# STOCKHOLM 1.0 #=GF ID DNA_pol3_a_NII #=GF AC PF11490.9 #=GF DE DNA polymerase III polC-type N-terminus II #=GF PI DNA_pol3_alph_N; #=GF AU Finn RD;0000-0001-8626-2148 #=GF AU Coggill P;0000-0001-5731-1588 #=GF SE Pfam-B_853 (release 23.0) #=GF GA 26.30 26.30; #=GF TC 26.30 26.30; #=GF NC 26.20 26.20; #=GF BM hmmbuild HMM.ann SEED.ann #=GF SM hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq #=GF TP Domain #=GF RN [1] #=GF RM 10048037 #=GF RT A 'gram-negative-type' DNA polymerase III is essential for #=GF RT replication of the linear chromosome of Streptomyces coelicolor #=GF RT A3(2). #=GF RA Flett F, de Mello Jungmann-Campello D, Mersinias V, Koh SL, #=GF RA Godden R, Smith CP; #=GF RL Mol Microbiol. 1999;31:949-958. #=GF RN [2] #=GF RM 17532183 #=GF RT Replication-associated purine asymmetry may contribute to #=GF RT strand-biased gene distribution. #=GF RA Hu J, Zhao X, Yu J; #=GF RL Genomics. 2007;90:186-194. #=GF RN [3] #=GF RM 21740522 #=GF RT The N-terminal region of the bacterial DNA polymerase PolC #=GF RT features a pair of domains, both distantly related to domain V #=GF RT of the DNA polymerase III tau subunit. #=GF RA Timinskas K, Venclovas C; #=GF RL FEBS J. 2011;278:3109-3118. #=GF DR INTERPRO; IPR024754; #=GF DR SO; 0000417; polypeptide_domain; #=GF CC This is the second N-terminal domain, NII domain, of the DNA #=GF CC polymerase III polC subunit A that is found only in Firmicutes. #=GF CC DNA polymerase polC-type III enzyme functions as the 'replicase' #=GF CC in low G + C Gram-positive bacteria [1]. Purine asymmetry is a #=GF CC characteristic of organisms with a heterodimeric DNA polymerase #=GF CC III alpha-subunit constituted by polC which probably plays a #=GF CC direct role in the maintenance of strand-biased gene #=GF CC distribution; since, among prokaryotic genomes, the distribution #=GF CC of genes on the leading and lagging strands of the replication #=GF CC fork is known to be biased [2]. It has been predicted that the #=GF CC N-terminus of polC folds into two globular domains, NI and NII. #=GF CC A predicted hydrophobic surface patch suggests this domain may #=GF CC be involved in protein binding [3]. This domain is associated #=GF CC with DNA_pol3_alpha Pfam:PF07733 and DNA_pol3_a_NI Pfam:PF14480. #=GF SQ 49 #=GS Q3AB92_CARHZ/76-190 AC Q3AB92.1 #=GS R6N7H0_9CLOT/84-201 AC R6N7H0.1 #=GS Q97DN0_CLOAB/82-198 AC Q97DN0.1 #=GS Q24PE2_DESHY/83-194 AC Q24PE2.1 #=GS DPO3_CLOPE/89-202 AC Q8XJR3.1 #=GS DPO3_CLOTE/85-199 AC Q895K2.1 #=GS A5I4J9_CLOBH/89-201 AC A5I4J9.1 #=GS A5N837_CLOK5/89-205 AC A5N837.1 #=GS A0Q0R1_CLONN/88-201 AC A0Q0R1.1 #=GS A6TRL2_ALKMQ/92-207 AC A6TRL2.1 #=GS A8MHH9_ALKOO/94-208 AC A8MHH9.1 #=GS Q18BG8_PEPD6/91-213 AC Q18BG8.1 #=GS DPO3_STAA8/92-205 AC Q2G1Z8.1 #=GS DPO3_STRT2/92-207 AC Q5M6H0.1 #=GS DPO3_STRA5/92-205 AC P63984.1 #=GS DPO3_STRP1/92-207 AC P0C0B8.1 #=GS DPO3_STRMU/92-207 AC Q8DWE0.1 #=GS DPO3_STRSY/92-207 AC A4VXT1.1 #=GS DPO3_STRR6/92-206 AC Q8DRA5.1 #=GS Q6F1H8_MESFL/90-208 AC Q6F1H8.1 #=GS Q6MTP4_MYCMS/90-208 AC Q6MTP4.1 #=GS Q3XZ68_ENTFC/94-209 AC Q3XZ68.1 #=GS Q831W8_ENTFA/95-209 AC Q831W8.1 #=GS Q03YC3_LEUMM/93-205 AC Q03YC3.1 #=GS Q5FJN1_LACAC/92-207 AC Q5FJN1.1 #=GS Q74IS3_LACJO/92-207 AC Q74IS3.1 #=GS DPO3_PEDPA/91-206 AC Q03FS8.1 #=GS DPO3_LACPL/91-206 AC Q88VK2.1 #=GS DPO3_LACBA/94-210 AC Q03QS9.1 #=GS DPO3_LACS1/95-210 AC Q1WUF9.1 #=GS DPO3_LACSS/95-210 AC Q38W73.1 #=GS DPO3_LACRD/94-207 AC A5VJD5.1 #=GS DPO3_LISMO/98-210 AC Q8Y7G1.1 #=GS B1YI67_EXIS2/93-206 AC B1YI67.1 #=GS A0A0J1I0J1_BACAN/96-205 AC A0A0J1I0J1.1 #=GS Q5L0J3_GEOKA/105-218 AC Q5L0J3.1 #=GS U5L7T9_9BACI/96-208 AC U5L7T9.1 #=GS A8FDC2_BACP2/97-210 AC A8FDC2.1 #=GS Q65JJ0_BACLD/97-210 AC Q65JJ0.1 #=GS Q5WFT7_BACSK/96-209 AC Q5WFT7.1 #=GS DPO3_BACHD/97-210 AC Q9KA72.1 #=GS DPO3_OCEIH/94-206 AC Q8EQU6.1 #=GS DPO3_CALS4/72-184 AC Q8RA32.1 #=GS R5UBP6_9FIRM/98-208 AC R5UBP6.1 #=GS R7G242_9FIRM/93-209 