Psyllid ID: psy3887

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
MENCPVGSRFRKGGCVHSPHRVDAVNRRGFVEAVYGFSHRLCLRVDTALQSDKTFEKYRERILEPNASLLRSGDLAKVHISIVINRPTTIMRLVRTEDSKKKLVALTWVMFQSHRAGKMRTDGIFLFLLRLLDPEINRFKKYRRPLSGIALSQIALKVGLSLYESSLLLSRPLSGIALSQIAEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRTVGRSVGYPTIRTSKGGASSQVQTYAVPGNSRRV
ccccccccccccccccccccccccccccHHHHHHHccccHHHHHHHHccccHHHHHHHHHHHccccHHHHcccccccccccHHHHHHHHHHHccccccHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHcccHHHccccccccccccccHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHccccEEEEcccccccHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccc
ccccccccccccccccccccccHHEcccccEEEEEccccEEEEEEccHccccHHHHHHHHHHHcccHHHHHHcHHHHHHHHHHHcccHHHHHccccccHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHcccccEEEEEcccccccHHHHHHHHHHccccHHHHHHHHHHHcccccccccEEcccccccc
mencpvgsrfrkggcvhsphrvdavnrRGFVEAVYGFSHRLCLRVDTALQSDKTFEKYRERILepnasllrsgdlakVHISIVINRPTTIMRLVRTEDSKKKLVALTWVMFQshragkmrtDGIFLFLLRLLDPEInrfkkyrrplsgIALSQIALKVGLSLYESSlllsrplsgIALSQIAEQLLELHRGqgmeiywrdnytcpseeeyrTMTIRtvgrsvgyptirtskggassqvqtyavpgnsrrv
mencpvgsrfrkggcvhsphrvdavnRRGFVEAVYGFSHRLCLRVDTALQSDKTFEKYRERILepnasllrsgdlakVHISivinrpttimrlVRTEDSKKKLVALTWVMfqshragkmrtDGIFLFLLRLLDPEINRFKKYRRPLSGIALSQIALKVGLSLYESSLLLSRPLSGIALSQIAEQLLELHRGQGMEIYWRDNYTCPSEEEYRTmtirtvgrsvGYPTirtskggassqvqtyavpgnsrrv
MENCPVGSRFRKGGCVHSPHRVDAVNRRGFVEAVYGFSHRLCLRVDTALQSDKTFEKYRERILEPNASLLRSGDLAKVHISIVINRPTTIMRLVRTEDSKKKLVALTWVMFQSHRAGKMRTDGIFLFLLRLLDPEINRFKKYRRPLSGIALSQIALKVGlslyesslllsrplsGIALSQIAEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRTVGRSVGYPTIRTSKGGASSQVQTYAVPGNSRRV
************GGCVHSPHRVDAVNRRGFVEAVYGFSHRLCLRVDTALQSDKTFEKYRERILEPNASLLRSGDLAKVHISIVINRPTTIMRLVRTEDSKKKLVALTWVMFQSHRAGKMRTDGIFLFLLRLLDPEINRFKKYRRPLSGIALSQIALKVGLSLYESSLLLSRPLSGIALSQIAEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRTVGRSVGYPTI***********************
********RFRKGGCVHSPHRVDAVNRRGFVEAVYGFSHRLCLRVD**************RILEPNAS*LR*****KVHISIVINRPTTIMRLVRTEDSKKKLVALTWVMFQSHRAGKMRTDGIFLFLLRLLDPEINRFKKYRRPLSGIALSQIALKVGLSLYESSLLLSRPLSGIALSQIAEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRTVGRSVGYPTIRTSKGGA***V*****PG*****
********RFRKGGCVHSPHRVDAVNRRGFVEAVYGFSHRLCLRVDTALQSDKTFEKYRERILEPNASLLRSGDLAKVHISIVINRPTTIMRLVRTEDSKKKLVALTWVMFQSHRAGKMRTDGIFLFLLRLLDPEINRFKKYRRPLSGIALSQIALKVGLSLYESSLLLSRPLSGIALSQIAEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRTVGRSVGYPTIRTSKGGASSQVQTYA********
********************RVDAVNRRGFVEAVYGFSHRLCLRVDTALQSDKTFEKYRERILEPNASLLRSGDLAKVHISIVINRPTTIMRLVRTEDSKKKLVALTWVMFQSHRAGKMRTDGIFLFLLRLLDPEINRFKKYRRPLSGIALSQIALKVGLSLYESSLLLSRPLSGIALSQIAEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRTVGRSVGYPTIRTSKGGASSQVQTY*********
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MENCPVGSRFRKGGCVHSPHRVDAVNRRGFVEAVYGFSHRLCLRVDTALQSDKTFEKYRERILEPNASLLRSGDLAKVHISIVINRPTTIMRLVRTEDSKKKLVALTWVMFQSHRAGKMRTDGIFLFLLRLLDPEINRFKKYRRPLSGIALSQIALKVGLSLYESSLLLSRPLSGIALSQIAEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRTVGRSVGYPTIRTSKGGASSQVQTYAVPGNSRRV
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 ?
Query250 2.2.26 [Sep-21-2011]
P56966 300 Geranylgeranyl pyrophosph yes N/A 0.228 0.19 0.516 2e-11
O95749 300 Geranylgeranyl pyrophosph yes N/A 0.228 0.19 0.516 2e-11
Q6F596 300 Geranylgeranyl pyrophosph yes N/A 0.228 0.19 0.5 2e-10
Q9WTN0 300 Geranylgeranyl pyrophosph yes N/A 0.228 0.19 0.5 2e-10
P24322 433 Geranylgeranyl pyrophosph N/A N/A 0.172 0.099 0.511 5e-08
Q9P885 303 Geranylgeranyl pyrophosph N/A N/A 0.132 0.108 0.636 2e-07
Q758K0 320 Geranylgeranyl pyrophosph yes N/A 0.188 0.146 0.458 1e-06
B2DBE9 424 Geranylgeranyl pyrophosph N/A N/A 0.172 0.101 0.488 2e-06
Q92236 418 Geranylgeranyl pyrophosph N/A N/A 0.156 0.093 0.465 1e-05
Q54BK1 303 Geranylgeranyl pyrophosph yes N/A 0.152 0.125 0.526 2e-05
>sp|P56966|GGPPS_BOVIN Geranylgeranyl pyrophosphate synthase OS=Bos taurus GN=GGPS1 PE=1 SV=2 Back     alignment and function desciption
 Score = 69.7 bits (169), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/60 (51%), Positives = 40/60 (66%), Gaps = 3/60 (5%)

