Citrus Sinensis ID: 044623

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480------
KNTREGKAVRSLEEWRPERLLVRYRIQVQRVEVTGASKFFFLSKKNNFYSMSVALLWVVSPNSQLSNCFGFVDSVREENRLFYSSRFLYQHQTRTAVFNSRPKQFNNSNKQRRNSYPLDTDLRHPCSSGIDLPEISCMVASTAGEVAMSSEEMVYNVVLKQAALVNKQPSGVTRDLDVNPDIALPGTLSLLSEAYDRCGEVCAEYAKTFYLGTLLMTSERRRAIWAIYVWCRRTDELVDGPNASHITPTALDRWESRLEDLFRGRPFDMLDAALSDTVTKFPVDIQPFRDMIEGMRMDLRKSRYKNFDELYLYCYYVAGTVGLMSVPVMGIAPDSQATTESVYNAALALGIANQLTNILRDVGEDAQRGRVYLPQDELAQAGLSDDDIFAGEVTNKWRNFMKNQIKRARMFFDMAENGVTELSEASRWPVWASLLLYRQILDEIEANDYNNFTKRAYVSKAKKIAALPIAYAKSLLRPSRIYTSKA
cccccccHHHHHccccccccEEEEEEEEEEEEEEcccEEEEEEcccccEEEEEEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHcccHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHcccccHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHccccHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHHccccccccccc
ccccccHHHHcHHccccHHEEEEEEEEEEEEEEccccEEEEEEcccccHHHHEEEEEEEcccccccccccccccccccccccccccccccccccEEEEcccccHcccccccccccccccccccccccccccccEEEEEEEcccccccccHHHHHHHHHHHHHHHHHHHHccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHcccccccHHHHHHcccccccccccccHHHHHHHHHHHHHHHcHEEccEcccccccccccHHHHHHHHHHHHHHHHHHHHHHHcHHHccccEEccHHHHHHHcccHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHccccccHHccHHHHHHHHHHHHHHHHHHHccccccccEEEccHHHHHHHHHHHHHHHcccccccccccc
kntregkavrsleeWRPERLLVRYRIQVQRVEVTGASKFFFLSKKNNFYSMSVALLWVvspnsqlsncfgfVDSVREENRLFYSSRFLYQHQTRtavfnsrpkqfnnsnkqrrnsypldtdlrhpcssgidlpeisCMVASTAGEVAMSSEEMVYNVVLKQAALvnkqpsgvtrdldvnpdialpgTLSLLSEAYDRCGEVCAEYAKTFYLGTLLMTSERRRAIWAIYVWCRrtdelvdgpnashitptALDRWESRLEDlfrgrpfdmlDAALSdtvtkfpvdiqpfRDMIEGMRMDLRksryknfdELYLYCYYVAGTvglmsvpvmgiapdsqatTESVYNAALALGIANQLTNILRDvgedaqrgrvylpqdelaqaglsdddifaGEVTNKWRNFMKNQIKRARMFFDMAENgvtelseasrwpVWASLLLYRQILDEIeandynnftKRAYVSKAKKIAALPIAYAKsllrpsriytska
kntregkavrsleewrperllvryriqvqrveVTGASKFFFLSKKNNFYSMSVALLWVVSPNSQLSNCFGFVDSVREENRLFYSSRFLYQHQtrtavfnsrpkqfnnsnkqrrnsyplDTDLRHPCSSGIDLPEISCMVASTAGEVAMSSEEMVYNVVLKQAALVNkqpsgvtrdldvnpdIALPGTLSLLSEAYDRCGEVCAEYAKTFYLGTLLMTSERRRAIWAIYVWCRRTdelvdgpnashitptaldrWESRLEDLFRGRPFDMLDAAlsdtvtkfpvdiqpfrDMIEGMRMDLRKSRYKNFDELYLYCYYVAGTVGLMSVPVMGIAPDSQATTESVYNAALALGIANQLTNILRDVGEDAQRGRVYLPQDElaqaglsdddiFAGEVTNKWRNFMKNQIKRARMFFDMAENGVTelseasrwpVWASLLLYRQILDEIEANDYNNFTKRAYVSKAKKIAALPIAyaksllrpsriytska
KNTREGKAVRSLEEWRPERLLVRYRIQVQRVEVTGAskffflskknnfYSMSVALLWVVSPNSQLSNCFGFVDSVREENRLFYSSRFLYQHQTRTAVFNSRPKQFNNSNKQRRNSYPLDTDLRHPCSSGIDLPEISCMVASTAGEVAMSSEEMVYNVVLKQAALVNKQPSGVTRDLDVNPDIALPGTLSLLSEAYDRCGEVCAEYAKTFYLGTLLMTSERRRAIWAIYVWCRRTDELVDGPNASHITPTALDRWESRLEDLFRGRPFDMLDAALSDTVTKFPVDIQPFRDMIEGMRMDLRKSRYKNFDELYLYCYYVAGTVGLMSVPVMGIAPDSQATTESVYNAALALGIANQLTNILRDVGEDAQRGRVYLPQDELAQAGLSDDDIFAGEVTNKWRNFMKNQIKRARMFFDMAENGVTELSEASRWPVWASLLLYRQILDEIEANDYNNFTKRAYVSKAKKIAALPIAYAKSLLRPSRIYTSKA
*************EWRPERLLVRYRIQVQRVEVTGASKFFFLSKKNNFYSMSVALLWVVSPNSQLSNCFGFVDSVREENRLFYSSRFLYQHQTRTAVF******************************GIDLPEISCMVASTAGEVAMSSEEMVYNVVLKQAALVNKQPSGVTRDLDVNPDIALPGTLSLLSEAYDRCGEVCAEYAKTFYLGTLLMTSERRRAIWAIYVWCRRTDELVDGPNASHITPTALDRWESRLEDLFRGRPFDMLDAALSDTVTKFPVDIQPFRDMIEGMRMDLRKSRYKNFDELYLYCYYVAGTVGLMSVPVMGIAPDSQATTESVYNAALALGIANQLTNILRDVGEDAQRGRVYLPQDELAQAGLSDDDIFAGEVTNKWRNFMKNQIKRARMFFDMAENGVTELSEASRWPVWASLLLYRQILDEIEANDYNNFTKRAYVSKAKKIAALPIAYAKSLLR*********
***********LEEWRPERLLVRYRIQVQRVEVTGASKFFFLSKKNNFYSMSVALLWVVSPNSQLSNCFGFVDSVREENRLFYSSRFL********************************************PEISCMVA************MVYNVVLKQAA*****************************EAYDRCGEVCAEYAKTFYLGTLLMTSERRRAIWAIYVWCRRTDELVDGPNASHITPTALDRWESRLEDLFRGRPFDMLDAALSDTVTKFPVDIQPFRDMIEGMRMDLRKSRYKNFDELYLYCYYVAGTVGLMSVPVMGIAPDSQATTESVYNAALALGIANQLTNILRDVGEDAQRGRVYLPQDELAQAGLSDDDIFAGEVTNKWRNFMKNQIKRARMFFDMAENGVTELSEASRWPVWASLLLYRQILDEIEANDYNNFTKRAYVSKAKKIAALPIAYAKSL***********
***********LEEWRPERLLVRYRIQVQRVEVTGASKFFFLSKKNNFYSMSVALLWVVSPNSQLSNCFGFVDSVREENRLFYSSRFLYQHQTRTAVFNSRPKQFNNSNKQRRNSYPLDTDLRHPCSSGIDLPEISCMVASTAGEVAMSSEEMVYNVVLKQAALVNKQPSGVTRDLDVNPDIALPGTLSLLSEAYDRCGEVCAEYAKTFYLGTLLMTSERRRAIWAIYVWCRRTDELVDGPNASHITPTALDRWESRLEDLFRGRPFDMLDAALSDTVTKFPVDIQPFRDMIEGMRMDLRKSRYKNFDELYLYCYYVAGTVGLMSVPVMGIAPDSQATTESVYNAALALGIANQLTNILRDVGEDAQRGRVYLPQDELAQAGLSDDDIFAGEVTNKWRNFMKNQIKRARMFFDMAENGVTELSEASRWPVWASLLLYRQILDEIEANDYNNFTKRAYVSKAKKIAALPIAYAKSLLRPSRIYTSKA
********VRSLEEWRPERLLVRYRIQVQRVEVTGASKFFFLSKKNNFYSMSVALLWVVSPNSQLSNCFGFVDSVREENRLFYSSRFLYQHQTRTAVFNSR***************************GIDLPEISCMVASTAGEVAMSSEEMVYNVVLKQAALVNKQPSGVTRDLDVNPDIALPGTLSLLSEAYDRCGEVCAEYAKTFYLGTLLMTSERRRAIWAIYVWCRRTDELVDGPNASHITPTALDRWESRLEDLFRGRPFDMLDAALSDTVTKFPVDIQPFRDMIEGMRMDLRKSRYKNFDELYLYCYYVAGTVGLMSVPVMGIAPDSQATTESVYNAALALGIANQLTNILRDVGEDAQRGRVYLPQDELAQAGLSDDDIFAGEVTNKWRNFMKNQIKRARMFFDMAENGVTELSEASRWPVWASLLLYRQILDEIEANDYNNFTKRAYVSKAKKIAALPIAYAKSLL**********
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KNTREGKAVRSLEEWRPERLLVRYRIQVQRVEVTGASKFFFLSKKNNFYSMSVALLWVVSPNSQLSNCFGFVDSVREENRLFYSSRFLYQHQTRTAVFNSRPKQFNNSNKQRRNSYPLDTDLRHPCSSGIDLPEISCMVASTAGEVAMSSEEMVYNVVLKQAALVNKQPSGVTRDLDVNPDIALPGTLSLLSEAYDRCGEVCAEYAKTFYLGTLLMTSERRRAIWAIYVWCRRTDELVDGPNASHITPTALDRWESRLEDLFRGRPFDMLDAALSDTVTKFPVDIQPFRDMIEGMRMDLRKSRYKNFDELYLYCYYVAGTVGLMSVPVMGIAPDSQATTESVYNAALALGIANQLTNILRDVGEDAQRGRVYLPQDELAQAGLSDDDIFAGEVTNKWRNFMKNQIKRARMFFDMAENGVTELSEASRWPVWASLLLYRQILDEIEANDYNNFTKRAYVSKAKKIAALPIAYAKSLLRPSRIYTSKA
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query486 2.2.26 [Sep-21-2011]
P37272419 Phytoene synthase, chloro N/A no 0.860 0.997 0.748 1e-180
P49293422 Phytoene synthase, chloro N/A no 0.837 0.964 0.746 1e-179
P08196412 Phytoene synthase 1, chlo N/A no 0.835 0.985 0.734 1e-177
P37271422 Phytoene synthase, chloro yes no 0.841 0.969 0.729 1e-177
P53797423 Phytoene synthase, chloro N/A no 0.777 0.893 0.759 1e-170
P49085410 Phytoene synthase, chloro N/A no 0.728 0.863 0.763 1e-160
P37273310 Phytoene synthase 2, chlo N/A no 0.617 0.967 0.866 1e-156
Q9SSU8398 Phytoene synthase, chloro N/A no 0.755 0.922 0.663 1e-150
P37269308 Phytoene synthase OS=Syne yes no 0.590 0.931 0.604 2e-99
O07333309 Phytoene synthase OS=Spir N/A no 0.609 0.957 0.562 4e-94
>sp|P37272|PSY_CAPAN Phytoene synthase, chloroplastic OS=Capsicum annuum GN=PSY1 PE=2 SV=1 Back     alignment and function desciption
 Score =  630 bits (1626), Expect = e-180,   Method: Compositional matrix adjust.
 Identities = 322/430 (74%), Positives = 351/430 (81%), Gaps = 12/430 (2%)

