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