Citrus Sinensis ID: 020845

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
MAKALSVLNLPAHVAPRRNHSRPSLSYRPMMVTMAMSTPNKNKSYWTSVHEDIGAHLRQAVVVKEPVEVYEPMRHFVFAAPVNMAPALCVAACELVGGHREQAIVAAAALHVMHAASFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVEMTYETYKKKEGRLHACGAACGAILGGGSEKEIELLRRYGFYVGMIQGIVSRRLGPTEEIEELKKLAFKLREVNSFNDENAEVIFSLVDDNITHVLGFNLG
ccccccccccccccccccccccccccccccHHcccccccccHHHHHHHHHHHHHHHHHHHccccccccHHHHHccccccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHccccHHHHHHHHHHHccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHcHHHHcccccHHHHHHHHHHHHHHHHHHHccccc
cccccccccccccccccHcccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHcccccHcHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHcccccEEEEEEEEcccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcHHEEEHHcHHcccccHHHccccccHHHHcccccHHHHHHHHHHHHHHHHHHHccccc
MAKALSVLnlpahvaprrnhsrpslsyrpmMVTMAmstpnknksyWTSVHEDIGAHLRQAVVVKepvevyepmrhfvfaapvnmAPALCVAACELVGGHREQAIVAAAALHVMHAASfihenlplsdrtslipkskptmyhafkpnTELLVADAMLPFGLELLassdnpagnnsgRILRVMVEMTRAmgsqgvvegqynelqcsqcddddrklngitdVEMTYETYkkkegrlhaCGAACgailgggsEKEIELLRRYGFYVGMIQGIvsrrlgpteEIEELKKLAFKLREvnsfndenAEVIFSLVDdnithvlgfnlg
makalsvlnlpahvaprrnhsrpslsyrpMMVTMAMSTPNKNKSYWTSVHEDIGAHLRQAVVVKEPVEVYEPMRHFVFAAPVNMAPALCVAACELVGGHREQAIVAAAALHVMHAASFIhenlplsdRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGLELLassdnpagnnsGRILRVMVEMTRAMGSQGVVEGQYNELQcsqcddddrklnGITDVEMTYETYKKKEGRLHACGAACGAILGGGSEKEIELLRRYGFYVGMIQGIVSRRLGPTEEIEELKKLAFKLREVNSFNDENAEVIFSLVDDNITHVLGFNLG
MAKALSVLNLPAHVAPRRNHSRPSLSYRPMMVTMAMSTPNKNKSYWTSVHEDIGAHLRQAvvvkepvevyepMRHFVFAAPVNMAPALCVAACELVGGHREQaivaaaalhvmhaaSFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVEMTYETYKKKEGRLHacgaacgailgggSEKEIELLRRYGFYVGMIQGIVSRRLGPTEEIEELKKLAFKLREVNSFNDENAEVIFSLVDDNITHVLGFNLG
*******************************************SYWTSVHEDIGAHLRQAVVVKEPVEVYEPMRHFVFAAPVNMAPALCVAACELVGGHREQAIVAAAALHVMHAASFIHENLPLSDRTSLIP**KPTMYHAFKPNTELLVADAMLPFGLELLA***********RILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVEMTYETYKKKEGRLHACGAACGAILGGGSEKEIELLRRYGFYVGMIQGIVSRRLGPTEEIEELKKLAFKLREVNSFNDENAEVIFSLVDDNITHVLGFN**
*****************************************NKSYWTSVHEDIGAHLRQAVVVKEPVEVYEPMRHFVFAAPVNMAPALCVAACELVGGHREQAIVAAAALHVMHAASFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVEMTYETYKKKEGRLHACGAACGAILGGGSEKEIELLRRYGFYVGMIQGIVSRRLGPTEEIEELKKLAFKLREVNSFNDENAEVIFSLVDDNITHVLGFNL*
MAKALSVLNLPAHVAPRRNHSRPSLSYRPMMVTMAMSTPNKNKSYWTSVHEDIGAHLRQAVVVKEPVEVYEPMRHFVFAAPVNMAPALCVAACELVGGHREQAIVAAAALHVMHAASFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVEMTYETYKKKEGRLHACGAACGAILGGGSEKEIELLRRYGFYVGMIQGIVSRRLGPTEEIEELKKLAFKLREVNSFNDENAEVIFSLVDDNITHVLGFNLG
*************************************TPNKNKSYWTSVHEDIGAHLRQAVVVKEPVEVYEPMRHFVFAAPVNMAPALCVAACELVGGHREQAIVAAAALHVMHAASFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVEMTYETYKKKEGRLHACGAACGAILGGGSEKEIELLRRYGFYVGMIQGIVSRRLGPTEEIEELKKLAFKLREVNSFNDENAEVIFSLVDDNITHVLGF***
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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
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MAKALSVLNLPAHVAPRRNHSRPSLSYRPMMVTMAMSTPNKNKSYWTSVHEDIGAHLRQAVVVKEPVEVYEPMRHFVFAAPVNMAPALCVAACELVGGHREQAIVAAAALHVMHAASFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVEMTYETYKKKEGRLHACGAACGAILGGGSEKEIELLRRYGFYVGMIQGIVSRRLGPTEEIEELKKLAFKLREVNSFNDENAEVIFSLVDDNITHVLGFNLG
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 ?
Query320 2.2.26 [Sep-21-2011]
Q39108326 Heterodimeric geranylgera yes no 0.696 0.684 0.353 1e-34
P80042369 Geranylgeranyl pyrophosph N/A no 0.821 0.712 0.313 3e-34
P34802371 Heterodimeric geranylgera no no 0.743 0.641 0.342 4e-33
Q9ZU77347 Geranylgeranyl pyrophosph no no 0.728 0.671 0.348 9e-33
Q94ID7370 Geranylgeranyl pyrophosph N/A no 0.734 0.635 0.341 6e-32
Q9SLG2372 Geranylgeranyl pyrophosph no no 0.828 0.712 0.314 1e-31
Q43133366 Geranylgeranyl pyrophosph N/A no 0.740 0.647 0.330 9e-31
Q42698357 Geranylgeranyl pyrophosph N/A no 0.728 0.652 0.326 3e-30
O04046376 Heterodimeric geranylgera no no 0.821 0.699 0.291 3e-28
Q9LJY2344 Geranylgeranyl pyrophosph no no 0.815 0.758 0.335 2e-27
>sp|Q39108|GGR_ARATH Heterodimeric geranylgeranyl pyrophosphate synthase small subunit, chloroplastic OS=Arabidopsis thaliana GN=GGR PE=1 SV=2 Back     alignment and function desciption
 Score =  147 bits (370), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 87/246 (35%), Positives = 129/246 (52%), Gaps = 23/246 (9%)

Query: 43  KSYWTSVHEDIGAHLRQAVVVKEPVEVYEPMRHFVFAAPVNMAP-ALCVAACELVGGHRE 101
           ++YWT++  +I   L +A+ VK P  +YE MR+ V A     AP  +CVAACEL GG R 
Sbjct: 48  RTYWTTLITEINQKLDEAIPVKHPAGIYEAMRYSVLAQGAKRAPPVMCVAACELFGGDRL 107

Query: 102 QAIVAAAALHVMHAASFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGLE 161
            A   A AL ++HAAS IH++LP  D    + + KP+ +  +     +L  DA+ P   +
Sbjct: 108 AAFPTACALEMVHAASLIHDDLPCMDDDP-VRRGKPSNHTVYGSGMAILAGDALFPLAFQ 166

Query: 162 LLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVEM 221
            + S   P       ILR++ E+ R +GS G+  GQY +L+            G   +  
Sbjct: 167 HIVSHTPPDLVPRATILRLITEIARTVGSTGMAAGQYVDLE-----------GGPFPLSF 215

Query: 222 TYETYKKKEGRLHACGAACGAILGGGSEKEIELLRRYGFYVGMIQGIVSRRLGPTEEIEE 281
             E   KK G +  C A CG +LGG +E E++ LRRYG  VGM+  +V       ++I E
Sbjct: 216 VQE---KKFGAMGECSAVCGGLLGGATEDELQSLRRYGRAVGMLYQVV-------DDITE 265

