Psyllid ID: psy9101

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-----
ISTSSVLSQKSKILSHDPPLAATNTVLSKDESRDFMAIFPDLVRDLTDAGRHSDIPDVTKWYAKVLQYNKAISNNVYLGTYFIVQVLQYNVPSGKKNRGLALVVAYKMLAQPSELTPENLHLAQILGWCVEIVSLKTSMGQSLDLSTANDLSKFTMDRYEAIVKYKTAFYSFQLPVALAMHMAGMQDVEVHRQARTLLLEMGHFFQVQDDYLDCFGTPDVTGKIGTDIEDGKCSWLAVVALQRATPAQRKLMEVN
cccccccHHHHHHHccccccccccccccHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHccccHHHHHccccccccccccccHHHccccHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccHHccccHHHHHHHHHHccHHHHHHHHHc
cccHHHHHHHHHHHHccccccccccccEcHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccEEHHHHHHccccccHHHHHHHHHHHHHccHHHccHHHHHHHHHHHHHHHHEEEHHHHHHHHHHccccccccccHHHHHHHHHHHcHHHHcHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccHHHHHHcccccHHHHHHHHHH
istssvlsqkskilshdpplaatntvlskdesrdfmAIFPDLVRDltdagrhsdipdvTKWYAKVLQYNKaisnnvylGTYFIVQVLQynvpsgkknrGLALVVAYKMlaqpseltpenlHLAQILGWCVEIVSLKTsmgqsldlstandlsKFTMDRYEAIVKYKTAFYSFQLPVALAMHMAGMQDVEVHRQARTLLLEMGhffqvqddyldcfgtpdvtgkigtdiedgkcSWLAVVALQRATPAQRKLMEVN
istssvlsqkskilshdpplaatntvlskdesRDFMAIFPDLVRDLTDAGRHSDIPDVTKWYAKVLQYNKAISNNVYLGTYFIVQVLQYNVPSGKKNRGLALVVAYKMLAQPSELTPENLHLAQILGWCVEIVSLKTSMGQSLDLSTANDLSKFTMDRYEAIVKYKTAFYSFQLPVALAMHMAGMQDVEVHRQARTLLLEMGHFFQVQDDYLDCFGTPDVTGKIGTDIEDGKCSWLAVVALQratpaqrklmevn
ISTSSVLSQKSKILSHDPPLAATNTVLSKDESRDFMAIFPDLVRDLTDAGRHSDIPDVTKWYAKVLQYNKAISNNVYLGTYFIVQVLQYNVPSGKKNRGLALVVAYKMLAQPSELTPENLHLAQILGWCVEIVSLKTSMGQSLDLSTANDLSKFTMDRYEAIVKYKTAFYSFQLPVALAMHMAGMQDVEVHRQARTLLLEMGHFFQVQDDYLDCFGTPDVTGKIGTDIEDGKCSWLAVVALQRATPAQRKLMEVN
*********************************DFMAIFPDLVRDLTDAGRHSDIPDVTKWYAKVLQYNKAISNNVYLGTYFIVQVLQYNVPSGKKNRGLALVVAYKMLAQPSELTPENLHLAQILGWCVEIVSLKTSMGQSLDLSTANDLSKFTMDRYEAIVKYKTAFYSFQLPVALAMHMAGMQDVEVHRQARTLLLEMGHFFQVQDDYLDCFGTPDVTGKIGTDIEDGKCSWLAVVALQR************
******************************ESRDFMAIFPDLVRDLTDAGRHSDIPDVTKWYAKVLQYNKAISNNVYLGTYFIVQVLQYNVPSGKKNRGLALVVAYKMLAQPSELTPENLHLAQILGWCVEIVSLKTSMGQSLDLSTANDLSKFTMDRYEAIVKYKTAFYSFQLPVALAMHMAGMQDVEVHRQARTLLLEMGHFFQVQDDYLDCFGTPDVTGKIGTDIEDGKCSWLAVVALQRATPAQ*KLM***
************ILSHDPPLAATNTVLSKDESRDFMAIFPDLVRDLTDAGRHSDIPDVTKWYAKVLQYNKAISNNVYLGTYFIVQVLQYNVPSGKKNRGLALVVAYKMLAQPSELTPENLHLAQILGWCVEIVSLKTSMGQSLDLSTANDLSKFTMDRYEAIVKYKTAFYSFQLPVALAMHMAGMQDVEVHRQARTLLLEMGHFFQVQDDYLDCFGTPDVTGKIGTDIEDGKCSWLAVVALQRATPAQRKLMEVN
ISTSSVLSQKSKILSHDPPLAATNTVLSKDESRDFMAIFPDLVRDLTDAGRHSDIPDVTKWYAKVLQYNKAISNNVYLGTYFIVQVLQYNVPSGKKNRGLALVVAYKMLAQPSELTPENLHLAQILGWCVEIVSLKTSMGQSLDLSTANDLSKFTMDRYEAIVKYKTAFYSFQLPVALAMHMAGMQDVEVHRQARTLLLEMGHFFQVQDDYLDCFGTPDVTGKIGTDIEDGKCSWLAVVALQRATPAQRKLMEVN
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
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ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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ISTSSVLSQKSKILSHDPPLAATNTVLSKDESRDFMAIFPDLVRDLTDAGRHSDIPDVTKWYAKVLQYNKAISNNVYLGTYFIVQVLQYNVPSGKKNRGLALVVAYKMLAQPSELTPENLHLAQILGWCVEIVSLKTSMGQSLDLSTANDLSKFTMDRYEAIVKYKTAFYSFQLPVALAMHMAGMQDVEVHRQARTLLLEMGHFFQVQDDYLDCFGTPDVTGKIGTDIEDGKCSWLAVVALQRATPAQRKLMEVN
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 ?
Query255 2.2.26 [Sep-21-2011]
P08836367 Farnesyl pyrophosphate sy no N/A 0.572 0.397 0.538 3e-41
Q8WMY2353 Farnesyl pyrophosphate sy yes N/A 0.478 0.345 0.611 1e-39
P14324419 Farnesyl pyrophosphate sy no N/A 0.478 0.291 0.611 1e-38
P05369353 Farnesyl pyrophosphate sy yes N/A 0.478 0.345 0.603 2e-38
Q920E5353 Farnesyl pyrophosphate sy yes N/A 0.478 0.345 0.595 3e-38
O14230347 Farnesyl pyrophosphate sy yes N/A 0.482 0.354 0.559 2e-34
P08524352 Farnesyl pyrophosphate sy yes N/A 0.482 0.349 0.535 3e-34
O24241342 Farnesyl pyrophosphate sy N/A N/A 0.478 0.356 0.535 5e-33
O24242342 Farnesyl pyrophosphate sy N/A N/A 0.478 0.356 0.543 8e-33
Q9NH03382 Farnesyl diphosphate synt yes N/A 0.470 0.314 0.544 1e-32
>sp|P08836|FPPS_CHICK Farnesyl pyrophosphate synthase OS=Gallus gallus GN=FDPS PE=1 SV=2 Back     alignment and function desciption
 Score =  168 bits (426), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 83/154 (53%), Positives = 106/154 (68%), Gaps = 8/154 (5%)

