFNMKAWKEGVKDDDPRWKYGVPPDGNANFAWMQHMI
HHLAPHGSMALLLANGSMSSNTNNEGEIRKALIEADLVECMVALPGQLFT
NTQIPACIWFLTRSKAERKAKRSRHGEVLFIDARQLGYMKDRVLRDFKPE
DLAKVADTFHAWQRGVGYADEAGFCKAATLADIGKADYVLTPGRYVGAAA
QEADAEPFEDKMARLTAALGDQFKESARLEAAIRKNLAGLGYEV
>Rfer_0012 putative exonuclease, RdgC
MERVQVFKNIIVYRIGAGWSATVAQMEEGLEADRFVECGASQEKSVGWVE
PRGEAHGLLVEAVGGQLILKLMVESRALPGSVVTRKVKERVAQIEASTGR
KPGKKEIRDLKDDIRLELLPMAFTKQAAVLIWIDPQARWLVIDASSQARA
DEVVTLLVKSLTGLAVTLLNTQVSPTAAMSEWLISQEPPAGFTVDRECEL
KAADESKAVVRYARHPLDNEEVKQHVVGGKLPTRLALTWDSRVSFVLTEG
LQLKKLTFLEVVFEGAAAGKDDGFDADTAIATGELRKLLPDLLQALGGEV
ALA
>Rfer_2580 replicative DNA helicase
MSAVLSAVPFDYGQDAQVAQLRIPPHSIEAESSVLGGLLLDNGAWDRVND
LLTEGDFYRYEHRMVFIALGALINATKPADVITVFEQLQNQGKAEEIGGL
AYLNSLAQYVPSAGNIRRYAEIVRERSILRKLVAASDEISTNAFNPKGRA
VAAILDEAEQKIFNIGEEGARTRQGFQAMDSLVVALLDRVQEMADNPNDV
TGVPTGFYDLDRMTAGFQAGDLVVLAARPSMGKTALAINIAEHVALNEGL
PVAVFSMEMGAAQLAVRIVGSIGRINQGHLRTGKLTDEEWPRLTEAIEKL
RTISLHIDETAGLTSSELRANARRLSRQCGKLGLIVVDYLQLMSGSNSDG
ENRATELGEISRGLKMLAKELQCPVIALSQLNRSVETRPDKRPMMSDLRE
SGAIEQDADIIMFIYRDEYYTKDACKEPGVAEIIIAKQRNGPTGVVKLAF
LNTITKFESLASGGSGDF
>Rfer_1354 phage integrase
MSLTDTAIKKAKPGDKPVKLSDGKGLYLLVNPVGSKLWRWKYRFLGKEKV
MSLGAYPDVSLAQARDGMGAARKLLASGTDPMAQRATDKITKQASAENSF
QSVALLWWDHWHGAKSARHADDVMRRLKADVFPAIGARPVSEIQAHELVG
MVQTISKRGALDIAKRALQTSGQVFRYAVAHGLAQRNPASDIKPSDVLAS
RKAANYARISAKELPELLRHIEGYAGAAVTRLAMKLMALTFVRTSELIGA
RWAEFDLEARRWDIPASRMKMKTPHIVPLSTQAVNVLQTLQLVSGRGTLL
FPGERDHEKSMSNNTILGALDRMGYKGRMTGHGFRGVASTLLHEMGFDHA
HIELQLAHQERNEVSAAYNHATYLKQRTKMMQHWADYLDSCTTGQVLAFQ
RAAA
>Rfer_3955 DNA topoisomerase III
MCERPGAREKLDCSQMKTLIIAEKPSVAQDIVRALTPVAGKFDKHDEHFE
SDSYVVTSAVGHLLEIQAPEEFDVKRGKWSFAHLPVIPPHFDLKPVDKTK
TRLNAVVKLAKRKDVDQLINACDAGREGELIFRLIEQYAGGAKPLGKPVR
RLWLQSMTPQAIRDGFNTLRSNEQMLPLADAARCRSEADWLVGINGTRAM
TAFNSRDGGFFLTTVGRVQTPTLSVVVEREEKIRAFVSRDYWEVHATFAA
