HHsearch alignment for GI: 254780268 and conserved domain: pfam00289

>pfam00289 CPSase_L_chain Carbamoyl-phosphate synthase L chain, N-terminal domain. Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both the urea cycle and the biosynthesis of arginine and/or pyrimidines. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. The small chain promotes the hydrolysis of glutamine to ammonia, which is used by the large chain to synthesize carbamoyl phosphate. See pfam00988. The small chain has a GATase domain in the carboxyl terminus. See pfam00117.
Probab=100.00  E-value=7.7e-36  Score=274.91  Aligned_cols=109  Identities=62%  Similarity=0.958  Sum_probs=107.0

Q ss_pred             CEEEEEECCCHHHHHHHHHHHHCCCEEEEECCCHHHCCCCHHHCCEEEECCCCCCCCHHCCHHHHHHHHHHCCCCEEECC
Q ss_conf             70686644709999999988880965999858557718776758579991899853000698999999987099899458
Q gi|254780268|r    2 ISKILIANRGEIALRILRACKELGIPTVAVHSTADSGAMHVRLADESVCIGPPSSKDSYLNIQQIVAACEVTGADAIHPG   81 (443)
Q Consensus         2 ~~~iLianrGeia~riira~~elGi~tv~v~s~~D~~a~~~~~ADe~~~i~~~~~~~sYldi~~ii~~a~~~~~daihPG   81 (443)
T Consensus         1 i~kvLIanrGeiA~ri~rt~re~gi~~v~i~s~~d~~s~~~~~ad~~~~~~~~~~~~~Yl~~~~Ii~ia~~~~~~aihpG   80 (109)
T pfam00289         1 IKKVLVANRGEIAVRIIRALRELGIETVAVNSNPDTVSTHVRLADEAYFLGPGPASESYLNIERILDIAEKEGADAIHPG   80 (109)
T ss_pred             CCEEEEECCCHHHHHHHHHHHHCCCCEEEEECHHHCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCCEEECC
T ss_conf             94899988879999999999986997999963344152256650576534799832111379999999998188968779


Q ss_pred             CCHHHCCHHHHHHHHHCCCEEECCCHHHH
Q ss_conf             53131097666889845921626898999
Q gi|254780268|r   82 YGFLSENAKFAEILEDHHIKFIGPSSEHI  110 (443)
Q Consensus        82 yGfLsEn~~fa~~~e~~Gi~fIGPs~~ai  110 (443)
T Consensus        81 yGflsEn~~fa~~~~~~Gi~fiGPs~~~i  109 (109)
T pfam00289        81 YGFLSENAEFAEACEKAGITFIGPSPEAI  109 (109)
T ss_pred             CCCCCCCHHHHHHHHHCCCEEECCCHHHC
T ss_conf             76233599999999988898999583549