Query: 106 YKMLAQPSELTPENLHLAQILGWCVEIVSLKTSMGQSLDLSTAN----DLSKFTMDRYEA 161
           Y++L +     P  +HL ++        + +T +GQ LDL TA     DLS F+ +RY+A
Sbjct: 154 YRVLKKYCRQRPYYVHLLELFLQ----TAYQTELGQMLDLITAPVSKVDLSHFSEERYKA 209

Query: 162 IVKYKTAFYSFQLPVALAMHMAGMQDVEVHRQARTLLLEMGHFFQVQDDYLDCFGTPDVT 221
           IVKYKTAFYSF LPVA AM+M G+   E H  A+ +LLEMG +FQ+QDDYLDCFG P +T
Sbjct: 210 IVKYKTAFYSFYLPVAAAMYMVGIDSKEEHENAKAILLEMGEYFQIQDDYLDCFGDPALT 269

Query: 222 GKIGTDIEDGKCSWLAVVALQRATPAQRKLMEVN 255
           GK+GTDI+D KCSWL V  LQR TP QR+L+E N
Sbjct: 270 GKVGTDIQDNKCSWLVVQCLQRVTPEQRQLLEDN 303
Catalyzes the sequential condensation of isopentenyl pyrophosphate with the allylic pyrophosphates, dimethylallyl pyrophosphate, and then with the resultant geranylpyrophosphate to the ultimate product farnesyl pyrophosphate.
Gallus gallus (taxid: 9031)
EC: 2EC: .EC: 5EC: .EC: 1EC: .EC: 1
>sp|Q8WMY2|FPPS_BOVIN Farnesyl pyrophosphate synthase OS=Bos taurus GN=FDPS PE=1 SV=1 Back     alignment and function description
>sp|P14324|FPPS_HUMAN Farnesyl pyrophosphate synthase OS=Homo sapiens GN=FDPS PE=1 SV=4 Back     alignment and function description
>sp|P05369|FPPS_RAT Farnesyl pyrophosphate synthase OS=Rattus norvegicus GN=Fdps PE=2 SV=2 Back     alignment and function description
>sp|Q920E5|FPPS_MOUSE Farnesyl pyrophosphate synthase OS=Mus musculus GN=Fdps PE=2 SV=1 Back     alignment and function description
>sp|O14230|FPPS_SCHPO Farnesyl pyrophosphate synthase OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=fps1 PE=1 SV=1 Back     alignment and function description
>sp|P08524|FPPS_YEAST Farnesyl pyrophosphate synthase OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=ERG20 PE=1 SV=2 Back     alignment and function description
>sp|O24241|FPPS1_PARAR Farnesyl pyrophosphate synthase 1 OS=Parthenium argentatum GN=FPS1 PE=2 SV=1 Back     alignment and function description
>sp|O24242|FPPS2_PARAR Farnesyl pyrophosphate synthase 2 OS=Parthenium argentatum GN=FPS2 PE=2 SV=1 Back     alignment and function description
>sp|Q9NH03|FPS_DICDI Farnesyl diphosphate synthase OS=Dictyostelium discoideum GN=fps 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 ?
Query255
282935089 394 mitochondrial farnesyl diphosphate synth 0.913 0.591 0.470 1e-61
119167460 394 putative mitochondrial isoprenyl diphosp 0.913 0.591 0.470 2e-61
340367010 394 isoprenyl diphosphate synthase [Rhopalos 0.913 0.591 0.467 2e-61
209870011 394 mitochondrial isoprenyl diphosphate synt 0.913 0.591 0.464 5e-61
254729448 394 mitochondrial farnesyl diphosphate synth 0.913 0.591 0.470 5e-61
345485558 404 PREDICTED: farnesyl pyrophosphate syntha 0.901 0.569 0.472 3e-60
162538561 394 farnesyl diphosphate synthase 1 [Myzus p 0.913 0.591 0.455 7e-60
190149251 394 putative mitochondrial isoprenyl diphosp 0.913 0.591 0.453 8e-60
63103171 394 bifunctional putative mitochondrial GPPS 0.913 0.591 0.455 8e-60
63103173 362 bifunctional GPPS/FPPS isoprenyl diphosp 0.913 0.643 0.453 9e-60
>gi|282935089|gb|ACT79809.3| mitochondrial farnesyl diphosphate synthase [Aphis gossypii] Back     alignment and taxonomy information
 Score =  242 bits (617), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 138/293 (47%), Positives = 178/293 (60%), Gaps = 60/293 (20%)

Query: 19  PLAATNTVLSKDESRDFMAIFPDLVRDLTDAGRHSDIPDVTKWYAKVLQYN--------- 69
           P   T T +SKDE+RDFMA+FPD+VRDLTD GR+ DIPDVTKW AKVLQYN         
Sbjct: 42  PPVITGTAVSKDETRDFMAVFPDVVRDLTDTGRNLDIPDVTKWLAKVLQYNVPGGKKNRG 101

Query: 70  -------KAISN-------NVYLGTY--FIVQVLQ-YNV---------------PSGKKN 97
                  K +S+       N+ L     + V++LQ Y +               P   ++
Sbjct: 102 LALVLSFKMLSSPSDQTDENLRLSYILGWCVEILQAYQLVLDDIMDNAITRRGRPCWYRH 161

Query: 98  RGLALVVA----------YKMLAQPSELTPENLHLAQILGWCVEIVSLKTSMGQSLDLST 147
             + L+            Y+++ +  +  P  +H+ ++       V++KTSMGQ LD+ T
Sbjct: 162 NDIGLMAVNDGILLEQTIYQLIKKYFKDKPYYVHILELF----YDVTMKTSMGQCLDMLT 217

Query: 148 AND-----LSKFTMDRYEAIVKYKTAFYSFQLPVALAMHMAGMQDVEVHRQARTLLLEMG 202
           AN      L K+TM+ Y AIVKYKTA+YSF LPV LAM M  + D E+ RQA+T+LLEMG
Sbjct: 218 ANSFKTKKLEKYTMENYTAIVKYKTAYYSFFLPVCLAMRMTNINDPEIFRQAKTILLEMG 277

Query: 203 HFFQVQDDYLDCFGTPDVTGKIGTDIEDGKCSWLAVVALQRATPAQRKLMEVN 255
           HFFQVQDD+LDC+G P+V GKIGTDIEDGKCSWLAVVALQ+    Q+KLME N
Sbjct: 278 HFFQVQDDFLDCYGDPEVMGKIGTDIEDGKCSWLAVVALQKVNSEQKKLMEEN 330

Source: Aphis gossypii

Species: Aphis gossypii

Genus: Aphis

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|119167460|gb|AAY33488.2| putative mitochondrial isoprenyl diphosphate synthase precursor [Aphis fabae] Back     alignment and taxonomy information
>gi|340367010|gb|AEK32003.1| isoprenyl diphosphate synthase [Rhopalosiphum padi] Back     alignment and taxonomy information
>gi|209870011|ref|NP_001119633.3| mitochondrial isoprenyl diphosphate synthase [Acyrthosiphon pisum] Back     alignment and taxonomy information
>gi|254729448|gb|ACT79808.1| mitochondrial farnesyl diphosphate synthase [Aphis gossypii] Back     alignment and taxonomy information
>gi|345485558|ref|XP_001604464.2| PREDICTED: farnesyl pyrophosphate synthase-like [Nasonia vitripennis] Back     alignment and taxonomy information
>gi|162538561|gb|ABY19312.1| farnesyl diphosphate synthase 1 [Myzus persicae] Back     alignment and taxonomy information
>gi|190149251|gb|AAY33490.3| putative mitochondrial isoprenyl diphosphate synthase precursor [Acyrthosiphon pisum] Back     alignment and taxonomy information
>gi|63103171|gb|AAY33491.1| bifunctional putative mitochondrial GPPS/FPPS isorpenyl diphosphate synthase precursor [Myzus persicae] Back     alignment and taxonomy information
>gi|63103173|gb|AAY33492.1| bifunctional GPPS/FPPS isoprenyl diphosphate synthase precursor [Myzus persicae] 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 ?
Query255
FB|FBgn0025373419 Fpps "Farnesyl pyrophosphate s 0.454 0.276 0.649 1.8e-71
UNIPROTKB|D0G6X4421 FDPS "Uncharacterized protein" 0.478 0.289 0.611 4.1e-52
UNIPROTKB|F1N431421 RUSC1 "Uncharacterized protein 0.478 0.289 0.619 1.4e-48
UNIPROTKB|Q8WMY2353 FDPS "Farnesyl pyrophosphate s 0.478 0.345 0.619 1.4e-48
UNIPROTKB|E9PCI9353 FDPS "Farnesyl pyrophosphate s 0.478 0.345 0.619 9.8e-48
UNIPROTKB|P14324419 FDPS "Farnesyl pyrophosphate s 0.478 0.291 0.619 9.8e-48
UNIPROTKB|F1P926421 FDPS "Uncharacterized protein" 0.478 0.289 0.619 6.8e-47
SGD|S000003703352 ERG20 "Farnesyl pyrophosphate 0.482 0.349 0.535 6.8e-47
MGI|MGI:104888353 Fdps "farnesyl diphosphate syn 0.478 0.345 0.595 1.1e-46
POMBASE|SPAC6F12.13c347 fps1 "geranyltranstransferase 0.482 0.354 0.559 3e-43
FB|FBgn0025373 Fpps "Farnesyl pyrophosphate synthase" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
 Score = 408 (148.7 bits), Expect = 1.8e-71, Sum P(3) = 1.8e-71
 Identities = 76/117 (64%), Positives = 98/117 (83%)

Query:   137 TSMGQSLDLSTAND-LSKFTMDRYEAIVKYKTAFYSFQLPVALAMHMAGMQDVEVHRQAR 195
             T+ GQSLD   +N  +S+FTM+ Y+AIV+ KTA+YSF LP ALA+H+AG +D E  RQ++
Sbjct:   236 TTCGQSLDQLNSNRCVSEFTMENYKAIVENKTAYYSFYLPFALALHLAGYKDAEAFRQSK 295

Query:   196 TLLLEMGHFFQVQDDYLDCFGTPDVTGKIGTDIEDGKCSWLAVVALQRATPAQRKLM 252
             T+LLEMG+FFQVQDD+LDCFG P+VTGKIGTDI+D KCSWLAVVA+QRA   Q+++M
Sbjct:   296 TILLEMGNFFQVQDDFLDCFGNPEVTGKIGTDIQDNKCSWLAVVAMQRANVEQKQIM 352
GO:0004337 "geranyltranstransferase activity" evidence=ISS;NAS
GO:0004161 "dimethylallyltranstransferase activity" evidence=NAS
GO:0045337 "farnesyl diphosphate biosynthetic process" evidence=IC
GO:0008299 "isoprenoid biosynthetic process" evidence=IEA
GO:0008354 "germ cell migration" evidence=IMP
GO:0035220 "wing disc development" evidence=IGI
UNIPROTKB|D0G6X4 FDPS "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|F1N431 RUSC1 "Uncharacterized protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|Q8WMY2 FDPS "Farnesyl pyrophosphate synthase" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|E9PCI9 FDPS "Farnesyl pyrophosphate synthase" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|P14324 FDPS "Farnesyl pyrophosphate synthase" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|F1P926 FDPS "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
SGD|S000003703 ERG20 "Farnesyl pyrophosphate synthetase" [Saccharomyces cerevisiae (taxid:4932)] Back     alignment and assigned GO terms
MGI|MGI:104888 Fdps "farnesyl diphosphate synthetase" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
POMBASE|SPAC6F12.13c fps1 "geranyltranstransferase Fps1" [Schizosaccharomyces pombe (taxid:4896)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

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

Original result of BLAST against SWISS-PROT

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
P05369FPPS_RAT2, ., 5, ., 1, ., 10.60310.47840.3456yesN/A
P49349FPPS_KLULA2, ., 5, ., 1, ., 10.51960.48230.3524yesN/A
Q8WMY2FPPS_BOVIN2, ., 5, ., 1, ., 10.61110.47840.3456yesN/A
P08524FPPS_YEAST2, ., 5, ., 1, ., 10.53540.48230.3494yesN/A
Q920E5FPPS_MOUSE2, ., 5, ., 1, ., 10.59520.47840.3456yesN/A
O14230FPPS_SCHPO2, ., 5, ., 1, ., 10.55900.48230.3544yesN/A
Q9NH03FPS_DICDI2, ., 5, ., 1, ., 10.54470.47050.3141yesN/A

EC Number Prediction by EFICAz Software ?

Prediction LevelEC numberConfidence of Prediction
4th Layer2.5.1.100.824
4th Layer2.5.1.10.824
3rd Layer2.5.10.766

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 ?
Query255
cd00685259 cd00685, Trans_IPPS_HT, Trans-Isoprenyl Diphosphat 2e-35
pfam00348260 pfam00348, polyprenyl_synt, Polyprenyl synthetase 3e-31
cd00867236 cd00867, Trans_IPPS, Trans-Isoprenyl Diphosphate S 4e-28
COG0142322 COG0142, IspA, Geranylgeranyl pyrophosphate syntha 7e-23
cd00385243 cd00385, Isoprenoid_Biosyn_C1, Isoprenoid Biosynth 2e-16
PRK10581299 PRK10581, PRK10581, geranyltranstransferase; Provi 0.001
>gnl|CDD|173833 cd00685, Trans_IPPS_HT, Trans-Isoprenyl Diphosphate Synthases, head-to-tail Back     alignment and domain information 
 Score =  126 bits (320), Expect = 2e-35
 Identities = 37/112 (33%), Positives = 56/112 (50%), Gaps = 4/112 (3%)

Query: 133 VSLKTSMGQSLDLSTANDLSKFTMDRYEAIVKYKTAFYSFQLPVALAMHMAGMQDVEVHR 192
             L+   GQ LDL +  D    T + Y  I++ KTA      P+  A+      D E   
Sbjct: 116 AILELVEGQLLDLLSEYDTD-VTEEEYLRIIRLKTAALFAAAPLLGALLAGA--DEEEAE 172

Query: 193 QARTLLLEMGHFFQVQDDYLDCFGTPDVTGK-IGTDIEDGKCSWLAVVALQR 243
             +     +G  FQ+QDD LD FG P+  GK +G+D+ +GKC+   ++AL+ 
Sbjct: 173 ALKRFGRNLGLAFQIQDDILDLFGDPETLGKPVGSDLREGKCTLPVLLALRE 224

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|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|223220 COG0142, IspA, Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism] Back     alignment and domain information
>gnl|CDD|173830 cd00385, Isoprenoid_Biosyn_C1, Isoprenoid Biosynthesis enzymes, Class 1 Back     alignment and domain information
>gnl|CDD|182567 PRK10581, PRK10581, geranyltranstransferase; Provisional Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 255
KOG0711|consensus347 100.0
COG0142322 IspA Geranylgeranyl pyrophosphate synthase [Coenzy 100.0
PRK10888323 octaprenyl diphosphate synthase; Provisional 100.0
PLN02890422 geranyl diphosphate synthase 100.0
TIGR02749322 prenyl_cyano solanesyl diphosphate synthase. Membe 100.0
TIGR02748319 GerC3_HepT heptaprenyl diphosphate synthase compon 100.0
PRK10581299 geranyltranstransferase; Provisional 100.0
CHL00151323 preA prenyl transferase; Reviewed 100.0
PLN02857416 octaprenyl-diphosphate synthase 100.0
PF00348260 polyprenyl_synt: Polyprenyl synthetase; InterPro: 100.0
cd00685259 Trans_IPPS_HT Trans-Isoprenyl Diphosphate Synthase 99.98
KOG0776|consensus384 99.94
cd00867236 Trans_IPPS Trans-Isoprenyl Diphosphate Synthases. 99.91
KOG0777|consensus322 99.71
cd00385243 Isoprenoid_Biosyn_C1 Isoprenoid Biosynthesis enzym 99.12
cd00683265 Trans_IPPS_HH Trans-Isoprenyl Diphosphate Synthase 92.7
PLN02632334 phytoene synthase 90.21
TIGR03465266 HpnD squalene synthase HpnD. The genes of this fam 89.52
TIGR03464266 HpnC squalene synthase HpnC. This family of genes 86.72
PF00494267 SQS_PSY: Squalene/phytoene synthase; InterPro: IPR 86.1
TIGR01559 336 squal_synth farnesyl-diphosphate farnesyltransfera 82.37
>KOG0711|consensus Back     alignment and domain information 
Probab=100.00  E-value=8.4e-44  Score=320.08  Aligned_cols=208  Identities=52%  Similarity=0.909  Sum_probs=193.4

Q ss_pred             chHHHHHHHHHHhhHHHHHHHhccCCCCCc-hHHHHHHHHHhHHHHHHhhhhcchhhHHHHhhcccCCCCccchHHHHHH
Q psy9101          27 LSKDESRDFMAIFPDLVRDLTDAGRHSDIP-DVTKWYAKVLQYNKAISNNVYLGTYFIVQVLQYNVPSGKKNRGLALVVA  105 (255)
Q Consensus        27 ~~~~~~~~f~~~~~~l~~~l~~~~~~~~~~-~~~~~~~~~l~~~~~l~~~~~~~~~~i~~a~~y~~~gGKr~Rpll~lla  105 (255)
                      ..++++++|+++||.+++++.+.+.....+ ++.+|+.++|                     .|++.|||.+|++.++.+
T Consensus         4 ~~~~~k~~f~~~f~~~vr~i~~~~~~~~~~~da~~~~~~~L---------------------~yN~~GGK~nRgl~vv~s   62 (347)
T KOG0711|consen    4 VYAQEKQDFLQVFPVLVRVLTEDLMAHGESGDATEWLKEVL---------------------DYNVIGGKLNRGLSVVDS   62 (347)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhccCCChHHHHHHHHHH---------------------hccCcccccccchhHHHH
Confidence            457899999999999999999998766555 9999999999                     999999999999999999


Q ss_pred             HHHhcCCCCCCHHHHHHHHHHHHHHHHH----------------------------------------------------
Q psy9101         106 YKMLAQPSELTPENLHLAQILGWCVEIV----------------------------------------------------  133 (255)
Q Consensus       106 ~~~l~~~~~~~~~~~~~a~~lA~avEll----------------------------------------------------  133 (255)
                      ++.|.++..++++++.++..+|||||++                                                    
T Consensus        63 ~~~L~~~~~l~~~~~~~a~~lGw~vElLQaffLiaDDIMDnS~tRRGqpCWy~~~gVG~~AINDA~lLea~Iy~lLkk~f  142 (347)
T KOG0711|consen   63 FKALVEPRKLDEEELQLALILGWCVELLQAFFLVADDIMDNSKTRRGQPCWYQKPGVGLDAINDAFLLEAAIYKLLKKHF  142 (347)
T ss_pred             HHHhcCccCCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhccccccCCCcceeecCCcchhhhhHHHHHHHHHHHHHHHhc
Confidence            9999887788999999999999999999                                                    


Q ss_pred             ----------------HHHhhcccchhcccCC-CCCCCCHHHHHHHHhccccchhHHHHHHHHHHHhCCCCHHHHHHHHH
Q psy9101         134 ----------------SLKTSMGQSLDLSTAN-DLSKFTMDRYEAIVKYKTAFYSFQLPVALAMHMAGMQDVEVHRQART  196 (255)
Q Consensus       134 ----------------~~~~~~GQ~lDl~~~~-~~~~~t~~~y~~i~~~KTa~Ltf~~~~~lga~lag~~~~~~~~~l~~  196 (255)
                                      .+.|+.||+++....+ +++.+|.+.|..|+.+|||+|||++|+++|++++|..+.+.....+.
T Consensus       143 r~~~~y~~l~elf~ev~f~T~lGdllt~~~~~~~ls~fsl~~y~~Iv~~KTa~YsFYLPialAl~~ag~~~~k~~~~~k~  222 (347)
T KOG0711|consen  143 RNIYCYVDLVELFHEVTFQTELGDLLTTPEGNKDLSKFSLEKYVFIVEYKTAYYSFYLPVALALLLAGIANLKEHACEKK  222 (347)
T ss_pred             cCCccHHHHHHHHHHHHHHHhhhccccCcccchhHhhhhHHHHHHHhhccccceeeecHHHHHHHHhhhhhHHHhhhHHH
Confidence                            5778999888766544 56679999999999999999999999999999999767888999999


Q ss_pred             HHHHHHHHHHHHhhhhccCCCCCccCCccchHhcCCchHHHHHHHhhCCHHHHHHHHhC
Q psy9101         197 LLLEMGHFFQVQDDYLDCFGTPDVTGKIGTDIEDGKCSWLAVVALQRATPAQRKLMEVN  255 (255)
Q Consensus       197 ~g~~iGiaFQI~DD~lD~~gd~~~~GK~g~Di~~gK~T~p~i~al~~a~~~~r~~l~~n  255 (255)
                      +...+|.+||+|||||||+|||+++||+|+||+++||||.+++|+++++++|++.+++|
T Consensus       223 v~~~lg~~FQvQDDYLd~fgDp~vtgkiGtDIqDnKCsWlv~~al~~~~~eq~~~l~~~  281 (347)
T KOG0711|consen  223 VLLLLGEYFQVQDDYLDCFGDPEVTGKIGTDIQDNKCSWLVVKALQRASAEQYKILFEN  281 (347)
T ss_pred             HHHHHHHHHhcchHHHHhcCChhhcCCCCCccccCceeeehHHHHhhcCHHHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999876

>COG0142 IspA Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism] Back     alignment and domain information
>PRK10888 octaprenyl diphosphate synthase; Provisional Back     alignment and domain information
>PLN02890 geranyl diphosphate synthase Back     alignment and domain information
>TIGR02749 prenyl_cyano solanesyl diphosphate synthase Back     alignment and domain information
>TIGR02748 GerC3_HepT heptaprenyl diphosphate synthase component II Back     alignment and domain information
>PRK10581 geranyltranstransferase; Provisional 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
>cd00685 Trans_IPPS_HT Trans-Isoprenyl Diphosphate Synthases, head-to-tail Back     alignment and domain information
>KOG0776|consensus Back     alignment and domain information
>cd00867 Trans_IPPS Trans-Isoprenyl Diphosphate Synthases Back     alignment and domain information
>KOG0777|consensus Back     alignment and domain information
>cd00385 Isoprenoid_Biosyn_C1 Isoprenoid Biosynthesis enzymes, Class 1 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
>TIGR03464 HpnC squalene synthase HpnC Back     alignment and domain information
>PF00494 SQS_PSY: Squalene/phytoene synthase; InterPro: IPR002060 Squalene synthase 2 Back     alignment and domain information
>TIGR01559 squal_synth farnesyl-diphosphate farnesyltransferase Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query255
1ubx_A367 Structure Of Farnesyl Pyrophosphate Synthetase Leng 2e-42
1fps_A348 Crystal Structure Of Recombinant Farnesyl Diphospha 2e-42
1ubv_A367 Structure Of Farnesyl Pyrophosphate Synthetase Leng 9e-42
3rye_A349 Human Fdps Synthase In Complex With A N-Methyl Pyri 3e-40
2f7m_F350 Crystal Structure Of Unliganded Human Fpps Length = 4e-40
1zw5_A355 X-Ray Structure Of Farnesyl Diphosphate Synthase Pr 4e-40
4h5d_F375 Crystal Structure Of Human Fpps In Complex With Ys_ 5e-40
3b7l_A356 Human Farnesyl Diphosphate Synthase Complexed With 5e-40
1yq7_A374 Human Farnesyl Diphosphate Synthase Complexed With 5e-40
2rah_A378 Human Fdps Synthase In Complex With Novel Inhibitor 6e-40
2qis_A374 Crystal Structure Of Human Farnesyl Pyrophosphate S 1e-39
3cp6_A376 Crystal Structure Of Human Farnesyl Diphosphate Syn 2e-39
3egt_A413 T. Brucei Farnesyl Diphosphate Synthase Complexed W 9e-22
2ewg_A390 T. Brucei Farnesyl Diphosphate Synthase Complexed W 9e-22
4e1e_A361 Crystal Structure Of Trypanosome Cruzi Farnesyl Dip 8e-21
4dzw_A362 Crystal Structure Of Trypanosome Cruzi Farnesyl Dip 8e-21
1yhk_A362 Trypanosoma Cruzi Farnesyl Diphosphate Synthase Len 9e-21
1yhm_A362 Structure Of The Complex Of Trypanosoma Cruzi Farne 3e-20
3mav_A395 Crystal Structure Of Plasmodium Vivax Putative Farn 3e-15
3cc9_A396 Crystal Structure Of Plasmodium Vivax Putative Poly 3e-15
3lk5_A380 Crystal Structure Of Putative Geranylgeranyl Pyroph 1e-08
1rtr_A301 Crystal Structure Of S. Aureus Farnesyl Pyrophospha 2e-04
2o1o_A368 Cryptosporidium Parvum Putative Polyprenyl Pyrophos 2e-04
2for_A323 Crystal Structure Of The Shigella Flexneri Farnesyl 7e-04
1rqj_A299 Active Conformation Of Farnesyl Pyrophosphate Synth 8e-04
1rqi_A300 Active Conformation Of Farnesyl Pyrophosphate Synth 8e-04
>pdb|1UBX|A Chain A, Structure Of Farnesyl Pyrophosphate Synthetase Length = 367 Back     alignment and structure 
Iteration: 1

 Score =  169 bits (427), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 83/154 (53%), Positives = 106/154 (68%), Gaps = 8/154 (5%)
Query: 106 YKMLAQPSELTPENLHLAQILGWCVEIVSLKTSMGQSLDLSTAN----DLSKFTMDRYEA 161
           Y++L +     P  +HL ++        + +T +GQ LDL TA     DLS F+ +RY+A
Sbjct: 154 YRVLKKYCRQRPYYVHLLELFLQ----TAYQTELGQMLDLITAPVSKVDLSHFSEERYKA 209
Query: 162 IVKYKTAFYSFQLPVALAMHMAGMQDVEVHRQARTLLLEMGHFFQVQDDYLDCFGTPDVT 221
           IVKYKTAFYSF LPVA AM+M G+   E H  A+ +LLEMG +FQ+QDDYLDCFG P +T
Sbjct: 210 IVKYKTAFYSFYLPVAAAMYMVGIDSKEEHENAKAILLEMGEYFQIQDDYLDCFGDPALT 269
Query: 222 GKIGTDIEDGKCSWLAVVALQRATPAQRKLMEVN 255
           GK+GTDI+D KCSWL V  LQR TP QR+L+E N
Sbjct: 270 GKVGTDIQDNKCSWLVVQCLQRVTPEQRQLLEDN 303
>pdb|1FPS|A Chain A, Crystal Structure Of Recombinant Farnesyl Diphosphate Synthase At 2.6 Angstroms Resolution Length = 348 Back     alignment and structure
>pdb|1UBV|A Chain A, Structure Of Farnesyl Pyrophosphate Synthetase Length = 367 Back     alignment and structure
>pdb|3RYE|A Chain A, Human Fdps Synthase In Complex With A N-Methyl Pyridinum Bisphosphonate Length = 349 Back     alignment and structure
>pdb|2F7M|F Chain F, Crystal Structure Of Unliganded Human Fpps Length = 350 Back     alignment and structure
>pdb|1ZW5|A Chain A, X-Ray Structure Of Farnesyl Diphosphate Synthase Protein Length = 355 Back     alignment and structure
>pdb|4H5D|F Chain F, Crystal Structure Of Human Fpps In Ternary Complex With Ys0470 And Inorganic Pyrophosphate Length = 375 Back     alignment and structure
>pdb|3B7L|A Chain A, Human Farnesyl Diphosphate Synthase Complexed With Mg And Minodronate Length = 356 Back     alignment and structure
>pdb|1YQ7|A Chain A, Human Farnesyl Diphosphate Synthase Complexed With Risedronate Length = 374 Back     alignment and structure
>pdb|2RAH|A Chain A, Human Fdps Synthase In Complex With Novel Inhibitor Length = 378 Back     alignment and structure
>pdb|2QIS|A Chain A, Crystal Structure Of Human Farnesyl Pyrophosphate Synthase T210s Mutant Bound To Risedronate Length = 374 Back     alignment and structure
>pdb|3CP6|A Chain A, Crystal Structure Of Human Farnesyl Diphosphate Synthase (T201a Mutant) Complexed With Mg And Biphosphonate Inhibitor Length = 376 Back     alignment and structure
>pdb|3EGT|A Chain A, T. Brucei Farnesyl Diphosphate Synthase Complexed With Bisphosphonate Bph-722 Length = 413 Back     alignment and structure
>pdb|2EWG|A Chain A, T. Brucei Farnesyl Diphosphate Synthase Complexed With Minodronate Length = 390 Back     alignment and structure
>pdb|4E1E|A Chain A, Crystal Structure Of Trypanosome Cruzi Farnesyl Diphosphate Synthase In Complex With [2-(n-hexylamino)ethane-1,1-diyl]bisphosphonic Acid And Mg2+ Length = 361 Back     alignment and structure
>pdb|4DZW|A Chain A, Crystal Structure Of Trypanosome Cruzi Farnesyl Diphosphate Synthase In Complex With [2-(cyclohexylamino)ethane-1,1-diyl]bisphosphonic Acid And Mg2+ Length = 362 Back     alignment and structure
>pdb|1YHK|A Chain A, Trypanosoma Cruzi Farnesyl Diphosphate Synthase Length = 362 Back     alignment and structure
>pdb|1YHM|A Chain A, Structure Of The Complex Of Trypanosoma Cruzi Farnesyl Disphosphate Synthase With Alendronate, Isopentenyl Diphosphate And Mg+2 Length = 362 Back     alignment and structure
>pdb|3MAV|A Chain A, Crystal Structure Of Plasmodium Vivax Putative Farnesyl Pyrophosphate Synthase (Pv092040) Length = 395 Back     alignment and structure
>pdb|3CC9|A Chain A, Crystal Structure Of Plasmodium Vivax Putative Polyprenyl Pyrophosphate Synthase In Complex With Geranylgeranyl Diphosphate Length = 396 Back     alignment and structure
>pdb|3LK5|A Chain A, Crystal Structure Of Putative Geranylgeranyl Pyrophosphate Synthase From Corynebacterium Glutamicum Length = 380 Back     alignment and structure
>pdb|1RTR|A Chain A, Crystal Structure Of S. Aureus Farnesyl Pyrophosphate Synthase Length = 301 Back     alignment and structure
>pdb|2O1O|A Chain A, Cryptosporidium Parvum Putative Polyprenyl Pyrophosphate Synthase (Cgd4_2550) In Complex With Risedronate. Length = 368 Back     alignment and structure
>pdb|2FOR|A Chain A, Crystal Structure Of The Shigella Flexneri Farnesyl Pyrophosphate Synthase Complex With An Isopentenyl Pyrophosphate Length = 323 Back     alignment and structure
>pdb|1RQJ|A Chain A, Active Conformation Of Farnesyl Pyrophosphate Synthase Bound To Isopentyl Pyrophosphate And Risedronate Length = 299 Back     alignment and structure
>pdb|1RQI|A Chain A, Active Conformation Of Farnesyl Pyrophosphate Synthase Bound To Isopentyl Pyrophosphate And Dimethylallyl S- Thiolodiphosphate Length = 300 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 ?
Query255
2qis_A374 Farnesyl pyrophosphate synthetase; trans-prenyltra 3e-56
2qis_A 374 Farnesyl pyrophosphate synthetase; trans-prenyltra 1e-19
1uby_A367 FPS, farnesyl diphosphate synthase; transferase, i 5e-56
1uby_A 367 FPS, farnesyl diphosphate synthase; transferase, i 6e-22
1yhl_A362 Farnesyl pyrophosphate synthase; farnesyl diphosph 4e-52
1yhl_A 362 Farnesyl pyrophosphate synthase; farnesyl diphosph 1e-11
3dyh_A390 Farnesyl pyrophosphate synthase; protein-bisphosph 6e-52
3dyh_A 390 Farnesyl pyrophosphate synthase; protein-bisphosph 2e-17
2her_A368 Fragment, farnesyl pyrophosphate synthase; farnesy 3e-50
2her_A 368 Fragment, farnesyl pyrophosphate synthase; farnesy 3e-14
2ihi_A395 Pyrophosphate synthase; PV092040, structural genom 7e-47
2ihi_A 395 Pyrophosphate synthase; PV092040, structural genom 1e-13
3lk5_A380 Geranylgeranyl pyrophosphate synthase; structural 8e-25
1wmw_A330 Geranylgeranyl diphosphate synthetase; GGPP, preny 2e-19
3nf2_A352 Putative polyprenyl synthetase; isoprenyl diphosph 4e-19
1wy0_A342 Geranylgeranyl pyrophosphate synthetase; pyrococcu 4e-18
2q80_A301 Geranylgeranyl pyrophosphate synthetase; isoprenoi 3e-14
2e8v_A340 Geranylgeranyl pyrophosphate synthetase; prenyltra 2e-13
4dhd_A358 Polyprenyl synthetase; isoprenoid synthesis, isopr 2e-13
3mzv_A341 Decaprenyl diphosphate synthase; transferase, stru 1e-10
3pko_A334 Geranylgeranyl pyrophosphate synthase; isoprenyl d 1e-10
3oyr_A345 Trans-isoprenyl diphosphate synthase; isoprenyl sy 1e-10
3lmd_A360 Geranylgeranyl pyrophosphate synthase; isoprenyl d 6e-10
3aqb_B325 Component B of hexaprenyl diphosphate synthase; pr 8e-10
3tc1_A315 Octaprenyl pyrophosphate synthase; all alpha-helic 6e-09
2azj_A289 Geranylgeranyl pyrophosphate synthetase; hexpps, t 2e-08
1v4e_A299 Octoprenyl-diphosphate synthase; trans-type prenyl 2e-08
3rmg_A334 Octaprenyl-diphosphate synthase; structural genomi 3e-08
3m0g_A297 Farnesyl diphosphate synthase; structural genomics 9e-08
3apz_A348 Geranyl diphosphate synthase; prenyltransferase, a 3e-07
3lom_A313 Geranyltranstransferase; geranyltransferase, struc 4e-07
3ipi_A295 Geranyltranstransferase; isoprene biosynthesis, he 6e-07
4fp4_A285 Polyprenyl synthetase; isoprenoid synthesis, isopr 8e-07
1rqj_A299 Geranyltranstransferase; bisphosphonate, isoprenyl 8e-07
4f62_A317 Geranyltranstransferase; enzyme function initiativ 9e-07
3p8r_A302 Geranyltranstransferase; isoprenyl synthase, struc 1e-06
3ts7_A324 Geranyltranstransferase; isoprenoid synthesis, far 2e-06
3uca_A324 Geranyltranstransferase; isoprenoid synthesis, iso 2e-06
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 3e-06
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-04
1rtr_A301 Geranyltranstransferase; 2.50A {Staphylococcus aur 4e-06
3lsn_A304 Geranyltranstransferase; structural genomics, prot 7e-06
2h8o_A335 Geranyltranstransferase; geranyltransferase,agroba 1e-05
3llw_A311 Geranyltranstransferase (ISPA); structural genomic 1e-05
3p8l_A302 Geranyltranstransferase; isoprenyl synthase, struc 3e-05
3pde_A309 Farnesyl-diphosphate synthase; isoprenyl diphospha 6e-05
3npk_A291 Geranyltranstransferase; isoprene biosynthesis, SG 5e-04
>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
 Score =  183 bits (465), Expect = 3e-56
 Identities = 81/158 (51%), Positives = 105/158 (66%), Gaps = 8/158 (5%)