QAGDYPAKWFDPQWKKAAANAAAGNLEEADPELKADRLWQQREAQAIADA
VRGQTASVTEESKPTTQASPLLFDLTSLQREANGKFGFSAKTTLSIAQSL
YERHKALTYPRTDSRALPEDYLPVVKQTFEMLSKSAMRHLAPHALTALNN
NYIRPSKRIFDNSKVSDHFAIIPTLQAPSGLSEAEQKIYDLVVRRFMAVF
FPNAEYQITTRISVAAGHSFKTEGKVLVKPGWLAIYGKEAVDEVTDRDGA
KDGDKGQRLVPVQAGERVTAQTVEARGLKTRPPARYTEATLLGAMEGAGK
TIEDDELRAAMHEKGLGTPATRASIIEGLLTQKYMLREGRELIPTASAFQ
LMTLLRGLDVKELSKAELTGEWEHKLALMEHGQLSRAEFMAEIAAMTERM
VKQAKEYDRDTVPGNYATLTAPCPNCGGIIKENYRRYTCTGKTGAEEGCG
FSFGKTPAGRTFEVAEVEQFLRDKKIGPLEGFRSKAGWPFTAEMVIKFDE
ESKNYKLEFDFGDDKKGEESGELIDFSGQESLGACPKCGAPVFEHGKNYV
CEKSVPTDAQATPSCDFKTGQIILQQPIEREQIAKLLATGKTDLLDKFVS
MRTRRGFKAMLAWDAEAGKVNFEFAPSKFPPRKTAAKSAAGASVAAKTGA
ARAATTGAAAKKAAKKVASPKAAAKASAKTPRKAAVKKVASPAAGLQPSA
ALAAVIGAEPVARPQVIKKLWDYIKANNLQDAVNKRNINADAKLLAVFGK
PQVTMFELAGIVGKHLA
>Rfer_4203 Integrase
MKQRPRIYYSDNQKALMWERRKKGESLQQIAQLFDRNHSSISRILGETGG
IRPAQRCRSQFALSLAEREEISRALAVGRSIRSIACLLGRAPSTVSREIQ
RNGGQGCHRATLADQAAWDRACRPKTCKLVEKLKLASLVAGKLQLQWSPQ
QIAGWLKQAYADDENYQVSHETIYRSLFIQARGALKKELLQHLRRTRTMR
RSRHHTQKTDNHGKITNAVSISERPASVEDRAIPGHWEGDLLFGSLNNQI
ATLVERQTRYVMLVKVAHKDTQTVINALIQKARKLPQELYKSLTWDRGHE
MADHKRFTLATDISVYFCDPQSPWQRGSNENTNGLLRQYFPKGIDISNYS
QAQLNAVARKLNERPRKTLNYETPAERFSQLVASTG
>Rfer_4007 Restriction endonuclease S subunits-like
MNELLEASVEQLPDGWSLVTVGQLVNEGVIAKPLDGNHGEIHPKGSDFVS
DGIPFVMATDINAGKVDLVNCKFITKKQADSLAKGFAIPEDVLLTHKATL
GRTAIVGELRTPYIMLTPQVTYYRTIKKDRLHNRFLKYYFDSPFFQDTLV
NHGDSGSTRAYVGITAQRDLPIILPNLVREQESIAAVLASLDDKIDLLHR
QNQTLEAIAETLFRQWFVEDAQEGWDERPLSSIANFLNGLACQKYPPTND
LEKLPVLKIRELSSGISETADWATSQVKPGYIVEAGDVIFAWSASLMVKV
WDGEKCVLNQHLFKVTSDEFPKWFYLRWCKHHLAEFIAVAASHATTMGHI
KRGDLDAAMVLVPPPPVLETMSRQMQPLLNKQIAIARQRKTLEKLRDTLL
PKLMSGEVRVAY
>Rfer_2194 putative primosomal replication protein
MNHVANQLVLTACIAGIDSLRYTPAGLPALNIRLEHESEIQEAGQIRQVK
VTLKAVAFGAMAERLAKQAIASAWRFNGFLATPRNGKHVVFHIQEFQQD