Query: 51  MSVALLWVVSPNSQLSNCFGFVDSVREENRLFYSSRFLYQHQTRTAVFNSRPKQFNNSNK 110
           MSVALLWVVSP   +SN  GF+ SVRE NR+F SS        R    N R K+     +
Sbjct: 1   MSVALLWVVSP-CDVSNGTGFLVSVREGNRIFDSS------GRRNLACNERIKRGGGKQR 53

Query: 111 QRRNSYPLDTDLRHPCSSGIDLPEISCMVASTAGEVAMSSEEMVYNVVLKQAALVNKQPS 170
               SY           SG      S +VA+ AGE+ MSSE MVY+VVL+QAALV +Q  
Sbjct: 54  WSFGSYLGGAQ----TGSGRKFSVRSAIVATPAGEMTMSSERMVYDVVLRQAALVKRQLR 109

Query: 171 GVTRDLDVNPDIALPGTLSLLSEAYDRCGEVCAEYAKTFYLGTLLMTSERRRAIWAIYVW 230
             T +LDV  DI +PGTL LLSEAYDRC EVCAEYAKTFYLGT+LMT ERR+AIWAIYVW
Sbjct: 110 S-TDELDVKKDIPIPGTLGLLSEAYDRCSEVCAEYAKTFYLGTMLMTPERRKAIWAIYVW 168

Query: 231 CRRTDELVDGPNASHITPTALDRWESRLEDLFRGRPFDMLDAALSDTVTKFPVDIQPFRD 290
           CRRTDELVDGPNASHITP ALDRWE RLED+F GRPFDMLDAALSDTV+KFPVDIQPFRD
Sbjct: 169 CRRTDELVDGPNASHITPAALDRWEDRLEDVFSGRPFDMLDAALSDTVSKFPVDIQPFRD 228

Query: 291 MIEGMRMDLRKSRYKNFDELYLYCYYVAGTVGLMSVPVMGIAPDSQATTESVYNAALALG 350
           MIEGMRMDLRKSRY+NFDELYLYCYYVAGTVGLMSVP+MGIAP+S+ATTESVYNAALALG
Sbjct: 229 MIEGMRMDLRKSRYRNFDELYLYCYYVAGTVGLMSVPIMGIAPESKATTESVYNAALALG 288

Query: 351 IANQLTNILRDVGEDAQRGRVYLPQDELAQAGLSDDDIFAGEVTNKWRNFMKNQIKRARM 410
           IANQLTNILRDVGEDA+RGRVYLPQDELAQAGLSD+DIFAG VT+KWR FMK QI+RAR 
Sbjct: 289 IANQLTNILRDVGEDARRGRVYLPQDELAQAGLSDEDIFAGRVTDKWRIFMKKQIQRARK 348

Query: 411 FFDMAENGVTELSEASRWPVWASLLLYRQILDEIEANDYNNFTKRAYVSKAKKIAALPIA 470
           FFD AE GVTELS ASRWPV ASLLLYR+ILDEIEANDYNNFTKRAYVSK KK+ ALPIA
Sbjct: 349 FFDEAEKGVTELSAASRWPVLASLLLYRRILDEIEANDYNNFTKRAYVSKPKKLIALPIA 408

Query: 471 YAKSLLRPSR 480
           YAKSL+  +R
Sbjct: 409 YAKSLVPSTR 418
Catalyzes the reaction from prephytoene diphosphate to phytoene.
Capsicum annuum (taxid: 4072)
EC: 2EC: .EC: 5EC: .EC: 1EC: .EC: 3EC: 2
>sp|P49293|PSY_CUCME Phytoene synthase, chloroplastic OS=Cucumis melo GN=PSY PE=2 SV=1 Back     alignment and function description
>sp|P08196|PSY1_SOLLC Phytoene synthase 1, chloroplastic OS=Solanum lycopersicum GN=PSY1 PE=1 SV=2 Back     alignment and function description
>sp|P37271|PSY_ARATH Phytoene synthase, chloroplastic OS=Arabidopsis thaliana GN=PSY1 PE=2 SV=2 Back     alignment and function description
>sp|P53797|PSY_NARPS Phytoene synthase, chloroplastic OS=Narcissus pseudonarcissus GN=PSY PE=2 SV=1 Back     alignment and function description
>sp|P49085|PSY_MAIZE Phytoene synthase, chloroplastic OS=Zea mays GN=Y1 PE=3 SV=1 Back     alignment and function description
>sp|P37273|PSY2_SOLLC Phytoene synthase 2, chloroplastic (Fragment) OS=Solanum lycopersicum GN=PSY2 PE=2 SV=1 Back     alignment and function description
>sp|Q9SSU8|PSY_DAUCA Phytoene synthase, chloroplastic OS=Daucus carota GN=PSY PE=2 SV=1 Back     alignment and function description
>sp|P37269|CRTB_SYNE7 Phytoene synthase OS=Synechococcus elongatus (strain PCC 7942) GN=crtB PE=3 SV=2 Back     alignment and function description
>sp|O07333|CRTY_SPIPL Phytoene synthase OS=Spirulina platensis GN=crtB PE=3 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query486
6959860436 phytoene synthase [Citrus unshiu] gi|113 0.897 1.0 0.993 0.0
13542332436 phytoene synthase [Citrus x paradisi] 0.897 1.0 0.988 0.0
166343816436 phytoene synthase [x Citrofortunella mic 0.897 1.0 0.974 0.0
166343818437 phytoene synthase [Citrus maxima] 0.897 0.997 0.981 0.0
380850954431 phytoene synthase [Mangifera indica] 0.870 0.981 0.806 0.0
262292925429 phytoene synthase 2 [Manihot esculenta] 0.866 0.981 0.791 0.0
110348215438 phytoene synthase protein [Carica papaya 0.882 0.979 0.782 0.0
262292933429 phytoene synthase 2 [Manihot esculenta] 0.866 0.981 0.789 0.0
262292935429 phytoene synthase 2 [Manihot esculenta] 0.866 0.981 0.789 0.0
225466263437 PREDICTED: phytoene synthase, chloroplas 0.872 0.970 0.766 0.0
>gi|6959860|gb|AAF33237.1|AF220218_1 phytoene synthase [Citrus unshiu] gi|11344507|dbj|BAB18514.1| phytoene synthase [Citrus unshiu] gi|82394887|gb|ABB72444.1| phytoene synthase [Citrus sinensis] Back     alignment and taxonomy information
 Score =  900 bits (2326), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 433/436 (99%), Positives = 434/436 (99%)

Query: 51  MSVALLWVVSPNSQLSNCFGFVDSVREENRLFYSSRFLYQHQTRTAVFNSRPKQFNNSNK 110
           MSV LLWVVSPNSQLSNCFGFVDSVREENRLFYSSRFLYQHQTRTAVFNSRPKQFNNSNK
Sbjct: 1   MSVTLLWVVSPNSQLSNCFGFVDSVREENRLFYSSRFLYQHQTRTAVFNSRPKQFNNSNK 60

Query: 111 QRRNSYPLDTDLRHPCSSGIDLPEISCMVASTAGEVAMSSEEMVYNVVLKQAALVNKQPS 170
           QRRNSYPLDTDLRHPCSSGIDLPEISCMVASTAGEVAMSSEEMVYNVVLKQAALVNKQPS
Sbjct: 61  QRRNSYPLDTDLRHPCSSGIDLPEISCMVASTAGEVAMSSEEMVYNVVLKQAALVNKQPS 120

Query: 171 GVTRDLDVNPDIALPGTLSLLSEAYDRCGEVCAEYAKTFYLGTLLMTSERRRAIWAIYVW 230
           GVTRDLDVNPDIALPGTLSLLSEAYDRCGEVCAEYAKTFYLGTLLMTSERRRAIWAIYVW
Sbjct: 121 GVTRDLDVNPDIALPGTLSLLSEAYDRCGEVCAEYAKTFYLGTLLMTSERRRAIWAIYVW 180

Query: 231 CRRTDELVDGPNASHITPTALDRWESRLEDLFRGRPFDMLDAALSDTVTKFPVDIQPFRD 290
           CRRTDELVDGPNASHITPTALDRWESRLEDLFRGRPFDMLDAALSDTVTKFPVDIQPFRD
Sbjct: 181 CRRTDELVDGPNASHITPTALDRWESRLEDLFRGRPFDMLDAALSDTVTKFPVDIQPFRD 240

Query: 291 MIEGMRMDLRKSRYKNFDELYLYCYYVAGTVGLMSVPVMGIAPDSQATTESVYNAALALG 350
           MIEGMRMDLRKSRYKNFDELYLYCYYVAGTVGLMSVPVMGIAPDSQATTESVYNAALALG
Sbjct: 241 MIEGMRMDLRKSRYKNFDELYLYCYYVAGTVGLMSVPVMGIAPDSQATTESVYNAALALG 300

Query: 351 IANQLTNILRDVGEDAQRGRVYLPQDELAQAGLSDDDIFAGEVTNKWRNFMKNQIKRARM 410
           IANQLTNILRDVGEDA+RGRVYLPQDELAQAGLSDDDIFAGEVT KWRNFMKNQIKRARM
Sbjct: 301 IANQLTNILRDVGEDARRGRVYLPQDELAQAGLSDDDIFAGEVTIKWRNFMKNQIKRARM 360

Query: 411 FFDMAENGVTELSEASRWPVWASLLLYRQILDEIEANDYNNFTKRAYVSKAKKIAALPIA 470
           FFDMAENGVTELSEASRWPVWASLLLYRQILDEIEANDYNNFTKRAYVSKAKKIAALPIA
Sbjct: 361 FFDMAENGVTELSEASRWPVWASLLLYRQILDEIEANDYNNFTKRAYVSKAKKIAALPIA 420

