>cd07903 Adenylation_DNA_ligase_IV The Adenylation domain of DNA Ligase IV 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 ligase in eukaryotic cells (I, III and IV). DNA ligase IV is required for DNA non-homologous end joining pathways, including recombination of the V(D)J immunoglobulin gene segments in cells of the mammalian immune system. DNA ligase IV is stabilized by forming a complex with XRCC4, a nuclear phosphoprotein, which is phosphorylated by DNA-dependent protein kinase. DNA ligases have a highly modular architecture consist

Probab=98.30 E-value=6.2e-05 Score=57.33 Aligned_cols=172 Identities=18% Similarity=0.166 Sum_probs=92.9 Q ss_pred CCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHH----HHCCCCCCCC--CCCCCEEEEEEEEEEECHHH Q ss_conf 61199994158189999985998998886598655666999775----3102432233--54455048999999852021 Q gi|254781172|r 125 SIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIR----AIPTIPRVLS--LNIPEIIEVRGEVYISKNDF 198 (731) Q Consensus 125 ~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~----~i~~iP~~l~--~~~~~~ieiRGEv~m~~~~F 198 (731) T Consensus 32 ~~~~~~E~K~DG~R~~~h~~~~~-v~l~SR----ng~d~t~~fpe~~~~~~~~~~~~~~~~~~~~~~ILDGElv~~d~~~ 106 (227) T cd07903 32 GDPFYIETKFDGERIQLHKDGEE-FKYFSR----NGNDYTYLYGESLDEGSLTPYIHLAFAKSVKSCILDGEMMVWDKET 106 (227) T ss_pred CCCEEEEEEECEEEEEEEEECCE-EEEEEC----CCCCCHHHCCCHHHHHHHCHHHHHHHHCCCCCEEEEEEEEEEECCC T ss_conf 98469998775189999995999-999977----8870023253056553202556777513688689960598873677 Q ss_pred HHHHHHHHHCCCCCCCCHHHHHHHHHHCCCH--HHHHCCCEEEEEEECCCCCCC--CCCCHHHHHHHHHCCCCCCCCE-- Q ss_conf 2345564314854334234567777523455--553011105664102454332--1000036899997599665414-- Q gi|254781172|r 199 LALNDEMIAVGRKPYANPRNAASGILRRLNP--TDITRYLNFFVHGLGKTSEIF--AKGQYEMLQKMRCLGFPVNNGV-- 272 (731) Q Consensus 199 ~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~--~~~~r~L~f~ay~~~~~~~~~--~~~~~e~l~~L~~~GF~v~~~~-- 272 (731) T Consensus 107 ~~---------~~~f~~l~~----~~~~~~~~~~~~~~~~~~~~FDiL~l~g~~l~~~p~~eR~~~L~~~~~~~~~~i~~ 173 (227) T cd07903 107 KR---------FLPFGTLKD----VAALRESRLEDSNLQPCFVVFDILYLNGKSLTNLPLHERKELLRKIITPVPGRIEI 173 (227) T ss_pred CC---------CCCCCHHHH----HHHHCCCCCCCCCCCEEEEEEEEEEECCHHHHHHHHHHHHHHHHHHHCCCCCCEEE T ss_conf 75---------255303667----98742344333455427999877515883165437899999999862568982798 Q ss_pred ---EEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCC Q ss_conf ---8874032113455665531001123437637773110001115876568663 Q gi|254781172|r 273 ---RQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRW 324 (731) Q Consensus 273 ---~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~Prw 324 (731) T Consensus 174 ~~~~~~~~~~~i~~~~~~~~~~------g~EGimiK~~~s~Y~~--g--kRs~~W 218 (227) T cd07903 174 VKRKEASTKEDIEEALNEAIDN------REEGIVVKDLDSKYRP--G--KRGDGW 218 (227) T ss_pred EEEEECCCHHHHHHHHHHHHHC------CCCEEEEECCCCCCCC--C--CCCCCC T ss_conf 7778739999999999999987------9978998179996479--9--989982

HHsearch alignment for GI: 254781172 and conserved domain: cd07903