HHsearch alignment for GI: 254780268 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=100.00  E-value=0  Score=450.68  Aligned_cols=370  Identities=23%  Similarity=0.340  Sum_probs=312.1

Q ss_pred             EEEEEECCCHH-----------HHHHHHHHHHCCCEEEEECCCHHHCCCCHHHCCEEEECCCCCCCCHHCCHHHHHHHHH
Q ss_conf             06866447099-----------9999998888096599985855771877675857999189985300069899999998
Q gi|254780268|r    3 SKILIANRGEI-----------ALRILRACKELGIPTVAVHSTADSGAMHVRLADESVCIGPPSSKDSYLNIQQIVAACE   71 (443)
Q Consensus         3 ~~iLianrGei-----------a~riira~~elGi~tv~v~s~~D~~a~~~~~ADe~~~i~~~~~~~sYldi~~ii~~a~   71 (443)
T Consensus       574 k~~lvlGSGp~RIGqgvEFDYc~Vh~~~aLr~~Gye~ImiN~NPETVSTDyD~sDrLYFEp--------lt~E~Vm~I~e  645 (1089)
T TIGR01369       574 KKVLVLGSGPNRIGQGVEFDYCCVHAVLALREAGYETIMINYNPETVSTDYDTSDRLYFEP--------LTFEDVMNIIE  645 (1089)
T ss_pred             CEEEEECCCCEECCCCEEEHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCHHHHHHCCCCC--------CCCCCCEEHEE
T ss_conf             5689987845140663120567899999998729959999778997436666510115876--------35031001100


Q ss_pred             HCCCCEE---ECCCCHHHCCHHHHHHHHHCC-CEEECCCHHHHHHHHCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf             7099899---458531310976668898459-216268989998721899887766422443324333455799987320
Q gi|254780268|r   72 VTGADAI---HPGYGFLSENAKFAEILEDHH-IKFIGPSSEHIKIMGDKITAKKTAQQLGIPVVPGSGEVYPHTAMPIAK  147 (443)
Q Consensus        72 ~~~~dai---hPGyGfLsEn~~fa~~~e~~G-i~fIGPs~~ai~~~gDK~~~k~~a~~~GVP~~p~~~~~~~~ea~~~a~  147 (443)
T Consensus       646 ~E~~~GVIVq~GGQtp~----nlA~~L~~~GG~~iLGTS~~~ID~AEDR~kFs~~l~~Lgi~QP~~~~a~s~eea~~~A~  721 (1089)
T TIGR01369       646 LEKPEGVIVQFGGQTPL----NLAKELEEAGGVPILGTSPESIDRAEDREKFSELLDELGIPQPEWKIATSVEEAKEFAS  721 (1089)
T ss_pred             ECCCCEEEEECCCHHHH----HHHHHHHHCCCCEEECCCHHHHHHHCCHHHHHHHHHHCCCCCCCCCEECCHHHHHHHHH
T ss_conf             05866799974873267----89999997089317368857875131867999999715879898852728799999985


Q ss_pred             CCCCHHHHHCCCCCCCCEEEEEEECHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEEEEECCEEEEEECCCCC--------
Q ss_conf             033012200023457821688875066899999875432125899816884434201103315777347870--------
Q gi|254780268|r  148 EIGFPVLVKASAGGGGRGMRIAYSENDLSEAIDQARSEALAAFGNDAVYIEKYLENPRHIEVQIFGDGMGNA--------  219 (443)
Q Consensus       148 ~iGyPviiKp~~gGGG~Gi~vv~~~~el~~a~~~a~~ea~~~fgd~~vlvEk~i~~~rhiEvqVl~D~~g~~--------  219 (443)
T Consensus       722 ~iGYPvlvRPSYVLgG~aM~iv~~~eeL~~yl~~a~~~S~----~~PVlidky~e~A~E~dVD~v~Dg~-~v~i~gI~EH  796 (1089)
T TIGR01369       722 EIGYPVLVRPSYVLGGRAMEIVYNEEELARYLEEAVEVSP----EHPVLIDKYLEDAVEIDVDAVSDGE-EVLIPGIMEH  796 (1089)
T ss_pred             HCCCCEEECCCCCCCCCCHHEECCHHHHHHHHHHHHHHCC----CCCEEEEEECCCCEEEEEEEEEECC-EEEEEEHHHH
T ss_conf             4699289816830033621002678899999999997208----9976988852888899998997288-4899623123