AC R7G242.1 #=GS A9KMW9_LACP7/95-205 AC A9KMW9.1 #=GS R5K4Z0_9CLOT/97-209 AC R5K4Z0.1 #=GS A3DE49_CLOTH/94-208 AC A3DE49.1 #=GS B8I6E2_CLOCE/94-208 AC B8I6E2.1 Q3AB92_CARHZ/76-190 LLLEDINYLLVQ.KLPRLRGELREAGLTF.DGENII.FETANEIVFDTIKRKKVVETITKFLAKVAP...DYKFIAKFKEEAN.........EVLDWQLEMEEELVQKLWEE...KVAEREGQENKEEVPVKL R6N7H0_9CLOT/84-201 DYYPELVEELRR.RIASLNGTVKDSTARV.KGERLT..VTLAHGGAEILKSKRFDKELSRLIREEFG....KSFQVEFDGVTSIEADSAVYQEHRTIRRVKEER...KKVVE...EIETYESKNFEGKRKDT. Q97DN0_CLOAB/82-198 DEIKDIIFSMSD.KHPVLKSVINNSECKV.ENNTIN..FNFKIAAAEFFKSMKYDKHLQDAIKTLYG....TSYNINFVDDITSEEL.....MLQQEARDQEMLAISKQIKE...AIGSGGISNSSAPKAPKE Q24PE2_DESHY/83-194 .ELKKIISLLAR.KHPLLKSALNNCDFDI.TDQSIQ..LTFKIAVSYLLKGKGYDKIIQEAIKNLYG....AHYTVHFADKVNPED.L....VRLQEATQEKEL...QLIQK...ERLAVPPSPTPAERPKE. DPO3_CLOPE/89-202 QHWNHVCEKIIE.KHPVLKEVLLNSPIVI.EGEKII.IKNGSEFLCTFVNKKHIDREIKGYIKSFFG....INSLVEVKYDESLAN......KNYNDEKLNENK...EIAKK...VIETMKAQAAQEKPVKKE DPO3_CLOTE/85-199 KYWIDIVNSILT.YIPFCKECLISSKRKVIDENTLK.LQYGNDFLYNILKEKNFEKILSSTIKDVFG....VECKVKFILDKSNGK......CNYLDFKEEQEA...LIIKN...IIKESRIEKTIPKKDNNY A5I4J9_CLOBH/89-201 KYWVDIVNLASS.SVPIARDCLLKSKREV.LEDSIN.ITYNNEFLCRFLSKNKFEGKLKSYIRDIFG....IKCNIKLEYDKSFNE......EDYFKTIETMEK...SMIKN...VLSEIKSKEKKVIRKEN. A5N837_CLOK5/89-205 VHWIELTGIMAS.YIPVCREFLEKCSKKV.EGDLLK.ISTGNEFICNLLKNKNIEKLMCRTIRDLFG....VECSVVVNYDKALNI......KDYLEKSEREEK...KYIENIFKYRDEKFRKSSGISSAAKK A0Q0R1_CLONN/88-201 KYWVDIVENVSK.IIPVCKQVLMSCNKVV.EENLLV.IHIGDKFMCNLLQNKNLNKIIQNVISDIFG....VKTIVTIKYNSQLKE......TNYIAVKEQEEK...EIIVS...TLKENKANISSGASKESS A6TRL2_ALKMQ/92-207 QDWNNIIYFLKN.MIPSIKGTLNETSYIL.KDGDLR.ITVSDSFTLKKAKERNVHIQIEDHLKNWFG....LNIKCVLELDEKSAFHV....DDYESQKEKESM...QFVQE...INKASQNSEMVTSNKGKR A8MHH9_ALKOO/94-208 MNWSNILYILQK.NIPSFNSIEGDIDKVI.EGSTLK.IILTSNIVAHKMKDRKIDLQIERYFVEQFN....VGIKCYIDVDTKSKFVL....EEYEKQKEHENS...ALVSQ....IKIQNPMDYGKAENVST Q18BG8_PEPD6/91-213 KYWNNILYILKY.LCPSIAGWYKQVEFLC.LEEELK.IKLPKGIFYERLMKKNVTYVLKTVLSEELGLDLNITIEKAVDEKVNKERLIRINDREMEEKIRALEI...GKVNN....CEENEEESYVIKSDVDE