NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1039745489|ref|XP_017171333|]
View 

squalene synthase isoform X1 [Mus musculus]

Protein Classification

isoprenoid biosynthesis enzyme family protein( domain architecture ID 89)

isoprenoid biosynthesis enzyme family protein

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

Name Accession Description Interval E-value
Isoprenoid_Biosyn_C1 super family cl00210
Isoprenoid Biosynthesis enzymes, Class 1; Superfamily of trans-isoprenyl diphosphate synthases ...
38-370 0e+00

Isoprenoid Biosynthesis enzymes, Class 1; Superfamily of trans-isoprenyl diphosphate synthases (IPPS) and class I terpene cyclases which either synthesis geranyl/farnesyl diphosphates (GPP/FPP) or longer chained products from isoprene precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), or use geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate as substrate. These enzymes produce a myriad of precursors for such end products as steroids, cholesterol, sesquiterpenes, heme, carotenoids, retinoids, and diterpenes; and are widely distributed among archaea, bacteria, and eukaryota.The enzymes in this superfamily share the same 'isoprenoid synthase fold' and include several subgroups. The head-to-tail (HT) IPPS catalyze the successive 1'-4 condensation of the 5-carbon IPP to the growing isoprene chain to form linear, all-trans, C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid diphosphates. Cyclic monoterpenes, diterpenes, and sesquiterpenes, are formed from their respective linear isoprenoid diphosphates by class I terpene cyclases. The head-to-head (HH) IPPS catalyze the successive 1'-1 condensation of 2 farnesyl or 2 geranylgeranyl isoprenoid diphosphates. Cyclization of these 30- and 40-carbon linear forms are catalyzed by class II cyclases. Both the isoprenoid chain elongation reactions and the class I terpene cyclization reactions proceed via electrophilic alkylations in which a new carbon-carbon single bond is generated through interaction between a highly reactive electron-deficient allylic carbocation and an electron-rich carbon-carbon double bond. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions located on opposite walls. These residues mediate binding of prenyl phosphates via bridging Mg2+ ions, inducing proposed conformational changes that close the active site to solvent, stabilizing reactive carbocation intermediates. Generally, the enzymes in this family exhibit an all-trans reaction pathway, an exception, is the cis-trans terpene cyclase, trichodiene synthase. Mechanistically and structurally distinct, class II terpene cyclases and cis-IPPS are not included in this CD.


The actual alignment was detected with superfamily member TIGR01559:

Pssm-ID: 469660  Cd Length: 337  Bit Score: 587.10  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039745489  38 SSLKTCYKYLNQTSRSFAAVIQALDGDIRHAICVFYLVLRALDTVEDDMSISVEKKIPLLCNFHTFLYDPEWRFTES-KE 116
Cdd:TIGR01559   1 PSLGFCYELLNLTSRSFAAVIQELPPELRNAVCIFYLVLRALDTVEDDMTISVDKKIPLLRDFHEKIYDPDWRFTESdNE 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039745489 117 KDRQVLEDFPTISLEFRNLAEKYQTVIDDICHRMGCGMAEFVDKDVTSKQ---DWDKYCHYVAGLVGIGLSRLFSASEFE 193
Cdd:TIGR01559  81 KDRQVLDDFPVVSLEFLKLKPKYQEVIADITRRMGNGMADFIDKEVTNEQtvgDYDKYCHYVAGLVGIGLSRLFVASGFE 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039745489 194 DPIVGEDIECANSMGLFLQKTNIIRDYLEDQQEGRKFWPQEVWGRYIKKLEDFAKPENVDVAVQCLNELITNTLQHIPDV 273
Cdd:TIGR01559 161 DPSLGESEALSNSMGLFLQKTNIIRDYLEDINEGRMFWPREIWSKYAKKLGDFKKPENSDKALQCLNELVTNALHHATDC 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039745489 274 LTYLSRLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGVVKIRKGQAVTLMMDATNMPAVKAIIYQYIEEIYHRIPNSD 353
Cdd:TIGR01559 241 LTYLSRLRDQSIFNFCAIPQVMAIATLALCYNNPQVFQGNVKIRKGTTVKLILDSTNMPAVYDIFYRYARKIYHKIDPND 320
                         330
                  ....*....|....*..
gi 1039745489 354 PSSSKTKQVISKIRTQN 370
Cdd:TIGR01559 321 PNFSKTLIIISKIEQQC 337
 