Query: 471 YAKSLLRPSRIYTSKA 486
           YAKSLLRPSRIYTSKA
Sbjct: 421 YAKSLLRPSRIYTSKA 436

Source: Citrus unshiu

Species: Citrus unshiu

Genus: Citrus

Family: Rutaceae

Order: Sapindales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|13542332|gb|AAD38051.2| phytoene synthase [Citrus x paradisi] Back     alignment and taxonomy information
>gi|166343816|gb|ABY86651.1| phytoene synthase [x Citrofortunella microcarpa] Back     alignment and taxonomy information
>gi|166343818|gb|ABY86652.1| phytoene synthase [Citrus maxima] Back     alignment and taxonomy information
>gi|380850954|gb|AFE85918.1| phytoene synthase [Mangifera indica] Back     alignment and taxonomy information
>gi|262292925|gb|ACY42665.1| phytoene synthase 2 [Manihot esculenta] gi|262292929|gb|ACY42667.1| phytoene synthase 2 [Manihot esculenta] gi|262292931|gb|ACY42668.1| phytoene synthase 2 [Manihot esculenta] Back     alignment and taxonomy information
>gi|110348215|gb|ABG72805.1| phytoene synthase protein [Carica papaya] Back     alignment and taxonomy information
>gi|262292933|gb|ACY42669.1| phytoene synthase 2 [Manihot esculenta] Back     alignment and taxonomy information
>gi|262292935|gb|ACY42670.1| phytoene synthase 2 [Manihot esculenta] Back     alignment and taxonomy information
>gi|225466263|ref|XP_002271575.1| PREDICTED: phytoene synthase, chloroplastic [Vitis vinifera] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query486
UNIPROTKB|Q6ED64421 Q6ED64 "Phytoene synthase 1" [ 0.771 0.890 0.706 1.4e-144
TAIR|locus:2167225437 PSY "PHYTOENE SYNTHASE" [Arabi 0.847 0.942 0.660 1.3e-141
UNIPROTKB|Q9UUQ6614 CARRP "Bifunctional lycopene c 0.434 0.343 0.246 1e-11
UNIPROTKB|Q9P854602 carRA "Bifunctional lycopene c 0.572 0.461 0.267 4.3e-11
UNIPROTKB|Q67GH9608 carRA "Bifunctional lycopene c 0.438 0.350 0.240 1.3e-08
UNIPROTKB|P37295602 al-2 "Bifunctional lycopene cy 0.374 0.302 0.262 1.6e-07
ZFIN|ZDB-GENE-100112-1344 ndufaf6 "NADH dehydrogenase (u 0.674 0.953 0.198 8.4e-07
UNIPROTKB|Q7Z859673 crtYB "Bifunctional lycopene c 0.257 0.185 0.323 1.3e-06
UNIPROTKB|Q8X0Z1612 carRA "Bifunctional lycopene c 0.399 0.316 0.274 1.8e-06
UNIPROTKB|Q60AN4362 sqs "Squalene synthase" [Methy 0.195 0.262 0.350 4.4e-06
UNIPROTKB|Q6ED64 Q6ED64 "Phytoene synthase 1" [Oryza sativa Indica Group (taxid:39946)] Back     alignment and assigned GO terms
 Score = 1413 (502.5 bits), Expect = 1.4e-144, P = 1.4e-144
 Identities = 275/389 (70%), Positives = 322/389 (82%)

Query:   107 NSNKQRRNSYPLDTDLRHPCSSGID---------LPEISCMVASTAGEVAMSSEEMVYNV 157
             ++NK+++  + L   L++ C  G+D          P  S +  + AGE  +SSE+ VY+V
Sbjct:    36 SNNKEKKRRWIL-CSLKYACL-GVDPAPGEIARTSPVYSSLTVTPAGEAVISSEQKVYDV 93

Query:   158 VLKQAALVNKQPSGVTRDLDVNP-DIALPGTLSLLSEAYDRCGEVCAEYAKTFYLGTLLM 216
             VLKQAAL+ +        + + P D+ LP   + L +AY RCGE+C EYAKTFYLGT+LM
Sbjct:    94 VLKQAALLKRHLRPQPHTIPIVPKDLDLPR--NGLKQAYHRCGEICEEYAKTFYLGTMLM 151

Query:   217 TSERRRAIWAIYVWCRRTDELVDGPNASHITPTALDRWESRLEDLFRGRPFDMLDAALSD 276
             T +RRRAIWAIYVWCRRTDELVDGPNASHITP+ALDRWE RL+DLF GRP+DMLDAALSD
Sbjct:   152 TEDRRRAIWAIYVWCRRTDELVDGPNASHITPSALDRWEKRLDDLFTGRPYDMLDAALSD 211

Query:   277 TVTKFPVDIQPFRDMIEGMRMDLRKSRYKNFDELYLYCYYVAGTVGLMSVPVMGIAPDSQ 336
             T++K P+DIQPFRDMIEGMR DLRK+RYKNFDELY+YCYYVAGTVGLMSVPVMGIAP+S+
Sbjct:   212 TISKSPIDIQPFRDMIEGMRSDLRKTRYKNFDELYMYCYYVAGTVGLMSVPVMGIAPESK 271

Query:   337 ATTESVYNAALALGIANQLTNILRDVGEDAQRGRVYLPQDELAQAGLSDDDIFAGEVTNK 396
             ATTESVY+AALALGIANQLTNILRDVGEDA+RGR+YLPQDELA+AGLSD+DIF G VTNK
Sbjct:   272 ATTESVYSAALALGIANQLTNILRDVGEDARRGRIYLPQDELAEAGLSDEDIFNGVVTNK 331

Query:   397 WRNFMKNQIKRARMFFDMAENGVTELSEASRWPVWASLLLYRQILDEIEANDYNNFTKRA 456
             WR+FMK QIKRARMFF+ AE GVTELS+ASRWPVWASLLLYRQILDEIEANDYNNFTKR 
Sbjct:   332 WRSFMKRQIKRARMFFEEAERGVTELSQASRWPVWASLLLYRQILDEIEANDYNNFTKRT 391

Query:   457 YVSKAKKIAALPIAYAKSLLRPSRIYTSK 485
             YV KAKK+ ALP+AY +SLL P  +  S+
Sbjct:   392 YVGKAKKLLALPVAYGRSLLMPYSLRNSQ 420
GO:0009536 "plastid" evidence=IC
TAIR|locus:2167225 PSY "PHYTOENE SYNTHASE" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|Q9UUQ6 CARRP "Bifunctional lycopene cyclase/phytoene synthase" [Mucor circinelloides f. lusitanicus (taxid:29924)] Back     alignment and assigned GO terms
UNIPROTKB|Q9P854 carRA "Bifunctional lycopene cyclase/phytoene synthase" [Phycomyces blakesleeanus NRRL 1555(-) (taxid:763407)] Back     alignment and assigned GO terms
UNIPROTKB|Q67GH9 carRA "Bifunctional lycopene cyclase/phytoene synthase" [Blakeslea trispora (taxid:4850)] Back     alignment and assigned GO terms
UNIPROTKB|P37295 al-2 "Bifunctional lycopene cyclase/phytoene synthase" [Neurospora crassa OR74A (taxid:367110)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-100112-1 ndufaf6 "NADH dehydrogenase (ubiquinone) complex I, assembly factor 6" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
UNIPROTKB|Q7Z859 crtYB "Bifunctional lycopene cyclase/phytoene synthase" [Xanthophyllomyces dendrorhous (taxid:5421)] Back     alignment and assigned GO terms
UNIPROTKB|Q8X0Z1 carRA "Bifunctional lycopene cyclase/phytoene synthase" [Fusarium fujikuroi (taxid:5127)] Back     alignment and assigned GO terms
UNIPROTKB|Q60AN4 sqs "Squalene synthase" [Methylococcus capsulatus str. Bath (taxid:243233)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
P49085PSY_MAIZE2, ., 5, ., 1, ., 3, 20.76380.72830.8634N/Ano
P49293PSY_CUCME2, ., 5, ., 1, ., 3, 20.74640.83740.9644N/Ano
P53797PSY_NARPS2, ., 5, ., 1, ., 3, 20.75900.77770.8936N/Ano
P08196PSY1_SOLLC2, ., 5, ., 1, ., 3, 20.73480.83530.9854N/Ano
P37273PSY2_SOLLC2, ., 5, ., 1, ., 3, 20.86660.61720.9677N/Ano
P37272PSY_CAPAN2, ., 5, ., 1, ., 3, 20.74880.86000.9976N/Ano
P37271PSY_ARATH2, ., 5, ., 1, ., 3, 20.72930.84150.9691yesno

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

Prediction LevelEC numberConfidence of Prediction
3rd Layer2.5.1.320.991
3rd Layer2.5.10.976

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query486
PLN02632334 PLN02632, PLN02632, phytoene synthase 0.0
cd00683265 cd00683, Trans_IPPS_HH, Trans-Isoprenyl Diphosphat 1e-109
pfam00494262 pfam00494, SQS_PSY, Squalene/phytoene synthase 2e-89
COG1562288 COG1562, ERG9, Phytoene/squalene synthetase [Lipid 7e-85
TIGR03465266 TIGR03465, HpnD, squalene synthase HpnD 8e-67
cd00385243 cd00385, Isoprenoid_Biosyn_C1, Isoprenoid Biosynth 5e-42
TIGR03464266 TIGR03464, HpnC, squalene synthase HpnC 1e-41
cd00867236 cd00867, Trans_IPPS, Trans-Isoprenyl Diphosphate S 4e-40
TIGR01559337 TIGR01559, squal_synth, farnesyl-diphosphate farne 4e-05
>gnl|CDD|215339 PLN02632, PLN02632, phytoene synthase Back     alignment and domain information 
 Score =  631 bits (1629), Expect = 0.0
 Identities = 269/340 (79%), Positives = 293/340 (86%), Gaps = 10/340 (2%)

Query: 143 AGEVAMSSEEMVYNVVLKQAALVNKQP--SGVTRDLDVNPDIALPGTLSLLSEAYDRCGE 200
               A SSEE VY VVLKQAALV K    S   R   ++P         LL EAYDRCGE
Sbjct: 3   VAPAAASSEEKVYEVVLKQAALVRKAARRSVRPRATSLSPA--------LLEEAYDRCGE 54

Query: 201 VCAEYAKTFYLGTLLMTSERRRAIWAIYVWCRRTDELVDGPNASHITPTALDRWESRLED 260
           VCAEYAKTFYLGTLLMT ERR+AIWAIYVWCRRTDELVDGPNASHITP ALDRWE+RLED
Sbjct: 55  VCAEYAKTFYLGTLLMTPERRKAIWAIYVWCRRTDELVDGPNASHITPAALDRWEARLED 114

Query: 261 LFRGRPFDMLDAALSDTVTKFPVDIQPFRDMIEGMRMDLRKSRYKNFDELYLYCYYVAGT 320
           LF GRP+DMLDAAL+DTV+KFP+DIQPFRDMIEGMRMDL KSRY+NFDELYLYCYYVAGT
Sbjct: 115 LFDGRPYDMLDAALADTVSKFPLDIQPFRDMIEGMRMDLVKSRYENFDELYLYCYYVAGT 174

Query: 321 VGLMSVPVMGIAPDSQATTESVYNAALALGIANQLTNILRDVGEDAQRGRVYLPQDELAQ 380
           VGLMSVPVMGIAP+S+A+TESVYNAALALGIANQLTNILRDVGEDA+RGRVYLPQDELAQ
Sbjct: 175 VGLMSVPVMGIAPESKASTESVYNAALALGIANQLTNILRDVGEDARRGRVYLPQDELAQ 234

Query: 381 AGLSDDDIFAGEVTNKWRNFMKNQIKRARMFFDMAENGVTELSEASRWPVWASLLLYRQI 440
            GL+D+DIFAG+VT+KWR FMK QIKRARM+F  AE GV+EL  ASRWPVWASLLLYRQI
Sbjct: 235 FGLTDEDIFAGKVTDKWRAFMKFQIKRARMYFAEAEEGVSELDPASRWPVWASLLLYRQI 294