Q ss_pred             -----CCCCCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECC-CCEEEEECCCCCCCC
Q ss_conf             -----23656654211356225540344558899999999999998865154341024589728-834998227654332
Q gi|254780268|r  220 -----IHFGERDCSVQRRNQKIWEEAHSPVISAQDRTEIGETCVKAMKKIDYRGAGTIEFLYEN-GQFYFIEMNTRLQVE  293 (443)
Q Consensus       220 -----v~l~erdCSiQrr~qkiiEeaPap~l~~~~~~~i~~~A~~~~~~~g~~g~~tvEFl~~~-~~~yflEvN~Rlqve  293 (443)
T Consensus       797 iE~AGVHSGDs~~~~-----------Pp~~L~~~~~~~i~~~~~~iA~~L~v~Gl~NiQf~~~~E~~~yVIE~NpRASRt  865 (1089)
T TIGR01369       797 IEEAGVHSGDSTCVL-----------PPQTLSEDIVKRIKDIVRKIAKELNVKGLFNIQFVVKDEGEVYVIEVNPRASRT  865 (1089)
T ss_pred             HHHCCCCCCCHHHCC-----------CCCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCEEEEEECCCCCCC
T ss_conf             421367613053117-----------697778899999999999999870660722245556169967999971742066


Q ss_pred             CHHHHHHHCCCCHHHHHHHHHCCCCCCCCC------CCCCCHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCEEEECC
Q ss_conf             016788632562011232221022222113------33320124533024566221111244215886689984467776
Q gi|254780268|r  294 HPVTEAITGIDLVHEQIYVASENRLSVQQK------DITFSGHAIECRINAEDPENFIPNPGEITYFHAPGGLGIRMDSA  367 (443)
Q Consensus       294 h~vte~~tgvdlv~~~~~~a~g~~l~~~~~------~i~~~g~aie~Ri~aEdp~~f~Ps~G~i~~~~~p~~~gvRvDt~  367 (443)
T Consensus       866 VPFvSKa~Gipl~~~A~~~~~G~~l~~~~~~~gv~~~~~~~~vav-----------------K~~vFSF~kL~g~Dp~LG  928 (1089)
T TIGR01369       866 VPFVSKATGIPLAKLAVRVMLGKKLEELGKDLGVGKEKESKYVAV-----------------KVPVFSFSKLAGVDPVLG  928 (1089)
T ss_pred             CCCEEEECCCCHHHHHHHHHHCCCCHHCCCCCCCCCCCCCCEEEE-----------------EEEECCCHHHCCCCEEEC
T ss_conf             541321037887999999970882010275401123268872799-----------------642377122148871117


Q ss_pred             CCCCCEECCCCCCCEEEEEEECCCHHHHHHHHHHHHHHCE--------ECCCCCCHHHHHHHHCCHHHHC
Q ss_conf             0238770777684338999955998999999998765408--------8263778889998968988955
Q gi|254780268|r  368 SYQGYTVPSYYDSLIAKLIVHGKNRKECMMRLNRALNEII--------IDGIKTTIPLFQKLIKNEDIIE  429 (443)
Q Consensus       368 ~~~G~~i~~~yDsmlaKiI~~g~~R~~Ai~~l~~aL~~~~--------I~Gv~TN~~~l~~il~~~~f~~  429 (443)
T Consensus       929 pE----MkS-----TGEvmg~g~d~~~A~~Ka~~~~~-~~~p~kg~~~~~~~d~dk~~~~~~a~--~L~~  986 (1089)
T TIGR01369       929 PE----MKS-----TGEVMGIGRDLEEAFLKAMLSSG-NRIPKKGSVLLSVRDKDKEELLDLAK--KLAE  986 (1089)
T ss_pred             CC----CCC-----CCEEEEECCCHHHHHHHHHHHCC-CCCCCCCEEEEEECCCCHHHHHHHHH--HHHH
T ss_conf             75----551-----32256412788999999999818-70578877999803443457999999--9986