HHsearch alignment for GI: 254780546 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=98.48  E-value=3.1e-06  Score=63.15  Aligned_cols=140  Identities=14%  Similarity=0.145  Sum_probs=88.9

Q ss_pred             CCCCEEEEEECCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEEECCC---
Q ss_conf             79983999966942489999999999986489972999999667798784689999999998718988999975047---
Q gi|254780546|r   17 VYPAHILVAVSGGSDSMGLLIALHSVLSDRSFGKIKFSAISVDHCLRETAKDEVRYVSDVCSRLRIAHSVVSWKNSK---   93 (423)
Q Consensus        17 ~~~~~i~vAvSGG~DS~aLl~ll~~~~~~~~~~~~~l~a~~vdHglr~~s~~e~~~v~~~~~~lgi~~~~~~~~~~~---   93 (423)
T Consensus        21 ~g~~~~viGlSGGIDSav~a~La~~Alg-----~~~v~~v~mP~~~--ss~~s~~~A~~la~~lgi~~~~i~I~~~~~~~   93 (248)
T cd00553          21 SGFKGVVLGLSGGIDSALVAALAVRALG-----RENVLALFMPSRY--SSEETREDAKELAEALGIEHVNIDIDPAVEAF   93 (248)
T ss_pred             CCCCCEEEECCCCHHHHHHHHHHHHHCC-----CCEEEEEECCCCC--CCHHHHHHHHHHHHHHCCCEEEECHHHHHHHH
T ss_conf             1999199958888999999999999728-----8759998899978--98758999999999958916871559999999


Q ss_pred             ---------------CCCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf             ---------------87780378885455554320012344201234566656689999862365444332235764100
Q gi|254780546|r   94 ---------------PQTGLMAAAREARYALISEHAKTINATLIMTAHTFDDQLETVYMRSQRDYAEKGMGLSGMCDTIL  158 (423)
Q Consensus        94 ---------------~~~~~~~~ar~~r~~~~~~~~~~~~~~~l~~ah~~dD~~Et~l~rl~r~sg~~g~~l~~~~~~~~  158 (423)
T Consensus        94 ~~~~~~~~~~~~~~~~~~Niqa---RlRm~~Ly~~An~~~~lVlgTg----NksE~~-----~Gy~T------------k  149 (248)
T cd00553          94 LALLGESGGSELEDLALGNIQA---RLRMVILYALANKLGGLVLGTG----NKSELL-----LGYFT------------K  149 (248)
T ss_pred             HHHHHHHCCCCHHHHHHHHHHH---HHHHHHHHHHHHHCCCEEECCC----CHHHHH-----HCCCE------------E
T ss_conf             9986440487055678742487---8889999999974499896287----460787-----57210------------0


Q ss_pred             CCCCCEEECCHHCCCHHHHHHHHHHHCCC
Q ss_conf             35796871012104289999989981893
Q gi|254780546|r  159 YDLNLWISRPFLRCRREDIRSFLLQRNIS  187 (423)
Q Consensus       159 ~~~~~~i~RPLL~~~r~~l~~~~~~~~i~  187 (423)
T Consensus       150 yGD~~~d~~Pi~~L~Kt~V~~la~~l~vp  178 (248)
T cd00553         150 YGDGAADINPIGDLYKTQVRELARYLGVP  178 (248)
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHCCH
T ss_conf             07877582213688499999999996888