HHsearch alignment for GI: 254780420 and conserved domain: pfam00988

>pfam00988 CPSase_sm_chain Carbamoyl-phosphate synthase small chain, CPSase domain. The carbamoyl-phosphate synthase domain is in the amino terminus of protein. 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 pfam00289. The small chain has a GATase domain in the carboxyl terminus. See pfam00117.
Probab=100.00  E-value=0  Score=433.86  Aligned_cols=130  Identities=54%  Similarity=0.843  Sum_probs=127.6

Q ss_pred             CEEEEECCCCEEEEEEECCCCEEEEEEEEECCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCHHHHCCCCCCCCCEEEE
Q ss_conf             66899728987999975676248888985378888760141614256173216897368458823420465333210236
Q gi|254780420|r   13 TAVLVLADGSVIEGMGCGATGSIQAEICFNTSLTGYQEILTDPSYLGQIVNFTFPHIGNVGVNSEDFESISRKNFKGAVG   92 (396)
Q Consensus        13 ~A~L~LedGt~f~G~~fG~~~~~~GEvVFnT~mtGYqE~lTDPSY~gQIlvfT~P~IGNyGvn~~d~ES~~~~~~~~~~g   92 (396)
T Consensus         2 ka~L~LedG~~f~G~~fG~~~~~~GEvvFnT~mtGYqE~lTDPSY~gQIl~fT~P~IGNyGin~~d~ES----~~~~~~G   77 (131)
T pfam00988         2 KAYLVLEDGTVFEGESFGAEGEAVGEVVFNTGMTGYQEILTDPSYAGQIVVFTYPLIGNYGINPEDFES----DKPHAKG   77 (131)
T ss_pred             CEEEEECCCCEEEEEECCCCCCEEEEEEEECCCCCCCEECCCCCCCCEEEEECCCCCCCCCCCCCCCCC----CCCCCCE
T ss_conf             379995799999879737776577799997887654403258765774899746640441779743200----4764057


Q ss_pred             EEEECCCCCCCCCCCCCCHHHHHHHCCCCEECCCCHHHHHHHHHHCCCCCEEEE
Q ss_conf             664046544345524179899997427832112576899999985398423663
Q gi|254780420|r   93 LVIKAEITEPSNYRANMHFDAWLKSCGIIGLSGIDTRALTVWIRDYGVSNSVIA  146 (396)
Q Consensus        93 ~Iv~~~~~~~Sn~rs~~sL~~wL~~~~IpgI~GIDTRaLTk~IRe~G~~~a~I~  146 (396)
T Consensus        78 ~iv~~~~~~~S~~~s~~sL~~~L~~~~IpgI~gIDTRaLt~~iR~~G~~~~~I~  131 (131)
T pfam00988        78 LIVRELSDIPSNWRSEESLDEFLKEHGIPGISGVDTRALTRKLREKGAMKGVIS  131 (131)
T ss_pred             EEECCCCCCCCCHHHHCCHHHHHHHCCCCEEECCCHHHHHHHHHHCCCCCEEEC
T ss_conf             985356657665323359999999779722706618999999986698516849