HHsearch alignment for GI: 254781225 and conserved domain: cd00525

>cd00525 AE_Prim_S_like AE_Prim_S_like: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases. The replication machineries of A/Es are distinct from that of bacteria. Primases are DNA-dependent RNA polymerases which synthesis the short RNA primers required for DNA replication. In eukaryotes, this small catalytically active primase subunit (p50) and a larger primase subunit (p60), referred to jointly as the core primase, associate with the B subunit and the DNA polymerase alpha subunit in a complex, called Pol alpha-pri. In addition to its catalytic role in replication, eukaryotic DNA primase may play a role in coupling replication to DNA damage repair and in checkpoint control during S phase. Pfu41 and Pfu46 comprise the primase complex of the archaea Pyrococcus furiosus; these proteins have sequence identity to the eukaryotic p50 and p60 primase proteins respectively. Pfu41 preferentially uses dNTPs as substrate. Pfu46 regulates the pri
Probab=98.98  E-value=2e-09  Score=80.31  Aligned_cols=113  Identities=21%  Similarity=0.252  Sum_probs=76.8

Q ss_pred             CEEEEECCCCCCCCCCCCCCC-CCCCHHHHHHH----HHCCEEEEECCC----CCCEEEEEEECCCC---HHHHHHHHHH
Q ss_conf             859773567787877565456-56898999742----007889992347----79879999646881---2567899987
Q gi|254781225|r   18 FKLIPLRLGDKRPQRLGKWEE-QLLSSEKIDKL----PACGFGFVCGVG----EQPLYAFDIDSKDE---KTANTFKDTF   85 (789)
Q Consensus        18 ~~viPi~pg~KrP~~~~~w~~-~~~~~~~i~~~----~~~giGi~~G~~----s~glv~iDiD~~d~---~~~~~~~~~~   85 (789)
T Consensus         1 r~~~p~~~~~k~p~~-~~~~~~~~~~~~~~~~w~~~~~~~~i~~~~~~~~~~~~~~~lv~DlD~~~~~~~~~~~~~a~~~   79 (136)
T cd00525           1 RPVSPIRPPGKGPFQ-RHWPFGATTDDAEILAWLANLPPGNIGLSLGRYDKLWKPDLLVFDLDPDDYDCWEDVKEAALLL   79 (136)
T ss_pred             CCCCCCCCCCCCCCC-CCCCCCCCCCHHHHHHHHHHCCCEEEECCCCCCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHH
T ss_conf             984455789888766-7886547558099999886338575017766567567998799826899999899999999999


Q ss_pred             HHCCC-----CCEEEECCCCCEEEEEEECCCCCCCCCCCCCCCCCEEEECC--CCEEEECCCCCC-CCCCEE
Q ss_conf             64189-----97699678896599995073102445444457675348526--843880477688-887457
Q gi|254781225|r   86 EILHG-----TPIVRIGQKPKILIPFRMNKEGIKKKKTTESTQGHLDILGC--GQYFVAYNIHPK-TKKEYT  149 (789)
Q Consensus        86 ~~l~g-----~p~~~~g~~~~~~~~yr~~~~~~~~~~~~~~~~~~iEi~~~--G~q~V~~gshp~-Tg~~Y~  149 (789)
T Consensus        80 ~~ll~~~~~~~~~~~TG~-~G~H~~~~~-----------------iD~~~~~~~~~~v~p~S~~~~~~~~p~  133 (136)
T cd00525          80 RELLDEDGLNTLVVTSGS-RGLHVYVRL-----------------IDIRVNARGRLLVAPPSVHPRPGGPPS  133 (136)
T ss_pred             HHHHHHCCCCEEEECCCC-CEEEEEEEC-----------------CHHHCCCCCCEEECCCCCCCCCCCCCC
T ss_conf             999988499554374389-834999976-----------------456435789727636556689989787