Query: 282 LKKLAF 287
            KK ++
Sbjct: 266 DKKKSY 271
Heterodimeric geranyl(geranyl)-diphosphate (GPP) synthase small subunit. The small subunit alone is inactive in vitro while the large subunit GGPPS1 catalyzes mainly the production of geranygeranyl-diphosphate in vitro. Upon association of the two subunits, the product profile changes and the production of gerany-diphosphate is strongly increased.
Arabidopsis thaliana (taxid: 3702)
>sp|P80042|GGPPS_CAPAN Geranylgeranyl pyrophosphate synthase, chloroplastic OS=Capsicum annuum GN=GGPS1 PE=3 SV=1 Back     alignment and function description
>sp|P34802|GGPP1_ARATH Heterodimeric geranylgeranyl pyrophosphate synthase large subunit 1, chloroplastic OS=Arabidopsis thaliana GN=GGPPS1 PE=1 SV=2 Back     alignment and function description
>sp|Q9ZU77|GGPP7_ARATH Geranylgeranyl pyrophosphate synthase 7, chloroplastic OS=Arabidopsis thaliana GN=At2g18620 PE=2 SV=1 Back     alignment and function description
>sp|Q94ID7|GGPPS_HEVBR Geranylgeranyl pyrophosphate synthase, chloroplastic OS=Hevea brasiliensis GN=GGPS PE=1 SV=1 Back     alignment and function description
>sp|Q9SLG2|GGPP4_ARATH Geranylgeranyl pyrophosphate synthase 4 OS=Arabidopsis thaliana GN=GGPP4 PE=2 SV=1 Back     alignment and function description
>sp|Q43133|GGPPS_SINAL Geranylgeranyl pyrophosphate synthase, chloroplastic/chromoplastic OS=Sinapis alba GN=GGPS1 PE=1 SV=1 Back     alignment and function description
>sp|Q42698|GGPPS_CATRO Geranylgeranyl pyrophosphate synthase, chloroplastic OS=Catharanthus roseus GN=GGPS1 PE=3 SV=1 Back     alignment and function description
>sp|O04046|GGPP2_ARATH Heterodimeric geranylgeranyl pyrophosphate synthase large subunit 2 OS=Arabidopsis thaliana GN=GGPPS2 PE=1 SV=2 Back     alignment and function description
>sp|Q9LJY2|GGPPA_ARATH Geranylgeranyl pyrophosphate synthase 10, mitochondrial OS=Arabidopsis thaliana GN=At3g20160 PE=2 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 ?
Query320
164605008306 geranyl-diphosphate synthase [Hevea bras 0.915 0.957 0.507 7e-78
225460953298 PREDICTED: geranylgeranyl pyrophosphate 0.896 0.963 0.490 3e-72
147776970298 hypothetical protein VITISV_007690 [Viti 0.903 0.969 0.487 6e-72
255583629308 geranyl geranyl pyrophosphate synthase, 0.853 0.886 0.520 8e-72
46241272297 geranyl diphosphate synthase small subun 0.881 0.949 0.475 1e-67
323463187273 Chain B, Crystal Structure Of Geranyl Di 0.775 0.908 0.509 2e-65
224135433236 predicted protein [Populus trichocarpa] 0.718 0.974 0.507 8e-65
229915238279 geranyl diphosphate synthase small subun 0.778 0.892 0.468 1e-61
374639379314 geranyl diphosphate synthase small subun 0.862 0.878 0.424 3e-59
342360000301 geranyl-diphosphate synthase [Medicago s 0.868 0.923 0.465 1e-57
>gi|164605008|dbj|BAF98300.1| geranyl-diphosphate synthase [Hevea brasiliensis] Back     alignment and taxonomy information
 Score =  296 bits (759), Expect = 7e-78,   Method: Compositional matrix adjust.
 Identities = 160/315 (50%), Positives = 216/315 (68%), Gaps = 22/315 (6%)

Query: 1   MAKALSVL---NLPAHVAPRRNHSRPSLSYRPMMVTMAMSTPNKNKSYWTSVHEDIGAHL 57
           MA ALS     NL A      N   P  S+RPM+V  AMST   ++SYW+SV+ D+  HL
Sbjct: 1   MAGALSSTIHGNLIARAVSSSNPKHPLFSHRPMVV--AMST---DQSYWSSVNADLDTHL 55

Query: 58  RQAVVVKEPVEVYEPMRHFVFAAPVNMAPALCVAACELVGGHREQAIVAAAALHVMHAAS 117
           +QA+ +++P+ V+EPMRH + +AP   APALC+AACELVGGHR QA+ AA+AL ++HA++
Sbjct: 56  KQAIPIRQPLAVFEPMRHLILSAPQTSAPALCIAACELVGGHRNQAMAAASALRLVHASA 115

Query: 118 FIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGRI 177
             HENLPL+DR   +P+++PT+Y    PN ELL+AD ++P+G ELLA  D+ A NNS R+
Sbjct: 116 STHENLPLTDRPRPMPRTRPTLY---GPNIELLIADGIIPYGFELLARDDDAAENNSNRV 172

Query: 178 LRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVEMTYETYKKKEGRLHACG 237
           LR ++E++RAMGSQGV+EGQYNE Q  + + ++     I  V       +KKEG LHAC 
Sbjct: 173 LRAIIEISRAMGSQGVIEGQYNESQYEESEGEE-----IFHVGWLQNVCRKKEGTLHACA 227

Query: 238 AACGAILGGGSEKEIELLRRYGFYVGMIQGIVS----RRLGPTEEIEELKKLAFKLREVN 293
            ACGAILGGGSE EIE LRRYG YVGM+QGI+S    R+  P +E+ +L+ LA  L+E+ 
Sbjct: 228 GACGAILGGGSEDEIEKLRRYGLYVGMVQGILSKVDERKEWPVKEVNKLRDLA--LKELK 285

Query: 294 SFNDENAEVIFSLVD 308
            FN    + I  LV+
Sbjct: 286 DFNQAKVKTISILVE 300

Source: Hevea brasiliensis

Species: Hevea brasiliensis

Genus: Hevea

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|225460953|ref|XP_002278023.1| PREDICTED: geranylgeranyl pyrophosphate synthase-related protein, chloroplastic [Vitis vinifera] Back     alignment and taxonomy information
>gi|147776970|emb|CAN63418.1| hypothetical protein VITISV_007690 [Vitis vinifera] Back     alignment and taxonomy information
>gi|255583629|ref|XP_002532570.1| geranyl geranyl pyrophosphate synthase, putative [Ricinus communis] gi|223527725|gb|EEF29831.1| geranyl geranyl pyrophosphate synthase, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|46241272|gb|AAS82859.1| geranyl diphosphate synthase small subunit [Antirrhinum majus] Back     alignment and taxonomy information
>gi|323463187|pdb|3QKC|B Chain B, Crystal Structure Of Geranyl Diphosphate Synthase Small Subunit From Antirrhinum Majus gi|323463188|pdb|3QKC|A Chain A, Crystal Structure Of Geranyl Diphosphate Synthase Small Subunit From Antirrhinum Majus Back     alignment and taxonomy information
>gi|224135433|ref|XP_002322072.1| predicted protein [Populus trichocarpa] gi|222869068|gb|EEF06199.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|229915238|gb|ACQ90681.1| geranyl diphosphate synthase small subunit [Humulus lupulus] Back     alignment and taxonomy information
>gi|374639379|gb|AEZ55678.1| geranyl diphosphate synthase small subunit type I [Salvia miltiorrhiza] Back     alignment and taxonomy information
>gi|342360000|gb|AEL29573.1| geranyl-diphosphate synthase [Medicago sativa] 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 ?
Query320
TAIR|locus:2093832357 AT3G29430 [Arabidopsis thalian 0.740 0.663 0.287 2.7e-20
TAIR|locus:2046283347 AT2G18620 [Arabidopsis thalian 0.643 0.593 0.300 9.2e-20
TAIR|locus:2115450371 GGPS1 "geranylgeranyl pyrophos 0.653 0.563 0.296 1.1e-19
TAIR|locus:2046258372 GGPS4 "geranylgeranyl pyrophos 0.828 0.712 0.268 1.9e-19
UNIPROTKB|P80042369 GGPS1 "Geranylgeranyl pyrophos 0.746 0.647 0.268 2.4e-19
TAIR|locus:2079028360 AT3G32040 [Arabidopsis thalian 0.734 0.652 0.289 1e-18
TAIR|locus:2121149326 GGR "geranylgeranyl reductase" 0.743 0.730 0.273 1.4e-18
TAIR|locus:2089626360 AT3G14530 "AT3G14530" [Arabido 0.737 0.655 0.282 3e-18
TAIR|locus:2010182336 GGPS6 "geranylgeranyl pyrophos 0.643 0.613 0.3 1.3e-15
TAIR|locus:2087550344 AT3G20160 [Arabidopsis thalian 0.815 0.758 0.273 9.2e-15
TAIR|locus:2093832 AT3G29430 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 240 (89.5 bits), Expect = 2.7e-20, P = 2.7e-20
 Identities = 71/247 (28%), Positives = 109/247 (44%)

Query:    43 KSYWTSVHEDIGAHLRQAXXXXXXXXXXXXMRHFVFAAPVNMAPALCVAACELVGGHREQ 102
             KSY     E + A L  +            +R+ + A    + P LC+AACELVGG    
Sbjct:    64 KSYMIRKAESVSAALNVSVPLQEPLTIQEAVRYSLLAGGKRVRPLLCIAACELVGGDEAT 123

Query:   103 XXXXXXXXXXXXXXSFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGLEL 162
                           S IH++LP  D   L  + KPT +  F  +  +L  DA+L    E 
Sbjct:   124 AMSAACAVEMIHTSSLIHDDLPCMDDADL-RRGKPTNHKEFGEDMAVLAGDALLALAFEH 182

