HHsearch alignment for GI: 254780696 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=98.73  E-value=3.5e-06  Score=60.92  Aligned_cols=266  Identities=20%  Similarity=0.342  Sum_probs=170.4

Q ss_pred             HCCCCCCCHHHHHHHHHHCCCEEEEEE--HHHEEEECCEEEEEEEEEEEECCCCCEEE-ECCCC---CCCHHHCCEEEEE
Q ss_conf             848476467999999998898899995--41248999899999999998077741265-04644---3521006366883
Q gi|254780696|r   16 TVKVKEDSTFAIALEAQVRGYQIFHYT--PDQLYMRDSKIYANTQPLSLDEKKEQYYS-LGEEK---IIDLSQMDVILIR   89 (316)
Q Consensus        16 ~i~~~~DTT~~Lm~eAq~RGheV~~~~--~~dL~~~~g~v~A~~~~i~i~~~~~~~f~-~~~~~---~~~L~~fD~i~iR   89 (316)
T Consensus       589 gvEFD-Yc~Vh~~~aLr~~Gye~ImiN~NPETVSTD------------yD~sDrLYFEplt~E~Vm~I~e~E~~~GVIVq  655 (1089)
T TIGR01369       589 GVEFD-YCCVHAVLALREAGYETIMINYNPETVSTD------------YDTSDRLYFEPLTFEDVMNIIELEKPEGVIVQ  655 (1089)
T ss_pred             CEEEH-HHHHHHHHHHHHCCCEEEEEECCCCCCCCC------------HHHHHHCCCCCCCCCCCEEHEEECCCCEEEEE
T ss_conf             31205-678999999987299599997789974366------------66510115876350310011000586679997


Q ss_pred             CCCCCCHHHHHHHHHHHHHC-CC-CEEE-CCHHHHHHCCCHHHHHHHHH----HCCCCEEECCHHHHHHHHHHHH-HHHH
Q ss_conf             28862247999999998623-58-5041-17488752565034334543----0443100037245568888521-4331
Q gi|254780696|r   90 QDPPFNMHYITSTYLLEKIN-PE-TLIV-NNPFWIRNSPEKIFVTEFSE----LMPPTLISRDITQITRFYLEMK-DIII  161 (316)
Q Consensus        90 ~dPp~d~~yi~~~~~Le~~~-~~-~~vi-N~p~~i~~~~eKl~~~~~~~----~~P~T~vt~~~~~~~~f~~~~~-~vVi  161 (316)
T Consensus       656 ------~GGQtp~nlA~~L~~~GG~~iLGTS~~~ID~AEDR~kFs~~l~~Lgi~QP~~~~a~s~eea~~~A~~iGYPvlv  729 (1089)
T TIGR01369       656 ------FGGQTPLNLAKELEEAGGVPILGTSPESIDRAEDREKFSELLDELGIPQPEWKIATSVEEAKEFASEIGYPVLV  729 (1089)
T ss_pred             ------CCCHHHHHHHHHHHHCCCCEEECCCHHHHHHHCCHHHHHHHHHHCCCCCCCCCEECCHHHHHHHHHHCCCCEEE
T ss_conf             ------48732678999999708931736885787513186799999971587989885272879999998546992898


Q ss_pred             HCCCCCCCCCEEEECCCCCCHHHHHHHHHHHC-CCCCCEEECCCCCCCCCEEEEEECCEEEE-EEEEECCCCCCCCCCCC
Q ss_conf             11688543446874488711588999998400-13340021053445682699998998863-21220456860000001
Q gi|254780696|r  162 KPLYGNGGTGVFRITLGDRNFSSLIEMLFEKY-PEPLMIQSYLPQIRDGDKRILLLNGKPVG-AVNRIPSEVDNRSNIHA  239 (316)
Q Consensus       162 KPl~g~~G~gV~~i~~~~~~~~~~~e~~~~~~-~~~ii~Qefi~~~~~gD~Rv~vi~g~~v~-a~~R~~~~~~~r~Nl~~  239 (316)
T Consensus       730 RPSYVLgG~aM~iv-~~~eeL~~yl~~a~~~S~~~PVlidky~e~A~E~dVD~v~Dg~~v~i~gI-~EHiE---~AGVHS  804 (1089)
T TIGR01369       730 RPSYVLGGRAMEIV-YNEEELARYLEEAVEVSPEHPVLIDKYLEDAVEIDVDAVSDGEEVLIPGI-MEHIE---EAGVHS  804 (1089)
T ss_pred             CCCCCCCCCCHHEE-CCHHHHHHHHHHHHHHCCCCCEEEEEECCCCEEEEEEEEEECCEEEEEEH-HHHHH---HCCCCC
T ss_conf             16830033621002-67889999999999720899769888528888999989972884899623-12342---136761


Q ss_pred             CCCEEE---EECCHHH----HHHHHHHHHHHHHCCCEEEEEEEE--C-C--EEEEEECCCCHHHHH---HHHHCCCCHHH
Q ss_conf             473111---0077899----999999999999849879999511--7-8--788983688303788---99751999899
Q gi|254780696|r  240 GGKAEL---TKLTKID----LDICKRIGESLRERGLFFTGIDVI--G-D--YITEINVTSPTCIRE---IHRNGGENVAS  304 (316)
Q Consensus       240 Gg~~~~---~~lt~~~----~~i~~~~~~~L~~~gl~~~GiDii--g-~--~i~EvNvtsP~g~~~---~~~~~~~~i~~  304 (316)
T Consensus       805 GDs~~~~Pp~~L~~~~~~~i~~~~~~iA~~L~v~Gl~--NiQf~~~~E~~~yVIE~N---pRASRtVPFvSKa~Gipl~~  879 (1089)
T TIGR01369       805 GDSTCVLPPQTLSEDIVKRIKDIVRKIAKELNVKGLF--NIQFVVKDEGEVYVIEVN---PRASRTVPFVSKATGIPLAK  879 (1089)
T ss_pred             CCHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCE--EEEEEEECCCCEEEEEEC---CCCCCCCCCEEEECCCCHHH
T ss_conf             3053117697778899999999999999870660722--245556169967999971---74206654132103788799


Q ss_pred             HHHHHH
Q ss_conf             999999
Q gi|254780696|r  305 LFWDGI  310 (316)
Q Consensus       305 ~i~d~i  310 (316)
T Consensus       880 ~A~~~~  885 (1089)
T TIGR01369       880 LAVRVM  885 (1089)
T ss_pred             HHHHHH
T ss_conf             999997