Query: 164 ESSLLLSRPLSGIALSQIAEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRTVGRSVG 223
           E  L L+ P    A+     QLLELH+GQG++IYWRDNYTCP+EEEY+ M ++  G   G
Sbjct: 101 EKVLTLNHP---DAVKLFTRQLLELHQGQGLDIYWRDNYTCPTEEEYKAMVLQKTGGLFG 157
Catalyzes the trans-addition of the three molecules of IPP onto DMAPP to form geranylgeranyl pyrophosphate, an important precursor of carotenoids and geranylated proteins.
Bos taurus (taxid: 9913)
EC: 2EC: .EC: 5EC: .EC: 1EC: .EC: 1EC: 0
>sp|O95749|GGPPS_HUMAN Geranylgeranyl pyrophosphate synthase OS=Homo sapiens GN=GGPS1 PE=1 SV=1 Back     alignment and function description
>sp|Q6F596|GGPPS_RAT Geranylgeranyl pyrophosphate synthase OS=Rattus norvegicus GN=Ggps1 PE=2 SV=1 Back     alignment and function description
>sp|Q9WTN0|GGPPS_MOUSE Geranylgeranyl pyrophosphate synthase OS=Mus musculus GN=Ggps1 PE=2 SV=1 Back     alignment and function description
>sp|P24322|GGPPS_NEUCR Geranylgeranyl pyrophosphate synthase OS=Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) GN=al-3 PE=2 SV=2 Back     alignment and function description
>sp|Q9P885|GGPPS_MUCCL Geranylgeranyl pyrophosphate synthase OS=Mucor circinelloides f. lusitanicus GN=carG PE=1 SV=1 Back     alignment and function description
>sp|Q758K0|GGPPS_ASHGO Geranylgeranyl pyrophosphate synthase OS=Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) GN=BTS1 PE=3 SV=1 Back     alignment and function description
>sp|B2DBE9|GGS4_PHOAM Geranylgeranyl pyrophosphate synthase D OS=Phomopsis amygdali GN=GGS-D PE=1 SV=1 Back     alignment and function description
>sp|Q92236|GGPPS_GIBFU Geranylgeranyl pyrophosphate synthase OS=Gibberella fujikuroi GN=GGS PE=3 SV=1 Back     alignment and function description
>sp|Q54BK1|GGPPS_DICDI Geranylgeranyl pyrophosphate synthase OS=Dictyostelium discoideum GN=ggps1 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 ?
Query250
328714372327 PREDICTED: geranylgeranyl pyrophosphate 0.264 0.201 0.550 9e-13
156554759314 PREDICTED: geranylgeranyl pyrophosphate 0.148 0.117 0.864 9e-12
91076666307 PREDICTED: similar to AGAP006894-PA [Tri 0.172 0.140 0.697 4e-11
225709438303 Geranylgeranyl pyrophosphate synthetase 0.156 0.128 0.769 4e-11
158286675324 AGAP006894-PA [Anopheles gambiae str. PE 0.152 0.117 0.789 5e-11
326435055328 quemao protein [Salpingoeca sp. ATCC 508 0.536 0.408 0.301 5e-11
312376381299 hypothetical protein AND_12794 [Anophele 0.148 0.123 0.783 8e-11
322797846246 hypothetical protein SINV_16081 [Solenop 0.148 0.150 0.756 1e-10
383855382317 PREDICTED: geranylgeranyl pyrophosphate 0.152 0.119 0.789 1e-10
321466396298 hypothetical protein DAPPUDRAFT_305827 [ 0.188 0.157 0.659 1e-10
>gi|328714372|ref|XP_001947385.2| PREDICTED: geranylgeranyl pyrophosphate synthase-like [Acyrthosiphon pisum] Back     alignment and taxonomy information
 Score = 79.7 bits (195), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 38/69 (55%), Positives = 48/69 (69%), Gaps = 3/69 (4%)

Query: 154 IALKVGLSLYESSLLLSRPLS---GIALSQIAEQLLELHRGQGMEIYWRDNYTCPSEEEY 210
           +A  +  + Y S + L R LS    +A +   EQ+LELHRGQGMEIYWRDNYTCP+E+EY
Sbjct: 108 VASTINAANYMSFVALERTLSLGHPMATTVYTEQVLELHRGQGMEIYWRDNYTCPTEDEY 167

