HHsearch alignment for GI: 254780414 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=99.70  E-value=8.3e-16  Score=133.20  Aligned_cols=187  Identities=21%  Similarity=0.310  Sum_probs=130.0

Q ss_pred             CHHHHHHHHHHHHHHH---CCCCEEEEECCCCHHHHHHHHHHHHCC-CCEEEEEECCCCCCCCCHHHHHHHHHHCCCCCE
Q ss_conf             0678999999997650---444036640564047799999986223-656999973895515627899998862369857
Q gi|254780414|r  205 MSSYHKEIVSRIKEQV---GNERVICAVSGGVDSTVAAFLIYEAIG-INLTCVLVDHGFMRKNEVENIISLFKGYPNFPL  280 (520)
Q Consensus       205 ~~~~~~~~i~~Ir~~v---g~~kVi~~lSGGVDStV~A~Ll~kAig-~~l~~vfVD~GllRknE~~~v~~~~~~~~~~~l  280 (520)
T Consensus         3 ~~~~~~~lv~~l~~y~~~~g~~~~viGlSGGIDSav~a~La~~Alg~~~v~~v~mP~~~ss~~s~~~A~~l-a~~lgi~~   81 (248)
T cd00553           3 LEEIINALVLFLRDYLRKSGFKGVVLGLSGGIDSALVAALAVRALGRENVLALFMPSRYSSEETREDAKEL-AEALGIEH   81 (248)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCEEEECCCCHHHHHHHHHHHHHCCCCEEEEEECCCCCCCHHHHHHHHHH-HHHHCCCE
T ss_conf             89999999999999999819991999588889999999999997288759998899978987589999999-99958916


Q ss_pred             EEEEHHH---HHHHHHCCCCCHHHHHHHHHHHHHHHH----HHHHHHCCCCEEEEECCCCCHHHHHHCCCCCCCCEEEEE
Q ss_conf             9975889---999996689888999988756589999----999974399709986462202454202467776303443
Q gi|254780414|r  281 RVVDASE---RFIRKLKNIVDPETKRKVIGQLFIEVF----EEEAKKIGGAQFLGQGTLYPDVIESISFFGGPSSIIKSH  353 (520)
Q Consensus       281 ~~vda~~---~Fl~~L~gv~DPE~KRkiIG~~Fi~vf----~~~a~~~~~~~~L~QGTlypDvIES~~~~~~~~~~IKsH  353 (520)
T Consensus        82 ~~i~I~~~~~~~~~~~~~~~~~~~~~~~~~NiqaRlRm~~Ly~~An~---~~~lVlgTg--NksE~~~Gy-------~Tk  149 (248)
T cd00553          82 VNIDIDPAVEAFLALLGESGGSELEDLALGNIQARLRMVILYALANK---LGGLVLGTG--NKSELLLGY-------FTK  149 (248)
T ss_pred             EEECHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHH---CCCEEECCC--CHHHHHHCC-------CEE
T ss_conf             87155999999999864404870556787424878889999999974---499896287--460787572-------100


Q ss_pred             ECCCCHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHCCCCCCCCCCEEEECCCCCHHHH
Q ss_conf             023201132032022378987389999999981999889426888983111221000367899
Q gi|254780414|r  354 HNVGGLPEHMDMKLVEPLKELFKDEVRLLGKELRLPDSFVERHPCPGPGLAIRCIGEITEERI  416 (520)
Q Consensus       354 HNvgglp~~~~~~liEPl~~l~KdEVR~lg~~Lglp~~~~~RhPFPGPGLaiRi~g~vt~e~~  416 (520)
T Consensus       150 yGD~------~-~d~~Pi~~L~Kt~V~~la~~l~vp~~Ii~k~PSae--L~~---~Q~DE~~l  200 (248)
T cd00553         150 YGDG------A-ADINPIGDLYKTQVRELARYLGVPESIIDKPPSAE--LWP---GQTDEDEL  200 (248)
T ss_pred             CCCC------C-CCCCCCCCCCHHHHHHHHHHHCCHHHHHCCCCCCC--CCC---CCCCHHHC
T ss_conf             0787------7-58221368849999999999688898734799966--679---99898775