HHsearch alignment for GI: 254781179 and conserved domain: TIGR01369

>TIGR01369 CPSaseII_lrg carbamoyl-phosphate synthase, large subunit; InterPro: IPR006275 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates , . CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate . The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain . CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites . The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein . The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP . There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia . CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains . This entry represents glutamine-dependent CPSase (6.3.5.5 from EC) from prokaryotes and eukaryotes (CPSase II). ; GO: 0004086 carbamoyl-phosphate synthase activity, 0006807 nitrogen compound metabolic process.
Probab=100.00  E-value=7e-39  Score=269.37  Aligned_cols=270  Identities=21%  Similarity=0.311  Sum_probs=222.8

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHCCCEEEEECCC---------------------CCHHHHHHHCCCCEEEECCCCCCCCC
Q ss_conf             787127889999999999999879889996158---------------------65688887539989999254884343
Q gi|254781179|r    7 GISSEREVSLSSGKACASALEDAGFKVSQIDVD---------------------RSVGLVLAHLKPDLAFNVLHGNFGED   65 (300)
Q Consensus         7 G~s~E~~iSl~S~~~i~~aL~~~g~~v~~id~~---------------------~~~~~~l~~~~~D~vf~~lhG~~gEd   65 (300)
T Consensus        20 GQAaEFD---YSGsQAcKALkEEGy~viLVNsNpATimTD~~~AD~vY~ePlT~e~V~~IIEKERPDgiL~t~GGQTALN   96 (1089)
T TIGR01369        20 GQAAEFD---YSGSQACKALKEEGYEVILVNSNPATIMTDPEMADKVYIEPLTPEAVEKIIEKERPDGILPTLGGQTALN   96 (1089)
T ss_pred             HHHCCCH---HHHHHHHHHHHHCCCEEEEECCCCCCCCCCHHHCCCCCCCCCCHHHHHHHHHHCCCCCHHCCCCCHHHHH
T ss_conf             1202302---4789999998764957999758847233886686600252545888866653168660002576035777


Q ss_pred             CHH----HHHHHHHHHHCCCCCHHHHHHCCCCHHCCCCCCCCEEECCCEEEECCCCC--HHHHHCCCCEEEEECC--CCC
Q ss_conf             102----35666432100231002332036500100002121000012132022200--0122105862564324--776
Q gi|254781179|r   66 GLV----QAILELLEIPYTHSGILASALSMDKMRSKQVVSSCGVPVCPSILVNRFTM--DSQHLISPPYVIKPLK--GGS  137 (300)
Q Consensus        66 g~i----q~~le~~~ipy~Gs~~~~~~l~~dK~~~k~~l~~~gIptp~~~~~~~~~~--~~~~~~~~P~ivKP~~--ggs  137 (300)
T Consensus        97 lav~L~~~GVL~kYgV~vLGT~~eaI~kaEDRe~F~~~M~ei~~pvp~S~~~~~~eEA~~~a~~~GyPviVRpAftLGG~  176 (1089)
T TIGR01369        97 LAVELEESGVLEKYGVEVLGTPVEAIKKAEDRELFREAMKEIGEPVPKSEIVHSVEEALKAAKEIGYPVIVRPAFTLGGT  176 (1089)
T ss_pred             HHHHHHHCCCCHHHCCEEECCCHHHHHHHCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHCCCCEEECCCHHCCCC
T ss_conf             78866206851452917852342435202027999999997389988110027889999999626896898100323889


Q ss_pred             CCCEEEECCHHHHHHHHHHHCCCCCCCCCCCCCCCCC-CEEEEEECCCCCCCEEEE-----CCCCCCCCCCCCCCCCCCC
Q ss_conf             4211432598999998863003668854223335788-457887314444200220-----2554333311000011222
Q gi|254781179|r  138 SLGIIVIKKDQSIPLDLLQSSSWNHGDQLLIEQYVDG-IELTCGVMGDASLDVTEI-----AVPKSDFYSYELKYSSLNS  211 (300)
Q Consensus       138 S~Gv~~v~~~~el~~~~~~~~~~~~~~~vlVEefI~G-~E~~v~Vl~~~~~~~~ei-----~~~~~~~~dy~~Ky~~~~~  211 (300)
T Consensus       177 --GgGiA~n~eEL~~~~~~aL~~SpI~qvL~EkSl~GWKE~EYEVmRD~~dNCItVCNmEN~DPmG-V-------HTGdS  246 (1089)
T TIGR01369       177 --GGGIASNEEELKEIVERALSASPINQVLVEKSLAGWKEIEYEVMRDSKDNCITVCNMENFDPMG-V-------HTGDS  246 (1089)
T ss_pred             --CCCEECCHHHHHHHHHHHHHHCCCCEEEEEEECCCCEEEEEEEEEECCCCEEEEECCCCCCCCC-E-------EECCC
T ss_conf             --9852257789999999886308885575011003317889889862687889997454768984-5-------70783


Q ss_pred             CCCCCCC-CHHHHHHHHHHHHHHHHHHCCCCCE-EEEEEEEECCCCEEEEEEECCCCCCCHHHHH---------HHHHH-
Q ss_conf             2458652-1166655444444457753487645-7999999768983999974726588822389---------99999-
Q gi|254781179|r  212 THVLPAK-IPLDIYKEVQRLAFLAHQAIGCRGI-SRSDFLFDPLSRKVFWLEINVQPGMTPVSIF---------PEMAA-  279 (300)
Q Consensus       212 ~~~~Pa~-l~~~~~~~i~~~a~~~~~alg~~g~-~rvDf~~d~~~g~~~~lEvN~~PGlt~~s~~---------p~~~~-  279 (300)
T Consensus       247 IVVAPSQTLtD~EYQ~LR~~sikIIR~lGi~GgGCNvQFAL~P~s~~Y~vIEvNPR--vSRSSALASKATGYPiAkvAAK  324 (1089)
T TIGR01369       247 IVVAPSQTLTDKEYQMLRDASIKIIRELGIVGGGCNVQFALDPDSGRYYVIEVNPR--VSRSSALASKATGYPIAKVAAK  324 (1089)
T ss_pred             EEECCCCCCCCHHHHHHHHHHHHHHHHCCCEECCCCEEEEECCCCCCEEEEEECCC--CCHHHHHHHHHHCCHHHHHHHH
T ss_conf             36507636880789999999999998739121674213215078970699986788--2135898766516628999999


Q ss_pred             -HCCCCHHHHHHH
Q ss_conf             -839998999999
Q gi|254781179|r  280 -YAGYSFRELLLW  291 (300)
Q Consensus       280 -~~G~s~~~li~~  291 (300)
T Consensus       325 LAvGY~LdEl~N~  337 (1089)
T TIGR01369       325 LAVGYGLDELKNP  337 (1089)
T ss_pred             HHCCCCCCCCCCC
T ss_conf             8468878765688