Query:   163 LASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQ-CDDDDRKLNGITDVEM 221
             +    N       R++R ++E+ +A+G++G+V GQ  +L CSQ  + DD  L  +  + +
Sbjct:   183 MTFVSNGLVAPE-RMIRAVMELAKAIGTKGLVAGQVTDL-CSQGLNPDDVGLERLEFIHL 240

Query:   222 TYETYKKKEGRLHXXXXXXXXXXXXXSEKEIELLRRYGFYVGMIQGIVSRRLGPTEEIEE 281
                    K   L              +E+EIE LR+Y   +G++  +V   L  TE  +E
Sbjct:   241 ------HKTAALLEAAAVLGAIMGGGTEEEIEKLRKYARCIGLLFQVVDDILDVTESTKE 294

Query:   282 LKKLAFK 288
             L K A K
Sbjct:   295 LGKTAGK 301
GO:0005739 "mitochondrion" evidence=ISM
GO:0008299 "isoprenoid biosynthetic process" evidence=IEA
GO:0006744 "ubiquinone biosynthetic process" evidence=RCA
TAIR|locus:2046283 AT2G18620 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2115450 GGPS1 "geranylgeranyl pyrophosphate synthase 1" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2046258 GGPS4 "geranylgeranyl pyrophosphate synthase 4" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|P80042 GGPS1 "Geranylgeranyl pyrophosphate synthase, chloroplastic" [Capsicum annuum (taxid:4072)] Back     alignment and assigned GO terms
TAIR|locus:2079028 AT3G32040 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2121149 GGR "geranylgeranyl reductase" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2089626 AT3G14530 "AT3G14530" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2010182 GGPS6 "geranylgeranyl pyrophosphate synthase 6" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2087550 AT3G20160 [Arabidopsis thaliana (taxid:3702)] 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

No confident hit for EC number transfering in SWISSPROT detected by BLAST

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 Layer2.5.10.766

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 ?
Query320
cd00685259 cd00685, Trans_IPPS_HT, Trans-Isoprenyl Diphosphat 2e-22
COG0142322 COG0142, IspA, Geranylgeranyl pyrophosphate syntha 2e-19
pfam00348260 pfam00348, polyprenyl_synt, Polyprenyl synthetase 9e-17
cd00867236 cd00867, Trans_IPPS, Trans-Isoprenyl Diphosphate S 3e-13
PRK10888323 PRK10888, PRK10888, octaprenyl diphosphate synthas 1e-06
PRK10581299 PRK10581, PRK10581, geranyltranstransferase; Provi 2e-05
CHL00151323 CHL00151, preA, prenyl transferase; Reviewed 6e-05
TIGR02748319 TIGR02748, GerC3_HepT, heptaprenyl diphosphate syn 1e-04
cd00385243 cd00385, Isoprenoid_Biosyn_C1, Isoprenoid Biosynth 0.001
>gnl|CDD|173833 cd00685, Trans_IPPS_HT, Trans-Isoprenyl Diphosphate Synthases, head-to-tail Back     alignment and domain information 
 Score = 93.8 bits (234), Expect = 2e-22
 Identities = 56/203 (27%), Positives = 85/203 (41%), Gaps = 30/203 (14%)

Query: 69  VYEPMRHFVFAAPVNMAPALCVAACELVGGH-REQAIVAAAALHVMHAASFIHENLPLSD 127
           + E +R+ + A    + P L + A   +GG   E A+  AAA+ ++H AS +H      D
Sbjct: 6   LREALRYLLLAGGKRLRPLLVLLAARALGGPELEAALRLAAAIELLHTASLVH------D 59

Query: 128 RTSLIPKS-----KPTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMV 182
              ++  S     KPT++  F   T +L  D +L    ELLA   NP      R L +  
Sbjct: 60  D--VMDNSDLRRGKPTVHKVFGNATAILAGDYLLARAFELLARLGNPYYP---RALELFS 114

Query: 183 EMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVEMTYETYKKKEGRLHACGAACGA 242
           E    +     VEGQ          D   + +     E      + K   L A     GA
Sbjct: 115 EAILEL-----VEGQL--------LDLLSEYDTDVTEEEYLRIIRLKTAALFAAAPLLGA 161

Query: 243 ILGGGSEKEIELLRRYGFYVGMI 265
           +L G  E+E E L+R+G  +G+ 
Sbjct: 162 LLAGADEEEAEALKRFGRNLGLA 184

These trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) catalyze head-to-tail (HT) (1'-4) condensation reactions. This CD includes all-trans (E)-isoprenyl diphosphate synthases which synthesize various chain length (C10, C15, C20, C25, C30, C35, C40, C45, and C50) linear isoprenyl diphosphates from precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). They catalyze the successive 1'-4 condensation of the 5-carbon IPP to allylic substrates geranyl-, farnesyl-, or geranylgeranyl-diphosphate. 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 (DDXX(XX)D) 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, protecting and stabilizing reactive carbocation intermediates. Farnesyl diphosphate synthases produce the precursors of steroids, cholesterol, sesquiterpenes, farnsylated proteins, heme, and vitamin K12; and geranylgeranyl diphosphate and longer chain synthases produce the precursors of carotenoids, retinoids, diterpenes, geranylgeranylated chlorophylls, ubiquinone, and archaeal ether linked lipids. Isoprenyl diphosphate synthases are widely distributed among archaea, bacteria, and eukareya. Length = 259
>gnl|CDD|223220 COG0142, IspA, Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism] Back     alignment and domain information
>gnl|CDD|215873 pfam00348, polyprenyl_synt, Polyprenyl synthetase Back     alignment and domain information
>gnl|CDD|173836 cd00867, Trans_IPPS, Trans-Isoprenyl Diphosphate Synthases Back     alignment and domain information
>gnl|CDD|182813 PRK10888, PRK10888, octaprenyl diphosphate synthase; Provisional Back     alignment and domain information
>gnl|CDD|182567 PRK10581, PRK10581, geranyltranstransferase; Provisional Back     alignment and domain information
>gnl|CDD|164542 CHL00151, preA, prenyl transferase; Reviewed Back     alignment and domain information
>gnl|CDD|131795 TIGR02748, GerC3_HepT, heptaprenyl diphosphate synthase component II Back     alignment and domain information
>gnl|CDD|173830 cd00385, Isoprenoid_Biosyn_C1, Isoprenoid Biosynthesis enzymes, Class 1 Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 320
PRK10581299 geranyltranstransferase; Provisional 100.0
COG0142322 IspA Geranylgeranyl pyrophosphate synthase [Coenzy 100.0
PRK10888323 octaprenyl diphosphate synthase; Provisional 100.0
TIGR02748319 GerC3_HepT heptaprenyl diphosphate synthase compon 100.0
TIGR02749322 prenyl_cyano solanesyl diphosphate synthase. Membe 100.0
CHL00151323 preA prenyl transferase; Reviewed 100.0
PLN02857416 octaprenyl-diphosphate synthase 100.0
PLN02890422 geranyl diphosphate synthase 100.0
KOG0776384 consensus Geranylgeranyl pyrophosphate synthase/Po 100.0
PF00348260 polyprenyl_synt: Polyprenyl synthetase; InterPro: 100.0
cd00685259 Trans_IPPS_HT Trans-Isoprenyl Diphosphate Synthase 100.0
cd00867236 Trans_IPPS Trans-Isoprenyl Diphosphate Synthases. 100.0
KOG0711347 consensus Polyprenyl synthetase [Coenzyme transpor 100.0
KOG0777322 consensus Geranylgeranyl pyrophosphate synthase/Po 99.97
cd00385243 Isoprenoid_Biosyn_C1 Isoprenoid Biosynthesis enzym 99.78
PF07307212 HEPPP_synt_1: Heptaprenyl diphosphate synthase (HE 97.37
cd00683265 Trans_IPPS_HH Trans-Isoprenyl Diphosphate Synthase 90.93
PLN02632334 phytoene synthase 90.18
TIGR03465266 HpnD squalene synthase HpnD. The genes of this fam 89.42
TIGR01559 336 squal_synth farnesyl-diphosphate farnesyltransfera 87.69
TIGR03464266 HpnC squalene synthase HpnC. This family of genes 86.61
>PRK10581 geranyltranstransferase; Provisional Back     alignment and domain information 
Probab=100.00  E-value=2.4e-56  Score=422.44  Aligned_cols=239  Identities=20%  Similarity=0.275  Sum_probs=211.1

