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Conserved domains on  [gi|150438878|sp|A2AIL4|]
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RecName: Full=NADH dehydrogenase (ubiquinone) complex I, assembly factor 6; Flags: Precursor

Protein Classification

phytoene/squalene synthase family protein( domain architecture ID 10452993)

phytoene/squalene synthase family protein may catalyze the head-to-head condensation of two isoprenyl diphosphates; similar to Homo sapiens NADH dehydrogenase (ubiquinone) complex I, assembly factor 6, which is involved in the assembly of mitochondrial NADH:ubiquinone oxidoreductase complex (complex I) at early stages

CATH:  1.10.600.10
EC:  2.5.1.-
Gene Ontology:  GO:0004659|GO:0046872|GO:0008299
PubMed:  12135472|11111076
SCOP:  3001615

Graphical summary

 Zoom to residue level

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List of domain hits

Name Accession Description Interval E-value
SQS_PSY pfam00494
Squalene/phytoene synthase;
65-311 4.55e-59

Squalene/phytoene synthase;


:

Pssm-ID: 425717 [Multi-domain]  Cd Length: 261  Bit Score: 190.58  E-value: 4.55e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150438878   65 LRKRDYESYLCSLLFPAECQRSASALRAFNVELAQVKDSVSE-KTIGLMRMQFWKKAVEDMYCDN--PPHQPVAIELWKA 141
Cdd:pfam00494   1 LRKVSRSFYLASLLLPPELRRAVFALYAFCREADDIVDEVSDpPAAKRARLDWWRDALDGAYARRlkPARHPVLRALADL 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150438878  142 VKKHNLTKRWLMRIIDEREKNLDDKAYRSMQELENYAENTQGSLLYLTLEVLGV--KDLHADHAASHIGKAQGIVTCLRA 219
Cdd:pfam00494  81 IRRYQLPKEPFLELIDGMEMDLEFTRYETLAELEEYCYYVAGVVGLLLLRLLGArsDEAALLEAASHLGLALQLTNILRD 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150438878  220 TPYHSSRRQVFLPMDVCVQHGVSQEDFLRRNQDKNVRDVVYDIASQAHLHLKHARSFHRSVPAEAFPAFLQTVSL-EDYL 298
Cdd:pfam00494 161 VGEDARRGRVYLPAEVLKRFGVSEEDLLRGRASPALRALLRELAERARAHLREARPLLALLPRRARPAVLLAAVLyRAIL 240
                         250
                  ....*....|...
gi 150438878  299 KKIQRVDFDIFHP 311
Cdd:pfam00494 241 RRLEAAGYDVLRR 253
 
Name Accession Description Interval E-value
SQS_PSY pfam00494
Squalene/phytoene synthase;
65-311 4.55e-59

Squalene/phytoene synthase;


Pssm-ID: 425717 [Multi-domain]  Cd Length: 261  Bit Score: 190.58  E-value: 4.55e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150438878   65 LRKRDYESYLCSLLFPAECQRSASALRAFNVELAQVKDSVSE-KTIGLMRMQFWKKAVEDMYCDN--PPHQPVAIELWKA 141
Cdd:pfam00494   1 LRKVSRSFYLASLLLPPELRRAVFALYAFCREADDIVDEVSDpPAAKRARLDWWRDALDGAYARRlkPARHPVLRALADL 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150438878  142 VKKHNLTKRWLMRIIDEREKNLDDKAYRSMQELENYAENTQGSLLYLTLEVLGV--KDLHADHAASHIGKAQGIVTCLRA 219
Cdd:pfam00494  81 IRRYQLPKEPFLELIDGMEMDLEFTRYETLAELEEYCYYVAGVVGLLLLRLLGArsDEAALLEAASHLGLALQLTNILRD 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150438878  220 TPYHSSRRQVFLPMDVCVQHGVSQEDFLRRNQDKNVRDVVYDIASQAHLHLKHARSFHRSVPAEAFPAFLQTVSL-EDYL 298
Cdd:pfam00494 161 VGEDARRGRVYLPAEVLKRFGVSEEDLLRGRASPALRALLRELAERARAHLREARPLLALLPRRARPAVLLAAVLyRAIL 240
                         250
                  ....*....|...
gi 150438878  299 KKIQRVDFDIFHP 311
Cdd:pfam00494 241 RRLEAAGYDVLRR 253
ERG9 COG1562
Phytoene/squalene synthetase [Lipid transport and metabolism];
60-310 7.22e-38

