HHsearch alignment for GI: 254781172 and conserved domain: cd00114

>cd00114 LIGANc NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction mechanism. The enzyme reacts with the cofactor to form a phosphoamide-linked AMP with the amino group of a conserved Lysine in the KXDG motif, and subsequently transfers it to the DNA substrate to yield adenylated DNA. This alignment contains members of the NAD+ dependent subfamily only.
Probab=100.00  E-value=0  Score=724.98  Aligned_cols=306  Identities=42%  Similarity=0.750  Sum_probs=293.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCHHHCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCH
Q ss_conf             99999999999999843317798208789999999999998977203115899996200364323577504516642570
Q gi|254781172|r   19 KELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGPLNKIGGEMNLSLFKVTHSIPTLSL   98 (731)
Q Consensus        19 ~~i~~L~~~i~~~~~~Yy~~~~p~isD~eYD~L~~~L~~le~~~p~~~~~~~p~spt~~Vg~~~~~~~~kv~H~~pMlSL   98 (731)
T Consensus         1 ~ri~~L~~~I~~~n~~Yy~~~~p~ISD~eYD~L~~eL~~le~~~p~l~---~~~spt~~VG~~~~~~~~kv~H~~pMlSL   77 (307)
T cd00114           1 ERIAELRELLNKHDYRYYVLDEPSVSDAEYDRLYRELRALEEEHPELK---TPDSPTQRVGGTPLSGFKKVRHPVPMLSL   77 (307)
T ss_pred             CHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCC---CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             979999999999999986489997988999999999999998682336---89998655587525667642178655453


Q ss_pred             HHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             21599999999999999861246777611999941581899999859989988865986556669997753102432233
Q gi|254781172|r   99 EKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLS  178 (731)
Q Consensus        99 ~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~  178 (731)
T Consensus        78 ~k~~~~~el~~w~~r~~~~~~----~~~~~~vepKlDGlaisl~Y~~G~L~~a~TRGDG~~GeDIT~nv~~i~~iP~~l~  153 (307)
T cd00114          78 DNAFDEEELRAFDERIKRFLG----EEPAYVVEPKIDGLSISLRYENGVLVQAATRGDGTTGEDVTENVRTIRSIPLTLA  153 (307)
T ss_pred             CCCCCHHHHHHHHHHHHHHHC----CCCCEEEEECCCCEEEEEEEECCEEEEEEECCCCCCCCCCCCCHHHHCCCHHHCC
T ss_conf             443889999999999998515----6744588761376368999809966676625898655483023212227313237


Q ss_pred             CCCCCEEEEEEEEEEECHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHH-HCCCEEEEEEECCCCCCCCCCCHHH
Q ss_conf             544550489999998520212345564314854334234567777523455553-0111056641024543321000036
Q gi|254781172|r  179 LNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDI-TRYLNFFVHGLGKTSEIFAKGQYEM  257 (731)
Q Consensus       179 ~~~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~-~r~L~f~ay~~~~~~~~~~~~~~e~  257 (731)
T Consensus       154 ~-~~~~levRGEi~~~~~~F~~~n~~~~~~~~~~f~NpRN~aAG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~t~~e~  232 (307)
T cd00114         154 G-APETLEVRGEVFMPKADFEALNKEREERGEKPFANPRNAAAGSLRQLDPKITAKRPLRFFIYGLGEAEGLGPKTQSEA  232 (307)
T ss_pred             C-CCCEEEEEEEEEECHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCHHHHCCCCEEEEEEECCCCCCCCCHHHH
T ss_conf             9-986299999997528879999999998178866573378761656248532440766178998552578886778999


Q ss_pred             HHHHHHCCCCCCCCEEEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCCEEEECCCC
Q ss_conf             899997599665414887403211345566553100112343763777311000111587656866312311456
Q gi|254781172|r  258 LQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMISHKFAE  332 (731)
Q Consensus       258 l~~L~~~GF~v~~~~~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~PrwaiA~Kf~~  332 (731)
T Consensus       233 l~~L~~~GF~~~~~~~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVvkvn~~~~~~~lG~ts~~PrwAiA~KfpA  307 (307)
T cd00114         233 LAFLKEWGFPVSPETRLCKNIEEVLAFYDEIEAKRDSLPYEIDGVVVKVDDLALQRELGFTSKAPRWAIAYKFPA  307 (307)
T ss_pred             HHHHHHCCCCCCCCCEEECCHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECHHHHHHHCCCCCCCCCEEEECCCC
T ss_conf             999997799668861897999999999999997642399887737999829899998487678987606856369