HHsearch alignment for GI: 254780206 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=99.96  E-value=3.7e-29  Score=230.71  Aligned_cols=360  Identities=20%  Similarity=0.289  Sum_probs=254.4

Q ss_pred             EEEEECCCH------HH------HHHHHHHHHCCCCCEEEEECCCHHHH----HCCEEEECCCCCHHHHHHHHHHHCCCE
Q ss_conf             589988658------89------99999998589967899954983575----117055128789899999998718979
Q gi|254780206|r    2 RVLLIGSGG------RE------HALAWKIAQSPLLSELWSIPGNPGIA----QHAQCVAIDIQNHSAIIHFCQEKHIDL   65 (424)
Q Consensus         2 kILviGsGg------rE------hAl~~~l~~s~~~~~v~~~pgN~g~~----~~~~~~~i~~~d~~~i~~~a~~~~iDl   65 (424)
T Consensus         8 kvLviGSGPi~IGQAaEFDYSGsQA-cKALkEEGy--~viLVNsNpATimTD~~~AD~vY~ePlT~e~V~~IIEKERPDg   84 (1089)
T TIGR01369         8 KVLVIGSGPIVIGQAAEFDYSGSQA-CKALKEEGY--EVILVNSNPATIMTDPEMADKVYIEPLTPEAVEKIIEKERPDG   84 (1089)
T ss_pred             EEEEECCCCCCHHHHCCCHHHHHHH-HHHHHHCCC--EEEEECCCCCCCCCCHHHCCCCCCCCCCHHHHHHHHHHCCCCC
T ss_conf             8999666731131202302478999-999876495--7999758847233886686600252545888866653168660


Q ss_pred             EEE--CCCHHHHHHH----HHHHHHCCCCEEECCHHHHHHHHCCHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCCE
Q ss_conf             999--7955787489----9898605880670106665552010235788876531011112234401111121012420
Q gi|254780206|r   66 VVV--GPELPLVNGI----SDALNAAGFKVFGPSQRAAKLESSKSFAKKFCTKYGIPTATYQHFSDPMKAKQYVQNKSMP  139 (424)
Q Consensus        66 viv--gpE~pL~~gi----~d~l~~~gi~v~Gp~~~aa~le~sK~~~K~~l~~~gIPt~~~~~~~~~~ea~~~~~~~g~P  139 (424)
T Consensus        85 iL~t~GGQTALNlav~L~~~GVL~kYgV~vLGT~~eaI~kaEDRe~F~~~M~ei~~pvp~S~~~~~~eEA~~~a~~~GyP  164 (1089)
T TIGR01369        85 ILPTLGGQTALNLAVELEESGVLEKYGVEVLGTPVEAIKKAEDRELFREAMKEIGEPVPKSEIVHSVEEALKAAKEIGYP  164 (1089)
T ss_pred             HHCCCCCHHHHHHHHHHHHCCCCHHHCCEEECCCHHHHHHHCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHCCCC
T ss_conf             00257603577778866206851452917852342435202027999999997389988110027889999999626896


Q ss_pred             EEEEECCCCCCCCCCCHHHHHHHHHHHHHHHCCC-CHHHHHHHHHHCC-CCCEEEECCCC-CCCCCCCCCCCCCCCCCCC
Q ss_conf             2563046534300023235677888788751445-3177788775205-75234421577-6310352000111356654
Q gi|254780206|r  140 IVVKADGLCAGKGVVVAATVDEATSAIDRCFQQI-NSTVIIEEYLEGF-EVSFFALCDGK-TAIPFTTARDHKRIHDGDI  216 (424)
Q Consensus       140 vVVKp~~~agGkGV~i~~~~~e~~~~~~~~~~~~-~~~VliEefl~G~-E~Sv~~i~dG~-~~~~l~~~~dyKr~~~~d~  216 (424)
T Consensus       165 viVRpAftLGG~GgGiA~n~eEL~~~~~~aL~~SpI~qvL~EkSl~GWKE~EYEVmRD~~dNCItVCNmEN~-----DPm  239 (1089)
T TIGR01369       165 VIVRPAFTLGGTGGGIASNEEELKEIVERALSASPINQVLVEKSLAGWKEIEYEVMRDSKDNCITVCNMENF-----DPM  239 (1089)
T ss_pred             EEECCCHHCCCCCCCEECCHHHHHHHHHHHHHHCCCCEEEEEEECCCCEEEEEEEEEECCCCEEEEECCCCC-----CCC
T ss_conf             898100323889985225778999999988630888557501100331788988986268788999745476-----898