DPO3_STAA8/92-205 KYFGHCIDQTA..LSPKVKGQLKQKKLIM.SGKVLK.VMVSNDIERNHFDKACNGSLIKAFRNCGFD...IDKIIFETND.NDQEQNL....ASLEAHIQEEDE...QSARL...ATEKLEKMKAEKAKQQD. DPO3_STRT2/92-207 AYFSYALDILKS.SHFSIYSLFSNLGIEI.SNNSIS.VKAPAHILRENLHERFIALIADVLSNVGLS...NVSISVLEDK.EASSSLE....EAYETNKISLQE...EAESQ...ARQALQSIVQSSPVPPPQ DPO3_STRA5/92-205 DYYQQAFCEPLC.NSASFKSSFSQLKVHY.NGSQMI.ISAPQFVNNNHFRQNHLPRLEQQFSLFGFG...KLAIDMVSDE.QMTQDLK....SSFETNREQLLE...KANQE...AMQALEAQKSLEDSAP.. DPO3_STRP1/92-207 AYYQEAFEHAPC.NSASFKSSFSKLKVTY.EDDKLI.IAAPGFVNNDHFRNNHLPNLVKQLEAFGFG...ILTIDMVSDQ.EMTEHLT....KNFVSSRQALVK...KAVQD...NLEAQKSLEAMMPPVEEA DPO3_STRMU/92-207 AYYQEAFKQPTC.NSASFKSSFSHLTVSY.TDGKVL.ISAPQFVNNDHFRKNHLPNLEKQFEAFGFG...KLSFDIVSNQ.KMTEEIK....HHFESSRQQQIQ...KASQE...TLEIQKSLEASIPPEEIP DPO3_STRSY/92-207 AYYPEAFTEDLC.QSAGFKALFQPLEVAY.RDGVLW.IKGPETIDTDHFRKNHLPNLVEQYKRFGFG...NLAVDIQVCQ.EMTQQQA....EIFHAQNAEIYQ...QANEE...NLAALEQLAQMAPPPEAA DPO3_STRR6/92-206 SYYREAFSEGPC.ASQGFKSLYQNLQVRA.EGNQLF.IEGSEAIDKEHFKKNHLPNLAKQLEKFGFP...TFNCQVEKND.VLTQEQE....EAFHAENEQIVQ...AANEE...ALRAMEQLEQMAPPPAE. Q6F1H8_MESFL/90-208 EYIEFIKNFKSQ.NKTIIWNFIEAEGFEYDADENLIKFVVDSNELKNQLTTE.LEYCLAKLKQFGFK...ELSYDIQVEDKTEEYIKQ...SLIIEQQTKEQYK...QFAPE...STEKSQNMIISKQKSQKW Q6MTP4_MYCMS/90-208 QYLEFIKMHKSLFNNRASWKLLDIYNFEL.INNQLV.FLVNSQTIKNEISLE.LDYCLAKLNQFGFK...DLSYLINVNEISLDTLDTK..QQINKTYDKPEYE...QQIIK...PIEKKPSVNNSYKNKRPS Q3XZ68_ENTFC/94-209 DYWAQALENQQC.DTPLAQQVLKTQVPVI.KDRKVI.LPIDSTGAISYLKQQYLPLVEELFVSYGFP...KFRIEPEVDE.QQAERVL....KLFEERKQEQAE...AFMKQ...AAESLVVHEQKKKERKEQ Q831W8_ENTFA/95-209 DYWQLALLNSQC.NTPLVQKVLKTQTPQF.EDRKII.LPVDNEAVIPYLKQQYLPIIEELYFSYGFP...KFHIEPKMDQ.QQAAEVL....KKFEEQKLEQAA...AFQQQ...AAESLVKHEQMKKEKQQ. Q03YC3_LEUMM/93-205 SYWHLALQESSL.NHATTQQLASNTILKTIETNHFG.VAVGASILYRALTAEVIDSIATVYHSFGLP...KIKLTPKLDEQLE.........QEIQENVAQHHA...RARED...LQKAIVANEQSKPKVSSE Q5FJN1_LACAC/92-207 