Name Accession Description Interval E-value
squal_synth TIGR01559
farnesyl-diphosphate farnesyltransferase; This model describes farnesyl-diphosphate ...
38-370 0e+00

farnesyl-diphosphate farnesyltransferase; This model describes farnesyl-diphosphate farnesyltransferase, also known as squalene synthase, as found in eukaryotes. This family is related to phytoene synthases. Tentatively identified archaeal homologs (excluded from this model) lack the C-terminal predicted transmembrane region universally conserved among members of this family.


Pssm-ID: 188157  Cd Length: 337  Bit Score: 587.10  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039745489  38 SSLKTCYKYLNQTSRSFAAVIQALDGDIRHAICVFYLVLRALDTVEDDMSISVEKKIPLLCNFHTFLYDPEWRFTES-KE 116
Cdd:TIGR01559   1 PSLGFCYELLNLTSRSFAAVIQELPPELRNAVCIFYLVLRALDTVEDDMTISVDKKIPLLRDFHEKIYDPDWRFTESdNE 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039745489 117 KDRQVLEDFPTISLEFRNLAEKYQTVIDDICHRMGCGMAEFVDKDVTSKQ---DWDKYCHYVAGLVGIGLSRLFSASEFE 193
Cdd:TIGR01559  81 KDRQVLDDFPVVSLEFLKLKPKYQEVIADITRRMGNGMADFIDKEVTNEQtvgDYDKYCHYVAGLVGIGLSRLFVASGFE 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039745489 194 DPIVGEDIECANSMGLFLQKTNIIRDYLEDQQEGRKFWPQEVWGRYIKKLEDFAKPENVDVAVQCLNELITNTLQHIPDV 273
Cdd:TIGR01559 161 DPSLGESEALSNSMGLFLQKTNIIRDYLEDINEGRMFWPREIWSKYAKKLGDFKKPENSDKALQCLNELVTNALHHATDC 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039745489 274 LTYLSRLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGVVKIRKGQAVTLMMDATNMPAVKAIIYQYIEEIYHRIPNSD 353
Cdd:TIGR01559 241 LTYLSRLRDQSIFNFCAIPQVMAIATLALCYNNPQVFQGNVKIRKGTTVKLILDSTNMPAVYDIFYRYARKIYHKIDPND 320
                         330
                  ....*....|....*..
gi 1039745489 354 PSSSKTKQVISKIRTQN 370
Cdd:TIGR01559 321 PNFSKTLIIISKIEQQC 337
Trans_IPPS_HH cd00683
Trans-Isoprenyl Diphosphate Synthases, head-to-head; These trans-Isoprenyl Diphosphate ...
41-321 5.37e-81

Trans-Isoprenyl Diphosphate Synthases, head-to-head; These trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) catalyze a head-to-head (HH) (1'-1) condensation reaction. This CD includes squalene and phytoene synthases which catalyze the 1'-1 condensation of two 15-carbon (farnesyl) and 20-carbon (geranylgeranyl) isoprenyl diphosphates, respectively. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions (DXXXD) located on opposite walls. These residues mediate binding of prenyl phosphates. A two-step reaction has been proposed for squalene synthase (farnesyl-diphosphate farnesyltransferase) in which, two molecules of FPP react to form a stable cyclopropylcarbinyl diphosphate intermediate, and then the intermediate undergoes heterolysis, isomerization, and reduction with NADPH to form squalene, a precursor of cholestrol. The carotenoid biosynthesis enzyme, phytoene synthase (CrtB), catalyzes the condensation reaction of two molecules of geranylgeranyl diphosphate to produce phytoene, a precursor of beta-carotene. These enzymes produce the triterpene and tetraterpene precursors for many diverse sterol and carotenoid end products and are widely distributed among eukareya, bacteria, and archaea.


Pssm-ID: 173831 [Multi-domain]  Cd Length: 265  Bit Score: 249.84  E-value: 5.37e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039745489  41 KTCYKYLNQTSRSFAAVIQALDGDIRHAICVFYLVLRALDTVEDDMSISVEKKIPLLCNFHTFLYDPEWrfteskekdrq 120
Cdd:cd00683     1 AYCRAILRKGSRSFYLASRLLPPELRRAVCALYAFCRAADDIVDDPAAPPDEKLALLDAFRAELDAAYW----------- 69
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039745489 121 VLEDFPTISLEFRNLAEkYQTVIDDICHRMGCGMAEFVDK-DVTSKQDWDKYCHYVAGLVGIGLSRLFSASEFEdpivgE 199
Cdd:cd00683    70 GGAPTHPVLRALADLAR-RYGIPREPFRDLLAGMAMDLDKrRYETLDELDEYCYYVAGVVGLMLLRVFGASSDE-----A 143
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039745489 200 DIECANSMGLFLQKTNIIRDYLEDQQEGRKFWPQEVWGRYIKKLEDFAKPENVDVAVQCLNELITNTLQHIPDVLTYLSR 279
Cdd:cd00683   144 ALERARALGLALQLTNILRDVGEDARRGRIYLPREELARFGVTLEDLLAPENSPAFRALLRRLIARARAHYREALAGLAA 223
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|..
gi 1039745489 280 LRnqSVFNFCAIPQVMAIATLAACYNNQQVFKGVVKIRKGQA 321
Cdd:cd00683   224 LP--RRSRFCVRAAAMLYRTILDEIEARGYDVLSVRVRVPKA 263
SQS_PSY pfam00494
Squalene/phytoene synthase;
47-320 1.66e-49

Squalene/phytoene synthase;


Pssm-ID: 425717 [Multi-domain]  Cd Length: 261  Bit Score: 168.62  E-value: 1.66e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039745489  47 LNQTSRSFAAVIQALDGDIRHAICVFYLVLRALDTVEDDMSISVEKKIPLLCNFHTFLYDPEWRfteskekdrQVLEDFP 126
Cdd:pfam00494   1 LRKVSRSFYLASLLLPPELRRAVFALYAFCREADDIVDEVSDPPAAKRARLDWWRDALDGAYAR---------RLKPARH 71
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039745489 127 TISLEFRNLAEKYQTVIDDiCHRMGCGMAEFVDKD-VTSKQDWDKYCHYVAGLVGIGLSRLFSASEFEDpivgEDIECAN 205
Cdd:pfam00494  72 PVLRALADLIRRYQLPKEP-FLELIDGMEMDLEFTrYETLAELEEYCYYVAGVVGLLLLRLLGARSDEA----ALLEAAS 146
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039745489 206 SMGLFLQKTNIIRDYLEDQQEGRKFWPQEVWGRYIKKLEDFAKPENVDVAVQCLNELITNTLQHIPDVLTYLSRLRNQSV 285
Cdd:pfam00494 147 HLGLALQLTNILRDVGEDARRGRVYLPAEVLKRFGVSEEDLLRGRASPALRALLRELAERARAHLREARPLLALLPRRAR 226
                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 1039745489 286 FnFCAIPQVMAIATLAACYNNQ-QVFKGVVKIRKGQ 320
Cdd:pfam00494 227 P-AVLLAAVLYRAILRRLEAAGyDVLRRRVKLSRRR 261
ERG9 COG1562
Phytoene/squalene synthetase [Lipid transport and metabolism];
36-328 1.61e-26

Phytoene/squalene synthetase [Lipid transport and metabolism];


