HHsearch alignment for GI: 254780306 and conserved domain: cd01025

>cd01025 TOPRIM_recR TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in Escherichia coli RecR. RecR participates in the RecFOR pathway of homologous recombinational repair in prokaryotes. This pathway provides a single-stranded DNA molecule coated with RecA to allow invasion of a homologous molecule. The RecFOR system directs the loading of RecA onto gapped DNA coated with SSB protein. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). In RecR sequences this glutamate in the first turn of the TOPRIM domain is semiconserved, the DXD motif is not conserved.
Probab=96.07  E-value=0.057  Score=33.83  Aligned_cols=87  Identities=25%  Similarity=0.435  Sum_probs=57.8

Q ss_pred             CEEEECCHHHHHHHHHHH--CCCCEEEEEECCCEECCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHH--HCCEEEE
Q ss_conf             189977904787788750--899899994251100786557867666744068877654899999999987--0998999
Q gi|254780306|r    2 NVIIVESPAKAKTISKYL--GSNYKVLSSFGHIRDLPAKKGSVLPEKEFEMIWNIDPSSQKHLQNIIHAVK--SSTILIL   77 (837)
Q Consensus         2 ~LvIvEsP~kak~I~~~L--g~~y~V~as~GHirdLp~~~~~v~~~~~f~p~y~v~~~~kk~~~~i~~~~k--~a~~iil   77 (837)
T Consensus         2 ~lcVVe~~~Dl~~iE~s~~y~G~YhVL~--G~l---spl~-g~~p~~-------------l~i~~L~~ri~~~~i~EvIl   62 (112)
T cd01025           2 KLCVVEEPRDVLAIEESGEYRGLYHVLG--GLI---SPLD-GIGPDD-------------LNIDKLLERIAKGQVKEVIL   62 (112)
T ss_pred             EEEEECCHHHHHHHHHHCCCCEEEEEEC--CCC---CCCC-CCCCCC-------------CCHHHHHHHHHCCCCEEEEE
T ss_conf             7999898999999972175656999852--634---7556-998330-------------31999999983589418999


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEE
Q ss_conf             4699702579999999997551257887169999
Q gi|254780306|r   78 ATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVS  111 (837)
Q Consensus        78 AtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~  111 (837)
T Consensus        63 A~~~t~EGe~Ta~yi~~~l~~~----~ikitrLA   92 (112)
T cd01025          63 ATNPTVEGEATALYIAKLLKDF----GVKVTRLA   92 (112)
T ss_pred             ECCCCCCCHHHHHHHHHHHHHC----CCCEEEEE
T ss_conf             7489966089999999985435----97279887