Query: 441 LDEIEANDYNNFTKRAYVSKAKKIAALPIAYAKSLLRPSR 480
           LD IEANDY+NFTKRAYV K KK+ ALP+AYA++L  PS 
Sbjct: 295 LDAIEANDYDNFTKRAYVGKWKKLLALPLAYARALFPPSS 334

Length = 334
>gnl|CDD|173831 cd00683, Trans_IPPS_HH, Trans-Isoprenyl Diphosphate Synthases, head-to-head Back     alignment and domain information
>gnl|CDD|215948 pfam00494, SQS_PSY, Squalene/phytoene synthase Back     alignment and domain information
>gnl|CDD|224478 COG1562, ERG9, Phytoene/squalene synthetase [Lipid metabolism] Back     alignment and domain information
>gnl|CDD|163278 TIGR03465, HpnD, squalene synthase HpnD Back     alignment and domain information
>gnl|CDD|173830 cd00385, Isoprenoid_Biosyn_C1, Isoprenoid Biosynthesis enzymes, Class 1 Back     alignment and domain information
>gnl|CDD|188327 TIGR03464, HpnC, squalene synthase HpnC Back     alignment and domain information
>gnl|CDD|173836 cd00867, Trans_IPPS, Trans-Isoprenyl Diphosphate Synthases Back     alignment and domain information
>gnl|CDD|188157 TIGR01559, squal_synth, farnesyl-diphosphate farnesyltransferase Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 486
PLN02632334 phytoene synthase 100.0
TIGR03465266 HpnD squalene synthase HpnD. The genes of this fam 100.0
TIGR03464266 HpnC squalene synthase HpnC. This family of genes 100.0
cd00683265 Trans_IPPS_HH Trans-Isoprenyl Diphosphate Synthase 100.0
COG1562288 ERG9 Phytoene/squalene synthetase [Lipid metabolis 100.0
PF00494267 SQS_PSY: Squalene/phytoene synthase; InterPro: IPR 100.0
TIGR01559336 squal_synth farnesyl-diphosphate farnesyltransfera 100.0
KOG4411292 consensus Phytoene/squalene synthetase [Lipid tran 100.0
KOG1459413 consensus Squalene synthetase [Lipid transport and 99.96
KOG1459413 consensus Squalene synthetase [Lipid transport and 99.96
cd00867236 Trans_IPPS Trans-Isoprenyl Diphosphate Synthases. 99.84
cd00385243 Isoprenoid_Biosyn_C1 Isoprenoid Biosynthesis enzym 99.79
cd00685259 Trans_IPPS_HT Trans-Isoprenyl Diphosphate Synthase 95.84
TIGR02749322 prenyl_cyano solanesyl diphosphate synthase. Membe 95.38
PLN02890422 geranyl diphosphate synthase 95.34
TIGR02748319 GerC3_HepT heptaprenyl diphosphate synthase compon 94.03
cd00687303 Terpene_cyclase_nonplant_C1 Non-plant Terpene Cycl 93.9
CHL00151323 preA prenyl transferase; Reviewed 93.31
PRK10581299 geranyltranstransferase; Provisional 93.03
PRK10888323 octaprenyl diphosphate synthase; Provisional 92.96
PLN02857416 octaprenyl-diphosphate synthase 92.52
cd00868284 Terpene_cyclase_C1 Terpene cyclases, Class 1. Terp 90.07
PF00348260 polyprenyl_synt: Polyprenyl synthetase; InterPro: 89.58
PF03936270 Terpene_synth_C: Terpene synthase family, metal bi 88.49
COG0142322 IspA Geranylgeranyl pyrophosphate synthase [Coenzy 87.28
>PLN02632 phytoene synthase Back     alignment and domain information 
Probab=100.00  E-value=3.2e-66  Score=531.42  Aligned_cols=329  Identities=81%  Similarity=1.277  Sum_probs=301.1

Q ss_pred             cccccCchhhHHHHHHHHhhhhccCCCccccccccCCCCCCCCChhhHHHHHHHHHHHHhhcCcchHHHHhcCCHHHHHH
Q 044623          144 GEVAMSSEEMVYNVVLKQAALVNKQPSGVTRDLDVNPDIALPGTLSLLSEAYDRCGEVCAEYAKTFYLGTLLMTSERRRA  223 (486)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~l~~a~~~C~evlr~~srSFyla~llLP~e~R~a  223 (486)
                      +++..+++++|+++++|++.......+. ..+   .+.+..  +...++++|++|.++++++|+|||+++++||++.|.+
T Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~---~~~~~~--~~~~l~~a~~~c~~i~r~~s~sFyla~~lLP~~~R~a   77 (334)
T PLN02632          4 APAAASSEEKVYEVVLKQAALVRKAARR-SVR---PRATSL--SPALLEEAYDRCGEVCAEYAKTFYLGTLLMTPERRKA   77 (334)
T ss_pred             ccCCCccHhHHHHHHHHHHHHHHHhccc-ccC---CCCCCC--CcccchHHHHHHHHHHhhcCchHHHHHHhCCHHHHHH
Confidence            3477899999999999999988777665 333   222222  2357899999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhhhcCCCCCCCCcHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhCCCChHHHHHHHHHHHhhccCCC
Q 044623          224 IWAIYVWCRRTDELVDGPNASHITPTALDRWESRLEDLFRGRPFDMLDAALSDTVTKFPVDIQPFRDMIEGMRMDLRKSR  303 (486)
Q Consensus       224 i~ALYAF~R~lDdIvDd~~~~~i~~~~L~~Wrd~Le~~f~G~p~~pv~~aL~~~v~~~~Lp~~~l~~mIegm~~DL~~~~  303 (486)
                      +++||+|||.+|||+|++..+.+++.+|+||++.++.++.|.+.||+..+|.+++.+|+++.++|.+||+||++|+...+
T Consensus        78 i~alYAf~R~~DdI~D~~~~~~~~~~~L~~w~~~l~~~~~g~~~~pv~~aL~~~~~~~~L~~~~~~~li~g~~~Dl~~~~  157 (334)
T PLN02632         78 IWAIYVWCRRTDELVDGPNASHITPAALDRWEARLEDLFDGRPYDMLDAALADTVSKFPLDIQPFRDMIEGMRMDLVKSR  157 (334)
T ss_pred             HHHHHHHHHHHhHHhcCCCCChhhHHHHHHHHHHHHHHhCCCCCChHHHHHHHHHHHCCCChHHHHHHHHHHHHHhccCC
Confidence            99999999999999999888777778899999999999999889999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHhhhhHHHHHHHhhhCCCCCCccchhhHHHHHHHHHHHHHHHHHHHhHHHHHHcCCCCCCHHhHHhcCC
Q 044623          304 YKNFDELYLYCYYVAGTVGLMSVPVMGIAPDSQATTESVYNAALALGIANQLTNILRDVGEDAQRGRVYLPQDELAQAGL  383 (486)
Q Consensus       304 ~~T~~DL~~Yc~~VAGtVG~Lll~ilg~~~~~~a~~e~~~~~A~~LG~ALQLTNILRDv~EDl~rGRiYLP~d~L~k~Gv  383 (486)
                      |+|++||+.|||+|||+||+|+++++|..+......+.+.+.|.+||+|+|+||||||++||+++||||||.|+|++||+
T Consensus       158 ~~t~~eL~~Ycy~vAgtVG~l~l~vlg~~~~~~~~~~~~~~~A~~lG~AlQltNILRDv~eD~~~GRvYLP~e~L~~~Gv  237 (334)
T PLN02632        158 YENFDELYLYCYYVAGTVGLMSVPVMGIAPESKASTESVYNAALALGIANQLTNILRDVGEDARRGRVYLPQDELAQFGL  237 (334)
T ss_pred             CCCHHHHHHHHHHhhHHHHHHHHHHhCCCCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCceeCCHHHHHHcCC
Confidence            99999999999999999999999999975522222244678999999999999999999999999999999999999999


Q ss_pred             ChhhhhccCCCHHHHHHHHHHHHHHHHHHHHHHHhhhhccccCchHHHHHHHHHHHHHHHHHHCCCCCCCCCccCCHHHH
Q 044623          384 SDDDIFAGEVTNKWRNFMKNQIKRARMFFDMAENGVTELSEASRWPVWASLLLYRQILDEIEANDYNNFTKRAYVSKAKK  463 (486)
Q Consensus       384 s~edL~~g~~~~~~r~li~~la~rAr~~l~~A~~~l~~Lp~~sr~pv~a~~~ly~~iL~~Ie~~~ydvf~~Rv~vsk~~K  463 (486)
                      +++||+.+..+++++.++.+++.+|+.||++|+.++..||+++++++++++.+|+.||++|+++||++|++|+++++++|
T Consensus       238 ~~edl~~~~~~~~~~~l~~~~~~~Ar~~~~~a~~~l~~lp~~~r~~v~~a~~~y~~iL~~i~~~~~~v~~~R~~l~~~~K  317 (334)
T PLN02632        238 TDEDIFAGKVTDKWRAFMKFQIKRARMYFAEAEEGVSELDPASRWPVWASLLLYRQILDAIEANDYDNFTKRAYVGKWKK  317 (334)
T ss_pred             CHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHhHhhCCHHhHHHHHHHHHHHHHHHHHHHHcCCCcCCCCCccCHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhhhcCC
Q 044623          464 IAALPIAYAKSLLRP  478 (486)
Q Consensus       464 l~ll~~a~~~~~~~~  478 (486)
                      +|+++++|.+....+
T Consensus       318 l~~~~~~~~~~~~~~  332 (334)
T PLN02632        318 LLALPLAYARALFPP  332 (334)
T ss_pred             HHHHHHHHHhhcccC
Confidence            999999988765443