Pssm-ID: 441170 [Multi-domain]  Cd Length: 278  Bit Score: 107.59  E-value: 1.61e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039745489  36 LSSSLKTCYKYLNQTSRSFAAVIQALDGDIRHAICVFYLVLRALDTVEDDMSISVEKKIpLLCNFHTFLYDPEWRFTEsk 115
Cdd:COG1562     1 LAAAYAYCRAITRRHSRSFYLASLLLPPELRRAVYALYAFCREADDIVDEVSDPAEREA-RLDWWRAELDAAYAGGPA-- 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039745489 116 ekDRQVLEDFPTISLEFrNLAEKY-QTVIDdichrmgcGMAEFVDKDV-TSKQDWDKYCHYVAGLVGIGLSRLFSASEfe 193
Cdd:COG1562    78 --DHPVLAALADTVRRY-GLPRELfLDLID--------GMEMDLTKTRyATFAELEDYCYRVAGVVGLLLLRVFGADD-- 144
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039745489 194 dpivGEDIECANSMGLFLQKTNIIRDYLEDQQEGRKFWPQEVWGRYIKKLEDFAKPENVDVAVQCLNELITNTLQHIPDV 273
Cdd:COG1562   145 ----PEALAAADALGVALQLTNILRDVGEDARRGRVYLPLDDLARFGVTEEDLLAGRASPALRALLRFLAARARALLREA 220
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1039745489 274 LTYLSRLRNQSVFnFCAIPQVMAIATLAACYNNQ-QVFKGVVKIRKGQAVTLMMDA 328
Cdd:COG1562   221 LAGIPALPRRARR-AVLLAAALYRAILDKIERRGyDVLRRRVRLSRLRKLWLLWRA 275
PLN02632 PLN02632
phytoene synthase
166-234 1.08e-06

phytoene synthase


Pssm-ID: 215339  Cd Length: 334  Bit Score: 50.10  E-value: 1.08e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1039745489 166 QDWDK---YCHYVAGLVGI------GLSRLFSASEfedpivgEDI-ECANSMGLFLQKTNIIRDYLEDQQEGRKFWPQE 234
Cdd:PLN02632  159 ENFDElylYCYYVAGTVGLmsvpvmGIAPESKAST-------ESVyNAALALGIANQLTNILRDVGEDARRGRVYLPQD 230
 
Name Accession Description Interval E-value
squal_synth TIGR01559
farnesyl-diphosphate farnesyltransferase; This model describes farnesyl-diphosphate ...
38-370 0e+00

farnesyl-diphosphate farnesyltransferase; This model describes farnesyl-diphosphate farnesyltransferase, also known as squalene synthase, as found in eukaryotes. This family is related to phytoene synthases. Tentatively identified archaeal homologs (excluded from this model) lack the C-terminal predicted transmembrane region universally conserved among members of this family.


Pssm-ID: 188157  Cd Length: 337  Bit Score: 587.10  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039745489  38 SSLKTCYKYLNQTSRSFAAVIQALDGDIRHAICVFYLVLRALDTVEDDMSISVEKKIPLLCNFHTFLYDPEWRFTES-KE 116
Cdd:TIGR01559   1 PSLGFCYELLNLTSRSFAAVIQELPPELRNAVCIFYLVLRALDTVEDDMTISVDKKIPLLRDFHEKIYDPDWRFTESdNE 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039745489 117 KDRQVLEDFPTISLEFRNLAEKYQTVIDDICHRMGCGMAEFVDKDVTSKQ---DWDKYCHYVAGLVGIGLSRLFSASEFE 193
Cdd:TIGR01559  81 KDRQVLDDFPVVSLEFLKLKPKYQEVIADITRRMGNGMADFIDKEVTNEQtvgDYDKYCHYVAGLVGIGLSRLFVASGFE 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039745489 194 DPIVGEDIECANSMGLFLQKTNIIRDYLEDQQEGRKFWPQEVWGRYIKKLEDFAKPENVDVAVQCLNELITNTLQHIPDV 273
Cdd:TIGR01559 161 DPSLGESEALSNSMGLFLQKTNIIRDYLEDINEGRMFWPREIWSKYAKKLGDFKKPENSDKALQCLNELVTNALHHATDC 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039745489 274 LTYLSRLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGVVKIRKGQAVTLMMDATNMPAVKAIIYQYIEEIYHRIPNSD 353
Cdd:TIGR01559 241 LTYLSRLRDQSIFNFCAIPQVMAIATLALCYNNPQVFQGNVKIRKGTTVKLILDSTNMPAVYDIFYRYARKIYHKIDPND 320
                         330
                  ....*....|....*..
gi 1039745489 354 PSSSKTKQVISKIRTQN 370
Cdd:TIGR01559 321 PNFSKTLIIISKIEQQC 337
Trans_IPPS_HH cd00683
Trans-Isoprenyl Diphosphate Synthases, head-to-head; These trans-Isoprenyl Diphosphate ...
41-321 5.37e-81

