HHsearch alignment for GI: 254781190 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=99.09  E-value=1.9e-10  Score=79.23  Aligned_cols=91  Identities=14%  Similarity=0.153  Sum_probs=65.2

Q ss_pred             CHHHHHCCCCCCEEEEECCC----CCCEEEEEEECCCH---HHHHHHHHHHHHHCC-----CCEEEECCCCCEEEEEECC
Q ss_conf             23787518616889970788----48889999548984---678999997764089-----8629867889539998447
Q gi|254781190|r    2 VATDVDHYVYNGFGILCGIG----THPVYAFDVDVLDE---QVVDRFNNEFQSCCG-----KPISRVGQAPKTLMLFRMQ   69 (233)
Q Consensus         2 va~~~~~~p~~giGi~~G~~----s~~l~~iDiD~~d~---~~~~~~~~~~~~~~~-----~~~~~~g~~~~~~~lfr~~   69 (233)
T Consensus        29 ~~~w~~~~~~~~i~~~~~~~~~~~~~~~lv~DlD~~~~~~~~~~~~~a~~~~~ll~~~~~~~~~~~TG~-~G~H~~~~~-  106 (136)
T cd00525          29 ILAWLANLPPGNIGLSLGRYDKLWKPDLLVFDLDPDDYDCWEDVKEAALLLRELLDEDGLNTLVVTSGS-RGLHVYVRL-  106 (136)
T ss_pred             HHHHHHHCCCEEEECCCCCCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEECCCC-CEEEEEEEC-
T ss_conf             999886338575017766567567998799826899999899999999999999988499554374389-834999976-


Q ss_pred             CCCCCCCCCCCCCCCCEEEEEC--CCEEEECCCCCC-CCCCEEE
Q ss_conf             4312433577767663589845--832895366888-8884574
Q gi|254781190|r   70 ETNLKKQKSEEKIQGHLEFLAY--GQQFVAYNIHPK-TQRAYTW  110 (233)
Q Consensus        70 ~~~~~~~~~~~~~~~~iEi~~~--g~q~V~~g~hp~-Tg~~Y~W  110 (233)
T Consensus       107 ----------------iD~~~~~~~~~~v~p~S~~~~~~~~p~~  134 (136)
T cd00525         107 ----------------IDIRVNARGRLLVAPPSVHPRPGGPPSW  134 (136)
T ss_pred             ----------------CHHHCCCCCCEEECCCCCCCCCCCCCCC
T ss_conf             ----------------4564357897276365566899897877