>TIGR03465 HpnD squalene synthase HpnD Back     alignment and domain information
>TIGR03464 HpnC squalene synthase HpnC Back     alignment and domain information
>cd00683 Trans_IPPS_HH Trans-Isoprenyl Diphosphate Synthases, head-to-head Back     alignment and domain information
>COG1562 ERG9 Phytoene/squalene synthetase [Lipid metabolism] Back     alignment and domain information
>PF00494 SQS_PSY: Squalene/phytoene synthase; InterPro: IPR002060 Squalene synthase 2 Back     alignment and domain information
>TIGR01559 squal_synth farnesyl-diphosphate farnesyltransferase Back     alignment and domain information
>KOG4411 consensus Phytoene/squalene synthetase [Lipid transport and metabolism] Back     alignment and domain information
>KOG1459 consensus Squalene synthetase [Lipid transport and metabolism] Back     alignment and domain information
>KOG1459 consensus Squalene synthetase [Lipid transport and metabolism] Back     alignment and domain information
>cd00867 Trans_IPPS Trans-Isoprenyl Diphosphate Synthases Back     alignment and domain information
>cd00385 Isoprenoid_Biosyn_C1 Isoprenoid Biosynthesis enzymes, Class 1 Back     alignment and domain information
>cd00685 Trans_IPPS_HT Trans-Isoprenyl Diphosphate Synthases, head-to-tail Back     alignment and domain information
>TIGR02749 prenyl_cyano solanesyl diphosphate synthase Back     alignment and domain information
>PLN02890 geranyl diphosphate synthase Back     alignment and domain information
>TIGR02748 GerC3_HepT heptaprenyl diphosphate synthase component II Back     alignment and domain information
>cd00687 Terpene_cyclase_nonplant_C1 Non-plant Terpene Cyclases, Class 1 Back     alignment and domain information
>CHL00151 preA prenyl transferase; Reviewed Back     alignment and domain information
>PRK10581 geranyltranstransferase; Provisional Back     alignment and domain information
>PRK10888 octaprenyl diphosphate synthase; Provisional Back     alignment and domain information
>PLN02857 octaprenyl-diphosphate synthase Back     alignment and domain information
>cd00868 Terpene_cyclase_C1 Terpene cyclases, Class 1 Back     alignment and domain information
>PF00348 polyprenyl_synt: Polyprenyl synthetase; InterPro: IPR000092 A variety of isoprenoid compounds are synthesized by various organisms Back     alignment and domain information
>PF03936 Terpene_synth_C: Terpene synthase family, metal binding domain; InterPro: IPR005630 Sequences containing this domain belong to the terpene synthase family Back     alignment and domain information
>COG0142 IspA Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism] Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query486
3ae0_A293 Crystal Structure Of The C(30) Carotenoid Dehydrosq 2e-22
2zco_A293 Crystal Structure Of The C(30) Carotenoid Dehydrosq 3e-22
4e9u_A287 Crystal Structure Of Dehydrosqualene Synthase (Crtm 3e-22
4f6v_A292 Crystal Structure Of Dehydrosqualene Synthase (Crtm 6e-22
3vjd_A293 Crystal Structure Of The Y248a Mutant Of C(30) Caro 3e-21
3adz_A293 Crystal Structure Of The C(30) Carotenoid Dehydrosq 3e-21
4hd1_A294 Crystal Structure Of Squalene Synthase Hpnc From Al 9e-21
1ezf_A340 Crystal Structure Of Human Squalene Synthase Length 6e-04
3lee_A340 Crystal Structure Of The Human Squalene Synthase Co 6e-04
3vj8_A343 Crystal Structure Of The Human Squalene Synthase Le 6e-04
>pdb|3AE0|A Chain A, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Complexed With Geranylgeranyl Thiopyrophosphate Length = 293 Back     alignment and structure 
Iteration: 1

 Score =  103 bits (258), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 72/282 (25%), Positives = 132/282 (46%), Gaps = 15/282 (5%)
Query: 188 LSLLSEAYDRCGEVCAEYAKTFYLGTLLMTSERRRAIWAIYVWCRRTDELVD------GP 241
           ++++   +  C ++  +++K+F     L+  ++R+A+WAIY  CR+ D+ +D        
Sbjct: 7   MTMMDMNFKYCHKIMKKHSKSFSYAADLLPEDQRKAVWAIYAVCRKIDDSIDVYGDIQFL 66
Query: 242 NASHITPTALDRWESRLEDLFRGRPFDMLDAALSDTVTKFPVDIQPFRDMIEGMRMDLRK 301
           N       +++++          R   M   AL        +  Q F ++I+ +  D   
Sbjct: 67  NQIKEDIQSIEKYPYEYHHFQSDRRIMM---ALQHVAQHKNIAFQSFYNLIDTVYKDQHF 123
Query: 302 SRYKNFDELYLYCYYVAGTVGLMSVPVMGIAPDSQATTESVYNAALALGIANQLTNILRD 361
           + ++   EL+ YCY VAGTVG +  P++     S   T   Y+ A  LG + QL NILRD
Sbjct: 124 TMFETDAELFGYCYGVAGTVGEVLTPIL-----SDHETHQTYDVARRLGESLQLINILRD 178
Query: 362 VGEDAQRGRVYLPQDELAQAGLSDDDIFAGEVTNKWRNFMKNQIKRARMFFDMAENGVTE 421
           VGED +  R+Y  +  L Q  +   +++   V N + +  +     A   F    + +  
Sbjct: 179 VGEDFENERIYFSKQRLKQYEVDIAEVYQNGVNNHYIDLWEYYAAIAEKDFRDVMDQIKV 238
Query: 422 LSEASRWPVWASLLLYRQILDEIEANDYNNFTKRAYVSKAKK 463
            S  ++  +  +  +Y +ILDE+   +Y    +R +V K KK
Sbjct: 239 FSIEAQPIIELAARIYIEILDEVRQANY-TLHERVFVEKRKK 279
>pdb|2ZCO|A Chain A, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Length = 293 Back     alignment and structure
>pdb|4E9U|A Chain A, Crystal Structure Of Dehydrosqualene Synthase (Crtm) From S. Aureus Complexed With A Thiocyanate Inhibitor Length = 287 Back     alignment and structure
>pdb|4F6V|A Chain A, Crystal Structure Of Dehydrosqualene Synthase (Crtm) From S. Aureus Complexed With Bph-1034, Mg2+ And Fmp. Length = 292 Back     alignment and structure
>pdb|3VJD|A Chain A, Crystal Structure Of The Y248a Mutant Of C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Length = 293 Back     alignment and structure
>pdb|3ADZ|A Chain A, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Complexed With Intermediate Pspp Length = 293 Back     alignment and structure
>pdb|4HD1|A Chain A, Crystal Structure Of Squalene Synthase Hpnc From Alicyclobacillus Acidocaldarius Length = 294 Back     alignment and structure
>pdb|1EZF|A Chain A, Crystal Structure Of Human Squalene Synthase Length = 340 Back     alignment and structure
>pdb|3LEE|A Chain A, Crystal Structure Of The Human Squalene Synthase Complexed With Bph- 652 Length = 340 Back     alignment and structure
>pdb|3VJ8|A Chain A, Crystal Structure Of The Human Squalene Synthase Length = 343 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query486
3acx_A293 Dehydrosqualene synthase; CRTM, carotenoid biosynt 1e-141
3vj8_A343 Squalene synthase; farnesyl-diphosphate farnesyltr 7e-91
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 3e-04
>3acx_A Dehydrosqualene synthase; CRTM, carotenoid biosynthesis, staphyloxanthin biosynthesis, transferase, head-TO-head condensation, inhibitor; HET: 673; 1.31A {Staphylococcus aureus} PDB: 2zcp_A* 2zcq_A* 2zcr_A* 2zcs_A* 2zy1_A* 3acw_A* 2zco_A* 3acy_A* 3npr_A* 3nri_A* 3tfn_A* 3tfp_A* 3tfv_A* 3adz_A* 3lgz_B* 3vjd_A* 3vje_A* 3ae0_A* 4ea2_A* 4e9u_A* ... Length = 293 Back     alignment and structure
 Score =  407 bits (1047), Expect = e-141
 Identities = 71/294 (24%), Positives = 131/294 (44%), Gaps = 9/294 (3%)

Query: 183 ALPGTLSLLSEAYDRCGEVCAEYAKTFYLGTLLMTSERRRAIWAIYVWCRRTDELVDGPN 242
           A    ++++   +  C ++  +++K+F     L+  ++R+A+WAIY  CR+ D+ +D   
Sbjct: 2   AAAAAMTMMDMNFKYCHKIMKKHSKSFSYAFDLLPEDQRKAVWAIYAVCRKIDDSIDVYG 61

Query: 243 ASHITPTA---LDRWESRLEDLFRGRPFDMLDAALSDTVTKFPVDIQPFRDMIEGMRMDL 299
                      +   E    +    +    +  AL        +  Q F ++I+ +  D 
Sbjct: 62  DIQFLNQIKEDIQSIEKYPYEYHHFQSDRRIMMALQHVAQHKNIAFQSFYNLIDTVYKDQ 121

Query: 300 RKSRYKNFDELYLYCYYVAGTVGLMSVPVMGIAPDSQATTESVYNAALALGIANQLTNIL 359
             + ++   EL+ YCY VAGTVG +  P++      Q      Y+ A  LG + QL NIL
Sbjct: 122 HFTMFETDAELFGYCYGVAGTVGEVLTPILSDHETHQT-----YDVARRLGESLQLINIL 176

Query: 360 RDVGEDAQRGRVYLPQDELAQAGLSDDDIFAGEVTNKWRNFMKNQIKRARMFFDMAENGV 419
           RDVGED +  R+Y  +  L Q  +   +++   V N + +  +     A   F    + +
Sbjct: 177 RDVGEDFENERIYFSKQRLKQYEVDIAEVYQNGVNNHYIDLWEYYAAIAEKDFRDVMDQI 236

