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Conserved domains on  [gi|699678152|ref|XP_009886241|]
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PREDICTED: squalene synthase [Charadrius vociferus]

Protein Classification

isoprenoid biosynthesis enzyme family protein( domain architecture ID 89)

isoprenoid biosynthesis enzyme family protein

Graphical summary

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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 ...
 1-285 1.36e-172

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: 482.33  E-value: 1.36e-172
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699678152    1 MTISLDVKVPMLHEFHSYLYQPEWKYMES-KEKDRQVLEDFPTISMEFRNLSKVYQDVISDICHKMGVGMAEFLEKKV-- 77
Cdd:TIGR01559  49 MTISVDKKIPLLRDFHEKIYDPDWRFTESdNEKDRQVLDDFPVVSLEFLKLKPKYQEVIADITRRMGNGMADFIDKEVtn 128

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699678152   78 -DSQHEWDKYCHYVAGLVGIGLSRLFSASELEDPVVGQDTELANSMGLFLQKTNIIRDYLEDQLEGREFWPREVWSRYAK 156
Cdd:TIGR01559 129 eQTVGDYDKYCHYVAGLVGIGLSRLFVASGFEDPSLGESEALSNSMGLFLQKTNIIRDYLEDINEGRMFWPREIWSKYAK 208

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699678152  157 KLSDLAKPENIDMAVQCLNELITNALHHVPDVLTYLSRLKNQSVFNFCAIPQVMAIATLAACYNNKQVFRGVVKIRKGQA 236
Cdd:TIGR01559 209 KLGDFKKPENSDKALQCLNELVTNALHHATDCLTYLSRLRDQSIFNFCAIPQVMAIATLALCYNNPQVFQGNVKIRKGTT 288

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 699678152  237 VTLMMDATNIQAVKAIMYQYVEEIYQKIPSTDPSSNKTQQIIASIRAMS 285
Cdd:TIGR01559 289 VKLILDSTNMPAVYDIFYRYARKIYHKIDPNDPNFSKTLIIISKIEQQC 337
 
Name Accession Description Interval E-value
squal_synth TIGR01559
farnesyl-diphosphate farnesyltransferase; This model describes farnesyl-diphosphate ...
 1-285 1.36e-172

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: 482.33  E-value: 1.36e-172
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699678152    1 MTISLDVKVPMLHEFHSYLYQPEWKYMES-KEKDRQVLEDFPTISMEFRNLSKVYQDVISDICHKMGVGMAEFLEKKV-- 77
Cdd:TIGR01559  49 MTISVDKKIPLLRDFHEKIYDPDWRFTESdNEKDRQVLDDFPVVSLEFLKLKPKYQEVIADITRRMGNGMADFIDKEVtn 128

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699678152   78 -DSQHEWDKYCHYVAGLVGIGLSRLFSASELEDPVVGQDTELANSMGLFLQKTNIIRDYLEDQLEGREFWPREVWSRYAK 156
Cdd:TIGR01559 129 eQTVGDYDKYCHYVAGLVGIGLSRLFVASGFEDPSLGESEALSNSMGLFLQKTNIIRDYLEDINEGRMFWPREIWSKYAK 208

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699678152  157 KLSDLAKPENIDMAVQCLNELITNALHHVPDVLTYLSRLKNQSVFNFCAIPQVMAIATLAACYNNKQVFRGVVKIRKGQA 236
Cdd:TIGR01559 209 KLGDFKKPENSDKALQCLNELVTNALHHATDCLTYLSRLRDQSIFNFCAIPQVMAIATLALCYNNPQVFQGNVKIRKGTT 288

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 699678152  237 VTLMMDATNIQAVKAIMYQYVEEIYQKIPSTDPSSNKTQQIIASIRAMS 285
Cdd:TIGR01559 289 VKLILDSTNMPAVYDIFYRYARKIYHKIDPNDPNFSKTLIIISKIEQQC 337
Trans_IPPS_HH cd00683
Trans-Isoprenyl Diphosphate Synthases, head-to-head; These trans-Isoprenyl Diphosphate ...
 1-236 8.33e-63

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: 200.54  E-value: 8.33e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699678152   1 MTISLDVKVPMLHEFHSYLYQPEWkymeskekdrqVLEDFPTISMEFRNLsKVYQDVISDICHKMGVGMAEFLEKK-VDS 79
Cdd:cd00683   46 PAAPPDEKLALLDAFRAELDAAYW-----------GGAPTHPVLRALADL-ARRYGIPREPFRDLLAGMAMDLDKRrYET 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699678152  80 QHEWDKYCHYVAGLVGIGLSRLFSASELEDPVvgqdtELANSMGLFLQKTNIIRDYLEDQLEGREFWPREVWSRYAKKLS 159
Cdd:cd00683  114 LDELDEYCYYVAGVVGLMLLRVFGASSDEAAL-----ERARALGLALQLTNILRDVGEDARRGRIYLPREELARFGVTLE 188

