HHsearch alignment for GI: 254780234 and conserved domain: cd00553

>cd00553 NAD_synthase NAD+ synthase is a homodimer, which catalyzes the final step in de novo nicotinamide adenine dinucleotide (NAD+) biosynthesis, an amide transfer from either ammonia or glutamine to nicotinic acid adenine dinucleotide (NaAD). The conversion of NaAD to NAD+ occurs via an NAD-adenylate intermediate and requires ATP and Mg2+. The intemediate is subsequently cleaved into NAD+ and AMP. In many prokaryotes, such as E. coli , NAD synthetase consists of a single domain and is strictly ammonia dependent. In contrast, eukaryotes and other prokaryotes have an additional N-terminal amidohydrolase domain that prefer glutamine, Interestingly, NAD+ synthases in these prokaryotes, can also utilize ammonia as an amide source .
Probab=97.96  E-value=0.00064  Score=48.44  Aligned_cols=151  Identities=21%  Similarity=0.238  Sum_probs=95.9

Q ss_pred             CCCEEEEEECCCHHHHHHHHHHHHHCC-CEEEEEEEECCC--CCHHHHHHHHHHHCCCEEEEEECHHHHHHHHHHHHHHH
Q ss_conf             777899991477259999999987189-869999945787--11068999999973980799820089999987999973
Q gi|254780234|r    4 DVKKVVLAYSGGLDTSIILKWLQVEKG-LEVIVFIADLGQ--GEELKIASDKARLLGAKEVYVKDLRREFVRDFVFPMFR   80 (404)
Q Consensus         4 ~~kkVvlaySGGLDTSv~i~~L~~e~g-~eVi~~~~d~Gq--~~d~~~~~~~A~~~Ga~~~~v~D~r~ef~~~~i~~~I~   80 (404)
T Consensus        22 g~~~~viGlSGGIDSav~a~La~~Alg~~~v~~v~mP~~~ss~~s~~~A~~la~~lgi-~~~~i~I~~~~-~~-~~~~~~   98 (248)
T cd00553          22 GFKGVVLGLSGGIDSALVAALAVRALGRENVLALFMPSRYSSEETREDAKELAEALGI-EHVNIDIDPAV-EA-FLALLG   98 (248)
T ss_pred             CCCCEEEECCCCHHHHHHHHHHHHHCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCC-CEEEECHHHHH-HH-HHHHHH
T ss_conf             9991999588889999999999997288759998899978987589999999999589-16871559999-99-999864


Q ss_pred             CCCCCCCCCCCCCCHHHH-HHH----HHHHHHHHHCCCCEEECHHHCCCCHHHHHHHHHHHHCCC-CEEEEEECCCCCCC
Q ss_conf             686547874201301243-359----999999885689287500111682156799999985879-70774410068763
Q gi|254780234|r   81 ANALYEGYYLLGTAIARP-LIA----KYLVDIANETGADAIAHGSTGKGNDQVRFELSAYSLNSD-IEIIAPWRHWSFKG  154 (404)
Q Consensus        81 ana~Yeg~Ypl~tslaRp-lia----~~lv~~a~~~ga~~iaHG~TgkGNDQvRFe~~~~~l~P~-l~viaP~Rd~~~~s  154 (404)
T Consensus        99 ~~~---~--~~~~~~~~~NiqaRlRm~~Ly~~An~~~~lVlg-----TgNksE~~~G-y~TkyGD~~~d~~Pi~~--L-~  164 (248)
T cd00553          99 ESG---G--SELEDLALGNIQARLRMVILYALANKLGGLVLG-----TGNKSELLLG-YFTKYGDGAADINPIGD--L-Y  164 (248)
T ss_pred             HHC---C--CCHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEC-----CCCHHHHHHC-CCEECCCCCCCCCCCCC--C-C
T ss_conf             404---8--705567874248788899999999744998962-----8746078757-21000787758221368--8-4


Q ss_pred             HHHHHHHHHHHCCCCCC
Q ss_conf             79999999970896756
Q gi|254780234|r  155 RQDLIDFAEKHAIPIDK  171 (404)
Q Consensus       155 Re~~i~ya~~~gIpv~~  171 (404)
T Consensus       165 Kt~V~~la~~l~vp~~I  181 (248)
T cd00553         165 KTQVRELARYLGVPESI  181 (248)
T ss_pred             HHHHHHHHHHHCCHHHH
T ss_conf             99999999996888987