Query: 211 RTMTIRTVG 219
           + MTIR  G
Sbjct: 168 KKMTIRKTG 176

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|156554759|ref|XP_001605679.1| PREDICTED: geranylgeranyl pyrophosphate synthase-like [Nasonia vitripennis] Back     alignment and taxonomy information
>gi|91076666|ref|XP_971444.1| PREDICTED: similar to AGAP006894-PA [Tribolium castaneum] gi|270002646|gb|EEZ99093.1| hypothetical protein TcasGA2_TC004978 [Tribolium castaneum] Back     alignment and taxonomy information
>gi|225709438|gb|ACO10565.1| Geranylgeranyl pyrophosphate synthetase [Caligus rogercresseyi] Back     alignment and taxonomy information
>gi|158286675|ref|XP_308860.3| AGAP006894-PA [Anopheles gambiae str. PEST] gi|157020582|gb|EAA03964.3| AGAP006894-PA [Anopheles gambiae str. PEST] Back     alignment and taxonomy information
>gi|326435055|gb|EGD80625.1| quemao protein [Salpingoeca sp. ATCC 50818] Back     alignment and taxonomy information
>gi|312376381|gb|EFR23484.1| hypothetical protein AND_12794 [Anopheles darlingi] Back     alignment and taxonomy information
>gi|322797846|gb|EFZ19754.1| hypothetical protein SINV_16081 [Solenopsis invicta] Back     alignment and taxonomy information
>gi|383855382|ref|XP_003703192.1| PREDICTED: geranylgeranyl pyrophosphate synthase-like [Megachile rotundata] Back     alignment and taxonomy information
>gi|321466396|gb|EFX77392.1| hypothetical protein DAPPUDRAFT_305827 [Daphnia pulex] 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 ?
Query250
UNIPROTKB|C9J6G3230 GGPS1 "Geranylgeranyl pyrophos 0.188 0.204 0.574 3.4e-11
FB|FBgn0019662 338 qm "quemao" [Drosophila melano 0.148 0.109 0.756 4e-11
UNIPROTKB|C9J7M1242 GGPS1 "Geranylgeranyl pyrophos 0.188 0.194 0.574 7.1e-11
UNIPROTKB|A8MVQ8 246 GGPS1 "Geranylgeranyl diphosph 0.188 0.191 0.574 8.3e-11
RGD|1359680 300 Ggps1 "geranylgeranyl diphosph 0.188 0.156 0.553 1.7e-10
UNIPROTKB|P56966 300 GGPS1 "Geranylgeranyl pyrophos 0.188 0.156 0.574 2.5e-10
UNIPROTKB|E2R3P8 300 GGPS1 "Uncharacterized protein 0.188 0.156 0.574 2.5e-10
UNIPROTKB|O95749 300 GGPS1 "Geranylgeranyl pyrophos 0.188 0.156 0.574 2.5e-10
UNIPROTKB|F1RGX0 300 GGPS1 "Uncharacterized protein 0.188 0.156 0.574 2.5e-10
MGI|MGI:1341724 300 Ggps1 "geranylgeranyl diphosph 0.188 0.156 0.553 2.7e-10
UNIPROTKB|C9J6G3 GGPS1 "Geranylgeranyl pyrophosphate synthase" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
 Score = 161 (61.7 bits), Expect = 3.4e-11, P = 3.4e-11
 Identities = 27/47 (57%), Positives = 35/47 (74%)

Query:   177 ALSQIAEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRTVGRSVG 223
             A+     QLLELH+GQG++IYWRDNYTCP+EEEY+ M ++  G   G
Sbjct:   111 AVKLFTRQLLELHQGQGLDIYWRDNYTCPTEEEYKAMVLQKTGGLFG 157
GO:0008299 "isoprenoid biosynthetic process" evidence=IEA
GO:0004337 "geranyltranstransferase activity" evidence=IEA
FB|FBgn0019662 qm "quemao" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
UNIPROTKB|C9J7M1 GGPS1 "Geranylgeranyl pyrophosphate synthase" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|A8MVQ8 GGPS1 "Geranylgeranyl diphosphate synthase 1, isoform CRA_b" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
RGD|1359680 Ggps1 "geranylgeranyl diphosphate synthase 1" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|P56966 GGPS1 "Geranylgeranyl pyrophosphate synthase" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|E2R3P8 GGPS1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|O95749 GGPS1 "Geranylgeranyl pyrophosphate synthase" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|F1RGX0 GGPS1 "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
MGI|MGI:1341724 Ggps1 "geranylgeranyl diphosphate synthase 1" [Mus musculus (taxid:10090)] 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 EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query250
cd00385243 cd00385, Isoprenoid_Biosyn_C1, Isoprenoid Biosynth 2e-04
cd00867236 cd00867, Trans_IPPS, Trans-Isoprenyl Diphosphate S 2e-04
cd00685259 cd00685, Trans_IPPS_HT, Trans-Isoprenyl Diphosphat 0.001
>gnl|CDD|173830 cd00385, Isoprenoid_Biosyn_C1, Isoprenoid Biosynthesis enzymes, Class 1 Back     alignment and domain information 
 Score = 41.3 bits (97), Expect = 2e-04
 Identities = 25/72 (34%), Positives = 35/72 (48%), Gaps = 2/72 (2%)

Query: 154 IALKVG-LSLYESSLLLSRPLSGIALSQIAEQLLELHRGQGMEIYWRDNYTCPSEEEYRT 212
            A+  G L L ++   L+R  S  AL  +AE LL+L  GQ +++ WR  Y  P+ EEY  
Sbjct: 56  EAILAGDLLLADAFEELAREGSPEALEILAEALLDLLEGQLLDLKWRREY-VPTLEEYLE 114

Query: 213 MTIRTVGRSVGY 224
                    VG 
Sbjct: 115 YCRYKTAGLVGA 126

Superfamily of trans-isoprenyl diphosphate synthases (IPPS) and class I terpene cyclases which either synthesis geranyl/farnesyl diphosphates (GPP/FPP) or longer chained products from isoprene precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), or use geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate as substrate. These enzymes produce a myriad of precursors for such end products as steroids, cholesterol, sesquiterpenes, heme, carotenoids, retinoids, and diterpenes; and are widely distributed among archaea, bacteria, and eukaryota.The enzymes in this superfamily share the same 'isoprenoid synthase fold' and include several subgroups. The head-to-tail (HT) IPPS catalyze the successive 1'-4 condensation of the 5-carbon IPP to the growing isoprene chain to form linear, all-trans, C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid diphosphates. Cyclic monoterpenes, diterpenes, and sesquiterpenes, are formed from their respective linear isoprenoid diphosphates by class I terpene cyclases. The head-to-head (HH) IPPS catalyze the successive 1'-1 condensation of 2 farnesyl or 2 geranylgeranyl isoprenoid diphosphates. Cyclization of these 30- and 40-carbon linear forms are catalyzed by class II cyclases. Both the isoprenoid chain elongation reactions and the class I terpene cyclization reactions proceed via electrophilic alkylations in which a new carbon-carbon single bond is generated through interaction between a highly reactive electron-deficient allylic carbocation and an electron-rich carbon-carbon double bond. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions located on opposite walls. These residues mediate binding of prenyl phosphates via bridging Mg2+ ions, inducing proposed conformational changes that close the active site to solvent, stabilizing reactive carbocation intermediates. Generally, the enzymes in this family exhibit an all-trans reaction pathway, an exception, is the cis-trans terpene cyclase, trichodiene synthase. Mechanistically and structurally distinct, class II terpene cyclases and cis-IPPS are not included in this CD. Length = 243
>gnl|CDD|173836 cd00867, Trans_IPPS, Trans-Isoprenyl Diphosphate Synthases Back     alignment and domain information
>gnl|CDD|173833 cd00685, Trans_IPPS_HT, Trans-Isoprenyl Diphosphate Synthases, head-to-tail Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 250
KOG0777|consensus 322 100.0
TIGR02748 319 GerC3_HepT heptaprenyl diphosphate synthase compon 100.0
PRK10888 323 octaprenyl diphosphate synthase; Provisional 100.0
COG0142 322 IspA Geranylgeranyl pyrophosphate synthase [Coenzy 100.0
PRK10581299 geranyltranstransferase; Provisional 99.97
cd00685259 Trans_IPPS_HT Trans-Isoprenyl Diphosphate Synthase 99.97
TIGR02749 322 prenyl_cyano solanesyl diphosphate synthase. Membe 99.97
PLN02890 422 geranyl diphosphate synthase 99.97
CHL00151 323 preA prenyl transferase; Reviewed 99.97
PLN02857 416 octaprenyl-diphosphate synthase 99.97
PF00348260 polyprenyl_synt: Polyprenyl synthetase; InterPro: 99.97
KOG0776|consensus 384 99.91
cd00867236 Trans_IPPS Trans-Isoprenyl Diphosphate Synthases. 99.88
cd00385243 Isoprenoid_Biosyn_C1 Isoprenoid Biosynthesis enzym 99.41
KOG0711|consensus 347 98.66
PF07307212 HEPPP_synt_1: Heptaprenyl diphosphate synthase (HE 96.57
cd00868284 Terpene_cyclase_C1 Terpene cyclases, Class 1. Terp 81.08
>KOG0777|consensus Back     alignment and domain information 
Probab=100.00  E-value=7.3e-39  Score=288.51  Aligned_cols=161  Identities=27%  Similarity=0.441  Sum_probs=152.8

Q ss_pred             HHHHhcc-CcchhhhhhhHHhHHHHHhc-CCCchHHHHHHHhcCcccccccccCChhHHHHHHHHHHHHhhccccccccc
Q psy3887          45 VDTALQS-DKTFEKYRERILEPNASLLR-SGDLAKVHISIVINRPTTIMRLVRTEDSKKKLVALTWVMFQSHRAGKMRTD  122 (250)
Q Consensus        45 v~~~l~~-~~~~~~~~~~l~~p~~yll~-~GKr~Rp~l~~l~~~~~~~~~~~~~~~~~~~~iA~~vE~lH~~~AS~~~~~  122 (250)
                      |++.+.. ..|.+..++.+++|+.|++. +||.+|..++.++|+      |+..|.+++..+..++||+||  +|     
T Consensus         5 i~~~~~~d~~tq~~~~~ill~Py~yilq~PGKqfR~~L~~afNh------wl~~P~dkLaii~~ivemLHN--sS-----   71 (322)
T KOG0777|consen    5 IDELINNDPVTQSQNESILLKPYNYILQKPGKQFRLNLIVAFNH------WLNLPKDKLAIISQIVEMLHN--SS-----   71 (322)
T ss_pred             HHHHhhcCcchHHHHHHHHhchHHHHHhCchHHHHHHHHHHHHH------HHhCCHHHHHHHHHHHHHHhc--cc-----
Confidence            4555543 46777888999999999999 999999999999999      999999999999999999999  99     


Q ss_pred             hhhhhhhhccccccccCCCCCCCC------CCchHHH-HHHHHHHHHHHHHHccCCCcHHHHHHHHHHHHHHHHhccccc
Q psy3887         123 GIFLFLLRLLDPEINRFKKYRRPL------SGIALSQ-IALKVGLSLYESSLLLSRPLSGIALSQIAEQLLELHRGQGME  195 (250)
Q Consensus       123 ~~~~~~~~LihDDI~D~s~~RRG~------~G~~~AI-~gd~l~~~a~~~~~~l~~p~~~~a~~~~~e~l~~l~~GQ~~d  195 (250)
                              |++|||+|+|++|||+      ||++.+| +++|+++.|++.++.+.+|+   +++++.+++.+||+||+||
T Consensus        72 --------LLIDDIEDNs~LRRG~pvaHsIyGvpStINtANY~yFlalekV~qLdhP~---a~kifteqLleLHrGQGld  140 (322)
T KOG0777|consen   72 --------LLIDDIEDNSPLRRGQPVAHSIYGVPSTINTANYMYFLALEKVSQLDHPN---AIKIFTEQLLELHRGQGLD  140 (322)
T ss_pred             --------eeeccccccchhhcCCcchhhhccCcchhhhhHHHHHHHHHHHHhcCCch---HHHHHHHHHHHHhcCCCcc
Confidence                    9999999999999999      9999999 99999999999999999998   9999999999999999999


Q ss_pred             hhcccCCCCCCHHHHHHHHhhhHHHHHHHHHHHH
Q psy3887         196 IYWRDNYTCPSEEEYRTMTIRTVGRSVGYPTIRT  229 (250)
Q Consensus       196 i~w~~~~~~pSeeeYl~mi~~KTg~Lf~~a~~~~  229 (250)
                      |||||+++||||++|..|+-+|||.||+++.++|
T Consensus       141 IYWRD~~tcPtee~Yk~Mv~~KTGGLF~La~rLM  174 (322)
T KOG0777|consen  141 IYWRDFLTCPTEEMYKNMVMNKTGGLFRLALRLM  174 (322)
T ss_pred             eeeeccCcCCCHHHHHHHHHHhcccHHHHHHHHH
Confidence            9999999999999999999999999999999874

>TIGR02748 GerC3_HepT heptaprenyl diphosphate synthase component II Back     alignment and domain information
>PRK10888 octaprenyl diphosphate synthase; Provisional Back     alignment and domain information
>COG0142 IspA Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism] Back     alignment and domain information
>PRK10581 geranyltranstransferase; Provisional 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
>CHL00151 preA prenyl transferase; Reviewed Back     alignment and domain information
>PLN02857 octaprenyl-diphosphate synthase 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
>KOG0776|consensus 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
>KOG0711|consensus 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
>cd00868 Terpene_cyclase_C1 Terpene cyclases, Class 1 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 ?
Query250
2q80_A 301 Crystal Structure Of Human Geranylgeranyl Pyrophosp 3e-12
2dh4_A 340 Geranylgeranyl Pyrophosphate Synthase Length = 340 8e-05
>pdb|2Q80|A Chain A, Crystal Structure Of Human Geranylgeranyl Pyrophosphate Synthase Bound To Ggpp Length = 301 Back     alignment and structure 
Iteration: 1

 Score = 68.6 bits (166), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 27/47 (57%), Positives = 35/47 (74%)
Query: 177 ALSQIAEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRTVGRSVG 223
           A+     QLLELH+GQG++IYWRDNYTCP+EEEY+ M ++  G   G
Sbjct: 112 AVKLFTRQLLELHQGQGLDIYWRDNYTCPTEEEYKAMVLQKTGGLFG 158
>pdb|2DH4|A Chain A, Geranylgeranyl Pyrophosphate Synthase Length = 340 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 ?
Query250
2q80_A 301 Geranylgeranyl pyrophosphate synthetase; isoprenoi 5e-11
2e8v_A 340 Geranylgeranyl pyrophosphate synthetase; prenyltra 2e-09
2her_A 368 Fragment, farnesyl pyrophosphate synthase; farnesy 1e-05
>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
 Score = 60.3 bits (147), Expect = 5e-11
 Identities = 25/37 (67%), Positives = 31/37 (83%)