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 699678152 160 DLAKPENIDMAVQCLNELITNALHHVPDVLTYLSRLKnqSVFNFCAIPQVMAIATLAACYNNKQVFRGVVKIRKGQA 236
Cdd:cd00683  189 DLLAPENSPAFRALLRRLIARARAHYREALAGLAALP--RRSRFCVRAAAMLYRTILDEIEARGYDVLSVRVRVPKA 263
SQS_PSY pfam00494
Squalene/phytoene synthase;
33-235 3.50e-33

Squalene/phytoene synthase;


Pssm-ID: 425717 [Multi-domain]  Cd Length: 261  Bit Score: 123.17  E-value: 3.50e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699678152   33 DRQVLEDFPTISMEFRNLSKVYQdVISDICHKMGVGMAEFLEKK-VDSQHEWDKYCHYVAGLVGIGLSRLFSASELEDPV 111
Cdd:pfam00494  63 ARRLKPARHPVLRALADLIRRYQ-LPKEPFLELIDGMEMDLEFTrYETLAELEEYCYYVAGVVGLLLLRLLGARSDEAAL 141

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699678152  112 VgqdtELANSMGLFLQKTNIIRDYLEDQLEGREFWPREVWSRYAKKLSDLAKPENIDMAVQCLNELITNALHHVPDVLTY 191
Cdd:pfam00494 142 L----EAASHLGLALQLTNILRDVGEDARRGRVYLPAEVLKRFGVSEEDLLRGRASPALRALLRELAERARAHLREARPL 217

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 699678152  192 LSRLKNQSVFnFCAIPQVMAIATLAACYNNK-QVFRGVVKIRKGQ 235
Cdd:pfam00494 218 LALLPRRARP-AVLLAAVLYRAILRRLEAAGyDVLRRRVKLSRRR 261
ERG9 COG1562
Phytoene/squalene synthetase [Lipid transport and metabolism];
68-243 5.71e-18

Phytoene/squalene synthetase [Lipid transport and metabolism];


Pssm-ID: 441170 [Multi-domain]  Cd Length: 278  Bit Score: 82.16  E-value: 5.71e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699678152  68 GMAEFLEKKV-DSQHEWDKYCHYVAGLVGIGLSRLFSASEledpvvGQDTELANSMGLFLQKTNIIRDYLEDQLEGREFW 146
Cdd:COG1562  105 GMEMDLTKTRyATFAELEDYCYRVAGVVGLLLLRVFGADD------PEALAAADALGVALQLTNILRDVGEDARRGRVYL 178

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699678152 147 PREVWSRYAKKLSDLAKPENIDMAVQCLNELITNALHHVPDVLTYLSRLKNQSVFnFCAIPQVMAIATLAACYNNK-QVF 225
Cdd:COG1562  179 PLDDLARFGVTEEDLLAGRASPALRALLRFLAARARALLREALAGIPALPRRARR-AVLLAAALYRAILDKIERRGyDVL 257

                        170
                 ....*....|....*...
gi 699678152 226 RGVVKIRKGQAVTLMMDA 243
Cdd:COG1562  258 RRRVRLSRLRKLWLLWRA 275
PLN02632 PLN02632
phytoene synthase
 86-149 5.00e-05

phytoene synthase


Pssm-ID: 215339  Cd Length: 334  Bit Score: 44.32  E-value: 5.00e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 699678152  86 YCHYVAGLVGiglsrLFSAseledPVVG------QDTEL----ANSMGLFLQKTNIIRDYLEDQLEGREFWPRE 149
Cdd:PLN02632 167 YCYYVAGTVG-----LMSV-----PVMGiapeskASTESvynaALALGIANQLTNILRDVGEDARRGRVYLPQD 230
 
Name Accession Description Interval E-value
squal_synth TIGR01559
farnesyl-diphosphate farnesyltransferase; This model describes farnesyl-diphosphate ...
 1-285 1.36e-172

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: 482.33  E-value: 1.36e-172
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699678152    1 MTISLDVKVPMLHEFHSYLYQPEWKYMES-KEKDRQVLEDFPTISMEFRNLSKVYQDVISDICHKMGVGMAEFLEKKV-- 77
Cdd:TIGR01559  49 MTISVDKKIPLLRDFHEKIYDPDWRFTESdNEKDRQVLDDFPVVSLEFLKLKPKYQEVIADITRRMGNGMADFIDKEVtn 128