Query: 420 TELSEASRWPVWASLLLYRQILDEIEANDYNNFTKRAYVSKAKKIAALPIAYAK 473
              S  ++  +  +  +Y +ILDE+   +Y    +R +V K KK        +K
Sbjct: 237 KVFSIEAQPIIELAARIYIEILDEVRQANY-TLHERVFVEKRKKAKLFHEINSK 289
>3vj8_A Squalene synthase; farnesyl-diphosphate farnesyltransferase, head-TO-head synth cholesterol biosynthesis, oxidoreductase, transferase; 1.52A {Homo sapiens} PDB: 3vj9_A 3vja_A 3vjb_A 3vjc_A* 3asx_A* 3lee_A* 3q2z_A* 3q30_A* 1ezf_A* Length = 343 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query486
4hd1_A294 Squalene synthase HPNC; MCSG, structural genomics, 100.0
3acx_A293 Dehydrosqualene synthase; CRTM, carotenoid biosynt 100.0
3vj8_A343 Squalene synthase; farnesyl-diphosphate farnesyltr 100.0
3rmg_A334 Octaprenyl-diphosphate synthase; structural genomi 96.01
3nf2_A352 Putative polyprenyl synthetase; isoprenyl diphosph 95.9
3kb9_A382 EPI-isozizaene synthase; terpenoid cyclase, alpha- 95.51
2q80_A301 Geranylgeranyl pyrophosphate synthetase; isoprenoi 95.27
1wy0_A342 Geranylgeranyl pyrophosphate synthetase; pyrococcu 95.21
4f62_A317 Geranyltranstransferase; enzyme function initiativ 95.08
3ts7_A324 Geranyltranstransferase; isoprenoid synthesis, far 94.97
2e8v_A340 Geranylgeranyl pyrophosphate synthetase; prenyltra 94.85
4dhd_A358 Polyprenyl synthetase; isoprenoid synthesis, isopr 94.83
3lom_A313 Geranyltranstransferase; geranyltransferase, struc 94.81
3p8r_A302 Geranyltranstransferase; isoprenyl synthase, struc 94.78
3lmd_A360 Geranylgeranyl pyrophosphate synthase; isoprenyl d 94.55
3lk5_A380 Geranylgeranyl pyrophosphate synthase; structural 94.45
3pko_A334 Geranylgeranyl pyrophosphate synthase; isoprenyl d 94.39
3apz_A348 Geranyl diphosphate synthase; prenyltransferase, a 94.39
3p8l_A302 Geranyltranstransferase; isoprenyl synthase, struc 94.38
3uca_A324 Geranyltranstransferase; isoprenoid synthesis, iso 94.24
3oyr_A345 Trans-isoprenyl diphosphate synthase; isoprenyl sy 94.16
3mzv_A341 Decaprenyl diphosphate synthase; transferase, stru 94.15
1rtr_A301 Geranyltranstransferase; 2.50A {Staphylococcus aur 94.12
1ps1_A337 Pentalenene synthase; antibiotic biosynthesis, ses 94.06
3aqb_B325 Component B of hexaprenyl diphosphate synthase; pr 93.94
3lsn_A304 Geranyltranstransferase; structural genomics, prot 93.72
1yhl_A362 Farnesyl pyrophosphate synthase; farnesyl diphosph 93.44
3tc1_A315 Octaprenyl pyrophosphate synthase; all alpha-helic 93.33
1v4e_A299 Octoprenyl-diphosphate synthase; trans-type prenyl 92.95
2her_A368 Fragment, farnesyl pyrophosphate synthase; farnesy 92.79
1wmw_A330 Geranylgeranyl diphosphate synthetase; GGPP, preny 92.62
2qis_A374 Farnesyl pyrophosphate synthetase; trans-prenyltra 92.59
1uby_A367 FPS, farnesyl diphosphate synthase; transferase, i 92.43
3ipi_A295 Geranyltranstransferase; isoprene biosynthesis, he 92.01
2azj_A289 Geranylgeranyl pyrophosphate synthetase; hexpps, t 91.48
2h8o_A335 Geranyltranstransferase; geranyltransferase,agroba 91.39
3pde_A309 Farnesyl-diphosphate synthase; isoprenyl diphospha 91.23
1di1_A300 Aristolochene synthase; sesquiterpene cyclase, iso 91.17
2j1p_A293 Geranylgeranyl pyrophosphate synthetase; transfera 90.83
2ihi_A395 Pyrophosphate synthase; PV092040, structural genom 90.79
1rqj_A299 Geranyltranstransferase; bisphosphonate, isoprenyl 90.31
3m0g_A297 Farnesyl diphosphate synthase; structural genomics 89.68
1n1b_A549 (+)-bornyl diphosphate synthase; terpene synthase 89.22
2ftz_A284 Geranyltranstransferase; TM0161, structural GE joi 88.16
3dyh_A390 Farnesyl pyrophosphate synthase; protein-bisphosph 87.32
3mav_A395 Farnesyl pyrophosphate synthase; PV092040, structu 83.57
3bny_A320 Aristolochene synthase; sesquiterpene cyclase, iso 82.75
3v1v_A433 2-MIB synthase, 2-methylisoborneol synthase; class 82.64
2ong_A543 4S-limonene synthase; monoterpene synthase, monote 82.15
3llw_A311 Geranyltranstransferase (ISPA); structural genomic 81.82
2q58_A368 Fragment, farnesyl pyrophosphate synthase; farnesy 81.53
3npk_A291 Geranyltranstransferase; isoprene biosynthesis, SG 81.53
>4hd1_A Squalene synthase HPNC; MCSG, structural genomics, PSI-biology, midwest center for S genomics, transferase; 2.40A {Alicyclobacillus acidocaldarius subsp} Back     alignment and structure
Probab=100.00  E-value=2.7e-63  Score=499.71  Aligned_cols=281  Identities=26%  Similarity=0.370  Sum_probs=246.2

Q ss_pred             hhhHHHHHHHHHHHHhhcCcchHHHHhcCCHHHHHHHHHHHHHHHHhhhhcCCCCCCCCcHHHHHHHHHHHHHHHcCCCC
Q 044623          188 LSLLSEAYDRCGEVCAEYAKTFYLGTLLMTSERRRAIWAIYVWCRRTDELVDGPNASHITPTALDRWESRLEDLFRGRPF  267 (486)
Q Consensus       188 ~~~l~~a~~~C~evlr~~srSFyla~llLP~e~R~ai~ALYAF~R~lDdIvDd~~~~~i~~~~L~~Wrd~Le~~f~G~p~  267 (486)
                      +..++++|++|.++++++|+|||+++++||++.|+++++||+|||.+|||+|++..  .+..+|+||++.++.++.|.+.
T Consensus         8 p~~l~~~y~~C~~i~~~~~~sF~~a~~~lp~~~R~~~~alYaf~R~~Ddi~D~~~~--~~~~~L~~~~~~l~~~~~g~~~   85 (294)
T 4hd1_A            8 PVELRGDFEVCRRLTRSHYENFSVVSLFVPRHLRPHFYSVYAFCRGVDDLGDEFAG--DRMAALDAYEEELRRAFAGEAT   85 (294)
T ss_dssp             CGGGHHHHHHHHHHHHHHCTTHHHHTTTCCTTTHHHHHHHHHHHHHHHHTSTTCCS--CHHHHHHHHHHHHHHHHHTCCC
T ss_pred             CHHHHHHHHHHHHHHHHhCCcHHHHHHHCCHHHHHHHHHHHHHHHHHHHhccCCCh--hHHHHHHHHHHHHHHHhcCCCC
Confidence            45789999999999999999999999999999999999999999999999998653  3456899999999999999999


Q ss_pred             CHHHHHHHHHHHhCCCChHHHHHHHHHHHhhccCCCCCCHHHHHHHHHhhhhHHHHHHHhhhCCCCCCccchhhHHHHHH
Q 044623          268 DMLDAALSDTVTKFPVDIQPFRDMIEGMRMDLRKSRYKNFDELYLYCYYVAGTVGLMSVPVMGIAPDSQATTESVYNAAL  347 (486)
Q Consensus       268 ~pv~~aL~~~v~~~~Lp~~~l~~mIegm~~DL~~~~~~T~~DL~~Yc~~VAGtVG~Lll~ilg~~~~~~a~~e~~~~~A~  347 (486)
                      ||+..+|.+++++|+||.++|.+||+||++|+.+.+|+|++||+.|||+|||+||+|++++||..++      ...+.|.
T Consensus        86 ~pv~~al~~~~~~~~l~~~~~~~li~g~~~Dl~~~~~~t~~dL~~Y~~~vAg~VG~m~~~i~g~~~~------~~~~~A~  159 (294)
T 4hd1_A           86 TPAFRALQFTIATCNLPMEPFLRLIEANRRDQRKHTYDTWEDLRDYCRYSADPVGRLVLGIFGCLDD------ERARLSD  159 (294)
T ss_dssp             SHHHHHHHHHHHHHTCCSHHHHHHHHHHHHHHHCSBCCSHHHHHHHHHHHTHHHHHHHHHHTTCCSH------HHHHHHH
T ss_pred             CHHHHHHHHHHHHcCCCHHHHHHHHHHHHhccccCCCCCHHHHHHHHHhccchHHHHHHHHhCCCCH------HHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999999997542      3567899