Query: 177 ALSQIAEQLLELHRGQGMEIYWRDNYTCPSEEEYRTM 213
           A+     QLLELH+GQG++IYWRDNYTCP+EEEY+ M
Sbjct: 112 AVKLFTRQLLELHQGQGLDIYWRDNYTCPTEEEYKAM 148
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query250
2q80_A 301 Geranylgeranyl pyrophosphate synthetase; isoprenoi 100.0
2e8v_A 340 Geranylgeranyl pyrophosphate synthetase; prenyltra 100.0
3mzv_A 341 Decaprenyl diphosphate synthase; transferase, stru 100.0
3kra_B274 Geranyl diphosphate synthase small subunit; prenyl 100.0
3rmg_A 334 Octaprenyl-diphosphate synthase; structural genomi 100.0
1wy0_A 342 Geranylgeranyl pyrophosphate synthetase; pyrococcu 100.0
3oyr_A 345 Trans-isoprenyl diphosphate synthase; isoprenyl sy 100.0
3ipi_A295 Geranyltranstransferase; isoprene biosynthesis, he 100.0
2ftz_A284 Geranyltranstransferase; TM0161, structural GE joi 100.0
3aqb_B 325 Component B of hexaprenyl diphosphate synthase; pr 100.0
3nf2_A 352 Putative polyprenyl synthetase; isoprenyl diphosph 100.0
4dhd_A 358 Polyprenyl synthetase; isoprenoid synthesis, isopr 100.0
3p8l_A302 Geranyltranstransferase; isoprenyl synthase, struc 100.0
1v4e_A299 Octoprenyl-diphosphate synthase; trans-type prenyl 100.0
1wmw_A 330 Geranylgeranyl diphosphate synthetase; GGPP, preny 100.0
3lmd_A 360 Geranylgeranyl pyrophosphate synthase; isoprenyl d 100.0
1rtr_A301 Geranyltranstransferase; 2.50A {Staphylococcus aur 100.0
3pde_A309 Farnesyl-diphosphate synthase; isoprenyl diphospha 99.98
3m0g_A297 Farnesyl diphosphate synthase; structural genomics 99.98
3pko_A 334 Geranylgeranyl pyrophosphate synthase; isoprenyl d 99.98
3lsn_A304 Geranyltranstransferase; structural genomics, prot 99.98
3npk_A291 Geranyltranstransferase; isoprene biosynthesis, SG 99.97
3ts7_A 324 Geranyltranstransferase; isoprenoid synthesis, far 99.97
3llw_A311 Geranyltranstransferase (ISPA); structural genomic 99.97
4f62_A 317 Geranyltranstransferase; enzyme function initiativ 99.97
3uca_A324 Geranyltranstransferase; isoprenoid synthesis, iso 99.97
2h8o_A335 Geranyltranstransferase; geranyltransferase,agroba 99.97
3p8r_A302 Geranyltranstransferase; isoprenyl synthase, struc 99.97
3lom_A313 Geranyltranstransferase; geranyltransferase, struc 99.97
1rqj_A299 Geranyltranstransferase; bisphosphonate, isoprenyl 99.97
2j1p_A293 Geranylgeranyl pyrophosphate synthetase; transfera 99.97
3apz_A 348 Geranyl diphosphate synthase; prenyltransferase, a 99.97
3tc1_A 315 Octaprenyl pyrophosphate synthase; all alpha-helic 99.97
3qkc_B273 Geranyl diphosphate synthase small subunit; struct 99.97
2azj_A289 Geranylgeranyl pyrophosphate synthetase; hexpps, t 99.97
4fp4_A285 Polyprenyl synthetase; isoprenoid synthesis, isopr 99.97
3lk5_A 380 Geranylgeranyl pyrophosphate synthase; structural 99.96
1yhl_A 362 Farnesyl pyrophosphate synthase; farnesyl diphosph 99.96
2qis_A 374 Farnesyl pyrophosphate synthetase; trans-prenyltra 99.96
2q58_A 368 Fragment, farnesyl pyrophosphate synthase; farnesy 99.96
1uby_A 367 FPS, farnesyl diphosphate synthase; transferase, i 99.96
2ihi_A 395 Pyrophosphate synthase; PV092040, structural genom 99.96
3dyh_A 390 Farnesyl pyrophosphate synthase; protein-bisphosph 99.95
3mav_A 395 Farnesyl pyrophosphate synthase; PV092040, structu 99.95
2her_A 368 Fragment, farnesyl pyrophosphate synthase; farnesy 99.95
>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
Probab=100.00  E-value=5.6e-35  Score=266.46  Aligned_cols=161  Identities=32%  Similarity=0.498  Sum_probs=144.3

Q ss_pred             hhhhhHHhHHHHHhc-CCCchHHHHHHHhcCcccccccccCChhHHHHHHHHHHHHhhccccccccchhhhhhhhccccc
Q psy3887          57 KYRERILEPNASLLR-SGDLAKVHISIVINRPTTIMRLVRTEDSKKKLVALTWVMFQSHRAGKMRTDGIFLFLLRLLDPE  135 (250)
Q Consensus        57 ~~~~~l~~p~~yll~-~GKr~Rp~l~~l~~~~~~~~~~~~~~~~~~~~iA~~vE~lH~~~AS~~~~~~~~~~~~~LihDD  135 (250)
                      ..++.|.+|..|++. +|||+||.|++++++      |++.+++++..+|+++||+|+  ||             |||||
T Consensus         8 ~~~~~l~~~~~y~~~~gGKr~Rp~l~l~~~~------~~~~~~~~~~~~A~avEliH~--as-------------LiHDD   66 (301)
T 2q80_A            8 TVQRILLEPYKYLLQLPGKQVRTKLSQAFNH------WLKVPEDKLQIIIEVTEMLHN--AS-------------LLIDD   66 (301)
T ss_dssp             CHHHHHTHHHHHHTTSSCHHHHHHHHHHHHH------HHCCCHHHHHHHHHHHHHHHH--HH-------------HHHHH
T ss_pred             CCcHHHHHHHHHHHhCCCccHHHHHHHHHHH------HhCCCHHHHHHHHHHHHHHHH--HH-------------HHHcc
Confidence            346679999999999 999999999999999      998888888999999999999  99             99999


Q ss_pred             cccCCCCCCCC------CCchHHH-HHHHHHHHHHHHHHccCCCcHHHHHHHHHHHHHHHHhccccchhcccCCCCCCHH
Q psy3887         136 INRFKKYRRPL------SGIALSQ-IALKVGLSLYESSLLLSRPLSGIALSQIAEQLLELHRGQGMEIYWRDNYTCPSEE  208 (250)
Q Consensus       136 I~D~s~~RRG~------~G~~~AI-~gd~l~~~a~~~~~~l~~p~~~~a~~~~~e~l~~l~~GQ~~di~w~~~~~~pSee  208 (250)
                      |+|+|+.|||+      ||+++|| +|||+++.|++.+.++..|.   +++.+++.+.+++.||.+|+.|+++..++|++
T Consensus        67 i~D~s~~RRG~pt~h~~~G~~~AIl~GD~l~~~a~~~l~~~~~~~---~~~~~~~~~~~~~~GQ~~dl~~~~~~~~~~~~  143 (301)
T 2q80_A           67 IEDNSKLRRGFPVAHSIYGIPSVINSANYVYFLGLEKVLTLDHPD---AVKLFTRQLLELHQGQGLDIYWRDNYTCPTEE  143 (301)
T ss_dssp             HHHTCSEETTEECHHHHHCHHHHHHHHHHHHHHHHHHHHTTCCTT---HHHHHHHHHHHHHHHHHHHHHHHHTTCCCCHH
T ss_pred             ccCCCCCCCCCcchhhccCcHHHHHHHHHHHHHHHHHHHHCCCHH---HHHHHHHHHHHHHHHHHHHHHhccCCCCCCHH
Confidence            99999999999      9999999 99999999999999987777   78889999999999999999998876689999


Q ss_pred             HHHHHHhhhHHHHHHHHHHHH-HcCCChhhhhhh
Q psy3887         209 EYRTMTIRTVGRSVGYPTIRT-SKGGASSQVQTY  241 (250)
Q Consensus       209 eYl~mi~~KTg~Lf~~a~~~~-l~Ggs~~~ie~y  241 (250)
                      +|++|+..|||+||.++|++. +.++.++....|
T Consensus       144 ~y~~~i~~KTa~L~~~~~~~ga~~a~~~~~l~~~  177 (301)
T 2q80_A          144 EYKAMVLQKTGGLFGLAVGLMQLFSDYKEDLKPL  177 (301)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCCCSCCHHH
T ss_pred             HHHHHHHcccHHHHHHHHHHHHHHCCChHHHHHH
Confidence            999999999999999999984 333333444444
>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
>3mzv_A Decaprenyl diphosphate synthase; transferase, structural genomics, PSI-2, protein structure initiative; 1.90A {Rhodobacter capsulatus} 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
>3rmg_A Octaprenyl-diphosphate synthase; structural genomics, protein structure initiative, isoprene biosynthesis, transferase; 2.30A {Bacteroides thetaiotaomicron} 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
>3oyr_A Trans-isoprenyl diphosphate synthase; isoprenyl synthase, PSI, protein structure initiative; HET: IPE; 2.00A {Caulobacter crescentus} 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
>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
>3aqb_B Component B of hexaprenyl diphosphate synthase; prenyltransferase, transferase; 2.40A {Micrococcus luteus} PDB: 3aqc_B* 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
>4dhd_A Polyprenyl synthetase; isoprenoid synthesis, isoprenoid diphosphate synthase, trans; 1.65A {Pyrobaculum calidifontis} PDB: 4gp1_A* 4gp2_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
>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
>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
>1rtr_A Geranyltranstransferase; 2.50A {Staphylococcus aureus} SCOP: a.128.1.1 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
>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
>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
>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
>3npk_A Geranyltranstransferase; isoprene biosynthesis, SGX, structural genomics protein structure initiative; 1.50A {Campylobacter jejuni} Back     alignment and structure
>3ts7_A Geranyltranstransferase; isoprenoid synthesis, farnesyl diphosphate synthase; 1.94A {Methylococcus capsulatus} 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
>4f62_A Geranyltranstransferase; enzyme function initiative, structural genomics; 2.10A {Marinomonas SP} Back     alignment and structure
>3uca_A Geranyltranstransferase; isoprenoid synthesis, isoprenoid diphosphate synthase; 2.00A {Clostridium perfringens} 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
>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
>3lom_A Geranyltranstransferase; geranyltransferase, structural genomics, PSI, protein structure initiative, nysgrc; 2.30A {Legionella pneumophila subsp} 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
>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
>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
>3tc1_A Octaprenyl pyrophosphate synthase; all alpha-helices fold, transferase; 2.00A {Helicobacter pylori} 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
>2azj_A Geranylgeranyl pyrophosphate synthetase; hexpps, trans-prenyltransferase; 2.40A {Sulfolobus solfataricus} PDB: 2azk_A 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
>3lk5_A Geranylgeranyl pyrophosphate synthase; structural genomics, protein structure initiative, geranylge pyrophosphate synthase; 1.90A {Corynebacterium glutamicum} PDB: 3qqv_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
>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
>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
>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

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query250
d2q80a1 291 Geranylgeranyl pyrophosphate synthetase {Human (Ho 100.0
d1v4ea_280 Octoprenyl-diphosphate synthase {Thermotoga mariti 99.96
d1rqja_299 Farnesyl diphosphate synthase (geranyltranstransfe 99.96
d1rtra_290 Farnesyl diphosphate synthase (geranyltranstransfe 99.96
d1fpsa_ 348 Farnesyl diphosphate synthase (geranyltranstransfe 99.95
d1ps1a_ 311 Pentalenene synthase {Streptomyces sp., UC5319 [Ta 89.11
>d2q80a1 a.128.1.1 (A:6-296) Geranylgeranyl pyrophosphate synthetase {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
class: All alpha proteins
fold: Terpenoid synthases
superfamily: Terpenoid synthases
family: Isoprenyl diphosphate synthases
domain: Geranylgeranyl pyrophosphate synthetase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.3e-35  Score=265.31  Aligned_cols=162  Identities=32%  Similarity=0.492  Sum_probs=147.6

Q ss_pred             hhhhhHHhHHHHHhc-CCCchHHHHHHHhcCcccccccccCChhHHHHHHHHHHHHhhccccccccchhhhhhhhccccc
Q psy3887          57 KYRERILEPNASLLR-SGDLAKVHISIVINRPTTIMRLVRTEDSKKKLVALTWVMFQSHRAGKMRTDGIFLFLLRLLDPE  135 (250)
Q Consensus        57 ~~~~~l~~p~~yll~-~GKr~Rp~l~~l~~~~~~~~~~~~~~~~~~~~iA~~vE~lH~~~AS~~~~~~~~~~~~~LihDD  135 (250)
                      ..++.|.+|++|++. ||||+||.|++++++      +++.+++++..+|+++|++|+  ||             |||||
T Consensus         2 ~~~~~l~e~~~y~~~~gGKr~Rp~l~~~~~~------~~~~~~~~~~~~a~aiEllH~--as-------------LihDD   60 (291)
T d2q80a1           2 TVQRILLEPYKYLLQLPGKQVRTKLSQAFNH------WLKVPEDKLQIIIEVTEMLHN--AS-------------LLIDD   60 (291)
T ss_dssp             CHHHHHTHHHHHHTTSSCHHHHHHHHHHHHH------HHCCCHHHHHHHHHHHHHHHH--HH-------------HHHHH
T ss_pred             chhHHHHHHHHHHHhCCCchHHHHHHHHHHH------HhCCCHHHHHHHHHHHHHHHH--HH-------------HHhcc
Confidence            346789999999999 999999999999999      999999999999999999999  99             99999


Q ss_pred             cccCCCCCCCC------CCchHHH-HHHHHHHHHHHHHHccCCCcHHHHHHHHHHHHHHHHhccccchhcccCCCCCCHH
Q psy3887         136 INRFKKYRRPL------SGIALSQ-IALKVGLSLYESSLLLSRPLSGIALSQIAEQLLELHRGQGMEIYWRDNYTCPSEE  208 (250)
Q Consensus       136 I~D~s~~RRG~------~G~~~AI-~gd~l~~~a~~~~~~l~~p~~~~a~~~~~e~l~~l~~GQ~~di~w~~~~~~pSee  208 (250)
                      |+|+++.|||+      ||++.|| +||++++.+++.+.++..+.   +...+++.+.+++.||.+|+.|+.+..++|++
T Consensus        61 i~D~~~~RRg~pt~~~~~G~~~Ail~gd~l~~~a~~~l~~~~~~~---~~~~~~~~~~~~~~gq~~d~~~~~~~~~~s~~  137 (291)
T d2q80a1          61 IEDNSKLRRGFPVAHSIYGIPSVINSANYVYFLGLEKVLTLDHPD---AVKLFTRQLLELHQGQGLDIYWRDNYTCPTEE  137 (291)
T ss_dssp             HHHTCSEETTEECHHHHHCHHHHHHHHHHHHHHHHHHHHTTCCTT---HHHHHHHHHHHHHHHHHHHHHHHHTTCCCCHH
T ss_pred             cccCcccccCCCccccccchhhhhhHHHHHHHHHHHhhhhhhhhH---HHHHHHHHHHHhHhccccccccccccccCCHH
Confidence            99999999999      9999999 99999999999999998888   78899999999999999999999888889999


Q ss_pred             HHHHHHhhhHHHHHHHHHHHH-HcCCChhhhhhhc
Q psy3887         209 EYRTMTIRTVGRSVGYPTIRT-SKGGASSQVQTYA  242 (250)
Q Consensus       209 eYl~mi~~KTg~Lf~~a~~~~-l~Ggs~~~ie~ya  242 (250)
                      +|++|+..|||+||.++|.+. +.++..+.+..|+
T Consensus       138 ~y~~ii~~KT~~Lf~~~~~~ga~~~~~~~~l~~~g  172 (291)
T d2q80a1         138 EYKAMVLQKTGGLFGLAVGLMQLFSDYKEDLKPLL  172 (291)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCCCSCCHHHH
T ss_pred             HHHHHHHhccchhhHhhhhhhhhhcccchhhHHHH
Confidence            999999999999999999873 3344445555543
>d1v4ea_ a.128.1.1 (A:) Octoprenyl-diphosphate synthase {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1rqja_ a.128.1.1 (A:) Farnesyl diphosphate synthase (geranyltranstransferase) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1rtra_ a.128.1.1 (A:) Farnesyl diphosphate synthase (geranyltranstransferase) {Staphylococcus aureus [TaxId: 1280]} 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
>d1ps1a_ a.128.1.4 (A:) Pentalenene synthase {Streptomyces sp., UC5319 [TaxId: 1931]} Back     information, alignment and structure