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Conserved domains on  [gi|1301426757|gb|PKB83928|]
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MAG: hypothetical protein BZY84_00055, partial [SAR202 cluster bacterium MP-SInd-SRR3963457-G1]

Protein Classification

inner membrane-spanning protein YciB( domain architecture ID 1903478)

inner membrane-spanning protein YciB plays a role in cell envelope biogenesis, maintenance of cell envelope integrity and membrane homeostasis

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
IspA super family cl43038
Geranylgeranyl pyrophosphate synthase [Coenzyme transport and metabolism]; Geranylgeranyl ...
 3-233 8.88e-34

Geranylgeranyl pyrophosphate synthase [Coenzyme transport and metabolism]; Geranylgeranyl pyrophosphate synthase is part of the Pathway/BioSystem: Isoprenoid biosynthesis


The actual alignment was detected with superfamily member COG0142:

Pssm-ID: 439912 [Multi-domain]  Cd Length: 329  Bit Score: 123.79  E-value: 8.88e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1301426757   3 RPSIWWVWGPAQAINAGDGLHALGrttmMRLAQNDVPADRVLRAVRSLDQACLSLCEGQYMDLQFQDQMLVSTADYMDMV 82
Cdd:COG0142    97 KPTVHARFGEATAILAGDALLALA----FELLAELGDPERRLRALRILARAARGMCEGQALDLEAEGRLDVTLEEYLRVI 172

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1301426757  83 ARK---------------AGalascsaesaalaagASDEVCAGFTDMGRSMGMAWQIARDIDDLWGEHGD-GMTP-SNVL 145
Cdd:COG0142   173 RLKtaalfaaalrlgailAG---------------ADEEQVEALRRYGRNLGLAFQIRDDILDVTGDPEVlGKPAgSDLR 237

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1301426757 146 NKKKSLPLVHTLETAGVSTKRELGAIYMKRVLESEDIAKMIEILDSAGARQISQAKAQELVGKALAGLDGVSQ-EGMDAL 224
Cdd:COG0142   238 EGKPTLPLLLALERADPEERAELRELLGKPDLDEEDLAEVRALLRESGALEYARELARELAEEALAALAALPDsEAREAL 317


                  ....*....
gi 1301426757 225 ASLGQWAAA 233
Cdd:COG0142   318 RALADYVVE 326
 
Name Accession Description Interval E-value
IspA COG0142
Geranylgeranyl pyrophosphate synthase [Coenzyme transport and metabolism]; Geranylgeranyl ...
 3-233 8.88e-34

Geranylgeranyl pyrophosphate synthase [Coenzyme transport and metabolism]; Geranylgeranyl pyrophosphate synthase is part of the Pathway/BioSystem: Isoprenoid biosynthesis


Pssm-ID: 439912 [Multi-domain]  Cd Length: 329  Bit Score: 123.79  E-value: 8.88e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1301426757   3 RPSIWWVWGPAQAINAGDGLHALGrttmMRLAQNDVPADRVLRAVRSLDQACLSLCEGQYMDLQFQDQMLVSTADYMDMV 82
Cdd:COG0142    97 KPTVHARFGEATAILAGDALLALA----FELLAELGDPERRLRALRILARAARGMCEGQALDLEAEGRLDVTLEEYLRVI 172

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1301426757  83 ARK---------------AGalascsaesaalaagASDEVCAGFTDMGRSMGMAWQIARDIDDLWGEHGD-GMTP-SNVL 145
Cdd:COG0142   173 RLKtaalfaaalrlgailAG---------------ADEEQVEALRRYGRNLGLAFQIRDDILDVTGDPEVlGKPAgSDLR 237

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1301426757 146 NKKKSLPLVHTLETAGVSTKRELGAIYMKRVLESEDIAKMIEILDSAGARQISQAKAQELVGKALAGLDGVSQ-EGMDAL 224
Cdd:COG0142   238 EGKPTLPLLLALERADPEERAELRELLGKPDLDEEDLAEVRALLRESGALEYARELARELAEEALAALAALPDsEAREAL 317


                  ....*....
gi 1301426757 225 ASLGQWAAA 233
Cdd:COG0142   318 RALADYVVE 326
polyprenyl_synt pfam00348
Polyprenyl synthetase;
3-188 1.05e-16

Polyprenyl synthetase;


Pssm-ID: 459773  Cd Length: 251  Bit Score: 76.39  E-value: 1.05e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1301426757   3 RPSIWWVWGPAQAINAGDGLHALGRTTMMRLAQNdvpadrvLRAVRSLDQACLSLCEGQYMDLQFQDQMLVST--ADYMD 80
Cdd:pfam00348  70 QPTWHRIFGNAIAINDGDYLYALAFQLLAKLFPN-------PELLELFSEVTLQTAEGQGLDLLWRNDDDLSCteEEYLE 142

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1301426757  81 MVARKAGALASCSAESAALAAGASDEVCAGFTDMGRSMGMAWQIARDIDDLWGEhgdgmtpSNVLNK---------KKSL 151
Cdd:pfam00348 143 IVKYKTAYLFALAVKLGAILSGADDEVIEALKDYGLNLGLAFQIQDDYLDLFGD-------PEVLGKpagtditegKCTW 215

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1301426757 152 PLVHTLETAGvSTKRELGAIYMKRVLESEDIAKMIEI 188
Cdd:pfam00348 216 PVIHALERTP-EQRKILLEIYGKRPEDVEKVKEAYEL 251
Trans_IPPS cd00867
Trans-Isoprenyl Diphosphate Synthases; Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) of ...
 3-160 4.66e-15

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: 71.61  E-value: 4.66e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1301426757   3 RPSIW-WVWGPAQAINAGDGLHALgrttmmrlAQNDVPADRVLRAVRSLDQACLSLCEGQYMDLQFQDQMLVSTADYMDM 81
Cdd:cd00867    50 KPTAHlRRFGNALAILAGDYLLAR--------AFQLLARLGYPRALELFAEALRELLEGQALDLEFERDTYETLDEYLEY 121

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1301426757  82 VARKAGALASCSAESAALAAGASDEVCAGFTDMGRSMGMAWQIARDIDDLWG-EHGDGMTPSNVLNKKKSLPLVHTLETA 160
Cdd:cd00867   122 CRYKTAGLVGLLCLLGAGLSGADDEQAEALKDYGRALGLAFQLTDDLLDVFGdAEELGKVGSDLREGRITLPVILARERA 201
 
Name Accession Description Interval E-value
IspA COG0142
Geranylgeranyl pyrophosphate synthase [Coenzyme transport and metabolism]; Geranylgeranyl ...
 3-233 8.88e-34

Geranylgeranyl pyrophosphate synthase [Coenzyme transport and metabolism]; Geranylgeranyl pyrophosphate synthase is part of the Pathway/BioSystem: Isoprenoid biosynthesis


Pssm-ID: 439912 [Multi-domain]  Cd Length: 329  Bit Score: 123.79  E-value: 8.88e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1301426757   3 RPSIWWVWGPAQAINAGDGLHALGrttmMRLAQNDVPADRVLRAVRSLDQACLSLCEGQYMDLQFQDQMLVSTADYMDMV 82
Cdd:COG0142    97 KPTVHARFGEATAILAGDALLALA----FELLAELGDPERRLRALRILARAARGMCEGQALDLEAEGRLDVTLEEYLRVI 172

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1301426757  83 ARK---------------AGalascsaesaalaagASDEVCAGFTDMGRSMGMAWQIARDIDDLWGEHGD-GMTP-SNVL 145
Cdd:COG0142   173 RLKtaalfaaalrlgailAG---------------ADEEQVEALRRYGRNLGLAFQIRDDILDVTGDPEVlGKPAgSDLR 237

