HHsearch alignment for GI: 254781225 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=6.8e-20 Score=149.84 Aligned_cols=143 Identities=27% Similarity=0.355 Sum_probs=101.3
Q ss_pred CEEEEECCCCCCCCCCCCCCCC--CCCHHHHHHH----HHCCEEEEECCCCCCEEEEEEECCCCHHHH-HHHHHHHHCCC
Q ss_conf 8597735677878775654565--6898999742----007889992347798799996468812567-89998764189
Q gi|254781225|r 18 FKLIPLRLGDKRPQRLGKWEEQ--LLSSEKIDKL----PACGFGFVCGVGEQPLYAFDIDSKDEKTAN-TFKDTFEILHG 90 (789)
Q Consensus 18 ~~viPi~pg~KrP~~~~~w~~~--~~~~~~i~~~----~~~giGi~~G~~s~glv~iDiD~~d~~~~~-~~~~~~~~l~g 90 (789)
T Consensus 1 ~~v~P~~~~~K~P~~-~~~~~~~at~d~~~i~~w~~~~p~~niGi~~G~--sglvviDiD~~~~~~~~~~~~~~~~~l~~ 77 (152)
T cd04859 1 FAVIPLDPGSKRPLI-KGWPKDAATTDPEQIEAWWRDGPDANIGLRTGP--SGLVVIDIDVKHDGAAALAALAELGKLPP 77 (152)
T ss_pred CEEEECCCCCCCCCC-CCCCCCCCCCCHHHHHHHHHHCCCCCEEEECCC--CCEEEEECCCCCCCHHHHHHHHHCCCCCC
T ss_conf 907746899871896-998874673999999999985998448888288--87799973267763468998776157787
Q ss_pred -CCEEEECCCCCEEEEEEECCCCCCCCCCCCCCCCCEEEECCCCEEEECCCCCCCCCCEEECCCCCCCCCCCCCCCCHHH
Q ss_conf -9769967889659999507310244544445767534852684388047768888745751776558722164689999
Q gi|254781225|r 91 -TPIVRIGQKPKILIPFRMNKEGIKKKKTTESTQGHLDILGCGQYFVAYNIHPKTKKEYTWTTPPHRFKVEDTPLLSEED 169 (789)
Q Consensus 91 -~p~~~~g~~~~~~~~yr~~~~~~~~~~~~~~~~~~iEi~~~G~q~V~~gshp~Tg~~Y~w~~~~~~~~~~~~P~i~~~~ 169 (789)
T Consensus 78 ~t~~~~T~-~gG~H~~f~~p~~~~~~~-~~~~~~~~vDir~~g~yvV~pPS~~~~g~~y~~~~------~~~~~~~P~wl 149 (152)
T cd04859 78 LTLTVRTG-SGGRHLYFRVPDGVPVKS-VKGKGGPGIDIRGGGGYVVAPPSVHPGGGYYVWKS------TVDPAPAPEWL 149 (152)
T ss_pred CCEEEECC-CCCEEEEEECCCCCCCCC-CCCCCCCCEEEEECCCEEECCCCCCCCCCEEEECC------CCCCCCCCHHH
T ss_conf 77478869-994499998999862233-22476786789835988981786848964698089------99866788678
Q ss_pred HH
Q ss_conf 99
Q gi|254781225|r 170 VE 171 (789)
Q Consensus 170 ~~ 171 (789)
T Consensus 150 ~~ 151 (152)
T cd04859 150 LD 151 (152)
T ss_pred HC
T ss_conf 63