HHsearch alignment for GI: 254781190 and conserved domain: cd04859
>cd04859 Prim_Pol Prim_Pol: Primase-polymerase (primpol) domain of the type found in bifunctional replicases from archaeal plasmids, including ORF904 protein of the crenarchaeal plasmid pRN1 from Sulfolobus islandicus (pRN1 primpol). These primpol domains belong to the archaeal/eukaryal primase (AEP) superfamily. This group includes archaeal plasmids and bacteriophage AEPs. The ORF904 protein is a multifunctional protein having ATPase, primase and DNA polymerase activity, and may play a role in the replication of the archaeal plasmid. The pRN1 primpol domain exhibits DNA polymerase and primase activities; a cluster of active site residues (three acidic residues, and a histidine) is required for both these activities. For pRN1 primpol, the primase activity prefers dNTPs to rNTPs; incorporation of dNTPs requires rNTP as cofactor. The pRN1 primpol contains an unusual zinc-binding stem, which is not conserved in other members of this group.
Probab=99.85 E-value=1.4e-20 Score=137.70 Aligned_cols=120 Identities=13% Similarity=0.079 Sum_probs=83.2
Q ss_pred CHHHHHCCCCCCEEEEECCCCCCEEEEEEECCCHHHHHHHHH--HHHHHCCCCEEEECCCCCEEEEEECCCCCCCCCCCC
Q ss_conf 237875186168899707884888999954898467899999--776408986298678895399984474312433577
Q gi|254781190|r 2 VATDVDHYVYNGFGILCGIGTHPVYAFDVDVLDEQVVDRFNN--EFQSCCGKPISRVGQAPKTLMLFRMQETNLKKQKSE 79 (233)
Q Consensus 2 va~~~~~~p~~giGi~~G~~s~~l~~iDiD~~d~~~~~~~~~--~~~~~~~~~~~~~g~~~~~~~lfr~~~~~~~~~~~~ 79 (233)
T Consensus 30 i~~w~~~~p~~niGi~~G~--sglvviDiD~~~~~~~-~~~~~~~~~~l~~~t~~~~T~~gG~H~~f~~p~~~~~~~-~~ 105 (152)
T cd04859 30 IEAWWRDGPDANIGLRTGP--SGLVVIDIDVKHDGAA-ALAALAELGKLPPLTLTVRTGSGGRHLYFRVPDGVPVKS-VK 105 (152)
T ss_pred HHHHHHHCCCCCEEEECCC--CCEEEEECCCCCCCHH-HHHHHHHCCCCCCCCEEEECCCCCEEEEEECCCCCCCCC-CC
T ss_conf 9999985998448888288--8779997326776346-899877615778777478869994499998999862233-22
Q ss_pred CCCCCCEEEEECCCEEEECCCCCCCCCCEEEECCCCCCCHHHCCCCCHHHHH
Q ss_conf 7676635898458328953668888884574216776882236768999999
Q gi|254781190|r 80 EKIQGHLEFLAYGQQFVAYNIHPKTQRAYTWSIAPHALKVEELPLLTPDEVE 131 (233)
Q Consensus 80 ~~~~~~iEi~~~g~q~V~~g~hp~Tg~~Y~W~~~~~~~~~~~lP~~~~~~l~ 131 (233)
T Consensus 106 ~~~~~~vDir~~g~yvV~pPS~~~~g~~y~~~~---~~---~~~~~P~wl~~ 151 (152)
T cd04859 106 GKGGPGIDIRGGGGYVVAPPSVHPGGGYYVWKS---TV---DPAPAPEWLLD 151 (152)
T ss_pred CCCCCCEEEEECCCEEECCCCCCCCCCEEEECC---CC---CCCCCCHHHHC
T ss_conf 476786789835988981786848964698089---99---86678867863