HHsearch alignment for GI: 254780306 and conserved domain: cd01027
>cd01027 TOPRIM_RNase_M5_like TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in Ribonuclease M5: (RNase M5) and other small primase-like proteins from bacteria and archaea. RNase M5 catalyzes the maturation of 5S rRNA in low G+C Gram-positive bacteria. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). 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.
Probab=93.80 E-value=0.45 Score=27.11 Aligned_cols=68 Identities=28% Similarity=0.415 Sum_probs=45.1
Q ss_pred CEEEECCHHHHHHHHHHHCCCCEEEEEECCCEECCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCEEEECCCC
Q ss_conf 18997790478778875089989999425110078655786766674406887765489999999998709989994699
Q gi|254780306|r 2 NVIIVESPAKAKTISKYLGSNYKVLSSFGHIRDLPAKKGSVLPEKEFEMIWNIDPSSQKHLQNIIHAVKSSTILILATDP 81 (837)
Q Consensus 2 ~LvIvEsP~kak~I~~~Lg~~y~V~as~GHirdLp~~~~~v~~~~~f~p~y~v~~~~kk~~~~i~~~~k~a~~iilAtD~ 81 (837)
T Consensus 3 evIvVEGk~D~~~l~~~~~~~-~ii~t~g~~------------------------~~~~~~~~i~~---~~~~VIIlTD~ 54 (81)
T cd01027 3 EVIIVEGKNDTESLKKLGIEA-EIIETNGSI------------------------INKETIELIKK---AYRGVIILTDP 54 (81)
T ss_pred EEEEEECCCHHHHHHHHCCCE-EEEEECCCC------------------------CCHHHHHHHHH---HCCCEEEEECC
T ss_conf 699995561899999863781-399989903------------------------45999999998---55985999689
Q ss_pred CCHHHHHHHHHHHHHH
Q ss_conf 7025799999999975
Q gi|254780306|r 82 DREGEAISWHVLDVLR 97 (837)
Q Consensus 82 DREGE~Iawhi~e~l~ 97 (837)
T Consensus 55 D~~Gekirk~i~~~l~ 70 (81)
T cd01027 55 DRKGEKIRKKLSEYLS 70 (81)
T ss_pred CCCHHHHHHHHHHHHC
T ss_conf 9670799999999822