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1301426757 146 NKKKSLPLVHTLETAGVSTKRELGAIYMKRVLESEDIAKMIEILDSAGARQISQAKAQELVGKALAGLDGVSQ-EGMDAL 224
Cdd:COG0142   238 EGKPTLPLLLALERADPEERAELRELLGKPDLDEEDLAEVRALLRESGALEYARELARELAEEALAALAALPDsEAREAL 317


                  ....*....
gi 1301426757 225 ASLGQWAAA 233
Cdd:COG0142   318 RALADYVVE 326
polyprenyl_synt pfam00348
Polyprenyl synthetase;
3-188 1.05e-16

Polyprenyl synthetase;


Pssm-ID: 459773  Cd Length: 251  Bit Score: 76.39  E-value: 1.05e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1301426757   3 RPSIWWVWGPAQAINAGDGLHALGRTTMMRLAQNdvpadrvLRAVRSLDQACLSLCEGQYMDLQFQDQMLVST--ADYMD 80
Cdd:pfam00348  70 QPTWHRIFGNAIAINDGDYLYALAFQLLAKLFPN-------PELLELFSEVTLQTAEGQGLDLLWRNDDDLSCteEEYLE 142

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1301426757  81 MVARKAGALASCSAESAALAAGASDEVCAGFTDMGRSMGMAWQIARDIDDLWGEhgdgmtpSNVLNK---------KKSL 151
Cdd:pfam00348 143 IVKYKTAYLFALAVKLGAILSGADDEVIEALKDYGLNLGLAFQIQDDYLDLFGD-------PEVLGKpagtditegKCTW 215

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1301426757 152 PLVHTLETAGvSTKRELGAIYMKRVLESEDIAKMIEI 188
Cdd:pfam00348 216 PVIHALERTP-EQRKILLEIYGKRPEDVEKVKEAYEL 251
Trans_IPPS cd00867
Trans-Isoprenyl Diphosphate Synthases; Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) of ...
 3-160 4.66e-15

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: 71.61  E-value: 4.66e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1301426757   3 RPSIW-WVWGPAQAINAGDGLHALgrttmmrlAQNDVPADRVLRAVRSLDQACLSLCEGQYMDLQFQDQMLVSTADYMDM 81
Cdd:cd00867    50 KPTAHlRRFGNALAILAGDYLLAR--------AFQLLARLGYPRALELFAEALRELLEGQALDLEFERDTYETLDEYLEY 121

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1301426757  82 VARKAGALASCSAESAALAAGASDEVCAGFTDMGRSMGMAWQIARDIDDLWG-EHGDGMTPSNVLNKKKSLPLVHTLETA 160
Cdd:cd00867   122 CRYKTAGLVGLLCLLGAGLSGADDEQAEALKDYGRALGLAFQLTDDLLDVFGdAEELGKVGSDLREGRITLPVILARERA 201
Isoprenoid_Biosyn_C1 cd00385
Isoprenoid Biosynthesis enzymes, Class 1; Superfamily of trans-isoprenyl diphosphate synthases ...
 6-187 4.77e-11

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: 60.59  E-value: 4.77e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1301426757   6 IWWVWGPAQAINAGDGLHALgrttmmrlAQNDVPADRVLRAVRSLDQACLSLCEGQYMDLQFQDQMLVSTADYMDMVARK 85
Cdd:cd00385    48 AVAIDGLPEAILAGDLLLAD--------AFEELAREGSPEALEILAEALLDLLEGQLLDLKWRREYVPTLEEYLEYCRYK 119

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1301426757  86 AGALASCSAESAALAAGASDEVCAGFTDMGRSMGMAWQIARDIDDLWGEhgdgmtpSNVLNKKKSLPLVHTLEtAGVSTK 165
Cdd:cd00385   120 TAGLVGALCLLGAGLSGGEAELLEALRKLGRALGLAFQLTNDLLDYEGD-------AERGEGKCTLPVLYALE-YGVPAE 191

                         170       180
                  ....*....|....*....|...
gi 1301426757 166 RELGAIYMKRVLESED-IAKMIE 187
Cdd:cd00385   192 DLLLVEKSGSLEEALEeLAKLAE 214
 
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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