HHsearch alignment for GI: 254780439 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=99.49  E-value=5.6e-14  Score=128.49  Aligned_cols=96  Identities=34%  Similarity=0.498  Sum_probs=89.8

Q ss_pred             CEEEEECCCCEEECCCCCCCHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCEEEEEE--------CCHHHHHHHHH
Q ss_conf             4189972763020147665318999999999659806996068652112324586379841--------67889999998
Q gi|254780439|r  619 KKIVILGGGPNRIGQGIEFDYCCCHASFSLKEAGFETIMINCNPETVSTDYDIADRLYFES--------LTEEDILEILR  690 (1162)
Q Consensus       619 kkviVlGsGp~RIGqgiEFDy~~v~a~~aLr~~G~~tImIN~NPETVSTDyd~sDrLYFEp--------lt~E~V~~I~~  690 (1162)
T Consensus         2 ~kvLIanrGei-----------A~ri~rt~re~gi~~v~i~s~~d~~s~~~~~ad~~~~~~~~~~~~~Yl~~~~Ii~ia~   70 (109)
T pfam00289         2 KKVLVANRGEI-----------AVRIIRALRELGIETVAVNSNPDTVSTHVRLADEAYFLGPGPASESYLNIERILDIAE   70 (109)
T ss_pred             CEEEEECCCHH-----------HHHHHHHHHHCCCCEEEEECHHHCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHH
T ss_conf             48999888799-----------9999999998699799996334415225665057653479983211137999999999


Q ss_pred             HHCCCCCCCEEEEECCCHHHHH----HHHHHHHCCCEEEECCCCHH
Q ss_conf             7485678227998445124668----98888875983861275203
Q gi|254780439|r  691 VEQQKGELVGIIVQFGGQTPLK----LSKILEKNQIPILGTQPDSI  732 (1162)
Q Consensus       691 ~E~p~g~~~~vi~q~gGqt~~~----la~~L~~~gv~ilGts~~~I  732 (1162)
T Consensus        71 ~~~-------~~aihpGyGflsEn~~fa~~~~~~Gi~fiGPs~~~i  109 (109)
T pfam00289        71 KEG-------ADAIHPGYGFLSENAEFAEACEKAGITFIGPSPEAI  109 (109)
T ss_pred             HHC-------CCEEECCCCCCCCCHHHHHHHHHCCCEEECCCHHHC
T ss_conf             818-------896877976233599999999988898999583549