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