Q ss_pred             HHHHHHHHHHHHHHHHHHhhccC--CcccHHhHHHhhccCCCCcchHHHHHHHHHHhCCChHHHhhHHHHHHHHHHHHHH
Q 020845           42 NKSYWTSVHEDIGAHLRQAVVVK--EPVEVYEPMRHFVFAAPVNMAPALCVAACELVGGHREQAIVAAAALHVMHAASFI  119 (320)
Q Consensus        42 ~~~~~~~~~~~ie~~L~~~i~~~--~~~~l~e~~~y~~~~gGKrlRp~L~l~~~~~~g~~~~~~~~lAaavEliH~asLI  119 (320)
                      |.++++...+.|++.|++.+...  .+..+.++++|++..||||+||+||+++++++|++++.+.++|++||++|+||||
T Consensus         3 ~~~~~~~~~~~i~~~l~~~~~~~~~~~~~l~~~~~~~~~~gGKrlRp~L~l~~~~~~g~~~~~~~~~A~avEliH~aSLi   82 (299)
T PRK10581          3 FPQQLQACVQQANQALSRFIAPLPFQNTPVVEAMQYGALLGGKRLRPFLVYATGQMFGVSTNTLDAPAAAVECIHAYSLI   82 (299)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhcccCchHHHHHHHHHHhcCcccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence            56777778888888888877542  2345899999999999999999999999999999888899999999999999999


Q ss_pred             HhCCCCCCCCCCCCCCCCcccccCChhHHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHhchhhhhHHHHH
Q 020845          120 HENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYN  199 (320)
Q Consensus       120 HDDlPi~D~Ds~~RRG~pt~h~~~G~~~AIl~GD~L~~~a~~ll~~~~~~~~~~~~~~~~~i~~~~~a~g~~~~~~GQ~l  199 (320)
                      |||||+||+ |++|||+||+|++||+++|||+||+|++.||+++++...+ ........+++.+++++.|..+++.||.+
T Consensus        83 HDDip~~D~-s~~RRG~pt~h~~~G~~~AIl~GD~L~~~a~~~l~~~~~~-~~~~~~~~~~~~~~~~~~~~~~l~~GQ~l  160 (299)
T PRK10581         83 HDDLPAMDD-DDLRRGLPTCHVKFGEANAILAGDALQTLAFSILSDAPMP-EVSDRDRISMISELASASGIAGMCGGQAL  160 (299)
T ss_pred             HcCcccccC-CCccCCCcChHHHhCcchHHHHHHHHHHHHHHHHHhCCCc-cCChHHHHHHHHHHHHhcccchhhHhhHH
Confidence            999888999 8899999999999999999999999999999999986532 12344567788888877666789999999


Q ss_pred             HhhcccCCCcccccCCCCCHHHHHHHHHhcHHHHHHHHHHHHHHhcCCCH-HHHHHHHHHHHHHHHHHHHHhhhcCCchh
Q 020845          200 ELQCSQCDDDDRKLNGITDVEMTYETYKKKEGRLHACGAACGAILGGGSE-KEIELLRRYGFYVGMIQGIVSRRLGPTEE  278 (320)
Q Consensus       200 Dl~~~~~~~~~~~~~~~~~~e~y~~ii~~KTg~Lf~~a~~~Gailag~~~-~~~~~l~~~G~~lG~afQi~DD~lD~~~~  278 (320)
                      |+.+...         ..+++.|++|+.+|||+||++||.+|++++|+++ +.++.+++||.++|+||||+||++|++++
T Consensus       161 d~~~~~~---------~~~~~~y~~i~~~KTa~L~~~~~~~gailag~~~~~~~~~l~~~g~~lG~aFQI~DDilD~~g~  231 (299)
T PRK10581        161 DLEAEGK---------QVPLDALERIHRHKTGALIRAAVRLGALSAGDKGRRALPVLDRYAESIGLAFQVQDDILDVVGD  231 (299)
T ss_pred             HHhccCC---------CCCHHHHHHHHHHhhHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHHHHHHHHHHHccccCC
Confidence            9988652         3688999999999999999999999999999864 57899999999999999999999999999


Q ss_pred             HHHh-hhHHHHHHH
Q 020845          279 IEEL-KKLAFKLRE  291 (320)
Q Consensus       279 ~~~~-k~~~~Dl~e  291 (320)
                      ++++ |+.++|++|
T Consensus       232 ~~~~GK~~g~Dl~~  245 (299)
T PRK10581        232 TATLGKRQGADQQL  245 (299)
T ss_pred             hHHHCCCcchhhhc
Confidence            9988 999999987

>COG0142 IspA Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism] Back     alignment and domain information
>PRK10888 octaprenyl diphosphate synthase; Provisional Back     alignment and domain information
>TIGR02748 GerC3_HepT heptaprenyl diphosphate synthase component II Back     alignment and domain information
>TIGR02749 prenyl_cyano solanesyl diphosphate synthase Back     alignment and domain information
>CHL00151 preA prenyl transferase; Reviewed Back     alignment and domain information
>PLN02857 octaprenyl-diphosphate synthase Back     alignment and domain information
>PLN02890 geranyl diphosphate synthase Back     alignment and domain information
>KOG0776 consensus Geranylgeranyl pyrophosphate synthase/Polyprenyl synthetase [Coenzyme transport and metabolism] 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
>cd00685 Trans_IPPS_HT Trans-Isoprenyl Diphosphate Synthases, head-to-tail Back     alignment and domain information
>cd00867 Trans_IPPS Trans-Isoprenyl Diphosphate Synthases Back     alignment and domain information
>KOG0711 consensus Polyprenyl synthetase [Coenzyme transport and metabolism] Back     alignment and domain information
>KOG0777 consensus Geranylgeranyl pyrophosphate synthase/Polyprenyl synthetase [Coenzyme transport and metabolism] Back     alignment and domain information
>cd00385 Isoprenoid_Biosyn_C1 Isoprenoid Biosynthesis enzymes, Class 1 Back     alignment and domain information
>PF07307 HEPPP_synt_1: Heptaprenyl diphosphate synthase (HEPPP synthase) subunit 1; InterPro: IPR009920 This family contains subunit 1 of bacterial heptaprenyl diphosphate synthase (HEPPP synthase) (2 Back     alignment and domain information
>cd00683 Trans_IPPS_HH Trans-Isoprenyl Diphosphate Synthases, head-to-head Back     alignment and domain information
>PLN02632 phytoene synthase Back     alignment and domain information
>TIGR03465 HpnD squalene synthase HpnD Back     alignment and domain information
>TIGR01559 squal_synth farnesyl-diphosphate farnesyltransferase Back     alignment and domain information
>TIGR03464 HpnC squalene synthase HpnC 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 ?
Query320
3qkc_B273 Crystal Structure Of Geranyl Diphosphate Synthase S 6e-50
3kra_B274 Mint Heterotetrameric Geranyl Pyrophosphate Synthas 2e-40
3oab_B264 Mint Deletion Mutant Of Heterotetrameric Geranyl Py 2e-36
3kra_A295 Mint Heterotetrameric Geranyl Pyrophosphate Synthas 3e-17
2j1p_A293 Geranylgeranyl Diphosphate Synthase From Sinapis Al 2e-16
2j1o_A268 Geranylgeranyl Diphosphate Synthase From Sinapis Al 2e-09
4f62_A317 Crystal Structure Of A Putative Farnesyl-Diphosphat 3e-08
3p8r_A302 Crystal Structure Of Polyprenyl Synthase From Vibri 7e-05
3uca_A324 Crystal Structure Of Isoprenoid Synthase (Target Ef 9e-05
3lom_A313 Crystal Structure Of Geranyltransferase From Legion 2e-04
2h8o_A335 The 1.6a Crystal Structure Of The Geranyltransferas 3e-04
>pdb|3QKC|B Chain B, Crystal Structure Of Geranyl Diphosphate Synthase Small Subunit From Antirrhinum Majus Length = 273 Back     alignment and structure 
Iteration: 1

 Score =  194 bits (493), Expect = 6e-50,   Method: Compositional matrix adjust.
 Identities = 110/265 (41%), Positives = 146/265 (55%), Gaps = 17/265 (6%)
Query: 40  NKNKSYWTSVHEDIGAHLRQAXXXXXXXXXXXXMRHFVFAAPVNMAPALCVAACELVGGH 99
            + ++Y  ++  DI ++L++A            M H  FAAP   A ALCVAACELVGG 
Sbjct: 4   TRTQTYRATIESDIESYLKKAIPIRAPESVFEPMHHLTFAAPRTSASALCVAACELVGGD 63
Query: 100 REQXXXXXXXXXXXXXXSFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFG 159
           R                ++ HENLPL+D     P SK  + H F PN ELL  D ++PFG
Sbjct: 64  RSDAMAAAAAVHLMHVAAYTHENLPLTDG----PMSKSEIQHKFDPNIELLTGDGIIPFG 119
Query: 160 LELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDV 219
           LEL+A S +P  NN  RILR ++E+TR MGS+G+VEGQY+EL           LN + D+
Sbjct: 120 LELMARSMDPTRNNPDRILRAIIELTRVMGSEGIVEGQYHEL----------GLNQLNDL 169
Query: 220 EMTYETYKKKEGRLHXXXXXXXXXXXXXSEKEIELLRRYGFYVGMIQGIVSR-RLGPTEE 278
           E+     KKKEG LH              E +IE LRR+G YVG +QG++ + R G    
Sbjct: 170 ELIEYVCKKKEGTLHACGAACGAILGGCDEDKIEKLRRFGLYVGTVQGLLGKNRSGFEGR 229
Query: 279 IEELKKLAFKLREVNSFNDENAEVI 303
           I+ELK+LA K  E+ SF  E  E+I
Sbjct: 230 IKELKELAVK--ELESFGGEKIELI 252
>pdb|3KRA|B Chain B, Mint Heterotetrameric Geranyl Pyrophosphate Synthase In Complex With Magnesium Length = 274 Back     alignment and structure
>pdb|3OAB|B Chain B, Mint Deletion Mutant Of Heterotetrameric Geranyl Pyrophosphate Synthase In Complex With Ligands Length = 264 Back     alignment and structure
>pdb|3KRA|A Chain A, Mint Heterotetrameric Geranyl Pyrophosphate Synthase In Complex With Magnesium Length = 295 Back     alignment and structure
>pdb|2J1P|A Chain A, Geranylgeranyl Diphosphate Synthase From Sinapis Alba In Complex With Ggpp Length = 293 Back     alignment and structure
>pdb|2J1O|A Chain A, Geranylgeranyl Diphosphate Synthase From Sinapis Alba Length = 268 Back     alignment and structure
>pdb|4F62|A Chain A, Crystal Structure Of A Putative Farnesyl-Diphosphate Synthase From Marinomonas Sp. Med121 (Target Efi-501980) Length = 317 Back     alignment and structure
>pdb|3P8R|A Chain A, Crystal Structure Of Polyprenyl Synthase From Vibrio Cholerae Length = 302 Back     alignment and structure
>pdb|3UCA|A Chain A, Crystal Structure Of Isoprenoid Synthase (Target Efi-501974) From Clostridium Perfringens Length = 324 Back     alignment and structure
>pdb|3LOM|A Chain A, Crystal Structure Of Geranyltransferase From Legionella Pneumophila Length = 313 Back     alignment and structure
>pdb|2H8O|A Chain A, The 1.6a Crystal Structure Of The Geranyltransferase From Agrobacterium Tumefaciens Length = 335 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 ?
Query320
3qkc_B273 Geranyl diphosphate synthase small subunit; struct 2e-75
3kra_B274 Geranyl diphosphate synthase small subunit; prenyl 1e-65
2j1p_A293 Geranylgeranyl pyrophosphate synthetase; transfera 1e-35
3ts7_A324 Geranyltranstransferase; isoprenoid synthesis, far 4e-32
2h8o_A335 Geranyltranstransferase; geranyltransferase,agroba 4e-32
3lom_A313 Geranyltranstransferase; geranyltransferase, struc 8e-31
3p8r_A302 Geranyltranstransferase; isoprenyl synthase, struc 2e-30
3uca_A324 Geranyltranstransferase; isoprenoid synthesis, iso 2e-30
3lsn_A304 Geranyltranstransferase; structural genomics, prot 4e-30
4f62_A317 Geranyltranstransferase; enzyme function initiativ 6e-30
1rqj_A299 Geranyltranstransferase; bisphosphonate, isoprenyl 8e-30
3pde_A309 Farnesyl-diphosphate synthase; isoprenyl diphospha 7e-29
3p8l_A302 Geranyltranstransferase; isoprenyl synthase, struc 1e-28
1rtr_A301 Geranyltranstransferase; 2.50A {Staphylococcus aur 1e-28
3m0g_A297 Farnesyl diphosphate synthase; structural genomics 6e-28
4dhd_A358 Polyprenyl synthetase; isoprenoid synthesis, isopr 8e-28
3llw_A311 Geranyltranstransferase (ISPA); structural genomic 9e-27
3npk_A291 Geranyltranstransferase; isoprene biosynthesis, SG 2e-26
1wy0_A342 Geranylgeranyl pyrophosphate synthetase; pyrococcu 1e-25
2ftz_A284 Geranyltranstransferase; TM0161, structural GE joi 3e-25
3nf2_A352 Putative polyprenyl synthetase; isoprenyl diphosph 2e-23
1wmw_A330 Geranylgeranyl diphosphate synthetase; GGPP, preny 1e-20
3ipi_A295 Geranyltranstransferase; isoprene biosynthesis, he 3e-18
3lk5_A380 Geranylgeranyl pyrophosphate synthase; structural 1e-17
4fp4_A285 Polyprenyl synthetase; isoprenoid synthesis, isopr 7e-17
3oyr_A345 Trans-isoprenyl diphosphate synthase; isoprenyl sy 1e-16
3mzv_A341 Decaprenyl diphosphate synthase; transferase, stru 5e-15
2ihi_A395 Pyrophosphate synthase; PV092040, structural genom 6e-15
1uby_A367 FPS, farnesyl diphosphate synthase; transferase, i 8e-15
1yhl_A362 Farnesyl pyrophosphate synthase; farnesyl diphosph 1e-14
3aqb_B325 Component B of hexaprenyl diphosphate synthase; pr 3e-14
3rmg_A334 Octaprenyl-diphosphate synthase; structural genomi 2e-13
2azj_A289 Geranylgeranyl pyrophosphate synthetase; hexpps, t 2e-13
2qis_A374 Farnesyl pyrophosphate synthetase; trans-prenyltra 4e-13
2e8v_A340 Geranylgeranyl pyrophosphate synthetase; prenyltra 5e-13
2q80_A301 Geranylgeranyl pyrophosphate synthetase; isoprenoi 2e-12
2her_A368 Fragment, farnesyl pyrophosphate synthase; farnesy 5e-12
3lmd_A360 Geranylgeranyl pyrophosphate synthase; isoprenyl d 7e-12
3dyh_A390 Farnesyl pyrophosphate synthase; protein-bisphosph 9e-12
3pko_A334 Geranylgeranyl pyrophosphate synthase; isoprenyl d 3e-11
3tc1_A315 Octaprenyl pyrophosphate synthase; all alpha-helic 3e-10
1v4e_A299 Octoprenyl-diphosphate synthase; trans-type prenyl 2e-09
3apz_A348 Geranyl diphosphate synthase; prenyltransferase, a 1e-07
>3qkc_B Geranyl diphosphate synthase small subunit; structural genomics, protein structure initiative, NEW YORK structural genomix research consortium; 2.20A {Antirrhinum majus} Length = 273 Back     alignment and structure
 Score =  232 bits (593), Expect = 2e-75
 Identities = 134/276 (48%), Positives = 181/276 (65%), Gaps = 20/276 (7%)

Query: 34  MAMSTPNKNKSYWTSVHEDIGAHLRQAVVVKEPVEVYEPMRHFVFAAPVNMAPALCVAAC 93
           M+++     ++Y  ++  DI ++L++A+ ++ P  V+EPM H  FAAP   A ALCVAAC
Sbjct: 1   MSLTRT---QTYRATIESDIESYLKKAIPIRAPESVFEPMHHLTFAAPRTSASALCVAAC 57

Query: 94  ELVGGHREQAIVAAAALHVMHAASFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVAD 153
           ELVGG R  A+ AAAA+H+MH A++ HENLPL+D     P SK  + H F PN ELL  D
Sbjct: 58  ELVGGDRSDAMAAAAAVHLMHVAAYTHENLPLTDG----PMSKSEIQHKFDPNIELLTGD 113

Query: 154 AMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKL 213
            ++PFGLEL+A S +P  NN  RILR ++E+TR MGS+G+VEGQY+EL            
Sbjct: 114 GIIPFGLELMARSMDPTRNNPDRILRAIIELTRVMGSEGIVEGQYHELGL---------- 163

Query: 214 NGITDVEMTYETYKKKEGRLHACGAACGAILGGGSEKEIELLRRYGFYVGMIQGIVSRRL 273
           N + D+E+     KKKEG LHACGAACGAILGG  E +IE LRR+G YVG +QG++ +  
Sbjct: 164 NQLNDLELIEYVCKKKEGTLHACGAACGAILGGCDEDKIEKLRRFGLYVGTVQGLLGKNR 223