DYWKYAVQNSDR.LQPMAREFLADQKPKK.VDGRWI.IQIDNNIIDGMIEQSTLDGLAEEMRNYGFF...NLKFITQLDQ.TSLQNSM....QSLQELHQEHEK...NMQEQ...YENTPDKPKPQPQAKQYP Q74IS3_LACJO/92-207 AYWTYAIQNSTN.LKPAVREFLQGQAPYL.EKEKWL.IPTQNQVVNGLLSEQVLAELNKEFRRYGFF...NIKFTTKVDE.TNIDENL....RSLEQEQAQHES...AMQEF...YEKQPAEPKKKMPVKSTR DPO3_PEDPA/91-206 DYWDWIIKNSGI.QSSLLQVLCDKSIPEF.KDGQLV.VKVDNQITKNFLNDDVLQTLSNTYQKVGFG...PIKIKPTIDD.NTAQERL....QAYHEEKIKRDQ...AIVQK...ATEAIKKAESKKKASDKA DPO3_LACPL/91-206 EYWEWIVQHSGI.KSPLVQSLCNSNVPTY.EDGRVI.LLAENEVIQNFLTNQALGPIESTYHRLGFP...KFSVHTMIDE.SASQAKI....KEFHEQKAKSDQ...ALAQK...AEAAIKKANEKRQKQADA DPO3_LACBA/94-210 DYWEWIVKNSGL.TSNLIQELCQSQVPELDENNRVL.LYAQNEVVKDFLSNQALGPIESAYRRAGFP...KFNIHVMIDE.SKSQAKI....DEFKARQEKTDA...QLAQQ...AAAAIEKANQKRQSQGDT DPO3_LACS1/95-210 DYWKWVVFNSGI.QSSFIQELSRSKVPYL.DNNRVI.LLAENEIVKRFLVDQALGPLESTYHKIGFP...KFSVNTLVDE.TKAQEII....ENIKEQKAKSDA...ELAQK...AVEAIKKQSEQREKSKAE DPO3_LACSS/95-210 AYWEYVVNHSGI.QSSLLHELCAKETPYI.EGRKVL.LVVENDIVKTFFINQAQTTIQAGYKRLGFP...NFAIQPLIDE.SASQKSI....EDFQAKRAVQDA...ERAQA...AAEAIKKNEALKEKRKTE DPO3_LACRD/94-207 .YWQFIINKAIS.DTPMLQQACLQTAPEV.KDGRVT.LVVENEVIKDLLAQKALDKIEKSYQELGFP...KFRIHPFVDQ.SASQAKI....EELKAKHEKADA...ALAAK...AAARIKKNEAAKKTAKK. DPO3_LISMO/98-210 DYWNLIVEPIGK.QSPMIGKLLMEQKPTF.KEPHFIEVAVHNDMEEATIQQRFQTKIIESYGKAGFP...RLAMKMHMLD.QSETDEY....KAFAQAKQEEDQ...KKAAE...AVQVMQKRQAEGQS.... B1YI67_EXIS2/93-206 DYWPYIVEDLAD.ASSAMRSHLSRVLPEY.RDNKLF.IPVRSEPEAGFLKNDLCSEMQLLYGAYGFP...KFVCEPVVQM...DQTEQ....EELRNQVKQEDI...DEAKR...MLELQFKREQSRDDDEGP A0A0J1I0J1_BACAN/96-205 AYWPLCTERIT...FSPMFAYLKKQLPQV.NGVKLL.INVNNELESTALKKNVAKPVGDQYEAFGFP...RFQLDTHIQQ...NTEEM....QKFREQTQQEDR...ERVIQ...AMEEMAKKQAEESSVV.. Q5L0J3_GEOKA/105-218 AYWPLCLAELQE.GMSPLVDWLSRQTPEL.KGNKLL.VVARHEAEALAIKRRFAKKIADVYASFGFP...PLQLDVSVEP...SKQEM....EQFLAQKQQEDE...ERALA...VLTDLAREEEKAASAPPS U5L7T9_9BACI/96-208 DYWKSCIQEIEG.ISPPLIKLLNEQTPKV.QGTKVI.LNVRNEMEGLAIKRKYAGMIANVFQTFGFP...MLTIDTEINADSSSNAEY....EQFLKAKQQEDQ...ERGRQ...AMIDMQKKEAEGDS.... A8FDC2_BACP2/97-210 