HHsearch alignment for GI: 254780414 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=100.00  E-value=0  Score=361.95  Aligned_cols=173  Identities=25%  Similarity=0.445  Sum_probs=146.5

Q ss_pred             EEEEECCCCHHHHHHHHHHHCCCEEEEECCCCCHHHHHHCCCCEEEECCCCCCCCCC-CCCCCCHHHHHCCCCEEEECHH
Q ss_conf             999988970578899888865940698528989889972399799998538899999-9975376898089988997789
Q gi|254780414|r   10 VLIIDFGSQFTQLIARRVRESKVYCEVIAFKNALDYFKEQNPQAIILSGSPASSLDI-DSPQIPKEILESNIPLLGICYG   88 (520)
Q Consensus        10 IlIlDfGSQytqLIaRriRelgVyseI~P~~~~~e~i~~~~p~GIILSGGP~SV~d~-~ap~~~~~I~~~~iPILGICyG   88 (520)
T Consensus         1 i~ilDfGsqy~--i~r~lrelg~~~~v~~~~~~~~~i~~~~p~giIlS~GPg~p~~~~~~~~~~~~~~~~~iPILGIClG   78 (178)
T cd01744           1 VVVIDFGVKHN--ILRELLKRGCEVTVVPYNTDAEEILKLDPDGIFLSNGPGDPALLDEAIKTVRKLLGKKIPIFGICLG   78 (178)
T ss_pred             CEEEECCCHHH--HHHHHHHCCCEEEEEECCCCHHHHHHCCCCEEEECCCCCCHHHHCCHHHHHHHHHHCCCCEEEECHH
T ss_conf             99998874999--9999998799799993989999998419997998999999577344499999997469988998121


Q ss_pred             HHHHHHHCCCEEEECCCCCCCEEEEEECCCCCCCCCCCCCCCCEEEEEECCCHHH--CCCCCCCEEECCC-CCCEEEEEE
Q ss_conf             9998997096999869866103667523886222787266553368600220110--1244421123239-831788986
Q gi|254780414|r   89 QQIMCQSLGGKTKNSQSREFGRAFIEIKKNCSLLKGMWEKGSKQQVWMSHGDQVE--HIPEGFEVIASSD-STPFAFIAD  165 (520)
Q Consensus        89 ~QlLa~~~GG~V~~~~~~EyG~~~I~i~~~~~lf~gl~~~~~~~~VwmSH~D~V~--~lP~gf~viA~S~-~~~iaai~~  165 (520)
T Consensus        79 ~Q~ia~~~Gg~v~k~~~g~~G~n-------~pv~~~~--~~~~~~~~~~H~~~v~~~~lp~~~~v~a~s~~d~~i~ai~h  149 (178)
T cd01744          79 HQLLALALGAKTYKMKFGHRGSN-------HPVKDLI--TGRVYITSQNHGYAVDPDSLPGGLEVTHVNLNDGTVEGIRH  149 (178)
T ss_pred             HHHHHHHCCCCCCCCCCCCCCCC-------CCCEECC--CCCEEEEECCCCEEEEECCCCCCCEEEEECCCCCCEEEEEE
T ss_conf             78899881983001566724787-------1216768--88388864475548762458998579996489985799998


Q ss_pred             CCCCEEEEEEEEHHHCCCH-HHHHHHHHH
Q ss_conf             3500112465212221520-257799875
Q gi|254780414|r  166 EKRKYYAVQFHPEVVHTVG-GSQLIDNFV  193 (520)
Q Consensus       166 ~~~~iyGVQFHPEV~hT~~-G~~iL~NFl  193 (520)
T Consensus       150 ~~~~i~GVQFHPEs~~~~~~~~~if~nFl  178 (178)
T cd01744         150 KDLPVFSVQFHPEASPGPHDTEYLFDEFL  178 (178)
T ss_pred             CCCCEEEEEECCCCCCCCCCCHHHHHHHC
T ss_conf             99999999859979999977489897239