Trans-Isoprenyl Diphosphate Synthases, head-to-head; These trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) catalyze a head-to-head (HH) (1'-1) condensation reaction. This CD includes squalene and phytoene synthases which catalyze the 1'-1 condensation of two 15-carbon (farnesyl) and 20-carbon (geranylgeranyl) isoprenyl diphosphates, respectively. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions (DXXXD) located on opposite walls. These residues mediate binding of prenyl phosphates. A two-step reaction has been proposed for squalene synthase (farnesyl-diphosphate farnesyltransferase) in which, two molecules of FPP react to form a stable cyclopropylcarbinyl diphosphate intermediate, and then the intermediate undergoes heterolysis, isomerization, and reduction with NADPH to form squalene, a precursor of cholestrol. The carotenoid biosynthesis enzyme, phytoene synthase (CrtB), catalyzes the condensation reaction of two molecules of geranylgeranyl diphosphate to produce phytoene, a precursor of beta-carotene. These enzymes produce the triterpene and tetraterpene precursors for many diverse sterol and carotenoid end products and are widely distributed among eukareya, bacteria, and archaea.


Pssm-ID: 173831 [Multi-domain]  Cd Length: 265  Bit Score: 249.84  E-value: 5.37e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039745489  41 KTCYKYLNQTSRSFAAVIQALDGDIRHAICVFYLVLRALDTVEDDMSISVEKKIPLLCNFHTFLYDPEWrfteskekdrq 120
Cdd:cd00683     1 AYCRAILRKGSRSFYLASRLLPPELRRAVCALYAFCRAADDIVDDPAAPPDEKLALLDAFRAELDAAYW----------- 69
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039745489 121 VLEDFPTISLEFRNLAEkYQTVIDDICHRMGCGMAEFVDK-DVTSKQDWDKYCHYVAGLVGIGLSRLFSASEFEdpivgE 199
Cdd:cd00683    70 GGAPTHPVLRALADLAR-RYGIPREPFRDLLAGMAMDLDKrRYETLDELDEYCYYVAGVVGLMLLRVFGASSDE-----A 143
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039745489 200 DIECANSMGLFLQKTNIIRDYLEDQQEGRKFWPQEVWGRYIKKLEDFAKPENVDVAVQCLNELITNTLQHIPDVLTYLSR 279
Cdd:cd00683   144 ALERARALGLALQLTNILRDVGEDARRGRIYLPREELARFGVTLEDLLAPENSPAFRALLRRLIARARAHYREALAGLAA 223
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|..
gi 1039745489 280 LRnqSVFNFCAIPQVMAIATLAACYNNQQVFKGVVKIRKGQA 321
Cdd:cd00683   224 LP--RRSRFCVRAAAMLYRTILDEIEARGYDVLSVRVRVPKA 263
SQS_PSY pfam00494
Squalene/phytoene synthase;
47-320 1.66e-49

Squalene/phytoene synthase;