SYWSHCVEELQG.ISPPIISLLQQQKPSL.SGHKII.IKTKSETEALAIKKKYSPMLQAAFKQVGFP...ELQFDTEIFV...SDQEI....QKFREQKLAEDQ...ERAMQ...ALTEMEKKESEEQEEGPS Q65JJ0_BACLD/97-210 DYWTRCIQELDG.ISPPILALLNDQKPKL.TGNKIL.LKTKTDTEASALKKKYSSLIQSSYRTFGFP...ELQLDTEIFV...SDQEI....QKFREQKMAEDQ...ERALQ...ALIEMEKQDKEAQDDEAP Q5WFT7_BACSK/96-209 SYWPLIANELAR.VSPPLAATLQKQAPTV.NDNKLS.LVAQNEAEAEAIRRKLADPFKDICGQFGLP...VLPLAVAVQQ...SQEAY....DEFVRKRAEEDR...SKVVE...AMLEKQRVEEEMAKQVKQ DPO3_BACHD/97-210 SYWPLIVAKLTN.ISQPLKEMLEKQTPRF.DGKRLV.IQVGNETEAIALKRKLTEPLQQAVQSFGFP...AVQLDAEVKE...SKQAF....EKFVEQRKQEDH...SKVVE...AILEKKKLEQQVEKKMKE DPO3_OCEIH/94-206 IYWKHFIAQTS..LSPAYRDLVLDQAPEV.SNNKIM.LTARNEAEASALKKRLEAKFHDFCLSIGSL...PYTLEVEVKT...NTEAM....QEFRDKKALEDQ...QLVMK...TVQEKEKRDKDKSVPDQQ DPO3_CALS4/72-184 ENWEKVVLELSE.EYPSSLSFLKTCDVAK.EGQNRITVKAPTYAIYEMAKSSKLDFAIREFLRNRYE....LNLDVELIFSEEG........EEIAEKIIEEDI...KAIEE...VIQKDEKSKKEKSRSEEN R5UBP6_9FIRM/98-208 EYKESLVLELEK.KSVLAASMFEQAELHF.EGEKIV.CVELLDSIVSEGKKEYIVTLLEEVLSRRFG....MQAEIRVLYREQEENQS....REYDEQRIQQEI...NAIFE....RRARQKGEILQKP.... R7G242_9FIRM/93-209 EYYDSFLMELDQ.RSVVERNMLQNASYEF.ENGNIL.CLTLTDTIVAQGKKDSLSTYLSDVFEERFH....RPVEIRVLYEK.AKDSK....LKYNEAKLEQEI...EAIREQSQAVKAKKAQELEQKEEKK. A9KMW9_LACP7/95-205 MHSDNILEELND.SSVMNYNILRMAEISF.DGYKM..IFKLPDTFLNQKKSEEIKVFLEPMFEQRFC....IPVDIRFEFY...........ELIEEAKEEEEY...PQARREKAKQNASGSMETSGEVSDEI R5K4Z0_9CLOT/97-209 .YKDSILYDVEK.ISHVGYRLLKRAEWYY.SDDIIT..LAMEDSKLSKSHSIGIKKYLEETYKKRFG....MDIKVGFDYTESDKEML....RRANEQKMKLEI...EAILS...NVHEDADLTLDGKSVDK. A3DE49_CLOTH/94-208 KYWDSILYIVKK.NIALCRGILSGCKWKI.EDKKLY.IYLKTKGT.EILKCKSCDTLIENIIKECFG....LEIKVEFKDFEIDEDKI....NEYIEFKENEEA...KIVTD...TVIKNNEKTQKTEKSEKT B8I6E2_CLOCE/94-208 IMWSELMQMLTS.KVALCRGILHGSKYEI.SGNKII.INLLTSGA.DILKAQNCHTMLEQHIKGTIC....QSVKVEFCDMHVDHVII....EEYVAEKVKNEA...KVVSS...AITALPENQKQKKYEFKS #=GC seq_cons pYWppllpphsp.psshhpshlpppp.ph.cssclh.lhstschhtshl+pptlstlhpphhphGFs....hplcsplpp.ptspp.h....cpappp+tpp-p...phspp...shpthpppcpptppptp. //