Query: 274 GPTE-EIEELKKLAFKLREVNSFNDENAEVIFSLVD 308
              E  I+ELK+LA K  E+ SF  E  E+I  + +
Sbjct: 224 SGFEGRIKELKELAVK--ELESFGGEKIELIRGVFE 257
>3kra_B Geranyl diphosphate synthase small subunit; prenyltransferase, isoprene biosynthesis, isoprenyl pyrophosphate synthase, transferase; 1.90A {Mentha x piperita} PDB: 3krc_B* 3krf_B* 3kro_B* 3krp_B* 3oab_B* 3oac_B* Length = 274 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* Length = 293 Back     alignment and structure
>3ts7_A Geranyltranstransferase; isoprenoid synthesis, farnesyl diphosphate synthase; 1.94A {Methylococcus capsulatus} Length = 324 Back     alignment and structure
>2h8o_A Geranyltranstransferase; geranyltransferase,agrobacterium tumefaciens, structural GEN PSI-2, protein structure initiative; 1.60A {Agrobacterium tumefaciens} Length = 335 Back     alignment and structure
>3lom_A Geranyltranstransferase; geranyltransferase, structural genomics, PSI, protein structure initiative, nysgrc; 2.30A {Legionella pneumophila subsp} Length = 313 Back     alignment and structure
>3p8r_A Geranyltranstransferase; isoprenyl synthase, structural genomics, PSI, protein struct initiative, nysgrc; 2.50A {Vibrio cholerae} Length = 302 Back     alignment and structure
>3uca_A Geranyltranstransferase; isoprenoid synthesis, isoprenoid diphosphate synthase; 2.00A {Clostridium perfringens} Length = 324 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* Length = 304 Back     alignment and structure
>4f62_A Geranyltranstransferase; enzyme function initiative, structural genomics; 2.10A {Marinomonas SP} Length = 317 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* Length = 299 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* Length = 309 Back     alignment and structure
>3p8l_A Geranyltranstransferase; isoprenyl synthase, structural genomics, PSI, protein struct initiative, nysgrc; 2.00A {Enterococcus faecalis} Length = 302 Back     alignment and structure
>1rtr_A Geranyltranstransferase; 2.50A {Staphylococcus aureus} SCOP: a.128.1.1 Length = 301 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 Length = 297 Back     alignment and structure
>4dhd_A Polyprenyl synthetase; isoprenoid synthesis, isoprenoid diphosphate synthase, trans; 1.65A {Pyrobaculum calidifontis} Length = 358 Back     alignment and structure
>3llw_A Geranyltranstransferase (ISPA); structural genomics, PSI, protein structure initiative, nysgrc; 2.30A {Helicobacter pylori} PDB: 3q1o_A* Length = 311 Back     alignment and structure
>3npk_A Geranyltranstransferase; isoprene biosynthesis, SGX, structural genomics protein structure initiative; 1.50A {Campylobacter jejuni} Length = 291 Back     alignment and structure
>1wy0_A Geranylgeranyl pyrophosphate synthetase; pyrococcus horikosh structural genomics, riken structural genomics/proteomics initiative, RSGI; 2.20A {Pyrococcus horikoshii} Length = 342 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} Length = 284 Back     alignment and structure
>3nf2_A Putative polyprenyl synthetase; isoprenyl diphosphate synthase, structural genomics, PSI, PR structure initiative, nysgrc; 2.20A {Streptomyces coelicolor} Length = 352 Back     alignment and structure
>1wmw_A Geranylgeranyl diphosphate synthetase; GGPP, prenyl diphosphate synthase, structural genom riken structural genomics/proteomics initiative; 1.55A {Thermus thermophilus} Length = 330 Back     alignment and structure
>3ipi_A Geranyltranstransferase; isoprene biosynthesis, helical bundle, protein structure initiative II (PSI II), structural genomics, nysgxrc; 1.90A {Methanosarcina mazei} Length = 295 Back     alignment and structure
>3lk5_A Geranylgeranyl pyrophosphate synthase; structural genomics, protein structure initiative, geranylge pyrophosphate synthase; 1.90A {Corynebacterium glutamicum} PDB: 3qqv_A* Length = 380 Back     alignment and structure
>4fp4_A Polyprenyl synthetase; isoprenoid synthesis, isoprenoid diphosphate synthase, trans; HET: GER UNL; 2.00A {Pyrobaculum calidifontis} Length = 285 Back     alignment and structure
>3oyr_A Trans-isoprenyl diphosphate synthase; isoprenyl synthase, PSI, protein structure initiative; HET: IPE; 2.00A {Caulobacter crescentus} Length = 345 Back     alignment and structure
>3mzv_A Decaprenyl diphosphate synthase; transferase, structural genomics, PSI-2, protein structure initiative; 1.90A {Rhodobacter capsulatus} Length = 341 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 Length = 367 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* Length = 362 Back     alignment and structure
>3aqb_B Component B of hexaprenyl diphosphate synthase; prenyltransferase, transferase; 2.40A {Micrococcus luteus} PDB: 3aqc_B* Length = 325 Back     alignment and structure
>3rmg_A Octaprenyl-diphosphate synthase; structural genomics, protein structure initiative, isoprene biosynthesis, transferase; 2.30A {Bacteroides thetaiotaomicron} Length = 334 Back     alignment and structure
>2azj_A Geranylgeranyl pyrophosphate synthetase; hexpps, trans-prenyltransferase; 2.40A {Sulfolobus solfataricus} PDB: 2azk_A Length = 289 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* ... Length = 374 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* ... Length = 340 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 Length = 301 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* Length = 360 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* Length = 390 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 Length = 334 Back     alignment and structure
>3tc1_A Octaprenyl pyrophosphate synthase; all alpha-helices fold, transferase; 2.00A {Helicobacter pylori} Length = 315 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 Length = 299 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* Length = 348 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query320
3ts7_A324 Geranyltranstransferase; isoprenoid synthesis, far 100.0
3lsn_A304 Geranyltranstransferase; structural genomics, prot 100.0
4f62_A317 Geranyltranstransferase; enzyme function initiativ 100.0
3pde_A309 Farnesyl-diphosphate synthase; isoprenyl diphospha 100.0
3lom_A313 Geranyltranstransferase; geranyltransferase, struc 100.0
2h8o_A335 Geranyltranstransferase; geranyltransferase,agroba 100.0
3m0g_A297 Farnesyl diphosphate synthase; structural genomics 100.0
3llw_A311 Geranyltranstransferase (ISPA); structural genomic 100.0
3p8l_A302 Geranyltranstransferase; isoprenyl synthase, struc 100.0
1rqj_A299 Geranyltranstransferase; bisphosphonate, isoprenyl 100.0
3qkc_B273 Geranyl diphosphate synthase small subunit; struct 100.0
3p8r_A302 Geranyltranstransferase; isoprenyl synthase, struc 100.0
3uca_A324 Geranyltranstransferase; isoprenoid synthesis, iso 100.0
1rtr_A301 Geranyltranstransferase; 2.50A {Staphylococcus aur 100.0
2j1p_A293 Geranylgeranyl pyrophosphate synthetase; transfera 100.0
3oyr_A345 Trans-isoprenyl diphosphate synthase; isoprenyl sy 100.0
3kra_B274 Geranyl diphosphate synthase small subunit; prenyl 100.0
3npk_A291 Geranyltranstransferase; isoprene biosynthesis, SG 100.0
3mzv_A341 Decaprenyl diphosphate synthase; transferase, stru 100.0
4dhd_A358 Polyprenyl synthetase; isoprenoid synthesis, isopr 100.0
1wy0_A342 Geranylgeranyl pyrophosphate synthetase; pyrococcu 100.0
3nf2_A352 Putative polyprenyl synthetase; isoprenyl diphosph 100.0
3rmg_A334 Octaprenyl-diphosphate synthase; structural genomi 100.0
4fp4_A285 Polyprenyl synthetase; isoprenoid synthesis, isopr 100.0
2ftz_A284 Geranyltranstransferase; TM0161, structural GE joi 100.0
3lmd_A360 Geranylgeranyl pyrophosphate synthase; isoprenyl d 100.0
3aqb_B325 Component B of hexaprenyl diphosphate synthase; pr 100.0
1wmw_A330 Geranylgeranyl diphosphate synthetase; GGPP, preny 100.0
3lk5_A380 Geranylgeranyl pyrophosphate synthase; structural 100.0
3pko_A334 Geranylgeranyl pyrophosphate synthase; isoprenyl d 100.0
3ipi_A295 Geranyltranstransferase; isoprene biosynthesis, he 100.0
3mav_A395 Farnesyl pyrophosphate synthase; PV092040, structu 100.0
2qis_A374 Farnesyl pyrophosphate synthetase; trans-prenyltra 100.0
2e8v_A340 Geranylgeranyl pyrophosphate synthetase; prenyltra 100.0
3tc1_A315 Octaprenyl pyrophosphate synthase; all alpha-helic 100.0
1v4e_A299 Octoprenyl-diphosphate synthase; trans-type prenyl 100.0
2ihi_A395 Pyrophosphate synthase; PV092040, structural genom 100.0
3dyh_A390 Farnesyl pyrophosphate synthase; protein-bisphosph 100.0
3apz_A348 Geranyl diphosphate synthase; prenyltransferase, a 100.0
1yhl_A362 Farnesyl pyrophosphate synthase; farnesyl diphosph 100.0
2q58_A368 Fragment, farnesyl pyrophosphate synthase; farnesy 100.0
1uby_A367 FPS, farnesyl diphosphate synthase; transferase, i 100.0
2q80_A301 Geranylgeranyl pyrophosphate synthetase; isoprenoi 100.0
2her_A368 Fragment, farnesyl pyrophosphate synthase; farnesy 100.0
2azj_A289 Geranylgeranyl pyrophosphate synthetase; hexpps, t 100.0
4hd1_A294 Squalene synthase HPNC; MCSG, structural genomics, 81.62
>3ts7_A Geranyltranstransferase; isoprenoid synthesis, farnesyl diphosphate synthase; 1.94A {Methylococcus capsulatus} Back     alignment and structure
Probab=100.00  E-value=2.1e-59  Score=445.70  Aligned_cols=246  Identities=20%  Similarity=0.265  Sum_probs=210.5