Q ss_pred             HHHHHHHHHHHHHhHHHHHHcCCCCCCHHhHHhcCCChhhhhccCCCHHHHHHHHHHHHHHHHHHHHHHHhhhhccccCc
Q 044623          348 ALGIANQLTNILRDVGEDAQRGRVYLPQDELAQAGLSDDDIFAGEVTNKWRNFMKNQIKRARMFFDMAENGVTELSEASR  427 (486)
Q Consensus       348 ~LG~ALQLTNILRDv~EDl~rGRiYLP~d~L~k~Gvs~edL~~g~~~~~~r~li~~la~rAr~~l~~A~~~l~~Lp~~sr  427 (486)
                      +||+|+|+||||||++||+++||+|||.|+|++||++++||..+..+++++.++.+++.+|+.||++|..++..||++++
T Consensus       160 ~lG~AlQltNilRDv~eD~~~gR~YlP~~~l~~~gv~~~dl~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~lp~~~r  239 (294)
T 4hd1_A          160 ATCTALQVANHMQDIDRDLALGRIYVPRADLEQFGATLDDIRARRATDGVRRCIALEVDRAQALFDEGRRLESLVPPRLA  239 (294)
T ss_dssp             HHHHHHHHHHHHHTHHHHHHTTCBCSCHHHHHTTTCCHHHHHTTCCCHHHHHHHHHHHHHHHHHHHHHGGGGGSSCHHHH
T ss_pred             HHHHHHHHHHHHHhchhhhccCceeCCHHHHHHcCCCHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHHHHHHHHCCCCCCCCCccCCHHHHHHHHHHHHHhhhc
Q 044623          428 WPVWASLLLYRQILDEIEANDYNNFTKRAYVSKAKKIAALPIAYAKSLL  476 (486)
Q Consensus       428 ~pv~a~~~ly~~iL~~Ie~~~ydvf~~Rv~vsk~~Kl~ll~~a~~~~~~  476 (486)
                      +++.++..+|+.||++|+++||++|++|+++++++|++++++++....+
T Consensus       240 ~~~~~~~~~y~~il~~i~~~~~~~~~~R~~vs~~~Kl~l~~~al~~~~~  288 (294)
T 4hd1_A          240 RQLKLYRLGGEAILAAIRRQGYNPFAGRPVVSGKQKLRIALSVLAGGAK  288 (294)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTTTCCC------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCCCCCCccCHHHHHHHHHHHHHHhhc
Confidence            9999999999999999999999999999999999999999999877543
>3acx_A Dehydrosqualene synthase; CRTM, carotenoid biosynthesis, staphyloxanthin biosynthesis, transferase, head-TO-head condensation, inhibitor; HET: 673; 1.31A {Staphylococcus aureus} PDB: 2zcp_A* 2zcq_A* 2zcr_A* 2zcs_A* 2zy1_A* 3acw_A* 2zco_A* 3acy_A* 3npr_A* 3nri_A* 3tfn_A* 3tfp_A* 3tfv_A* 3adz_A* 3lgz_B* 3vjd_A* 3vje_A* 3ae0_A* 4ea2_A* 4e9u_A* ... Back     alignment and structure
>3vj8_A Squalene synthase; farnesyl-diphosphate farnesyltransferase, head-TO-head synth cholesterol biosynthesis, oxidoreductase, transferase; 1.52A {Homo sapiens} PDB: 3vj9_A 3vja_A 3vjb_A 3vjc_A* 3v66_A* 3lee_A* 3q2z_A* 3q30_A* 3asx_A* 1ezf_A* Back     alignment and structure
>3rmg_A Octaprenyl-diphosphate synthase; structural genomics, protein structure initiative, isoprene biosynthesis, transferase; 2.30A {Bacteroides thetaiotaomicron} Back     alignment and structure
>3nf2_A Putative polyprenyl synthetase; isoprenyl diphosphate synthase, structural genomics, PSI, PR structure initiative, nysgrc; 2.20A {Streptomyces coelicolor} Back     alignment and structure
>3kb9_A EPI-isozizaene synthase; terpenoid cyclase, alpha-helical fold, farnesyl diphosphate, metal-binding, lyase, magnesium; HET: BTM; 1.60A {Streptomyces coelicolor} PDB: 3kbk_A 3lgk_A 3lg5_A* Back     alignment and structure
>2q80_A Geranylgeranyl pyrophosphate synthetase; isoprenoid pathway, isopentenyl transferase, structural GENO structural genomics consortium, SGC; HET: GRG; 2.70A {Homo sapiens} SCOP: a.128.1.1 Back     alignment and structure
>1wy0_A Geranylgeranyl pyrophosphate synthetase; pyrococcus horikosh structural genomics, riken structural genomics/proteomics initiative, RSGI; 2.20A {Pyrococcus horikoshii} Back     alignment and structure
>4f62_A Geranyltranstransferase; enzyme function initiative, structural genomics; 2.10A {Marinomonas SP} Back     alignment and structure
>3ts7_A Geranyltranstransferase; isoprenoid synthesis, farnesyl diphosphate synthase; 1.94A {Methylococcus capsulatus} Back     alignment and structure
>2e8v_A Geranylgeranyl pyrophosphate synthetase; prenyltransferase, farnesyl pyrophosphate, bisphosphonate; HET: GRG; 1.80A {Saccharomyces cerevisiae} PDB: 2e8t_A* 2e8u_A* 2dh4_A* 2e8w_A* 2e8x_A* 2e90_A* 2e91_A* 2e92_A* 2e93_A* 2e94_A* 2e95_A* 2z4v_A* 2z4w_A* 2z4x_A* 2z4y_A* 2z4z_A* 2z50_A* 2z52_A* 2z78_A* 2z7h_A* ... Back     alignment and structure
>4dhd_A Polyprenyl synthetase; isoprenoid synthesis, isoprenoid diphosphate synthase, trans; 1.65A {Pyrobaculum calidifontis} PDB: 4gp1_A* 4gp2_A* Back     alignment and structure
>3lom_A Geranyltranstransferase; geranyltransferase, structural genomics, PSI, protein structure initiative, nysgrc; 2.30A {Legionella pneumophila subsp} Back     alignment and structure
>3p8r_A Geranyltranstransferase; isoprenyl synthase, structural genomics, PSI, protein struct initiative, nysgrc; 2.50A {Vibrio cholerae} SCOP: a.128.1.1 Back     alignment and structure
>3lmd_A Geranylgeranyl pyrophosphate synthase; isoprenyl diphosphate synthase, structural genomics, PSI, protein structure initiative, nysgrc; 1.90A {Corynebacterium glutamicum} PDB: 3q2q_A* Back     alignment and structure
>3lk5_A Geranylgeranyl pyrophosphate synthase; structural genomics, protein structure initiative, geranylge pyrophosphate synthase; 1.90A {Corynebacterium glutamicum} PDB: 3qqv_A* Back     alignment and structure
>3pko_A Geranylgeranyl pyrophosphate synthase; isoprenyl diphosphate synthase, structural genomics, PSI, PR structure initiative, nysgrc; HET: CIT; 1.98A {Lactobacillus brevis} PDB: 3n3d_A Back     alignment and structure
>3apz_A Geranyl diphosphate synthase; prenyltransferase, all alpha-helices fold, chroloplast, TRAN isoprenoid biosynthetic process; 2.60A {Arabidopsis thaliana} PDB: 3aq0_A* Back     alignment and structure
>3p8l_A Geranyltranstransferase; isoprenyl synthase, structural genomics, PSI, protein struct initiative, nysgrc; 2.00A {Enterococcus faecalis} Back     alignment and structure
>3uca_A Geranyltranstransferase; isoprenoid synthesis, isoprenoid diphosphate synthase; 2.00A {Clostridium perfringens} Back     alignment and structure
>3oyr_A Trans-isoprenyl diphosphate synthase; isoprenyl synthase, PSI, protein structure initiative; HET: IPE; 2.00A {Caulobacter crescentus} Back     alignment and structure
>3mzv_A Decaprenyl diphosphate synthase; transferase, structural genomics, PSI-2, protein structure initiative; 1.90A {Rhodobacter capsulatus} Back     alignment and structure
>1rtr_A Geranyltranstransferase; 2.50A {Staphylococcus aureus} SCOP: a.128.1.1 Back     alignment and structure
>1ps1_A Pentalenene synthase; antibiotic biosynthesis, sesquiterpene cyclase, lyase; 2.60A {Streptomyces SP} SCOP: a.128.1.4 PDB: 1hm7_A 1hm4_A Back     alignment and structure
>3aqb_B Component B of hexaprenyl diphosphate synthase; prenyltransferase, transferase; 2.40A {Micrococcus luteus} PDB: 3aqc_B* Back     alignment and structure
>3lsn_A Geranyltranstransferase; structural genomics, protein structure initiative, NEW YORK structural genomix research consortium, nysgxrc; HET: MSE; 1.35A {Pseudomonas fluorescens} PDB: 3lji_A* 3p41_A* Back     alignment and structure
>1yhl_A Farnesyl pyrophosphate synthase; farnesyl diphosphate synthase, bisphosphonate, dimethyl ALLY pyrophosphate sulfate, FPPS, transferase; HET: DMA RIS; 1.95A {Trypanosoma cruzi} PDB: 1yhk_A* 1yhm_A* 3iba_A* 3ick_A* 3icm_A* 3icn_A* 3icz_A* 3id0_A* Back     alignment and structure
>3tc1_A Octaprenyl pyrophosphate synthase; all alpha-helices fold, transferase; 2.00A {Helicobacter pylori} Back     alignment and structure
>1v4e_A Octoprenyl-diphosphate synthase; trans-type prenyltransferase, thermophilic; 2.28A {Thermotoga maritima} SCOP: a.128.1.1 PDB: 1v4j_A 1wkz_A 1vg2_A 1wl3_A 1wl0_A 1wl2_A 1v4h_A 1v4i_A 1v4k_A 2azl_A 1wl1_A 1vg4_A 1vg3_A 1vg6_A 1vg7_A Back     alignment and structure
>1wmw_A Geranylgeranyl diphosphate synthetase; GGPP, prenyl diphosphate synthase, structural genom riken structural genomics/proteomics initiative; 1.55A {Thermus thermophilus} Back     alignment and structure
>2qis_A Farnesyl pyrophosphate synthetase; trans-prenyltransferase, structural genomics, structural GEN consortium, SGC, transferase; HET: RIS; 1.80A {Homo sapiens} PDB: 4dem_F* 1yv5_A* 1yq7_A* 2opm_A* 2opn_A* 3cp6_A* 2rah_A* 2vf6_A* 1zw5_A* 3b7l_A* 3s4j_A* 3rye_A* 3n45_F* 2f89_F* 2f7m_F* 2f8z_F* 2f8c_F* 2f92_F* 2f9k_F* 3n1v_F* ... Back     alignment and structure
>1uby_A FPS, farnesyl diphosphate synthase; transferase, isoprene biosynthesis, cholesterol biosynthesis; HET: DMA; 2.40A {Gallus gallus} SCOP: a.128.1.1 PDB: 1ubw_A* 1ubv_A* 1ubx_A* 1fps_A Back     alignment and structure
>3ipi_A Geranyltranstransferase; isoprene biosynthesis, helical bundle, protein structure initiative II (PSI II), structural genomics, nysgxrc; 1.90A {Methanosarcina mazei} Back     alignment and structure
>2azj_A Geranylgeranyl pyrophosphate synthetase; hexpps, trans-prenyltransferase; 2.40A {Sulfolobus solfataricus} PDB: 2azk_A Back     alignment and structure
>2h8o_A Geranyltranstransferase; geranyltransferase,agrobacterium tumefaciens, structural GEN PSI-2, protein structure initiative; 1.60A {Agrobacterium tumefaciens} Back     alignment and structure
>3pde_A Farnesyl-diphosphate synthase; isoprenyl diphosphate synthase, structural genomics, PSI, PR structure initiative; HET: IPE; 1.75A {Lactobacillus brevis} PDB: 3m9u_A* Back     alignment and structure
>1di1_A Aristolochene synthase; sesquiterpene cyclase, isoprenoid biosynthesis, lyase; 2.50A {Penicillium roqueforti} SCOP: a.128.1.4 PDB: 1dgp_A Back     alignment and structure
>2j1p_A Geranylgeranyl pyrophosphate synthetase; transferase, isoprene biosynthesis, multifunctional enzyme, carotenoid biosynthesis; HET: GRG; 1.8A {Sinapis alba} PDB: 2j1o_A 3kra_A 3krc_A* 3krf_A* 3kro_A* 3krp_A* 3oab_A* 3oac_A* Back     alignment and structure
>1rqj_A Geranyltranstransferase; bisphosphonate, isoprenyl synthase; HET: IPR RIS; 1.95A {Escherichia coli} SCOP: a.128.1.1 PDB: 1rqi_A* 2for_A* Back     alignment and structure
>3m0g_A Farnesyl diphosphate synthase; structural genomics, protein structure initiative, NYSGXRC, biosynthesis, transferase, PSI-2; 1.90A {Rhodobacter capsulatus} PDB: 3lvs_A Back     alignment and structure
>1n1b_A (+)-bornyl diphosphate synthase; terpene synthase fold, isomerase; 2.00A {Salvia officinalis} SCOP: a.102.4.1 a.128.1.3 PDB: 1n1z_A* 1n20_A* 1n21_A* 1n22_A* 1n23_A* 1n24_A* Back     alignment and structure
>2ftz_A Geranyltranstransferase; TM0161, structural GE joint center for structural genomics, JCSG, protein structu initiative, PSI; HET: MLY; 1.90A {Thermotoga maritima} Back     alignment and structure
>3dyh_A Farnesyl pyrophosphate synthase; protein-bisphosphonate complex, isoprene biosynthesis, transferase; HET: 721; 1.94A {Trypanosoma brucei} PDB: 2ewg_A* 2i19_A* 2p1c_A* 3dyf_A* 3dyg_A* 2ogd_A* 3efq_A* 3egt_A* Back     alignment and structure
>3mav_A Farnesyl pyrophosphate synthase; PV092040, structural genomics, structural genomics consortium, SGC, transferase, isoprene biosynthesis; 2.10A {Plasmodium vivax} PDB: 3cc9_A* 3ez3_A* 3ldw_A* 3mys_A* 3ph7_A* 3rbm_A* 3ryw_A* Back     alignment and structure
>3bny_A Aristolochene synthase; sesquiterpene cyclase, isoprenoid, farnesyl diphosphate, magnesium, cyclization, lyase; HET: FPF; 1.89A {Aspergillus terreus} PDB: 2e4o_A 2oa6_A* 3bnx_A* 3cke_A* Back     alignment and structure
>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid cyclase fold, DDXXXXD motif, NDXXSXXXE MOT methylisoborneol biosynthesis; HET: GST; 1.80A {Streptomyces coelicolor} PDB: 3v1x_A* Back     alignment and structure
>2ong_A 4S-limonene synthase; monoterpene synthase, monoterpene cyclase, geranyl diphosphate, 2 fluorogeranyl diphosphate linalyl diphosphate; HET: FPG BTB; 2.70A {Mentha spicata} PDB: 2onh_A* Back     alignment and structure
>3llw_A Geranyltranstransferase (ISPA); structural genomics, PSI, protein structure initiative, nysgrc; 2.30A {Helicobacter pylori} PDB: 3q1o_A* Back     alignment and structure
>2q58_A Fragment, farnesyl pyrophosphate synthase; farnesyl diphosphate synthase, structural genomics, structur genomics consortium, SGC; HET: ZOL; 2.37A {Cryptosporidium parvum} PDB: 2o1o_A* Back     alignment and structure
>3npk_A Geranyltranstransferase; isoprene biosynthesis, SGX, structural genomics protein structure initiative; 1.50A {Campylobacter jejuni} Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 486
d1ezfa_333 a.128.1.2 (A:) Squalene synthase {Human (Homo sapi 2e-68
>d1ezfa_ a.128.1.2 (A:) Squalene synthase {Human (Homo sapiens) [TaxId: 9606]} Length = 333 Back     information, alignment and structure

class: All alpha proteins
fold: Terpenoid synthases
superfamily: Terpenoid synthases
family: Squalene synthase
domain: Squalene synthase
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  220 bits (561), Expect = 2e-68
 Identities = 51/285 (17%), Positives = 89/285 (31%), Gaps = 13/285 (4%)

