HHsearch alignment for GI: 254780696 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=97.44  E-value=0.0025  Score=42.18  Aligned_cols=251  Identities=18%  Similarity=0.277  Sum_probs=150.7

Q ss_pred             HHHHHHCCCEEEEEEHHHEEEECCEEEEEEEEEEEECCCCCEEEECCCCCCCHHHCCEEEEECCCCCCHHHHHHHHH---
Q ss_conf             99999889889999541248999899999999998077741265046443521006366883288622479999999---
Q gi|254780696|r   28 ALEAQVRGYQIFHYTPDQLYMRDSKIYANTQPLSLDEKKEQYYSLGEEKIIDLSQMDVILIRQDPPFNMHYITSTYL---  104 (316)
Q Consensus        28 m~eAq~RGheV~~~~~~dL~~~~g~v~A~~~~i~i~~~~~~~f~~~~~~~~~L~~fD~i~iR~dPp~d~~yi~~~~~---  104 (316)
T Consensus        33 cKALkEEGy~viLVNsNpATimTD~~~AD~vY~e----PlT~e~V~--~IIEKERPDgiL~------t~GGQTALNlav~  100 (1089)
T TIGR01369        33 CKALKEEGYEVILVNSNPATIMTDPEMADKVYIE----PLTPEAVE--KIIEKERPDGILP------TLGGQTALNLAVE  100 (1089)
T ss_pred             HHHHHHCCCEEEEECCCCCCCCCCHHHCCCCCCC----CCCHHHHH--HHHHHCCCCCHHC------CCCCHHHHHHHHH
T ss_conf             9998764957999758847233886686600252----54588886--6653168660002------5760357777886


Q ss_pred             HHH---HCC-CCEEE-CCHHHHHHCCCH-HHH---HHHHHHCCCCEEECCHHHHHHHHHHHH-HHHHHCCCCCCCCCEEE
Q ss_conf             986---235-85041-174887525650-343---345430443100037245568888521-43311168854344687
Q gi|254780696|r  105 LEK---INP-ETLIV-NNPFWIRNSPEK-IFV---TEFSELMPPTLISRDITQITRFYLEMK-DIIIKPLYGNGGTGVFR  174 (316)
Q Consensus       105 Le~---~~~-~~~vi-N~p~~i~~~~eK-l~~---~~~~~~~P~T~vt~~~~~~~~f~~~~~-~vViKPl~g~~G~gV~~  174 (316)
T Consensus       101 L~~~GVL~kYgV~vLGT~~eaI~kaEDRe~F~~~M~ei~~pvp~S~~~~~~eEA~~~a~~~GyPviVRpAftLGG~GgG-  179 (1089)
T TIGR01369       101 LEESGVLEKYGVEVLGTPVEAIKKAEDRELFREAMKEIGEPVPKSEIVHSVEEALKAAKEIGYPVIVRPAFTLGGTGGG-  179 (1089)
T ss_pred             HHHCCCCHHHCCEEECCCHHHHHHHCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHCCCCEEECCCHHCCCCCCC-
T ss_conf             6206851452917852342435202027999999997389988110027889999999626896898100323889985-


Q ss_pred             ECCCCCCHHHHHHHHHHHCC-CCCCEEECCCCCCCCCEEEEEECC-----EEEEEEEE-----ECCCCCCCCCCCCCCCE
Q ss_conf             44887115889999984001-334002105344568269999899-----88632122-----04568600000014731
Q gi|254780696|r  175 ITLGDRNFSSLIEMLFEKYP-EPLMIQSYLPQIRDGDKRILLLNG-----KPVGAVNR-----IPSEVDNRSNIHAGGKA  243 (316)
Q Consensus       175 i~~~~~~~~~~~e~~~~~~~-~~ii~Qefi~~~~~gD~Rv~vi~g-----~~v~a~~R-----~~~~~~~r~Nl~~Gg~~  243 (316)
T Consensus       180 iA~n~eEL~~~~~~aL~~SpI~qvL~EkSl~GWKE--~EYEVmRD~~dNCItVCNmEN~DPmGVHTGdSIVV-------A  250 (1089)
T TIGR01369       180 IASNEEELKEIVERALSASPINQVLVEKSLAGWKE--IEYEVMRDSKDNCITVCNMENFDPMGVHTGDSIVV-------A  250 (1089)
T ss_pred             EECCHHHHHHHHHHHHHHCCCCEEEEEEECCCCEE--EEEEEEEECCCCEEEEECCCCCCCCCEEECCCEEE-------C
T ss_conf             22577899999998863088855750110033178--89889862687889997454768984570783365-------0


Q ss_pred             EEEECCHHHHH----HHHHHHHHHHHCCCEEEEEEE---EC-----CEEEEEECCCCHHHHH---HHHHCCCCHHHHH
Q ss_conf             11007789999----999999999984987999951---17-----8788983688303788---9975199989999
Q gi|254780696|r  244 ELTKLTKIDLD----ICKRIGESLRERGLFFTGIDV---IG-----DYITEINVTSPTCIRE---IHRNGGENVASLF  306 (316)
Q Consensus       244 ~~~~lt~~~~~----i~~~~~~~L~~~gl~~~GiDi---ig-----~~i~EvNvtsP~g~~~---~~~~~~~~i~~~i  306 (316)
T Consensus       251 PSQTLtD~EYQ~LR~~sikIIR~l---Gi~GgGCNvQFAL~P~s~~Y~vIEvN---PRvSRSSALASKATGYPiAkvA  322 (1089)
T TIGR01369       251 PSQTLTDKEYQMLRDASIKIIREL---GIVGGGCNVQFALDPDSGRYYVIEVN---PRVSRSSALASKATGYPIAKVA  322 (1089)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHC---CCEECCCCEEEEECCCCCCEEEEEEC---CCCCHHHHHHHHHHCCHHHHHH
T ss_conf             763688078999999999999873---91216742132150789706999867---8821358987665166289999