Q ss_pred             cCCCcchHHHHHHHHHHHHHHHHHHhhccC--CcccHHhHHHhhccCCCCcchHHHHHHHHHHhCCChHHHhhHHHHHHH
Q 020845           35 AMSTPNKNKSYWTSVHEDIGAHLRQAVVVK--EPVEVYEPMRHFVFAAPVNMAPALCVAACELVGGHREQAIVAAAALHV  112 (320)
Q Consensus        35 ~~~~~~~~~~~~~~~~~~ie~~L~~~i~~~--~~~~l~e~~~y~~~~gGKrlRp~L~l~~~~~~g~~~~~~~~lAaavEl  112 (320)
                      .+++.++|+.|++...+.||+.|.+.++..  .+..+.++++|.+..||||+||+||+++++++|++.+.+.++|++|||
T Consensus         2 ~~~~~~~~~~~l~~~~~~ve~~L~~~l~~~~~~~~~l~~a~~y~~~~gGKrlRP~L~l~~~~~~g~~~~~~~~~A~avEl   81 (324)
T 3ts7_A            2 VMNPERSLSDFMRSSQERVERALDARLPAADRMPERLHQAMRYSVLGGGKRMRPLLTYATGQTIGVAADLLDGPACAVEF   81 (324)
T ss_dssp             ----CCCHHHHHHHHHHHHHHHHHHTSCCTTSSSHHHHHHHHHHHHSCCCCHHHHHHHHHHHHHTCCGGGTHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHHHHHHHHHHHhhhccCCcHHHHHHHHHHHhCCCCcHHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            356677899999999999999999998753  356799999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhCCCCCCCCCCCCCCCCcccccCChhHHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHhchhh
Q 020845          113 MHAASFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQG  192 (320)
Q Consensus       113 iH~asLIHDDlPi~D~Ds~~RRG~pt~h~~~G~~~AIl~GD~L~~~a~~ll~~~~~~~~~~~~~~~~~i~~~~~a~g~~~  192 (320)
                      ||+|||||||||+||+ +++|||+||+|++||+++|||+||+|++.||+++++...+ ..++....+++..++++.|..+
T Consensus        82 iH~aSLIHDDip~mD~-~~~RRG~pt~h~~~G~~~AIlaGD~L~~~Af~~l~~~~~~-~~~~~~~~~~i~~la~a~g~~~  159 (324)
T 3ts7_A           82 IHVYSLIHDDLPAMDD-DDLRRGKPTCHKAYDEATAILAGDGLQALAFHVLAQDPSI-AVPAENRIAMIETLAKASGPAG  159 (324)
T ss_dssp             HHHHHHHHHTSTTTTC-CSEETTEECHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTS-CCCHHHHHHHHHHHHHHHSTTT
T ss_pred             HHHHHHhhcCcccccC-CCccCCCCchhhhcChHHHHHHHHHHHHHHHHHHHhcccc-CCCHHHHHHHHHHHHHHHhhhH
Confidence            9999999999999999 7889999999999999999999999999999999987421 1235566788888888877789


Q ss_pred             hhHHHHHHhhcccCCCcccccCCCCCHHHHHHHHHhcHHHHHHHHHHHHHHhcC-CCHHHHHHHHHHHHHHHHHHHHHhh
Q 020845          193 VVEGQYNELQCSQCDDDDRKLNGITDVEMTYETYKKKEGRLHACGAACGAILGG-GSEKEIELLRRYGFYVGMIQGIVSR  271 (320)
Q Consensus       193 ~~~GQ~lDl~~~~~~~~~~~~~~~~~~e~y~~ii~~KTg~Lf~~a~~~Gailag-~~~~~~~~l~~~G~~lG~afQi~DD  271 (320)
                      |+.||.+|+.+...         ..++++|.+|+++|||+||++||++|++++| ++++..+.+++||.++|+||||+||
T Consensus       160 m~~GQ~lDl~~~~~---------~~t~~~y~~i~~~KTg~L~~~a~~~Ga~lag~a~~~~~~~l~~~g~~lGlAFQI~DD  230 (324)
T 3ts7_A          160 MVGGQAIDLASVGK---------KLDLPGLENMHIRKTGALIRASVRLACLARPGLPAEQFDRLDHYAKCIGLAFQIQDD  230 (324)
T ss_dssp             HHHHHHHHHHTTTC---------CCCHHHHHHHHHHHTHHHHHHHHHHHHTTSTTCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhHHHHHHccCC---------CCCHHHHHHHHHhhHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999998762         3689999999999999999999999999999 8999999999999999999999999


Q ss_pred             hcCCchhHHHh-hhHHHHHHH
Q 020845          272 RLGPTEEIEEL-KKLAFKLRE  291 (320)
Q Consensus       272 ~lD~~~~~~~~-k~~~~Dl~e  291 (320)
                      ++|++++++++ |++|+|++|
T Consensus       231 iLD~~~d~~~~GK~~g~Dl~e  251 (324)
T 3ts7_A          231 ILDEESDTQTLGKTRGKDRDH  251 (324)
T ss_dssp             HHHHTCC--------------
T ss_pred             HHhccCCHHHhCCCccchhhc
Confidence            99999999888 999999976
>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
>4f62_A Geranyltranstransferase; enzyme function initiative, structural genomics; 2.10A {Marinomonas SP} 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
>3lom_A Geranyltranstransferase; geranyltransferase, structural genomics, PSI, protein structure initiative, nysgrc; 2.30A {Legionella pneumophila subsp} 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
>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
>3llw_A Geranyltranstransferase (ISPA); structural genomics, PSI, protein structure initiative, nysgrc; 2.30A {Helicobacter pylori} PDB: 3q1o_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
>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
>3qkc_B Geranyl diphosphate synthase small subunit; structural genomics, protein structure initiative, NEW YORK structural genomix research consortium; 2.20A {Antirrhinum majus} 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
>3uca_A Geranyltranstransferase; isoprenoid synthesis, isoprenoid diphosphate synthase; 2.00A {Clostridium perfringens} Back     alignment and structure
>1rtr_A Geranyltranstransferase; 2.50A {Staphylococcus aureus} SCOP: a.128.1.1 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
>3oyr_A Trans-isoprenyl diphosphate synthase; isoprenyl synthase, PSI, protein structure initiative; HET: IPE; 2.00A {Caulobacter crescentus} Back     alignment and structure
>3kra_B Geranyl diphosphate synthase small subunit; prenyltransferase, isoprene biosynthesis, isoprenyl pyrophosphate synthase, transferase; 1.90A {Mentha x piperita} PDB: 3krc_B* 3krf_B* 3kro_B* 3krp_B* 3oab_B* 3oac_B* Back     alignment and structure
>3npk_A Geranyltranstransferase; isoprene biosynthesis, SGX, structural genomics protein structure initiative; 1.50A {Campylobacter jejuni} 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
>4dhd_A Polyprenyl synthetase; isoprenoid synthesis, isoprenoid diphosphate synthase, trans; 1.65A {Pyrobaculum calidifontis} PDB: 4gp1_A* 4gp2_A* 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
>3nf2_A Putative polyprenyl synthetase; isoprenyl diphosphate synthase, structural genomics, PSI, PR structure initiative, nysgrc; 2.20A {Streptomyces coelicolor} 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
>4fp4_A Polyprenyl synthetase; isoprenoid synthesis, isoprenoid diphosphate synthase, trans; HET: GER UNL; 2.00A {Pyrobaculum calidifontis} 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
>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
>3aqb_B Component B of hexaprenyl diphosphate synthase; prenyltransferase, transferase; 2.40A {Micrococcus luteus} PDB: 3aqc_B* 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
>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
>3ipi_A Geranyltranstransferase; isoprene biosynthesis, helical bundle, protein structure initiative II (PSI II), structural genomics, nysgxrc; 1.90A {Methanosarcina mazei} 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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>2azj_A Geranylgeranyl pyrophosphate synthetase; hexpps, trans-prenyltransferase; 2.40A {Sulfolobus solfataricus} PDB: 2azk_A Back     alignment and structure
>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

