HHsearch alignment for GI: 254780222 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=90.70 E-value=1.2 Score=23.80 Aligned_cols=69 Identities=30% Similarity=0.506 Sum_probs=45.1
Q ss_pred EEEEEECCCCCCCCHHHCCCCCCEEEEEECCEECCHHHHHHHHHHCCHHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEC
Q ss_conf 37997327676421001011222012211231314454108776322889999988256654333334655251899977
Q gi|254780222|r 464 TELFIVEGDSAGGSAKQARNRSNQAVLPLRGKILNVASAGSEKIRNNQQIMDLVQALGCRTRSQYREEDLRYEKVIIMTD 543 (686)
Q Consensus 464 ~eL~lvEGDSA~gsAk~grdr~~qgi~PLRGKiLNv~~as~~ki~~N~Ei~~l~~~lGl~~g~~~~~~~LRYgkIiImTD 543 (686)
T Consensus 2 ~evIvVEGk~D~~~l~~~~~~--~~ii~t~g~~~~~------------~~~~~i~~--------------~~~~VIIlTD 53 (81)
T cd01027 2 GEVIIVEGKNDTESLKKLGIE--AEIIETNGSIINK------------ETIELIKK--------------AYRGVIILTD 53 (81)
T ss_pred CEEEEEECCCHHHHHHHHCCC--EEEEEECCCCCCH------------HHHHHHHH--------------HCCCEEEEEC
T ss_conf 769999556189999986378--1399989903459------------99999998--------------5598599968
Q ss_pred CCCCCHHHHHHHHHHHH
Q ss_conf 98771468899999999
Q gi|254780222|r 544 ADVDGAHIASLLLTFFY 560 (686)
Q Consensus 544 aD~DGsHI~~Lll~ff~ 560 (686)
T Consensus 54 ~D~~Gekirk~i~~~l~ 70 (81)
T cd01027 54 PDRKGEKIRKKLSEYLS 70 (81)
T ss_pred CCCCHHHHHHHHHHHHC
T ss_conf 99670799999999822