Q ss_pred             CCCCCCCCEEECCCCCCCCCCEEEECCHHHHHHHHHHHCCCEEEEE-EEEEEEEECCE--EEEEEEEEEECCCCCEEEEE
Q ss_conf             4444344300001234432220100000899999862046235664-45448985570--48999886514775104433
Q gi|254780206|r  217 GPNTGGMGACSPALGMSQELYSTVIQKIILPTIEGMQKEQNPFQGV-LFAGLMITEQG--PYLIEYNVRFGDPECQAMMM  293 (424)
Q Consensus       217 GpnTGGMGa~~p~~~~~~~~~~~i~~~i~~~~~~~l~~~~~~y~G~-l~~~~m~t~~g--p~viE~N~R~GDPE~q~ilp  293 (424)
T Consensus       240 GVHTGdSIVVAPSQTLtD~EYQ~LR~-~sikIIR~lGi~-----GgGCNvQFAL~P~s~~Y~vIEvNPRvSRS---S---  307 (1089)
T TIGR01369       240 GVHTGDSIVVAPSQTLTDKEYQMLRD-ASIKIIRELGIV-----GGGCNVQFALDPDSGRYYVIEVNPRVSRS---S---  307 (1089)
T ss_pred             CEEECCCEEECCCCCCCCHHHHHHHH-HHHHHHHHCCCE-----ECCCCEEEEECCCCCCEEEEEECCCCCHH---H---
T ss_conf             45707833650763688078999999-999999873912-----16742132150789706999867882135---8---


Q ss_pred             CCCC-----CCHHHHHHHHHCC-CCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEE-ECCE
Q ss_conf             2654-----4115666542013-3332123444420675422544668775797624876668986899833587-7887
Q gi|254780206|r  294 RLES-----DILEILNSCVHGN-LHNTHINWKAEYALTVVVATKGYPEEYPHGTIISKIPQNTGTTQLFHAGTAI-VNNN  366 (424)
Q Consensus       294 ~L~~-----dl~~il~~~~~g~-L~~~~~~~~~~~~v~Vvlas~GYP~~~~kg~~I~~l~~~~~~~~ifhagt~~-~~g~  366 (424)
T Consensus       308 ALASKATGYPiAkvAAKLAvGY~LdEl~N~vT~~T~A~---------FEPSLDYvVvKIPRW~f~-K-F-~~v~r~LGt~  375 (1089)
T TIGR01369       308 ALASKATGYPIAKVAAKLAVGYGLDELKNPVTKTTPAS---------FEPSLDYVVVKIPRWDFD-K-F-EGVDRKLGTQ  375 (1089)
T ss_pred             HHHHHHHCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCC---------CCCCCCEEEECCCCCCCH-H-H-CCCCCCCCCE
T ss_conf             98766516628999999846887876568888853541---------046748088606788722-1-0-5788541521


Q ss_pred             EEECCCCEEEEEEECCCHHHHHHHHHHHHHC
Q ss_conf             9981880799999628989999999999852
Q gi|254780206|r  367 LTANGGRVLSATALGKTITESRELAYHMVEN  397 (424)
Q Consensus       367 l~t~GGRVL~vv~~g~~l~eA~~~ay~~i~~  397 (424)
T Consensus       376 MKS----vGEVMAIGRtFEEALQKA~Rsle~  402 (1089)
T TIGR01369       376 MKS----VGEVMAIGRTFEEALQKALRSLEI  402 (1089)
T ss_pred             EEE----EEEEECCCCCHHHHHHHHHHHHCC
T ss_conf             015----777734671389999898876537