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 320
d1rqja_299 a.128.1.1 (A:) Farnesyl diphosphate synthase (gera 1e-13
d1rtra_290 a.128.1.1 (A:) Farnesyl diphosphate synthase (gera 3e-12
d2q80a1291 a.128.1.1 (A:6-296) Geranylgeranyl pyrophosphate s 4e-09
d1v4ea_280 a.128.1.1 (A:) Octoprenyl-diphosphate synthase {Th 1e-05
d1fpsa_348 a.128.1.1 (A:) Farnesyl diphosphate synthase (gera 4e-05
>d1rqja_ a.128.1.1 (A:) Farnesyl diphosphate synthase (geranyltranstransferase) {Escherichia coli [TaxId: 562]} Length = 299 Back     information, alignment and structure

class: All alpha proteins
fold: Terpenoid synthases
superfamily: Terpenoid synthases
family: Isoprenyl diphosphate synthases
domain: Farnesyl diphosphate synthase (geranyltranstransferase)
species: Escherichia coli [TaxId: 562]

 Score = 67.7 bits (164), Expect = 1e-13
 Identities = 44/231 (19%), Positives = 81/231 (35%), Gaps = 12/231 (5%)

Query: 43  KSYWTSVHEDIGAHLRQAV--VVKEPVEVYEPMRHFVFAAPVNMAPALCVAACELVGGHR 100
                +  +     L + +  +  +   V E M++        + P L  A   + G   
Sbjct: 4   PQQLEACVKQANQALSRFIAPLPFQNTPVVETMQYGALLGGKRLRPFLVYATGHMFGVST 63

Query: 101 EQAIVAAAALHVMHAASFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGL 160
                 AAA+  +HA S IH++LP  D   L  +  PT +  F     +L  DA+     
Sbjct: 64  NTLDAPAAAVECIHAYSLIHDDLPAMDDDDL-RRGLPTCHVKFGEANAILAGDALQTLAF 122

Query: 161 ELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVE 220
            +L+ +D P  ++    + ++ E+  A G  G+  GQ  +L           L  I    
Sbjct: 123 SILSDADMPEVSDR-DRISMISELASASGIAGMCGGQALDLDAEGKHVPLDALERI---- 177

Query: 221 MTYETYKKKEGRLHACGAACGAILGGGSEKEIELLRRYGFYVGMIQGIVSR 271
                  K    + A         G    + + +L +Y   +G+   +   
Sbjct: 178 ----HRHKTGALIRAAVRLGALSAGDKGRRALPVLDKYAESIGLAFQVQDD 224
>d1rtra_ a.128.1.1 (A:) Farnesyl diphosphate synthase (geranyltranstransferase) {Staphylococcus aureus [TaxId: 1280]} Length = 290 Back     information, alignment and structure
>d2q80a1 a.128.1.1 (A:6-296) Geranylgeranyl pyrophosphate synthetase {Human (Homo sapiens) [TaxId: 9606]} Length = 291 Back     information, alignment and structure
>d1v4ea_ a.128.1.1 (A:) Octoprenyl-diphosphate synthase {Thermotoga maritima [TaxId: 2336]} Length = 280 Back     information, alignment and structure
>d1fpsa_ a.128.1.1 (A:) Farnesyl diphosphate synthase (geranyltranstransferase) {Chicken (Gallus gallus) [TaxId: 9031]} Length = 348 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query320
d1rqja_299 Farnesyl diphosphate synthase (geranyltranstransfe 100.0
d1rtra_290 Farnesyl diphosphate synthase (geranyltranstransfe 100.0
d2q80a1291 Geranylgeranyl pyrophosphate synthetase {Human (Ho 100.0
d1fpsa_348 Farnesyl diphosphate synthase (geranyltranstransfe 100.0
d1v4ea_280 Octoprenyl-diphosphate synthase {Thermotoga mariti 100.0
>d1rqja_ a.128.1.1 (A:) Farnesyl diphosphate synthase (geranyltranstransferase) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: All alpha proteins
fold: Terpenoid synthases
superfamily: Terpenoid synthases
family: Isoprenyl diphosphate synthases
domain: Farnesyl diphosphate synthase (geranyltranstransferase)
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=2.9e-54  Score=404.76  Aligned_cols=240  Identities=20%  Similarity=0.275  Sum_probs=213.4

Q ss_pred             hHHHHHHHHHHHHHHHHHHhhccC--CcccHHhHHHhhccCCCCcchHHHHHHHHHHhCCChHHHhhHHHHHHHHHHHHH
Q 020845           41 KNKSYWTSVHEDIGAHLRQAVVVK--EPVEVYEPMRHFVFAAPVNMAPALCVAACELVGGHREQAIVAAAALHVMHAASF  118 (320)
Q Consensus        41 ~~~~~~~~~~~~ie~~L~~~i~~~--~~~~l~e~~~y~~~~gGKrlRp~L~l~~~~~~g~~~~~~~~lAaavEliH~asL  118 (320)
                      +|.++++...++|++.|++.++..  .+..+.++++|.+.+||||+||.|++++++++|++.+.+.++|+|+|++|+|||
T Consensus         2 ~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~l~e~~~y~~~~gGKrlRp~l~~~~~~~~g~~~~~~~~~A~aiEllH~asL   81 (299)
T d1rqja_           2 DFPQQLEACVKQANQALSRFIAPLPFQNTPVVETMQYGALLGGKRLRPFLVYATGHMFGVSTNTLDAPAAAVECIHAYSL   81 (299)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHTTSSSTTSHHHHHHHHHHHSSCCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHHHhhCCcccHHHHHHHHHHHHcCCcchhHHHHHHHHHHHHHHHH
Confidence            478999999999999999988643  234599999999999999999999999999999999999999999999999999


Q ss_pred             HHhCCCCCCCCCCCCCCCCcccccCChhHHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHhchhhhhHHHH
Q 020845          119 IHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQY  198 (320)
Q Consensus       119 IHDDlPi~D~Ds~~RRG~pt~h~~~G~~~AIl~GD~L~~~a~~ll~~~~~~~~~~~~~~~~~i~~~~~a~g~~~~~~GQ~  198 (320)
                      ||||||.+|+ +++|||+||+|++||+++|||+||+|++.+++++++...+ .......++++.+++.+.|..++++||.
T Consensus        82 iHDDI~d~d~-~~~RRG~pt~h~~~G~~~AIl~Gd~l~~~a~~~l~~~~~~-~~~~~~~~~~~~~l~~~~~~~~l~~GQ~  159 (299)
T d1rqja_          82 IHDDLPAMDD-DDLRRGLPTCHVKFGEANAILAGDALQTLAFSILSDADMP-EVSDRDRISMISELASASGIAGMCGGQA  159 (299)
T ss_dssp             HHHTSTTTTC-CCEETTEECHHHHHCHHHHHHHHHHHHHHHHHHHHHSCCT-TCCHHHHHHHHHHHHHHHSTTTHHHHHH
T ss_pred             HHccchhhhh-hhcccccccceeeeCcchhhhhcchHHHHHHHHHHhCCCc-cccHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence            9999655677 6789999999999999999999999999999999998654 2345677788888888877788999999


Q ss_pred             HHhhcccCCCcccccCCCCCHHHHHHHHHhcHHHHHHHHHHHHHHhcC-CCHHHHHHHHHHHHHHHHHHHHHhhhcCCch
Q 020845          199 NELQCSQCDDDDRKLNGITDVEMTYETYKKKEGRLHACGAACGAILGG-GSEKEIELLRRYGFYVGMIQGIVSRRLGPTE  277 (320)
Q Consensus       199 lDl~~~~~~~~~~~~~~~~~~e~y~~ii~~KTg~Lf~~a~~~Gailag-~~~~~~~~l~~~G~~lG~afQi~DD~lD~~~  277 (320)
                      +|+.+...         ..++++|..|+.+|||+||.+++.+|+++.+ .+.+..+.+++||.++|++|||+||++|+++
T Consensus       160 ldl~~~~~---------~~~~~~~~~i~~~KT~~l~~~~~~~~a~~~~~~~~~~~~~l~~~g~~lGiaFQi~DD~lD~~~  230 (299)
T d1rqja_         160 LDLDAEGK---------HVPLDALERIHRHKTGALIRAAVRLGALSAGDKGRRALPVLDKYAESIGLAFQVQDDILDVVG  230 (299)
T ss_dssp             HHHHTTTT---------CCCHHHHHHHHHHHTHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHhccC---------cccHHHHHHHHHHHHhhHHHHHHHhhhhhhcchhhHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            99987642         3688999999999999999999999887654 5566678999999999999999999999999


Q ss_pred             hHHHh-hhHHHHHHH
Q 020845          278 EIEEL-KKLAFKLRE  291 (320)
Q Consensus       278 ~~~~~-k~~~~Dl~e  291 (320)
                      +++++ |+.++||+|
T Consensus       231 ~~~~~GK~~g~Dl~e  245 (299)
T d1rqja_         231 DTATLGKRQGADQQL  245 (299)
T ss_dssp             CHHHHSSCTTHHHHH
T ss_pred             chhhcCCchhhHHHC
Confidence            99988 999999998
>d1rtra_ a.128.1.1 (A:) Farnesyl diphosphate synthase (geranyltranstransferase) {Staphylococcus aureus [TaxId: 1280]} 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