# 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 --cut_ga HMM metaseq #=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 15 #=GS 2004230754/3-113 DE [subseq from] 'DNA polymerase III, alpha subunit (gram-positive type) [Mouse Gut Community lean3 ]' #=GS 2004029353/81-182 DE [subseq from] 'DNA polymerase III, alpha subunit (gram-positive type) [Human Gut Community Subject 8]' #=GS EBB94312.1/40-135 DE [subseq from] hypothetical protein GOS_150173 [marine metagenome] #=GS EBV05343.1/116-206 DE [subseq from] hypothetical protein GOS_6963793 [marine metagenome] #=GS ECT21383.1/104-194 DE [subseq from] hypothetical protein GOS_7074135 [marine metagenome] #=GS EBR70124.1/21-111 DE [subseq from] hypothetical protein GOS_7555577 [marine metagenome] #=GS ECD28997.1/68-158 DE [subseq from] hypothetical protein GOS_4025063 [marine metagenome] #=GS EDE43556.1/106-205 DE [subseq from] hypothetical protein GOS_1131202 [marine metagenome] #=GS ECE56046.1/44-133 DE [subseq from] hypothetical protein GOS_6210597 [marine metagenome] #=GS EDG30939.1/24-116 DE [subseq from] hypothetical protein GOS_804124 [marine metagenome] #=GS ECO92716.1/44-133 DE [subseq from] hypothetical protein GOS_3530627 [marine metagenome] #=GS ECR76875.1/44-133 DE [subseq from] hypothetical protein GOS_3873071 [marine metagenome] #=GS ECT87712.1/44-133 DE [subseq from] hypothetical protein GOS_4221824 [marine metagenome] #=GS EDC21513.1/415-504 DE [subseq from] hypothetical protein GOS_1515765 [marine metagenome] #=GS EBS07049.1/44-131 DE [subseq from] hypothetical protein GOS_7495833 [marine metagenome] 2004230754/3-113 EYFDSFLLELDRRSVVERSVLQNSSYEF..EDENILCLTLRDSIVAQGKKEAITTYLTEV.F.RHRFC...-RPIEIKVQY-EKPKESALKYNDVKL.KQEVEEILKNNAAIQKEQAAGEE---- 2004029353/81-182 DYFPQLYAAVRRDIPSINGTLNNAEVRF..ENNTLTINLLNGGK-TLLDSKGFDKALIKL.I.SEEFNlyiSVNYTGTFEVEENSE----EYKAAIQ.DAQEKINRENLQKA------------- EBB94312.1/40-135 --WLDIFDLLD-LSGPSRAFFSNLQIEK..VEDNIIFFKGSDMFAERINKENIQNLIDSL.L.RLGYP...KYQVEIESSD-SA--KNTPSSKWAKQrAEEIKIFKEEI---------------- EBV05343.1/116-206 --------DLLDLSGPSRAFFSNLQIEK..VEDNIIFFKGSDMFAERINKENIQNLIDSL.L.RLGYP...KYQVEIESSD-SAK--NTPSSKWAKQrAEEIKIFKEEI---------------- ECT21383.1/104-194 --------DLLDLSGPSRAFFSNLQIEK..VEDNIIFFKGSDMFAERINKENIQNLIDSL.V.RLGYP...EYQVEIESSD-SAK--NTPSSKWAKQrAEEIKIFKEEI---------------- EBR70124.1/21-111 -----------DLSKSERYWLEQVNFEI..DNGSLSIFVGSDFVKSSIEKKLYKKIKKTF.NtSTGFK...----ECVFVLDKNMKKDIQAYEFEEK.NEDLLKNQEEIKKVQ------------ ECD28997.1/68-158 KHWPEVIENVKQKRRLTWSLLSASAKILsvDDTTITIAVSNSGAKDSFIRSASDAILSQA.F.QEVAG...-ITKRIEIQVDSAANVVIPDFVEDSE.--------------------------- EDE43556.1/106-205 KHWPAVIENVKQKRRLTWSLLSASARILsvDDTSITIAVSNSGAKDSFIRSASDAILSQA.F.QEVAG...-VTKKIEIQVDSAADVVIPDFVEDSE.SKPQLSAEE------------------ ECE56046.1/44-133 ------------LSKTERYWLEQVNFEI..DNESLSIFVGSDFVKSSIEKKLYKKIKKTFnI.STGFK...----ECVFVLDKNMKKDIQAYEFEEK.NEDLLKNQEEIKKVQ------------ EDG30939.1/24-116 --------DKTDLTGPSRAFFSNLQLKK.vEENTIY-FEGTEMFADRINKENIQNLIDSL.K.RLNFP...EYKVEIESTE-KAKNTPSSKWEQQRK.KDIEKFKKEIIN--------------- ECO92716.1/44-133 ------------LSKTERYWLEQVNFEI..DNESLSIFVGSDFVKSSIEKKLYKKIKKTFnI.STGFK...----ECVFVLDKNMKKDFQAYEFEEK.NEDLLKNQEEIKKVQ------------ ECR76875.1/44-133 ------------LSKTERYWLEQVNFEI..DNESLSIFVGSDFVKSSIEKKLYKKIKKTF.NtSTGFK...----ECVFVLDKNIKKDFQAYEFEEK.NEDLLKNQEEIKKVQ------------ ECT87712.1/44-133 ------------LSKTERYWLEQVNFEI..ENESLSIFVGSDFVKSSIEKKLYKKIKKTFnI.STGFK...----ECVFVLDKNMKKDLQAYKFEEK.NEDLLKNQEEIKKVQ------------ EDC21513.1/415-504 ---------LD-LTGPSRAFFSNLQVEK..VNDAKIFFRGSGMFAERINEENIQNLIDSL.Q.RLGFP...EYEIEIESSD-KADNTPSSKWAKQRA.KDIEKFKEEII---------------- EBS07049.1/44-131 ------------LSKTERYWLEQVNFEI..DNESLSIFVGSDFVKSSIEKKLYKKIKKTFnI.STGFK...----ECVFVLDKNMKKDFQAYEFEEK.NEDLLKNREEIKK-------------- #=GC PP_cons 6999999977787888999******999..999999************************.9.9****...89998888887677887788877777.77777777766765577766554.... #=GC RF xxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x.xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx //