HHsearch alignment for GI: 254781172 and conserved domain: cd07902

>cd07902 Adenylation_DNA_ligase_III The Adenylation domain of DNA Ligase III is a component of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase III is not found in lower eukaryotes and is present both in the nucleus and mitochondria. It has several isoforms; two splice forms, III-alpha and III-beta, differ in their carboxy-terminal sequences. DNA ligase III-beta is believed to play a role in homologous recombination during meiotic prophase. DNA ligase III-alpha interacts with X-ray Cross Complementing
Probab=97.83  E-value=0.00074  Score=48.98  Aligned_cols=176  Identities=15%  Similarity=0.131  Sum_probs=90.4

Q ss_pred             CCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHH-HHHH
Q ss_conf             664257021599999999999999861246777611999941581899999859989988865986556669997-7531
Q gi|254781172|r   92 SIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSAC-IRAI  170 (731)
Q Consensus        92 ~~pMlSL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n-~~~i  170 (731)
T Consensus        14 i~PMLA~-~~~~~~~~~~---~----------~~~~~~~E~K~DG~R~qih~~~~~-v~l~SR----n~~d~~~~~~~~~   74 (213)
T cd07902          14 VKPMLAE-ACKSVEYAMK---K----------CPNGMYAEIKYDGERVQLHKQGDN-FSFFSR----SLKPVLPHKVSHF   74 (213)
T ss_pred             CCCEECC-CCCCHHHHHH---H----------CCCCEEEEEEECEEEEEEEECCCE-EEEEEC----CCCCCCCCHHHHH
T ss_conf             8243589-8799799997---5----------799759997158189999982999-999927----8830364217789


Q ss_pred             C-CCCCCCCCCCCCEEEEEEEEEEECHHHHHHHHHHHHCCCC-CCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCC
Q ss_conf             0-2432233544550489999998520212345564314854-3342345677775234555530111056641024543
Q gi|254781172|r  171 P-TIPRVLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRK-PYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSE  248 (731)
Q Consensus       171 ~-~iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~-~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~  248 (731)
T Consensus        75 ~~~i~~~~~--~~~~~ILDGEiv~~d~~----------~g~~~~f~~l-----~-~~~~~~-~~~~~~~~~vFDlL~l~g  135 (213)
T cd07902          75 KDYIPKAFP--HGHSMILDSEVLLVDTK----------TGKPLPFGTL-----G-IHKKSA-FKDANVCLFVFDCLYFNG  135 (213)
T ss_pred             HHHHHHHCC--CCCCEEEEEEEEEEECC----------CCCCCCCHHH-----H-HHHHHH-CCCCCEEEEEEEEEEECC
T ss_conf             999998647--78747997047998668----------9975503004-----4-554541-245781699997700598


Q ss_pred             C--CCCCCHHHHHHHHHCCCCCCCCEEE-----EECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHC
Q ss_conf             3--2100003689999759966541488-----7403211345566553100112343763777311000
Q gi|254781172|r  249 I--FAKGQYEMLQKMRCLGFPVNNGVRQ-----ANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSL  311 (731)
Q Consensus       249 ~--~~~~~~e~l~~L~~~GF~v~~~~~~-----~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~  311 (731)
T Consensus       136 ~~l~~~pl~eRr~~L~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~a~~------~g~EGiv~K~~~S~Y  199 (213)
T cd07902         136 ESLMDKPLRERRKILEDNMVEIPNRIMFSEMKFVKKADDLAALITRVIR------EGLEGLVLKDIKSVY  199 (213)
T ss_pred             EEHHHCCHHHHHHHHHHHHCCCCCCEEEEEEEECCCHHHHHHHHHHHHH------CCCEEEEEECCCCCC
T ss_conf             1833088999999999740568984798744755999999999999997------698389975898976