Pssm-ID: 425717 [Multi-domain]  Cd Length: 261  Bit Score: 168.62  E-value: 1.66e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039745489  47 LNQTSRSFAAVIQALDGDIRHAICVFYLVLRALDTVEDDMSISVEKKIPLLCNFHTFLYDPEWRfteskekdrQVLEDFP 126
Cdd:pfam00494   1 LRKVSRSFYLASLLLPPELRRAVFALYAFCREADDIVDEVSDPPAAKRARLDWWRDALDGAYAR---------RLKPARH 71
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039745489 127 TISLEFRNLAEKYQTVIDDiCHRMGCGMAEFVDKD-VTSKQDWDKYCHYVAGLVGIGLSRLFSASEFEDpivgEDIECAN 205
Cdd:pfam00494  72 PVLRALADLIRRYQLPKEP-FLELIDGMEMDLEFTrYETLAELEEYCYYVAGVVGLLLLRLLGARSDEA----ALLEAAS 146
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039745489 206 SMGLFLQKTNIIRDYLEDQQEGRKFWPQEVWGRYIKKLEDFAKPENVDVAVQCLNELITNTLQHIPDVLTYLSRLRNQSV 285
Cdd:pfam00494 147 HLGLALQLTNILRDVGEDARRGRVYLPAEVLKRFGVSEEDLLRGRASPALRALLRELAERARAHLREARPLLALLPRRAR 226
                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 1039745489 286 FnFCAIPQVMAIATLAACYNNQ-QVFKGVVKIRKGQ 320
Cdd:pfam00494 227 P-AVLLAAVLYRAILRRLEAAGyDVLRRRVKLSRRR 261
ERG9 COG1562
Phytoene/squalene synthetase [Lipid transport and metabolism];
36-328 1.61e-26

Phytoene/squalene synthetase [Lipid transport and metabolism];


Pssm-ID: 441170 [Multi-domain]  Cd Length: 278  Bit Score: 107.59  E-value: 1.61e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039745489  36 LSSSLKTCYKYLNQTSRSFAAVIQALDGDIRHAICVFYLVLRALDTVEDDMSISVEKKIpLLCNFHTFLYDPEWRFTEsk 115
Cdd:COG1562     1 LAAAYAYCRAITRRHSRSFYLASLLLPPELRRAVYALYAFCREADDIVDEVSDPAEREA-RLDWWRAELDAAYAGGPA-- 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039745489 116 ekDRQVLEDFPTISLEFrNLAEKY-QTVIDdichrmgcGMAEFVDKDV-TSKQDWDKYCHYVAGLVGIGLSRLFSASEfe 193
Cdd:COG1562    78 --DHPVLAALADTVRRY-GLPRELfLDLID--------GMEMDLTKTRyATFAELEDYCYRVAGVVGLLLLRVFGADD-- 144
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039745489 194 dpivGEDIECANSMGLFLQKTNIIRDYLEDQQEGRKFWPQEVWGRYIKKLEDFAKPENVDVAVQCLNELITNTLQHIPDV 273
Cdd:COG1562   145 ----PEALAAADALGVALQLTNILRDVGEDARRGRVYLPLDDLARFGVTEEDLLAGRASPALRALLRFLAARARALLREA 220
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1039745489 274 LTYLSRLRNQSVFnFCAIPQVMAIATLAACYNNQ-QVFKGVVKIRKGQAVTLMMDA 328
Cdd:COG1562   221 LAGIPALPRRARR-AVLLAAALYRAILDKIERRGyDVLRRRVRLSRLRKLWLLWRA 275
Trans_IPPS cd00867
Trans-Isoprenyl Diphosphate Synthases; Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) of ...
64-245 7.54e-23

