HHsearch alignment for GI: 254780924 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=94.80  E-value=0.072  Score=29.70  Aligned_cols=99  Identities=15%  Similarity=0.255  Sum_probs=59.0

Q ss_pred             CCEEEECCCHHHHHHHHHHHHCCCCEEEECCCHHHHHHHHHCCCCEEE-CCCCCHHHHHHCCHHHCCEEEEECCCHHHHH
Q ss_conf             817997377489999999984799089971998999999976992999-7899989998489314679999359968999
Q gi|254780924|r  449 DHVILVGYGRIGKVIVQNLKAAGIALLVIEDSEKKIEELRSLGIDVIY-GNATITKILLMANIEKARSLVVSISTAFEAA  527 (609)
Q Consensus       449 ~~vii~G~g~~g~~~~~~L~~~~~~v~vid~~~~~~~~~~~~g~~~~~-gd~~~~~~l~~~~i~~a~~vi~~~~~~~~n~  527 (609)
T Consensus         2 ~kvLIanrGeiA~ri~rt~re~gi~~v~i~s~~d~~s~~~~~ad~~~~~~~~~~~------------------~~Yl~~~   63 (109)
T pfam00289         2 KKVLVANRGEIAVRIIRALRELGIETVAVNSNPDTVSTHVRLADEAYFLGPGPAS------------------ESYLNIE   63 (109)
T ss_pred             CEEEEECCCHHHHHHHHHHHHCCCCEEEEECHHHCCCHHHHHHHHHHHCCCCCCC------------------CCCCCHH
T ss_conf             4899988879999999999986997999963344152256650576534799832------------------1113799


Q ss_pred             HHHHHHHHHCCCCEEE----EEECCHHHHHHHHHCCCCEEECHH
Q ss_conf             9999999958988089----994698999999976998787658
Q gi|254780924|r  528 YITQEARNSNPSILII----ALADSDSEVEHLTRYGADTVVMSA  567 (609)
Q Consensus       528 ~~~~~~~~~~~~~~ii----a~~~~~~~~~~l~~~Ga~~vi~p~  567 (609)
T Consensus        64 ~Ii~ia~~~~~~-aihpGyGflsEn~~fa~~~~~~Gi~f-iGPs  105 (109)
T pfam00289        64 RILDIAEKEGAD-AIHPGYGFLSENAEFAEACEKAGITF-IGPS  105 (109)
T ss_pred             HHHHHHHHHCCC-EEECCCCCCCCCHHHHHHHHHCCCEE-ECCC
T ss_conf             999999981889-68779762335999999999888989-9958