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699678152   78 -DSQHEWDKYCHYVAGLVGIGLSRLFSASELEDPVVGQDTELANSMGLFLQKTNIIRDYLEDQLEGREFWPREVWSRYAK 156
Cdd:TIGR01559 129 eQTVGDYDKYCHYVAGLVGIGLSRLFVASGFEDPSLGESEALSNSMGLFLQKTNIIRDYLEDINEGRMFWPREIWSKYAK 208

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699678152  157 KLSDLAKPENIDMAVQCLNELITNALHHVPDVLTYLSRLKNQSVFNFCAIPQVMAIATLAACYNNKQVFRGVVKIRKGQA 236
Cdd:TIGR01559 209 KLGDFKKPENSDKALQCLNELVTNALHHATDCLTYLSRLRDQSIFNFCAIPQVMAIATLALCYNNPQVFQGNVKIRKGTT 288

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 699678152  237 VTLMMDATNIQAVKAIMYQYVEEIYQKIPSTDPSSNKTQQIIASIRAMS 285
Cdd:TIGR01559 289 VKLILDSTNMPAVYDIFYRYARKIYHKIDPNDPNFSKTLIIISKIEQQC 337
Trans_IPPS_HH cd00683
Trans-Isoprenyl Diphosphate Synthases, head-to-head; These trans-Isoprenyl Diphosphate ...
 1-236 8.33e-63

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: 200.54  E-value: 8.33e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699678152   1 MTISLDVKVPMLHEFHSYLYQPEWkymeskekdrqVLEDFPTISMEFRNLsKVYQDVISDICHKMGVGMAEFLEKK-VDS 79
Cdd:cd00683   46 PAAPPDEKLALLDAFRAELDAAYW-----------GGAPTHPVLRALADL-ARRYGIPREPFRDLLAGMAMDLDKRrYET 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699678152  80 QHEWDKYCHYVAGLVGIGLSRLFSASELEDPVvgqdtELANSMGLFLQKTNIIRDYLEDQLEGREFWPREVWSRYAKKLS 159
Cdd:cd00683  114 LDELDEYCYYVAGVVGLMLLRVFGASSDEAAL-----ERARALGLALQLTNILRDVGEDARRGRIYLPREELARFGVTLE 188

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 699678152 160 DLAKPENIDMAVQCLNELITNALHHVPDVLTYLSRLKnqSVFNFCAIPQVMAIATLAACYNNKQVFRGVVKIRKGQA 236
Cdd:cd00683  189 DLLAPENSPAFRALLRRLIARARAHYREALAGLAALP--RRSRFCVRAAAMLYRTILDEIEARGYDVLSVRVRVPKA 263
SQS_PSY pfam00494
Squalene/phytoene synthase;
33-235 3.50e-33

Squalene/phytoene synthase;


Pssm-ID: 425717 [Multi-domain]  Cd Length: 261  Bit Score: 123.17  E-value: 3.50e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699678152   33 DRQVLEDFPTISMEFRNLSKVYQdVISDICHKMGVGMAEFLEKK-VDSQHEWDKYCHYVAGLVGIGLSRLFSASELEDPV 111
Cdd:pfam00494  63 ARRLKPARHPVLRALADLIRRYQ-LPKEPFLELIDGMEMDLEFTrYETLAELEEYCYYVAGVVGLLLLRLLGARSDEAAL 141

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699678152  112 VgqdtELANSMGLFLQKTNIIRDYLEDQLEGREFWPREVWSRYAKKLSDLAKPENIDMAVQCLNELITNALHHVPDVLTY 191
Cdd:pfam00494 142 L----EAASHLGLALQLTNILRDVGEDARRGRVYLPAEVLKRFGVSEEDLLRGRASPALRALLRELAERARAHLREARPL 217

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 699678152  192 LSRLKNQSVFnFCAIPQVMAIATLAACYNNK-QVFRGVVKIRKGQ 235
Cdd:pfam00494 218 LALLPRRARP-AVLLAAVLYRAILRRLEAAGyDVLRRRVKLSRRR 261
Trans_IPPS cd00867
Trans-Isoprenyl Diphosphate Synthases; Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) of ...
 32-184 1.29e-19

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: 86.24  E-value: 1.29e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699678152  32 KDRQVLEDFPTISMEFRNLSK----VYQDVISDICHKMGVGMAEFLEKKVDSQHEWDKY---CHY-VAGLVGIGLSRLFS 103
Cdd:cd00867   60 NALAILAGDYLLARAFQLLARlgypRALELFAEALRELLEGQALDLEFERDTYETLDEYleyCRYkTAGLVGLLCLLGAG 139