Phytoene/squalene synthetase [Lipid transport and metabolism];


Pssm-ID: 441170 [Multi-domain]  Cd Length: 278  Bit Score: 136.09  E-value: 7.22e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150438878  60 YCLELLRKRDYESYLCSLLFPAECQRSASALRAFNVELAQVKDSVSEKTIGLMRMQFWKKAVEDMYCDNPPHQPVAIELW 139
Cdd:COG1562    7 YCRAITRRHSRSFYLASLLLPPELRRAVYALYAFCREADDIVDEVSDPAEREARLDWWRAELDAAYAGGPADHPVLAALA 86
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150438878 140 KAVKKHNLTKRWLMRIIDEREKNLDDKAYRSMQELENYAENTQGSLLYLTLEVLGVKDLHADHAASHIGKAQGIVTCLRA 219
Cdd:COG1562   87 DTVRRYGLPRELFLDLIDGMEMDLTKTRYATFAELEDYCYRVAGVVGLLLLRVFGADDPEALAAADALGVALQLTNILRD 166
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150438878 220 TPYHSSRRQVFLPMDVCVQHGVSQEDFLRRNQDKNVRDVVYDIASQAHLHLKHARSFHRSVPAEA-FPAFLQTVSLEDYL 298
Cdd:COG1562  167 VGEDARRGRVYLPLDDLARFGVTEEDLLAGRASPALRALLRFLAARARALLREALAGIPALPRRArRAVLLAAALYRAIL 246
                        250
                 ....*....|..
gi 150438878 299 KKIQRVDFDIFH 310
Cdd:COG1562  247 DKIERRGYDVLR 258
Trans_IPPS_HH cd00683
Trans-Isoprenyl Diphosphate Synthases, head-to-head; These trans-Isoprenyl Diphosphate ...
60-310 1.33e-12

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: 66.87  E-value: 1.33e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150438878  60 YCLELLRKRDYESYLCSLLFPAECQRSASALRAFNVELAQVKDSVS-EKTIGLMRMQFWKKAVEDMYCDNPPHQPVAIEL 138
Cdd:cd00683    2 YCRAILRKGSRSFYLASRLLPPELRRAVCALYAFCRAADDIVDDPAaPPDEKLALLDAFRAELDAAYWGGAPTHPVLRAL 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150438878 139 WKAVKKHNLTKRWLMRIIDEREKNLDDKAYRSMQELENYAENTQGSLLYLTLEVLGVKDLH-ADHAASHIGKAQGIVTCL 217
Cdd:cd00683   82 ADLARRYGIPREPFRDLLAGMAMDLDKRRYETLDELDEYCYYVAGVVGLMLLRVFGASSDEaALERARALGLALQLTNIL 161
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150438878 218 R--ATPYHSSRrqVFLPMDVCVQHGVSQEDFLRRNQDKNVRDVVYDIASQAHLHLKHARSFHRSVPAEA-FPAFLQTVSL 294
Cdd:cd00683  162 RdvGEDARRGR--IYLPREELARFGVTLEDLLAPENSPAFRALLRRLIARARAHYREALAGLAALPRRSrFCVRAAAMLY 239
                        250
                 ....*....|....*.
gi 150438878 295 EDYLKKIQRVDFDIFH 310
Cdd:cd00683  240 RTILDEIEARGYDVLS 255
PLN02632 PLN02632
phytoene synthase
34-325 2.62e-07

phytoene synthase


Pssm-ID: 215339  Cd Length: 334  Bit Score: 51.64  E-value: 2.62e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150438878  34 RRLPGPSAVRRSVAAASGPGIPGSHL---Y--CLELLRKRDYESYLCSLLFPAECQRSASALRAFNVELAQVKDSVSEKT 108
Cdd:PLN02632  20 KQAALVRKAARRSVRPRATSLSPALLeeaYdrCGEVCAEYAKTFYLGTLLMTPERRKAIWAIYVWCRRTDELVDGPNASH 99
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150438878 109 IGLMRMQFWKKAVEDMYCDNPpHQPVAIELWKAVKKHNLTKRWLMRIIDEREKNLDDKAYRSMQELENYAENTQGSLLYL 188
Cdd:PLN02632 100 ITPAALDRWEARLEDLFDGRP-YDMLDAALADTVSKFPLDIQPFRDMIEGMRMDLVKSRYENFDELYLYCYYVAGTVGLM 178
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150438878 189 TLEVLGV------KDLHADHAASHIGKAQGIVTCLRATPYHSSRRQVFLPMDVCVQHGVSQEDFLRRNQDKNVRDVVYDI 262
Cdd:PLN02632 179 SVPVMGIapeskaSTESVYNAALALGIANQLTNILRDVGEDARRGRVYLPQDELAQFGLTDEDIFAGKVTDKWRAFMKFQ 258
                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 150438878 263 ASQAHLHLKHARSFHRSVPAEA-FPAFLqtvSLEDY---LKKIQRVDFDIF----HPSLQQKNMLLPLSLY 325
Cdd:PLN02632 259 IKRARMYFAEAEEGVSELDPASrWPVWA---SLLLYrqiLDAIEANDYDNFtkraYVGKWKKLLALPLAYA 326
 
Name Accession Description Interval E-value
SQS_PSY pfam00494
Squalene/phytoene synthase;
65-311 4.55e-59

Squalene/phytoene synthase;


Pssm-ID: 425717 [Multi-domain]  Cd Length: 261  Bit Score: 190.58  E-value: 4.55e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150438878   65 LRKRDYESYLCSLLFPAECQRSASALRAFNVELAQVKDSVSE-KTIGLMRMQFWKKAVEDMYCDN--PPHQPVAIELWKA 141
Cdd:pfam00494   1 LRKVSRSFYLASLLLPPELRRAVFALYAFCREADDIVDEVSDpPAAKRARLDWWRDALDGAYARRlkPARHPVLRALADL 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150438878  142 VKKHNLTKRWLMRIIDEREKNLDDKAYRSMQELENYAENTQGSLLYLTLEVLGV--KDLHADHAASHIGKAQGIVTCLRA 219
Cdd:pfam00494  81 IRRYQLPKEPFLELIDGMEMDLEFTRYETLAELEEYCYYVAGVVGLLLLRLLGArsDEAALLEAASHLGLALQLTNILRD 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150438878  220 TPYHSSRRQVFLPMDVCVQHGVSQEDFLRRNQDKNVRDVVYDIASQAHLHLKHARSFHRSVPAEAFPAFLQTVSL-EDYL 298
Cdd:pfam00494 161 VGEDARRGRVYLPAEVLKRFGVSEEDLLRGRASPALRALLRELAERARAHLREARPLLALLPRRARPAVLLAAVLyRAIL 240
                         250
                  ....*....|...
gi 150438878  299 KKIQRVDFDIFHP 311
Cdd:pfam00494 241 RRLEAAGYDVLRR 253
ERG9 COG1562
Phytoene/squalene synthetase [Lipid transport and metabolism];
60-310 7.22e-38

Phytoene/squalene synthetase [Lipid transport and metabolism];


Pssm-ID: 441170 [Multi-domain]  Cd Length: 278  Bit Score: 136.09  E-value: 7.22e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150438878  60 YCLELLRKRDYESYLCSLLFPAECQRSASALRAFNVELAQVKDSVSEKTIGLMRMQFWKKAVEDMYCDNPPHQPVAIELW 139
Cdd:COG1562    7 YCRAITRRHSRSFYLASLLLPPELRRAVYALYAFCREADDIVDEVSDPAEREARLDWWRAELDAAYAGGPADHPVLAALA 86
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150438878 140 KAVKKHNLTKRWLMRIIDEREKNLDDKAYRSMQELENYAENTQGSLLYLTLEVLGVKDLHADHAASHIGKAQGIVTCLRA 219
Cdd:COG1562   87 DTVRRYGLPRELFLDLIDGMEMDLTKTRYATFAELEDYCYRVAGVVGLLLLRVFGADDPEALAAADALGVALQLTNILRD 166
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150438878 220 TPYHSSRRQVFLPMDVCVQHGVSQEDFLRRNQDKNVRDVVYDIASQAHLHLKHARSFHRSVPAEA-FPAFLQTVSLEDYL 298
Cdd:COG1562  167 VGEDARRGRVYLPLDDLARFGVTEEDLLAGRASPALRALLRFLAARARALLREALAGIPALPRRArRAVLLAAALYRAIL 246
                        250
                 ....*....|..
gi 150438878 299 KKIQRVDFDIFH 310
Cdd:COG1562  247 DKIERRGYDVLR 258
Trans_IPPS_HH cd00683
Trans-Isoprenyl Diphosphate Synthases, head-to-head; These trans-Isoprenyl Diphosphate ...
60-310 1.33e-12