>Rfer_0760 DNA polymerase III, delta subunit
MQLAPHQLANHLQKGLKSLYTVYGDEPLLVQEAADAIRAFARTQGFTERS
SHTVAGAHFDWSEVLAAGGSLSLFADKQIVELRIPSGKPGKEGGVALQQL
AEQARGNESTLTLVMLPRLDKLGKGSAWFGALESFGITLAVEPVERNALP
AWIAQRLAVQGQRVAAGEAGQHSLQFFADRVEGNLLAAHQEIQKLALLYP
PGELTFDQIESAVLNVARYDVFKLSDAVLSGQVVRVQRMLDGLQAEGEAA
VLVHYTLAEDIRALKRVKDAMNRGSPLPMALREQRVWGTRERLFERVLPR
LGDAALASLLRAAHQVDGVVKGLKSPDWPTEPWAALQQLAFDLCRECARV
PGKR
>Rfer_1306 nuclease (SNase-like)
MNQTILGHEPRKTVRFLLLVLFMAATHVQAKTIFTGNVSFVSDGDTLWVR
PDAGGPPRKLRIDGIDAPEICQTGGEAAREVLRQLVLHQHVEVTIRRNDD
YGRGLARIRLDGQDLGAQMVQAGQAWSYRWRRALGPYAAEEAVARQSRSG
LFAADTTELPRDFRQRHGSCHDAPR
>Rfer_3577 DEAD/DEAH box helicase-like
MSTTQTQAATATPSSSNKRFESLALNPATLANLQQLGYLEMTPIQAASLP
AALAGKDLIAQAETGSGKTAAFALALLERLNPRRFAVQALVLCPTRELAD
QVTIEIRRLARATDNIKVVTLCGGVALRGQRASLEQGAHIVVGTPGRVMD
HLAREYLNLEALNTLVLDEADRMLDMGFFDDMATVAKQCPKERQTLLFSA
TYPEGIEKLAQQFMREPLRVQVAAQQTESLIEQRFYEVTRANRFEAVALL
LNHFRPISTLAFCNTKQQCKDLVTYLQAQGFSALALYGELEQRERDQVLA
QFSNRSASVLVATDVASRGLDITQLEAVINVDITPDPEVHVHRIGRTGRA
GESGLALSLASMNEMGSVGKIEQYQKRESVWHKLDELKPTGQGPLLPPMV
TLQILGGRKEKIRPGDVLGALTADAGYSREQIGKIVVTEFTTFVAVQRDI
ALAAMQKLNAGKVKGKSVKVRLL
>Rfer_1138 transposase, IS4
MHQGKLVFAQLMLYVPLSTFRRCVADHRGEHKVKDFSCLDQFFAMAFAQL
TYRESLRDIEVNLRAQVRRLYHMGFRCQTISRNTLANANATRRWQIYADF
AQHLIGLARPLYATEPFGLELDAAVYAFDASTIDLCQSVFAWAPFRSTKA
AIKLHTLLDLRGNIPSFIHITDGKTHEVNVMDDLVLEPGAFCLMDRGYLD
FARLFVIHEAQAFFVTRAKSNTKFKRRYSHPVDRINTTVLCDQTGVLTTY
YAGKDYPTTLRRVVVKDDTGKRLVFLTNNFALKPELIADLYRQRWQVELF
FKWIKQHLRIKVFFGTSENAVKTQIWIAISTYLLIAITKKRLRLDHHSLY
EILQILSLSMFETIPINQLLMPPSTNSEPDFEPNQLALL
>Rfer_1331 transcription-repair coupling factor
MSRIGALATTCPAFMELPKLIPGKRFTLPRPVGSADALLLAQLGLREKSQ
HKVTAIITADALDAQRLIDEMAFFAPELRCVLFPDWETLPYDTFSPHQDL
ISERLATLWRISQRNKETGADVVLVPATTALYRLAPPSFLAGYTFHFKVK
QKLDEAKLKAQLTLAGYSHVTQVVSPGEYAVRGGLIDLFPMGSAVPYRVD
