HHsearch alignment for GI: 254780328 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=95.52  E-value=0.014  Score=35.14  Aligned_cols=232  Identities=18%  Similarity=0.162  Sum_probs=114.7

Q ss_pred             CCEEEEECCCCH-H---------HHHHHHHHHHCCCEEEEEECCCCCCHHHHCC-----CCEEEEECCCHHHHHHHHHHC
Q ss_conf             447999687882-7---------7999999998798899992687675213023-----867984268999999998756
Q gi|254780328|r    3 NKNVLVVGGAGY-I---------GAHTCRVLYERGFLPIVLDNLSSGHAEFVLW-----GPLEQVDICDYTNLRAVFAKY   67 (333)
Q Consensus         3 ~kkIlItG~tGf-i---------Gs~l~~~L~~~g~~v~~~d~~~~~~~~~~~~-----~~~~~~Di~d~~~l~~~~~~~   67 (333)
T Consensus       573 Kk~~lvlGSGp~RIGqgvEFDYc~Vh~~~aLr~~Gye~ImiN----~NPETVSTDyD~sDrLYFEpl-t~E~Vm~I~e~E  647 (1089)
T TIGR01369       573 KKKVLVLGSGPNRIGQGVEFDYCCVHAVLALREAGYETIMIN----YNPETVSTDYDTSDRLYFEPL-TFEDVMNIIELE  647 (1089)
T ss_pred             CCEEEEECCCCEECCCCEEEHHHHHHHHHHHHHCCCEEEEEE----CCCCCCCCCHHHHHHCCCCCC-CCCCCEEHEEEC
T ss_conf             856899878451406631205678999999987299599997----789974366665101158763-503100110005


Q ss_pred             CCC-EEEECHHHCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCC----CCCCCCCCCCCCCCC
Q ss_conf             988-9995714401122343100123301233322211222222-2222223333222222----222222222222222
Q gi|254780328|r   68 QPA-SVMHFAGLTNISESVKNPSLFYEINIKGSFNLIATAIESN-VRRFIFSSTCATYGIP----HNTIITENDPQESIT  141 (333)
Q Consensus        68 ~~d-~ViHlAa~~~~~~~~~~p~~~~~~Nv~gt~~ll~~~~~~~-~~~~i~~SS~~vYG~~----~~~~~~E~~~~~p~~  141 (333)
T Consensus       648 ~~~GVIVq~GGQtp~-------------------nlA~~L~~~GG~~-iLGTS~~~ID~AEDR~kFs~~l~~Lgi~QP~~  707 (1089)
T TIGR01369       648 KPEGVIVQFGGQTPL-------------------NLAKELEEAGGVP-ILGTSPESIDRAEDREKFSELLDELGIPQPEW  707 (1089)
T ss_pred             CCCEEEEECCCHHHH-------------------HHHHHHHHCCCCE-EECCCHHHHHHHCCHHHHHHHHHHCCCCCCCC
T ss_conf             866799974873267-------------------8999999708931-73688578751318679999997158798988


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC---------CCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             2222222333222222222222222222222222222222222333---------3322222222222222222222222
Q gi|254780328|r  142 PYGYTKYVVERELLQHNKVNGLRSVVLRYFNAAGATLDSIIGEWHN---------PETHVIPLAIKTAMGYQNSFKVFGQ  212 (333)
Q Consensus       142 ~Yg~sK~~~E~~~~~~~~~~~~~~~~~R~~~vyGp~~~~~~g~~~~---------~~~~~~~~~i~~~~~~~~~i~i~g~  212 (333)
T Consensus       708 ~~a~s~ee----a~~~A~~iGYP-vlvRPSYVLgG~aM~iv~~~eeL~~yl~~a~~~S~~~PVlidky~e~A~E~dV---  779 (1089)
T TIGR01369       708 KIATSVEE----AKEFASEIGYP-VLVRPSYVLGGRAMEIVYNEEELARYLEEAVEVSPEHPVLIDKYLEDAVEIDV---  779 (1089)
T ss_pred             CEECCHHH----HHHHHHHCCCC-EEECCCCCCCCCCHHEECCHHHHHHHHHHHHHHCCCCCEEEEEECCCCEEEEE---
T ss_conf             52728799----99998546992-89816830033621002678899999999997208997698885288889999---


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCC--CCEE------EEECCCCEEHHHHHHHHHHHHCCCCCEE
Q ss_conf             22222232211001111100000001110023587--3103------6417998029999999999837898759
Q gi|254780328|r  213 DYATRDGTCLRDYIHVLDLANAHIMALEYLINQGD--SIAI------NLGTGTGITVKEIISTIQSMYECAFPIT  279 (333)
Q Consensus       213 ~~~~~dg~~~Rdfi~v~D~~~a~~~~~~~~~~~~~--~~~~------Nig~~~~~si~~l~~~i~~~~g~~~~i~  279 (333)
T Consensus       780 -D~v~Dg~~v-----------~i~gI~EHiE~AGVHSGDs~~~~Pp~~L~~~~~~~i~~~~~~iA~~L~v~Gl~N  842 (1089)
T TIGR01369       780 -DAVSDGEEV-----------LIPGIMEHIEEAGVHSGDSTCVLPPQTLSEDIVKRIKDIVRKIAKELNVKGLFN  842 (1089)
T ss_pred             -EEEEECCEE-----------EEEEHHHHHHHCCCCCCCHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCEE
T ss_conf             -899728848-----------996231234213676130531176977788999999999999998706607222