HHsearch alignment for GI: 254780971 and conserved domain: cd01744

>cd01744 GATase1_CPSase Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II. This group of sequences represents the small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II. CPSase II catalyzes the production of carbomyl phosphate (CP) from bicarbonate, glutamine and two molecules of MgATP. The reaction is believed to proceed by a series of four biochemical reactions involving a minimum of three discrete highly reactive intermediates. The synthesis of CP is critical for the initiation of two separate biosynthetic pathways. In one CP is coupled to aspartate, its carbon and nitrogen nuclei ultimately incorporated into the aromatic moieties of pyrimidine nucleotides. In the second pathway CP is condensed with ornithine at the start of the urea cycle and is utilized for the detoxification of ammonia and biosynthesis of arginine. CPSases may be encoded by one or by several genes, depending on the species. The E.coli enzyme is
Probab=99.22  E-value=1.6e-10  Score=88.15  Aligned_cols=174  Identities=19%  Similarity=0.222  Sum_probs=96.9

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHCCCCEEEEECCC----CCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf             8998449706479999999985499639982154----644564789972873454311406775200212122332205
Q gi|254780971|r    3 TAIVQIPGLNRDNDMIKAITKIIGQSPILVWQSD----TDIPDVDLIVIPGGFSYGDYLRCGAIAARTPVMQAIKKKAQQ   78 (219)
Q Consensus         3 vaVl~~pGsNcd~e~~~A~~~~~~~~~~~v~~~~----~~l~~~d~lvipGGFSygD~l~aG~i~~~~~~~~~i~~~~~~   78 (219)
T Consensus         1 i~ilDfGs---qy~i~r~lrel-g~~~~v~~~~~~~~~i~~~~p~giIlS~GP--g~p~------~~~~~~~~~~~~~~~   68 (178)
T cd01744           1 VVVIDFGV---KHNILRELLKR-GCEVTVVPYNTDAEEILKLDPDGIFLSNGP--GDPA------LLDEAIKTVRKLLGK   68 (178)
T ss_pred             CEEEECCC---HHHHHHHHHHC-CCEEEEEECCCCHHHHHHCCCCEEEECCCC--CCHH------HHCCHHHHHHHHHHC
T ss_conf             99998874---99999999987-997999939899999984199979989999--9957------734449999999746


Q ss_pred             CCEEEEECCCHHHHEECCCHHHHHCCCCCCCEEEEEEEEEECCCHHHHHHHCCCCCEEEEEEECCCEEEEECHHHHHHHH
Q ss_conf             97178606403101000001011012443324542257675252357764137996899862013302330867741154
Q gi|254780971|r   79 GIKVMGICNGFQILVELNLLPGILMRNCSLKFVCKQVLLEVVNSNTAFTKSYKMNQIIKCPVAHHDGNYFIDAKGLAEIE  158 (219)
Q Consensus        79 g~~vLGICNGfQiL~elGLlPg~l~~N~s~rf~~r~~~~~v~~~~s~~~~~~~~~~~l~~piaHgEGrf~~~~~~l~~l~  158 (219)
T Consensus        69 ~iPILGIClG~Q~ia~~--~Gg~v~k~~~g~~G~----------n~pv~~~-~~~~~~~~~~~H~~---~v~~~---~lp  129 (178)
T cd01744          69 KIPIFGICLGHQLLALA--LGAKTYKMKFGHRGS----------NHPVKDL-ITGRVYITSQNHGY---AVDPD---SLP  129 (178)
T ss_pred             CCCEEEECHHHHHHHHH--CCCCCCCCCCCCCCC----------CCCCEEC-CCCCEEEEECCCCE---EEEEC---CCC
T ss_conf             99889981217889988--198300156672478----------7121676-88838886447554---87624---589


Q ss_pred             HCCEEEEECCCCCCCCCCCCCEEEEECCCCCEEEECCCCHHHCCCCCCCCCHHHHHHHHC
Q ss_conf             225036531688888988112668886999899984884343221006776289998642
Q gi|254780971|r  159 KNNQIVFRYASGTNPNGSLHDIAGVINRRGNVLGMMPHPENIIEKFHGGIDGRGLFASLL  218 (219)
Q Consensus       159 ~~~~i~~~Y~d~~NPNGS~~~IAgi~s~~G~vlgmMPHPER~~~~~~~~~dG~~~f~~~~  218 (219)
T Consensus       130 ~~~~v~a-~----s~~--d~~i~ai~h~~~~i~GVQFHPEs~----~~~~~~~~if~nFl  178 (178)
T cd01744         130 GGLEVTH-V----NLN--DGTVEGIRHKDLPVFSVQFHPEAS----PGPHDTEYLFDEFL  178 (178)
T ss_pred             CCCEEEE-E----CCC--CCCEEEEEECCCCEEEEEECCCCC----CCCCCCHHHHHHHC
T ss_conf             9857999-6----489--985799998999999998599799----99977489897239