LFDDEIDSIRTFDPDSQRSLYPVPEVRLLPGREFPMDDEARARFRNRWRE
LLEGDPTRSRIYKDIGNGVATAGIEYYLPLFFDDTATVFDYLGEAATVVL
HGDLEPAFAHFWQDTRERYRLVQGDPERPVLPPGALFLSTEQFYERVNQH
AQLALRPALDTASAYAEFEALPPLSVVRGAEDPLARLKAHIRNTQQRTLV
LAESEGRRASLLDFLHSSQFDPPAFDSLAEFERSDEPIGIATSSLSAGFG
WLEAGIDFVTETELFAAGPTTRRRKKQEQVSDVEALIKDLSELNIGDPVV
HSAHGIGRYRGLINLDLGNRLANGEPEVQEFLHLEYADKATLYVPVSQLQ
LISRYTGVAADEAPLHKLGSGQWDKAKRKAAEQVRDSAAELLNIYARRAL
REGHAFRYSAGDYEIFANDFGFEETADQSAAIHAVIQDMISPRPMDRLIC
GDVGFGKTEVALRAAFIAITGGKQVAFLAPTTLLAEQHYQTLVDRFSKWP
VKVAEMSRFRSAKEITAAMKGIADGTIDIVVGTHKLLSKDTHFKDLGLLI
IDEEHRFGVRHKEQMKALRAEVDVLTLTATPIPRTLGMALEGLRDLSVIA
TAPQRRLAIKTFVRTEGAGVIREAVLRELKRGGQVYFLHNEVETIENRRA
KLEELLPEARIAVAHGQMPERQLEAVMRDFVAQRFNLLLCSTIIETGIDV
PTANTIVMARADKFGLAQLHQLRGRVGRSHHQAYAYLMVPDLEGLTKQAQ
QRLDAIQQMEELGSGFYLAMHDLEIRGAGEVLGENQSGNMLEVGFQLYNE
MLSEAVRCLKAGIEPDLLSPLNVSTDINLHAPALLPNDFCGDVHLRLSFY
KKLATANNTNQIDALLEELVDRFGKLPNQAQTLIDVHRLRVLAKPFGVVK
VDAAPGVITITFKKNPPIDPMKIIAMIQKNKHIKLAGNEKLRIERELPEA
KDRAQMVRDVLRNLGQPVAPVATIA
>Rfer_1342 integration host factor, alpha subunit
MPALTKAQLAELLFEKIGLNKRESKDMVDAFFDLVADSLLKGEDVKISGF
GNFQIRTKAPRPGRNPRTGETIPIQARRVVTFHAGYKLKEQIQDQELVPL
AP
>Rfer_2897 conserved hypothetical protein
MAEIAKNHPVDQAWDRVMGQIRAEMAARGVHASRTVVLLPYAQLMQQARS
AWLRALEGATPGVNSPAHFLPRFETSMNWTRSLGGFEPGPDDLQLDCARD
VLTAASLLARAGLAPYQNLLAARLMEAAWSLARLAASVAPTARAQWGLRL
DSLLVSGLDAPVLALEAALARVALAWVASSSYPSDRLFAARPDLLVVLQG
FQSEPLALALQHGLGERVVVLALQQEDTPTGAAAGADTVALHAAQDAEDE
AQRAAACVLAHLAAGRSPVALVAQDRVLTRRVRAMLEERGVAVRDETGWT
LSTTRAAAALMSLLRASAWDASTDGVLDWLKNAPAFDPQLVTQAEASWRR
GAVREWRAVPLGDALQRPVQALRDSLQSGRPLARWLVDLRAVLQSAGQWT
GLMQDAAGQAVLQALRLHEGAHTEFADVAVSMSQSEFTAWVSQSLEAASF
LPEHPENSAPGQVVILPLSQLLGRPLAAVVLPGCDDVRLPMSPEPTGPWT
PAQRELLGLPARAQLAAASRAAWQYALQFPHVDVLWRQSEGGEHLMASGF
VQELQLGQIGAMAADPRPLRALTAKPGAMPSPRGDALALTRLSSTAYEDL