Trans-Isoprenyl Diphosphate Synthases; Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) of class 1 isoprenoid biosynthesis enzymes which either synthesis geranyl/farnesyl diphosphates (GPP/FPP) or longer chained products from isoprene precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), or use geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate as substrate. These enzymes produce a myriad of precursors for such end products as steroids, cholesterol, sesquiterpenes, heme, carotenoids, retinoids, diterpenes, ubiquinone, and archaeal ether linked lipids; and are widely distributed among archaea, bacteria, and eukareya. The enzymes in this family share the same 'isoprenoid synthase fold' and include the head-to-tail (HT) IPPS which catalyze the successive 1'-4 condensation of the 5-carbon IPP to the growing isoprene chain to form linear, all-trans, C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid diphosphates. The head-to-head (HH) IPPS catalyze the successive 1'-1 condensation of 2 farnesyl or 2 geranylgeranyl isoprenoid diphosphates. Isoprenoid chain elongation reactions proceed via electrophilic alkylations in which a new carbon-carbon single bond is generated through interaction between a highly reactive electron-deficient allylic carbocation and an electron-rich carbon-carbon double bond. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions located on opposite walls. These residues mediate binding of prenyl phosphates via bridging Mg2+ ions, inducing proposed conformational changes that close the active site to solvent, stabilizing reactive carbocation intermediates. Mechanistically and structurally distinct, cis-IPPS are not included in this CD.


Pssm-ID: 173836  Cd Length: 236  Bit Score: 96.26  E-value: 7.54e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039745489  64 DIRHAICVFYLVLRALDTVEDDMSISVEKKIPLLcnfhtflydpeWRFTEskekDRQVLEDFPTISLEFRNLAE----KY 139
Cdd:cd00867    22 RLAAAVELLHAASLVHDDIVDDSDLRRGKPTAHL-----------RRFGN----ALAILAGDYLLARAFQLLARlgypRA 86
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039745489 140 QTVIDDICHRMGCGMAEFVDKDVTSKQDWD---KYCHY-VAGLVGIGLSRLFSASEFEDPIVGEDIECANSMGLFLQKTN 215
Cdd:cd00867    87 LELFAEALRELLEGQALDLEFERDTYETLDeylEYCRYkTAGLVGLLCLLGAGLSGADDEQAEALKDYGRALGLAFQLTD 166
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1039745489 216 IIRDY----------LEDQQEGRKFWPQEVWGRYIKKLED 245
Cdd:cd00867   167 DLLDVfgdaeelgkvGSDLREGRITLPVILARERAAEYAE 206
Isoprenoid_Biosyn_C1 cd00385
Isoprenoid Biosynthesis enzymes, Class 1; Superfamily of trans-isoprenyl diphosphate synthases ...
53-298 1.74e-20

Isoprenoid Biosynthesis enzymes, Class 1; Superfamily of trans-isoprenyl diphosphate synthases (IPPS) and class I terpene cyclases which either synthesis geranyl/farnesyl diphosphates (GPP/FPP) or longer chained products from isoprene precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), or use geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate as substrate. These enzymes produce a myriad of precursors for such end products as steroids, cholesterol, sesquiterpenes, heme, carotenoids, retinoids, and diterpenes; and are widely distributed among archaea, bacteria, and eukaryota.The enzymes in this superfamily share the same 'isoprenoid synthase fold' and include several subgroups. The head-to-tail (HT) IPPS catalyze the successive 1'-4 condensation of the 5-carbon IPP to the growing isoprene chain to form linear, all-trans, C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid diphosphates. Cyclic monoterpenes, diterpenes, and sesquiterpenes, are formed from their respective linear isoprenoid diphosphates by class I terpene cyclases. The head-to-head (HH) IPPS catalyze the successive 1'-1 condensation of 2 farnesyl or 2 geranylgeranyl isoprenoid diphosphates. Cyclization of these 30- and 40-carbon linear forms are catalyzed by class II cyclases. Both the isoprenoid chain elongation reactions and the class I terpene cyclization reactions proceed via electrophilic alkylations in which a new carbon-carbon single bond is generated through interaction between a highly reactive electron-deficient allylic carbocation and an electron-rich carbon-carbon double bond. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions located on opposite walls. These residues mediate binding of prenyl phosphates via bridging Mg2+ ions, inducing proposed conformational changes that close the active site to solvent, stabilizing reactive carbocation intermediates. Generally, the enzymes in this family exhibit an all-trans reaction pathway, an exception, is the cis-trans terpene cyclase, trichodiene synthase. Mechanistically and structurally distinct, class II terpene cyclases and cis-IPPS are not included in this CD.


