HHsearch alignment for GI: 254780595 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=96.91 E-value=0.0031 Score=37.96 Aligned_cols=222 Identities=15% Similarity=0.147 Sum_probs=96.9
Q ss_pred EEEEECCC-----------HHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHCCCEEEECCCCCCCHHHHH-HHCCCCEEE
Q ss_conf 39998888-----------889999999998898899996794463455644982898067864023465-411563278
Q gi|254780595|r 2 HLMIFGAG-----------YTGKFIADAALKVGVYTCGTTRSVSNLLTLKHKGISPFLFADQKINNLLRE-KLYFTTHIV 69 (289)
Q Consensus 2 kIlI~GaG-----------~iG~~l~~~L~~~g~~V~~~~r~~~~~~~l~~~~~~~~~~~~~~~~~~~~~-~~~~~~~v~ 69 (289)
T Consensus 575 ~~lvlGSGp~RIGqgvEFDYc~Vh~~~aLr~~Gye~ImiN~NPETVSTDyD~-sDrLYFEplt~E~Vm~I~e~E~~~GVI 653 (1089)
T TIGR01369 575 KVLVLGSGPNRIGQGVEFDYCCVHAVLALREAGYETIMINYNPETVSTDYDT-SDRLYFEPLTFEDVMNIIELEKPEGVI 653 (1089)
T ss_pred EEEEECCCCEECCCCEEEHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCHHH-HHHCCCCCCCCCCCEEHEEECCCCEEE
T ss_conf 6899878451406631205678999999987299599997789974366665-101158763503100110005866799
Q ss_pred EEECCCCCCCEEECCCCCHHHHHHHC-C-CCCCCCCCEEEC--CCCC--CCCCCCCCCCCCCCHHHHHHHHHHHHHHHCC
Q ss_conf 76124443310001221013443201-2-334333320102--5762--1234532112343113455445555432001
Q gi|254780595|r 70 QCIKPSSEGDPCIISMSKDFYKFMPH-V-KWIGYLSSTSIY--GNRE--GQWVDEHSFVHPISCVATQRFNAEKEWLAIT 143 (289)
Q Consensus 70 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~-~~~i~~SS~~VY--g~~~--g~~i~E~~~~~P~~~y~~~k~~~E~~~~~~~ 143 (289)
T Consensus 654 Vq~G---------GQtp~nlA~~L~~~GG~~iLGTS~~~ID~AEDR~kFs~~l~~Lgi~QP~~~~a~s~e----ea~~~A 720 (1089)
T TIGR01369 654 VQFG---------GQTPLNLAKELEEAGGVPILGTSPESIDRAEDREKFSELLDELGIPQPEWKIATSVE----EAKEFA 720 (1089)
T ss_pred EECC---------CHHHHHHHHHHHHCCCCEEECCCHHHHHHHCCHHHHHHHHHHCCCCCCCCCEECCHH----HHHHHH
T ss_conf 9748---------732678999999708931736885787513186799999971587989885272879----999998
Q ss_pred CCCCCCCCCCCCCCCCCCC-------CCHHHHHH-------CCCCCCCCCCCCEEC-C--HHHHHHH--------HHHHH
Q ss_conf 2345676420347777898-------50344431-------134543222110001-0--2477779--------99999
Q gi|254780595|r 144 KKLNIKLAVLRLSGIYGPK-------RNPFIKIR-------QKNSLRLVKKNQVFN-R--IRVEDVA--------RCVIF 198 (289)
Q Consensus 144 ~~~~~~~~ilR~~~iyGp~-------r~~~~~~~-------~g~~~~~~~~~~~~~-~--ihv~Dva--------~~i~~ 198 (289)
T Consensus 721 ~~iGYPv-lvRPSYVLgG~aM~iv~~~eeL~~yl~~a~~~S~~~PVli---dky~e~A~E~dVD~v~Dg~~v~i~gI~EH 796 (1089)
T TIGR01369 721 SEIGYPV-LVRPSYVLGGRAMEIVYNEEELARYLEEAVEVSPEHPVLI---DKYLEDAVEIDVDAVSDGEEVLIPGIMEH 796 (1089)
T ss_pred HHCCCCE-EECCCCCCCCCCHHEECCHHHHHHHHHHHHHHCCCCCEEE---EEECCCCEEEEEEEEEECCEEEEEEHHHH
T ss_conf 5469928-9816830033621002678899999999997208997698---88528888999989972884899623123
Q ss_pred HHCCC--CC------CCEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf 95135--57------861626843333899999999995579986343101
Q gi|254780595|r 199 LMTHH--LG------GIFNLSDDEPAPPQNVIMEAASLMKITPPLEQCFDT 241 (289)
Q Consensus 199 l~~~~--~~------~iyni~~~~~~s~~e~~~~i~~~~g~~~~~~~~~~~ 241 (289)
T Consensus 797 iE~AGVHSGDs~~~~Pp~~L~~~~~~~i~~~~~~iA~~L~v~Gl~NiQf~~ 847 (1089)
T TIGR01369 797 IEEAGVHSGDSTCVLPPQTLSEDIVKRIKDIVRKIAKELNVKGLFNIQFVV 847 (1089)
T ss_pred HHHCCCCCCCHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEEE
T ss_conf 421367613053117697778899999999999999870660722245556