RRCPYRFFALRQLKLQESDELDTELGKRDFGNWLHTVLKLFHEALNESPA
PDFVGRLAMINAAAEQATLALGLSSSEFLPFAAAWPRVRAGYLEWLAGHE
ASGASFVAAERWRETALGHLTLVGKIDRIDRLQDGSALVIDYKTEPRAST
AQRIKDAPEDTQLAFYAALLGDDTLAAAYVNVGEKDGTKTYEQSDVVALR
DLLLAGIATDMARIADGAAMAAMGEGKACEFCAARGLCRKDFWDVA
>Rfer_0028 type I site-specific deoxyribonuclease, HsdR family
MVESDLEQLALTWFQDTGWDYRAGPDIAPDSDSPQRSDYRQMLLQGELRE
ALSRLNPQVPAAVLDDVAHQLSKPDHPSLIQSNRAFHEALVGGVPVEVEV
NGERRGDRVVLVDFDTPERNRFLVVNQFTVQGSKQPRRPDLVCFINGLPI
AVIELKNLAAEQVGVQDAFHQLQTYKDELADLFVTNEALVASDGLHARIG
SLTASFERFLPWRTVKNENDRPLLEFELEKVVRGFFAPALLLDYLRYFVL
FEMADGQVVKKIAAYHQFHAVRAAVKAAVIAATPPATNAAQEQWASYAER
VKPGSRMGGIVWHTQGSGKSISMVCFAAKLMQQPEMHNPTLVVVTDRNDL
DGQLFQTFVGARSLLREQPQQAGSRDELRALLAGRPSGGIIFTTVQKFTP
DAGEEVFPLLSERNNIVVMADEAHRSQYGFRAVLDKKTGKYKYGFAKHLR
DALKNATFVGFTGTPIEAGDHDTRAVFGEYVSIYDIQDAVDDGATVPIFY
ESRLAKLNLNQVEMEKLNADVEDVFEDEEDAALIEAEKTRWAALEKLVGA
KERVDLVAADIVQHFEARNTAVAGKGMVVAMSREICARLYAAIIKLRPDW
HSDDPAQGAIKVVMTGSAADATLLQPHIYNSAAKKLLERRFKDATDPLKL
VIVRDMWLTGFDVPCLHTMYIDKPMRDHNLMQAIARVNRVFRDKEGGLVV
DYIGIAAELRKALRTYTESKGKGQPTLDATEALAKLQELMEVARHLLHGF
DFSAYRTQATTLLLPAANFVLGLDDGKKRWADVVLAITKAFSLCGTLDDA
ALLREEIAFFQAIKAVIAKATTSDAKLSEEGRNAVLKQILDNAVVAEGVE
DIFKLAGLERPDIGILSDAFLEEVRQLPQRNFAVELLQKLLNDQVKSRMR
TNVVMERKFSERLQAALNRYLSRAVESAQVIEELIAMAKEFREAALRGNK
LGLNTSELAFYDALTDNESAVREMDDEVLKKIAVEITEKLRNSTSVDWQK
RESVRARLRNLVRITLRRYKYPPDMQEEAIRLVLEQAERLSDAWTK
>Rfer_2830 phage integrase
MLTDAECKNATCPPDKARARLACSGGLYLEISPAGSKRWFYKYRKHGKEG
RMALGSYPTVGPKKAREARDAAKSQKSDGADPVQARRVEKLKAARPGGDT
FKAVALEWYGKQSPQWSTSHAERSLRQFERDLFPYIGARPMAEIHPMELL
AALQKVEERGAIETADRVLMLARQVWDYWLPTATVQQRNITEGLKGRLTP
YRGKTFAAILDPVRMGGLMRAIKGYKGGPIVRTALQLTPFLYQRPGNLRM
MEWAELDLEAALWTIPSMKMKRTKLEKEQGEAHVVPLPTQAVALLRSIHP
LTGHGRYVFPGERSHDRPLSDNSVRSALYALGFGKEQSWHGFRASARTML
VDELNIDFNVIEANLAHAVKDANGRSYNRTQYVKQRFEMIQQWADYLDKL
AAGADVIQFKAA