Query: 194 AYDRCGEVCAEYAKTFYLGTLLMTSERRRAIWAIYVWCRRTDELVDGPNASHIT-PTALD 252
           +   C +   + +++F      +  E R A+   Y+  R  D L D    S       L 
Sbjct: 2   SLKTCYKYLNQTSRSFAAVIQALDGEMRNAVCIFYLVLRALDTLEDDMTISVEKKVPLLH 61

Query: 253 RWESRLEDLFRGRP------------FDMLDAALSDTVTKFPVDIQPFRDMIEGMRMDLR 300
            + S L                    F  +     +   K+   I      +     +  
Sbjct: 62  NFHSFLYQPDWRFMESKEKDRQVLEDFPTISLEFRNLAEKYQTVIADICRRMGIGMAEFL 121

Query: 301 KSRYKNFDELYLYCYYVAGTVGLMSVPVMGIAPDSQATTESVYNAALALGIANQLTNILR 360
                +  E   YC+YVAG VG+    +   +             A ++G+  Q TNI+R
Sbjct: 122 DKHVTSEQEWDKYCHYVAGLVGIGLSRLFSASEFEDPLVGEDTERANSMGLFLQKTNIIR 181

Query: 361 DVGEDAQRGRVYLPQDELAQAGLSDDDIFAGEVTNKWRNFMKNQIKRARMFFDMAENGVT 420
           D  ED Q GR + PQ+  ++      D    E  +     +   I  A          ++
Sbjct: 182 DYLEDQQGGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELITNALHHIPDVITYLS 241

Query: 421 ELSEASRWPVWASLLLYRQILDEIEANDYNNFTKRAYVSKAKKIA 465
            L   S +   A   +          N+   F     + K + + 
Sbjct: 242 RLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGAVKIRKGQAVT 286

Homologous Domains Detected by HHsearch ?

Original result of HHsearch against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query486
d1ezfa_333 Squalene synthase {Human (Homo sapiens) [TaxId: 96 100.0
d1ps1a_311 Pentalenene synthase {Streptomyces sp., UC5319 [Ta 95.97
d2q80a1291 Geranylgeranyl pyrophosphate synthetase {Human (Ho 93.24
d1fpsa_348 Farnesyl diphosphate synthase (geranyltranstransfe 90.69
d1v4ea_280 Octoprenyl-diphosphate synthase {Thermotoga mariti 90.1
d1n1ba2328 (+)-bornyl diphosphate synthase {Garden sage (Salv 89.54
d5easa2328 5-Epi-aristolochene synthase {Tobacco (Nicotiana t 87.32
d1rqja_299 Farnesyl diphosphate synthase (geranyltranstransfe 85.94
d1di1a_300 Aristolochene synthase {Fungus (Penicillium roquef 85.26
d1rtra_290 Farnesyl diphosphate synthase (geranyltranstransfe 83.51
>d1ezfa_ a.128.1.2 (A:) Squalene synthase {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
class: All alpha proteins
fold: Terpenoid synthases
superfamily: Terpenoid synthases
family: Squalene synthase
domain: Squalene synthase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=7.2e-53  Score=428.49  Aligned_cols=276  Identities=20%  Similarity=0.153  Sum_probs=224.0

Q ss_pred             HHHHHHHHHhhcCcchHHHHhcCCHHHHHHHHHHHHHHHHhhhhcCCCCCCCCc-HHHHHHHHHHHHHHHcCC-----CC
Q 044623          194 AYDRCGEVCAEYAKTFYLGTLLMTSERRRAIWAIYVWCRRTDELVDGPNASHIT-PTALDRWESRLEDLFRGR-----PF  267 (486)
Q Consensus       194 a~~~C~evlr~~srSFyla~llLP~e~R~ai~ALYAF~R~lDdIvDd~~~~~i~-~~~L~~Wrd~Le~~f~G~-----p~  267 (486)
                      ++++|.++++++|+|||+++++||+++|++++++|+|||.+|||+|++..+... ...|++|++.+.+...+.     ..
T Consensus         2 sl~~C~~~l~~~SrSF~~a~~~Lp~~~R~~v~~lYafcR~~DdI~D~~~~~~~~k~~~L~~~~~~l~~~~~~~~~~~~~~   81 (333)
T d1ezfa_           2 SLKTCYKYLNQTSRSFAAVIQALDGEMRNAVCIFYLVLRALDTLEDDMTISVEKKVPLLHNFHSFLYQPDWRFMESKEKD   81 (333)
T ss_dssp             HHHHHHHHHHHHCSSHHHHHHTSCTHHHHHHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHHTTCTTCCCCCCCSTT
T ss_pred             hHHHHHHHHHhhCccHHHHHHHCCHHHHHHHHHHHHHHHHhhhhHhCCCCCHHHHHHHHHHHHHHHHHhhhcccccCcch
Confidence            689999999999999999999999999999999999999999999998766443 457899999887654332     22


Q ss_pred             CHHHHHHHHHHHhC-------CCChHH-HHHHHHHHHhhccCCCCCCHHHHHHHHHhhhhHHHHHHHhhhCCCCCCccch
Q 044623          268 DMLDAALSDTVTKF-------PVDIQP-FRDMIEGMRMDLRKSRYKNFDELYLYCYYVAGTVGLMSVPVMGIAPDSQATT  339 (486)
Q Consensus       268 ~pv~~aL~~~v~~~-------~Lp~~~-l~~mIegm~~DL~~~~~~T~~DL~~Yc~~VAGtVG~Lll~ilg~~~~~~a~~  339 (486)
                      +++..++..++..+       ..++.. +..|..||.+++ ..+|+|++||+.|||+|||+||+|+++++|..+......
T Consensus        82 ~~ll~~~~~v~~~~~~l~~~~~~~i~~~~~~m~~gm~d~~-~~~~~t~~dL~~Ycy~VAG~VG~~l~~l~~~~~~~~~~~  160 (333)
T d1ezfa_          82 RQVLEDFPTISLEFRNLAEKYQTVIADICRRMGIGMAEFL-DKHVTSEQEWDKYCHYVAGLVGIGLSRLFSASEFEDPLV  160 (333)
T ss_dssp             HHHHHTHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHH-TSCCCSHHHHHHHHHHHTHHHHHHHHHHHHHHTSSCHHH
T ss_pred             HHHHhhccHHHHHHHHHHHHhccchHHHHHHHhccHHHHc-cCcCCCHHHHHHHHHHHHHHHHHHHHHHhCcCCCccccH
Confidence            35555555555443       333333 345556666665 568999999999999999999999999998765332233


Q ss_pred             hhHHHHHHHHHHHHHHHHHHHhHHHHHHcCCCCCCHHhHHhcCCChhhhhccCCCHHHHHHHHHHHHHHHHHHHHHHHhh
Q 044623          340 ESVYNAALALGIANQLTNILRDVGEDAQRGRVYLPQDELAQAGLSDDDIFAGEVTNKWRNFMKNQIKRARMFFDMAENGV  419 (486)
Q Consensus       340 e~~~~~A~~LG~ALQLTNILRDv~EDl~rGRiYLP~d~L~k~Gvs~edL~~g~~~~~~r~li~~la~rAr~~l~~A~~~l  419 (486)
                      +...+.|.+||+|+|+||||||++||+++||||||+|+|.+||++++++.+++..++++.++.+++.+|+.||++|..++
T Consensus       161 ~~~~~~A~~lG~AlQltNIlRDi~eD~~~gR~YlP~e~l~~~g~~~~dl~~~~~~~~~~~~~~~l~~~A~~~~~~a~~y~  240 (333)
T d1ezfa_         161 GEDTERANSMGLFLQKTNIIRDYLEDQQGGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELITNALHHIPDVITYL  240 (333)
T ss_dssp             HHCHHHHHHHHHHHHHHHHHHTHHHHHHHTCCCSCHHHHTTTCSSGGGGGSGGGHHHHHHHHHHHHHHHHTTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhHHHHhCCcEECCHHHHHHcCCCHHHHHhccchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45568899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhccccCchHHHHHHHHHHHHHHHHHHCCCCCCCCCccCCHHHHHHHHHHH
Q 044623          420 TELSEASRWPVWASLLLYRQILDEIEANDYNNFTKRAYVSKAKKIAALPIA  470 (486)
Q Consensus       420 ~~Lp~~sr~pv~a~~~ly~~iL~~Ie~~~ydvf~~Rv~vsk~~Kl~ll~~a  470 (486)
                      ..||.++++.+.+...+|..+.-++.++|+++|++++++++.+++.++.++
T Consensus       241 ~~lp~~~~~~~~~~~~~~a~~tl~~~~~~~~~~~~~vkisr~~~~~l~~~~  291 (333)
T d1ezfa_         241 SRLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGAVKIRKGQAVTLMMDA  291 (333)
T ss_dssp             HTCCCHHHHHHHHHHHHHHHHHHHHHTTCGGGGTSCCCC----------CT
T ss_pred             HHCCchhHHHHHHHHHHHHHHHHHHHHcCchhcCCCeEeeHHHHHHHHHHh
Confidence            999999888777777777777777778899999999999999998876443
>d1ps1a_ a.128.1.4 (A:) Pentalenene synthase {Streptomyces sp., UC5319 [TaxId: 1931]} Back     information, alignment and structure
>d2q80a1 a.128.1.1 (A:6-296) Geranylgeranyl pyrophosphate synthetase {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1fpsa_ a.128.1.1 (A:) Farnesyl diphosphate synthase (geranyltranstransferase) {Chicken (Gallus gallus) [TaxId: 9031]} Back     information, alignment and structure
>d1v4ea_ a.128.1.1 (A:) Octoprenyl-diphosphate synthase {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1n1ba2 a.128.1.3 (A:271-598) (+)-bornyl diphosphate synthase {Garden sage (Salvia officinalis) [TaxId: 38868]} Back     information, alignment and structure
>d5easa2 a.128.1.3 (A:221-548) 5-Epi-aristolochene synthase {Tobacco (Nicotiana tabacum) [TaxId: 4097]} Back     information, alignment and structure
>d1rqja_ a.128.1.1 (A:) Farnesyl diphosphate synthase (geranyltranstransferase) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1di1a_ a.128.1.4 (A:) Aristolochene synthase {Fungus (Penicillium roqueforti) [TaxId: 5082]} Back     information, alignment and structure
>d1rtra_ a.128.1.1 (A:) Farnesyl diphosphate synthase (geranyltranstransferase) {Staphylococcus aureus [TaxId: 1280]} Back     information, alignment and structure