Pssm-ID: 173830 [Multi-domain]  Cd Length: 243  Bit Score: 89.86  E-value: 1.74e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039745489  53 SFAAVIQAL--DGDIRHAICVFYLVLRALDTVEDDMSISVEKKIPLLCNFHTflydpewrfteskEKDRQVLEDFPTISL 130
Cdd:cd00385     1 FRPLAVLLEpeASRLRAAVEKLHAASLVHDDIVDDSGTRRGLPTAHLAVAID-------------GLPEAILAGDLLLAD 67
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039745489 131 EFRNLAE----KYQTVIDDICHRMGCGM---AEFVDKDVTSKQDWDKYCHYV-AGLVGIGLSRLFSASEFEDPIVGEDIE 202
Cdd:cd00385    68 AFEELARegspEALEILAEALLDLLEGQlldLKWRREYVPTLEEYLEYCRYKtAGLVGALCLLGAGLSGGEAELLEALRK 147
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039745489 203 CANSMGLFLQKTNIIRDYLEDQQ--EGRKFWPQEVWGRYIKKLEDFAKPENVDVAVQCLNELITNTLQHIPDVLTYLSRL 280
Cdd:cd00385   148 LGRALGLAFQLTNDLLDYEGDAErgEGKCTLPVLYALEYGVPAEDLLLVEKSGSLEEALEELAKLAEEALKELNELILSL 227
                         250
                  ....*....|....*...
gi 1039745489 281 RnqSVFNFCAIPQVMAIA 298
Cdd:cd00385   228 P--DVPRALLALALNLYR 243
HpnD TIGR03465
squalene synthase HpnD; The genes of this family are often found in the same genetic locus ...
49-239 5.57e-11

squalene synthase HpnD; The genes of this family are often found in the same genetic locus with squalene-hopene cyclase genes, and are never associated with genes for the metabolism of phytoene. In the organisms Zymomonas mobilis and Bradyrhizobium japonicum these genes have been characterized as squalene synthases (farnesyl-pyrophosphate ligases). Often, these genes appear in tandem with the HpnC gene which appears to have resulted from an ancient gene duplication event. Presumably these proteins form a heteromeric complex, but this has not yet been experimentally demonstrated.


Pssm-ID: 163278  Cd Length: 266  Bit Score: 62.68  E-value: 5.57e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039745489  49 QTSRSFAAVIQALDGDIRHAICVFYLVLRALDTVEDDMSISVEKKIPLlcnfhtflydPEWRftesKEKDR--------- 119
Cdd:TIGR03465   3 ASGSSFYYGMRLLPPERRRAMTALYAFCREVDDIVDEDSDPEVAQAKL----------AWWR----AEIDRlyagapshp 68
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039745489 120 --QVLED-FPTISLEfrnlAEKYQTVIDdichrmGCGMaefvDKDVTSKQDWDK---YCHYVAGLVGIGLSRLFSASEfe 193
Cdd:TIGR03465  69 vaRALADpARRFDLP----QEDFLEVID------GMEM----DLEQTRYPDFAEldlYCDRVAGAVGRLSARIFGATD-- 132
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1039745489 194 dpivGEDIECANSMGLFLQKTNIIRDYLEDQQEGRKFWPQEVWGRY 239
Cdd:TIGR03465 133 ----ARTLEYAHHLGRALQLTNILRDVGEDARRGRIYLPAEELQRF 174
PLN02632 PLN02632
phytoene synthase
166-234 1.08e-06

phytoene synthase


Pssm-ID: 215339  Cd Length: 334  Bit Score: 50.10  E-value: 1.08e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1039745489 166 QDWDK---YCHYVAGLVGI------GLSRLFSASEfedpivgEDI-ECANSMGLFLQKTNIIRDYLEDQQEGRKFWPQE 234
Cdd:PLN02632  159 ENFDElylYCYYVAGTVGLmsvpvmGIAPESKAST-------ESVyNAALALGIANQLTNILRDVGEDARRGRVYLPQD 230
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH