HHsearch alignment for GI: 254780195 and conserved domain: TIGR01368
>TIGR01368 CPSaseIIsmall carbamoyl-phosphate synthase, small subunit; InterPro: IPR006274 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 the small subunit of the glutamine-dependent form (6.3.5.5 from EC) of carbamoyl phosphate synthase, CPSase II. The small subunit catalyses the hydrolysis of glutamine to ammonia, which in turn used by the large chain to synthesize carbamoyl phosphate. The C-terminal domain of the small subunit of CPSase has glutamine amidotransferase activity. Note that the sequence from the mammalian urea cycle form has lost the active site Cys, resulting in an ammonia-dependent form, CPSase I (6.3.4.16 from EC). CPSases of pyrimidine biosynthesis, arginine biosynthesis, and the urea cycle may be encoded by one or by several genes, depending on the species. ; GO: 0004086 carbamoyl-phosphate synthase activity, 0006807 nitrogen compound metabolic process.
Probab=99.54 E-value=1.1e-12 Score=112.11 Aligned_cols=252 Identities=21% Similarity=0.289 Sum_probs=179.7
Q ss_pred HHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHH-HHCCCCHHHEEECCCCCCHHHHHHHHHHCCHHHHHHHHHCCCCC
Q ss_conf 89999999974998768999238758999999998-64198867724038986202668988764948899998387888
Q gi|254780195|r 192 TQHSVKELQALGVHPDILLIRADRDIPEMERRKIS-LFCNVPMSAVIPALDVDDIYKVPLSYHREGIDSVVLNAFGIENV 270 (544)
Q Consensus 192 TQhSVk~Lrs~GIqPDiivcRse~~l~~~~k~KIa-lfc~V~~~~Vi~~~Dv~sIY~VPl~l~~q~l~~~I~~~L~l~~~ 270 (544)
T Consensus 121 TRaLv~~iR~~G~m~g~I~~~~~~--~~~~~~~~~f~~p~~~---------------------~~nLv~~Vst~~~~~~- 176 (383)
T TIGR01368 121 TRALVKKIREKGTMKGVISTEDSN--DEELVEKAKFESPDID---------------------GINLVAEVSTKEPYTW- 176 (383)
T ss_pred HHHHHHHHHHCCCEEEEEEECCCC--HHHHHHHHHHHCCCCC---------------------CCCCCCCEECCCCEEE-
T ss_conf 799999986358547899606767--0356778654246757---------------------7652010011465560-
Q ss_pred CCCCHHHHHHHHHHHCCCCCCEEEEEEH---HHCCCCHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCHHHHHCCC
Q ss_conf 8620478999998741843437999952---0014813468888888888787367241677225656723445662169
Q gi|254780195|r 271 SLPQIDNWQTFCDRTLSLKNEVKVAIVG---KYIHLKDAYRSLIEALRHSGVSNYTKVQLSWIDAETLEKEDPVKHFYGV 347 (544)
Q Consensus 271 ~~~~l~~W~~~~~~~~~~~~~V~IaiVG---KY~~l~DaY~Si~EAL~hA~~~~~~kv~i~wIdse~le~~~~~~~L~~~ 347 (544)
T Consensus 177 ~~~~~~~~~~~-~~~~~g~~~~~Vv~~DfG~K~--------nIlr~L~------~rG~~v~vVP~~~----~~~~i~~~~ 237 (383)
T TIGR01368 177 GQGTWNLWKFF-VAKRNGKKPLRVVVIDFGVKQ--------NILRRLV------KRGCEVTVVPYDT----DAEEIKKYN 237 (383)
T ss_pred CCCCCHHHHHH-HHCCCCCCCEEEEEEECCCCH--------HHHHHHH------HCCCEEEEECCCC----CHHHHHHHC
T ss_conf 68864166432-211368973599998558875--------5898997------6698799967899----889998657
Q ss_pred -CEEEECCCCCCC--CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHCCC--CCCCCEECCCHHC
Q ss_conf -839973777865--50168889988740476322355769999999987516889997000356--6664121150112
Q gi|254780195|r 348 -HGILVPGGFGKR--GSEGKIAAIKFARENKIPFLGICFGMQMAVIEAARNLAGIPNACSTEFSE--AGVPVIALMSEWM 422 (544)
Q Consensus 348 -dGIlVPGGFG~R--GieGkI~Ai~yARen~iP~LGIClGmQ~avIEfARnvlgl~dAnStEf~~--~~~pvI~~l~e~~ 422 (544)
T Consensus 238 PDGiflSNGPGDPH~~~~~~i~~~~~l~~~~~P~fGICLGHQllALA~Ga~TyKlK------FGHRG~NhPV~~~~~g-- 309 (383)
T TIGR01368 238 PDGIFLSNGPGDPHAAVEPAIETVRELLEAKIPIFGICLGHQLLALAFGAKTYKLK------FGHRGGNHPVKDLRTG-- 309 (383)
T ss_pred CCEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCEEECC------CCCCCCCCCEEECCCC--
T ss_conf 88899908798805678999999999984489710026668999997388700046------5678875131442798--
Q ss_pred CCCCCCCCCCCCCCCCEEEECCEEEEECCCCHHHHHHCCCEEEEECCCCCCCCHHHHHHHHHCCCEEEEECCCCCEEEEE
Q ss_conf 34653001565546740231652578558706688637984766025233327889989997895999986999868999
Q gi|254780195|r 423 KGDQQEKRLPSDDLGATMRLGAYDVSLKEETLISRIYGLDLIPERHRHRYEVNVRYREKLEGCGLKFSGFSVDHALPEVV 502 (544)
Q Consensus 423 ~~~~~~~~~~~~~~GGTMRLG~~~~~l~~~S~~~~iYg~~~I~ERHRHRYEvN~~y~~~le~~Gl~~sg~~~d~~lvEii 502 (544)
T Consensus 310 -----------------------~v~IT----------------sQNHGyAVD~~sl---~~~~~~~th~nLNDgt~EG~ 347 (383)
T TIGR01368 310 -----------------------RVEIT----------------SQNHGYAVDEESL---LAGDLEVTHVNLNDGTVEGI 347 (383)
T ss_pred -----------------------EEEEE----------------EECCCEECCHHHC---CCCCEEEEEEECCCCCCCCC
T ss_conf -----------------------79999----------------7068712575355---78853899983597933153
Q ss_pred EECCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 83899849997248773278769884158999999
Q gi|254780195|r 503 EYINHPWFIGVQYHPELKSRPLDPHPLFVSFIQAT 537 (544)
Q Consensus 503 El~~HpffvgvQfHPEf~Srp~~phPLF~~fi~Aa 537 (544)
T Consensus 348 ~h~~~P~-fSVQyHPEA~PGPhD~~~lFd~F~~~~ 381 (383)
T TIGR01368 348 RHKDLPV-FSVQYHPEASPGPHDTEYLFDEFIDLI 381 (383)
T ss_pred CCCCCCE-EEEECCCCCCCCCHHHHHHHHHHHHHH
T ss_conf 0058786-677006888887002379999999998