HHsearch alignment for GI: 254780762 and conserved domain: cd03364

>cd03364 TOPRIM_DnaG_primases TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. E. coli DnaG is a single subunit enzyme.
Probab=90.89  E-value=1.7  Score=24.86  Aligned_cols=76  Identities=22%  Similarity=0.337  Sum_probs=50.5

Q ss_pred             CEEEEEECHHHHHHHHHHCCEEEEEEEHHHHCCCCCCCCHHHCCHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             36999835889999975174013421012100200026811128899999851578554999946997868999999998
Q gi|254780762|r   83 SVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIRELIFAISATIEGQTTAHYIMDK  162 (201)
Q Consensus        83 ~~lCVVE~~~Di~~IE~t~~y~G~YhVLgG~ispl~g~~p~~l~i~~L~~ri~~~~i~EVIlA~~~t~EGe~Ta~yi~~~  162 (201)
T Consensus         1 k~viivEG~~D~i~~~~~G~-~n~VA~~Gt~~t------~~q--~~~----L~~~-~~~vil~~D~D~AG~~Aa~r~~~~   66 (79)
T cd03364           1 KKVILVEGYMDVIALHQAGI-KNVVASLGTALT------EEQ--AEL----LKRL-AKEVILAFDGDEAGQKAALRALEL   66 (79)
T ss_pred             CEEEEEECHHHHHHHHHCCC-CCEEECCCCCCC------HHH--HHH----HHCC-CCCEEEEECCCHHHHHHHHHHHHH
T ss_conf             98999967799999998599-625625665471------999--997----7231-586799978988999999999999


Q ss_pred             HCCCCCEEEE
Q ss_conf             2017980887
Q gi|254780762|r  163 LKGIDVKITR  172 (201)
Q Consensus       163 lk~~~ikitr  172 (201)
T Consensus        67 l~~~g~~v~i   76 (79)
T cd03364          67 LLKLGLNVRV   76 (79)
T ss_pred             HHHCCCEEEE
T ss_conf             9977996999