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699678152 104 ASELEDPVVGQDTELANSMGLFLQKTNIIRDY----------LEDQLEGREFWPREVWSRYAKKLSDLAK------PENI 167
Cdd:cd00867  140 LSGADDEQAEALKDYGRALGLAFQLTDDLLDVfgdaeelgkvGSDLREGRITLPVILARERAAEYAEEAYaalealPPSL 219

                        170
                 ....*....|....*..
gi 699678152 168 DMAVQCLNELITNALHH 184
Cdd:cd00867  220 PRARRALIALADFLYRR 236
ERG9 COG1562
Phytoene/squalene synthetase [Lipid transport and metabolism];
68-243 5.71e-18

Phytoene/squalene synthetase [Lipid transport and metabolism];


Pssm-ID: 441170 [Multi-domain]  Cd Length: 278  Bit Score: 82.16  E-value: 5.71e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699678152  68 GMAEFLEKKV-DSQHEWDKYCHYVAGLVGIGLSRLFSASEledpvvGQDTELANSMGLFLQKTNIIRDYLEDQLEGREFW 146
Cdd:COG1562  105 GMEMDLTKTRyATFAELEDYCYRVAGVVGLLLLRVFGADD------PEALAAADALGVALQLTNILRDVGEDARRGRVYL 178

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699678152 147 PREVWSRYAKKLSDLAKPENIDMAVQCLNELITNALHHVPDVLTYLSRLKNQSVFnFCAIPQVMAIATLAACYNNK-QVF 225
Cdd:COG1562  179 PLDDLARFGVTEEDLLAGRASPALRALLRFLAARARALLREALAGIPALPRRARR-AVLLAAALYRAILDKIERRGyDVL 257

                        170
                 ....*....|....*...
gi 699678152 226 RGVVKIRKGQAVTLMMDA 243
Cdd:COG1562  258 RRRVRLSRLRKLWLLWRA 275
Isoprenoid_Biosyn_C1 cd00385
Isoprenoid Biosynthesis enzymes, Class 1; Superfamily of trans-isoprenyl diphosphate synthases ...
 48-213 2.28e-16

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: 77.15  E-value: 2.28e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699678152  48 RNLSKVYQDVISDICHKMGVGMAEFLEK---KVDSQHEWDKYCHYV-AGLVGIGLSRLFSASELEDPVVGQDTELANSMG 123
Cdd:cd00385   74 REGSPEALEILAEALLDLLEGQLLDLKWrreYVPTLEEYLEYCRYKtAGLVGALCLLGAGLSGGEAELLEALRKLGRALG 153

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699678152 124 LFLQKTNIIRDYLEDQ--LEGREFWPREVWSRYAKKLSDLAKPENIDMAVQCLNELITNALHHVPDVLTYLSRLKnqSVF 201
Cdd:cd00385  154 LAFQLTNDLLDYEGDAerGEGKCTLPVLYALEYGVPAEDLLLVEKSGSLEEALEELAKLAEEALKELNELILSLP--DVP 231

                        170
                 ....*....|..
gi 699678152 202 NFCAIPQVMAIA 213
Cdd:cd00385  232 RALLALALNLYR 243
HpnD TIGR03465
squalene synthase HpnD; The genes of this family are often found in the same genetic locus ...
 84-184 5.20e-09

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: 56.14  E-value: 5.20e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699678152   84 DKYCHYVAGLVGIGLSRLFSASEledpvvGQDTELANSMGLFLQKTNIIRDYLEDQLEGREFWPREVWSRYAKKLSDLAK 163
Cdd:TIGR03465 110 DLYCDRVAGAVGRLSARIFGATD------ARTLEYAHHLGRALQLTNILRDVGEDARRGRIYLPAEELQRFGVPAADILE 183

                          90       100
                  ....*....|....*....|.
gi 699678152  164 PENIDMAVQCLNELITNALHH 184
Cdd:TIGR03465 184 GRYSPALAALCRFQAERARAH 204
PLN02632 PLN02632
phytoene synthase
 86-149 5.00e-05

phytoene synthase


Pssm-ID: 215339  Cd Length: 334  Bit Score: 44.32  E-value: 5.00e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 699678152  86 YCHYVAGLVGiglsrLFSAseledPVVG------QDTEL----ANSMGLFLQKTNIIRDYLEDQLEGREFWPRE 149
Cdd:PLN02632 167 YCYYVAGTVG-----LMSV-----PVMGiapeskASTESvynaALALGIANQLTNILRDVGEDARRGRVYLPQD 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.
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