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: 66.87  E-value: 1.33e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150438878  60 YCLELLRKRDYESYLCSLLFPAECQRSASALRAFNVELAQVKDSVS-EKTIGLMRMQFWKKAVEDMYCDNPPHQPVAIEL 138
Cdd:cd00683    2 YCRAILRKGSRSFYLASRLLPPELRRAVCALYAFCRAADDIVDDPAaPPDEKLALLDAFRAELDAAYWGGAPTHPVLRAL 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150438878 139 WKAVKKHNLTKRWLMRIIDEREKNLDDKAYRSMQELENYAENTQGSLLYLTLEVLGVKDLH-ADHAASHIGKAQGIVTCL 217
Cdd:cd00683   82 ADLARRYGIPREPFRDLLAGMAMDLDKRRYETLDELDEYCYYVAGVVGLMLLRVFGASSDEaALERARALGLALQLTNIL 161
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150438878 218 R--ATPYHSSRrqVFLPMDVCVQHGVSQEDFLRRNQDKNVRDVVYDIASQAHLHLKHARSFHRSVPAEA-FPAFLQTVSL 294
Cdd:cd00683  162 RdvGEDARRGR--IYLPREELARFGVTLEDLLAPENSPAFRALLRRLIARARAHYREALAGLAALPRRSrFCVRAAAMLY 239
                        250
                 ....*....|....*.
gi 150438878 295 EDYLKKIQRVDFDIFH 310
Cdd:cd00683  240 RTILDEIEARGYDVLS 255
PLN02632 PLN02632
phytoene synthase
34-325 2.62e-07

phytoene synthase


Pssm-ID: 215339  Cd Length: 334  Bit Score: 51.64  E-value: 2.62e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150438878  34 RRLPGPSAVRRSVAAASGPGIPGSHL---Y--CLELLRKRDYESYLCSLLFPAECQRSASALRAFNVELAQVKDSVSEKT 108
Cdd:PLN02632  20 KQAALVRKAARRSVRPRATSLSPALLeeaYdrCGEVCAEYAKTFYLGTLLMTPERRKAIWAIYVWCRRTDELVDGPNASH 99
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150438878 109 IGLMRMQFWKKAVEDMYCDNPpHQPVAIELWKAVKKHNLTKRWLMRIIDEREKNLDDKAYRSMQELENYAENTQGSLLYL 188
Cdd:PLN02632 100 ITPAALDRWEARLEDLFDGRP-YDMLDAALADTVSKFPLDIQPFRDMIEGMRMDLVKSRYENFDELYLYCYYVAGTVGLM 178
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150438878 189 TLEVLGV------KDLHADHAASHIGKAQGIVTCLRATPYHSSRRQVFLPMDVCVQHGVSQEDFLRRNQDKNVRDVVYDI 262
Cdd:PLN02632 179 SVPVMGIapeskaSTESVYNAALALGIANQLTNILRDVGEDARRGRVYLPQDELAQFGLTDEDIFAGKVTDKWRAFMKFQ 258
                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 150438878 263 ASQAHLHLKHARSFHRSVPAEA-FPAFLqtvSLEDY---LKKIQRVDFDIF----HPSLQQKNMLLPLSLY 325
Cdd:PLN02632 259 IKRARMYFAEAEEGVSELDPASrWPVWA---SLLLYrqiLDAIEANDYDNFtkraYVGKWKKLLALPLAYA 326
 
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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