Query: 100 LALVVAYKMLAQPSELTPENLHLAQILGWCVEIVSLKTSMGQSLDLSTAN----DLSKFT 155
           L     Y++L       P  L+L ++        S +T +GQ+LDL TA     DL +FT
Sbjct: 155 LLEACIYRLLKLYCREQPYYLNLIELFLQ----SSYQTEIGQTLDLLTAPQGNVDLVRFT 210

Query: 156 MDRYEAIVKYKTAFYSFQLPVALAMHMAGMQDVEVHRQARTLLLEMGHFFQVQDDYLDCF 215
             RY++IVKYK+AFYSF LP+A AM+MAG+   + H  A+ +LLEMG FFQ+QDDYLD F
Sbjct: 211 EKRYKSIVKYKSAFYSFYLPIAAAMYMAGIDGEKEHANAKKILLEMGEFFQIQDDYLDLF 270

Query: 216 GTPDVTGKIGTDIEDGKCSWLAVVALQRATPAQRKLME 253
           G P VTGKIGTDI+D KCSWL V  LQRATP Q ++++
Sbjct: 271 GDPSVTGKIGTDIQDNKCSWLVVQCLQRATPEQYQILK 308
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>4dhd_A Polyprenyl synthetase; isoprenoid synthesis, isoprenoid diphosphate synthase, trans; 1.65A {Pyrobaculum calidifontis} Length = 358 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
>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
>3oyr_A Trans-isoprenyl diphosphate synthase; isoprenyl synthase, PSI, protein structure initiative; HET: IPE; 2.00A {Caulobacter crescentus} Length = 345 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
>3aqb_B Component B of hexaprenyl diphosphate synthase; prenyltransferase, transferase; 2.40A {Micrococcus luteus} PDB: 3aqc_B* Length = 325 Back     alignment and structure
>3tc1_A Octaprenyl pyrophosphate synthase; all alpha-helices fold, transferase; 2.00A {Helicobacter pylori} Length = 315 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
>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
>3rmg_A Octaprenyl-diphosphate synthase; structural genomics, protein structure initiative, isoprene biosynthesis, transferase; 2.30A {Bacteroides thetaiotaomicron} Length = 334 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
>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
>3lom_A Geranyltranstransferase; geranyltransferase, structural genomics, PSI, protein structure initiative, nysgrc; 2.30A {Legionella pneumophila subsp} Length = 313 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
>4fp4_A Polyprenyl synthetase; isoprenoid synthesis, isoprenoid diphosphate synthase, trans; HET: GER UNL; 2.00A {Pyrobaculum calidifontis} Length = 285 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
>4f62_A Geranyltranstransferase; enzyme function initiative, structural genomics; 2.10A {Marinomonas SP} Length = 317 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
>3ts7_A Geranyltranstransferase; isoprenoid synthesis, farnesyl diphosphate synthase; 1.94A {Methylococcus capsulatus} Length = 324 Back     alignment and structure
>3uca_A Geranyltranstransferase; isoprenoid synthesis, isoprenoid diphosphate synthase; 2.00A {Clostridium perfringens} Length = 324 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>1rtr_A Geranyltranstransferase; 2.50A {Staphylococcus aureus} SCOP: a.128.1.1 Length = 301 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
>2h8o_A Geranyltranstransferase; geranyltransferase,agrobacterium tumefaciens, structural GEN PSI-2, protein structure initiative; 1.60A {Agrobacterium tumefaciens} Length = 335 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
>3p8l_A Geranyltranstransferase; isoprenyl synthase, structural genomics, PSI, protein struct initiative, nysgrc; 2.00A {Enterococcus faecalis} Length = 302 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
>3npk_A Geranyltranstransferase; isoprene biosynthesis, SGX, structural genomics protein structure initiative; 1.50A {Campylobacter jejuni} Length = 291 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query255
1uby_A367 FPS, farnesyl diphosphate synthase; transferase, i 100.0
2ihi_A395 Pyrophosphate synthase; PV092040, structural genom 100.0
2qis_A374 Farnesyl pyrophosphate synthetase; trans-prenyltra 100.0
3dyh_A390 Farnesyl pyrophosphate synthase; protein-bisphosph 100.0
3mav_A395 Farnesyl pyrophosphate synthase; PV092040, structu 100.0
1yhl_A362 Farnesyl pyrophosphate synthase; farnesyl diphosph 100.0
2her_A368 Fragment, farnesyl pyrophosphate synthase; farnesy 100.0
2q58_A368 Fragment, farnesyl pyrophosphate synthase; farnesy 100.0
3oyr_A345 Trans-isoprenyl diphosphate synthase; isoprenyl sy 100.0
3mzv_A341 Decaprenyl diphosphate synthase; transferase, stru 100.0
4dhd_A358 Polyprenyl synthetase; isoprenoid synthesis, isopr 100.0
3pde_A309 Farnesyl-diphosphate synthase; isoprenyl diphospha 100.0
1wy0_A342 Geranylgeranyl pyrophosphate synthetase; pyrococcu 100.0
3rmg_A334 Octaprenyl-diphosphate synthase; structural genomi 100.0
3aqb_B325 Component B of hexaprenyl diphosphate synthase; pr 100.0
3pko_A334 Geranylgeranyl pyrophosphate synthase; isoprenyl d 100.0
3nf2_A352 Putative polyprenyl synthetase; isoprenyl diphosph 100.0
4f62_A317 Geranyltranstransferase; enzyme function initiativ 100.0
1wmw_A330 Geranylgeranyl diphosphate synthetase; GGPP, preny 100.0
3lmd_A360 Geranylgeranyl pyrophosphate synthase; isoprenyl d 100.0
3uca_A324 Geranyltranstransferase; isoprenoid synthesis, iso 100.0
3p8l_A302 Geranyltranstransferase; isoprenyl synthase, struc 100.0
3lsn_A304 Geranyltranstransferase; structural genomics, prot 100.0
3ts7_A324 Geranyltranstransferase; isoprenoid synthesis, far 100.0
3m0g_A297 Farnesyl diphosphate synthase; structural genomics 100.0
3llw_A311 Geranyltranstransferase (ISPA); structural genomic 100.0
3p8r_A302 Geranyltranstransferase; isoprenyl synthase, struc 100.0
3lom_A313 Geranyltranstransferase; geranyltransferase, struc 100.0
1v4e_A299 Octoprenyl-diphosphate synthase; trans-type prenyl 100.0
1rtr_A301 Geranyltranstransferase; 2.50A {Staphylococcus aur 100.0
2h8o_A335 Geranyltranstransferase; geranyltransferase,agroba 100.0
3apz_A348 Geranyl diphosphate synthase; prenyltransferase, a 100.0
1rqj_A299 Geranyltranstransferase; bisphosphonate, isoprenyl 100.0
3lk5_A380 Geranylgeranyl pyrophosphate synthase; structural 100.0
3tc1_A315 Octaprenyl pyrophosphate synthase; all alpha-helic 100.0
3npk_A291 Geranyltranstransferase; isoprene biosynthesis, SG 100.0
2e8v_A340 Geranylgeranyl pyrophosphate synthetase; prenyltra 100.0
2q80_A301 Geranylgeranyl pyrophosphate synthetase; isoprenoi 100.0
2ftz_A284 Geranyltranstransferase; TM0161, structural GE joi 100.0
3ipi_A295 Geranyltranstransferase; isoprene biosynthesis, he 100.0
2j1p_A293 Geranylgeranyl pyrophosphate synthetase; transfera 99.97
2azj_A289 Geranylgeranyl pyrophosphate synthetase; hexpps, t 99.97
4fp4_A285 Polyprenyl synthetase; isoprenoid synthesis, isopr 99.96
3qkc_B273 Geranyl diphosphate synthase small subunit; struct 99.93
3kra_B274 Geranyl diphosphate synthase small subunit; prenyl 99.93
3acx_A293 Dehydrosqualene synthase; CRTM, carotenoid biosynt 88.79
4hd1_A294 Squalene synthase HPNC; MCSG, structural genomics, 80.71
>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
Probab=100.00  E-value=1.5e-43  Score=330.35  Aligned_cols=210  Identities=53%  Similarity=0.901  Sum_probs=182.5

Q ss_pred             hhhhchHHHHHHHHHHhhHHHHHHHhccCCCCCc-hHHHHHHHHHhHHHHHHhhhhcchhhHHHHhhcccCCCCccchHH
Q psy9101          23 TNTVLSKDESRDFMAIFPDLVRDLTDAGRHSDIP-DVTKWYAKVLQYNKAISNNVYLGTYFIVQVLQYNVPSGKKNRGLA  101 (255)
Q Consensus        23 ~~~~~~~~~~~~f~~~~~~l~~~l~~~~~~~~~~-~~~~~~~~~l~~~~~l~~~~~~~~~~i~~a~~y~~~gGKr~Rpll  101 (255)
                      ..++..++++++|+++|+.+++++.+...+.+.+ +...|+.+++                     +|+++||||+||++
T Consensus        19 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~---------------------~y~~~gGKrlRp~l   77 (367)
T 1uby_A           19 LSPVVVEREREEFVGFFPQIVRDLTEDGIGHPEVGDAVARLKEVL---------------------QYNAPGGKCNRGLT   77 (367)
T ss_dssp             -CHHHHHHHHHHHHHTHHHHHHHHHTTTSSCTTTHHHHHHHHHHH---------------------HHHSSSSCCHHHHH
T ss_pred             CCCCCchHHHHHHHHHHHHHHHHHHHhhhcccCchhhHHHHHHHH---------------------hhhcCCCcchhHHH
Confidence            3345567889999999999999999987544444 6777888888                     99999999999999


Q ss_pred             HHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHH------------------------------------------------
Q psy9101         102 LVVAYKMLAQPSELTPENLHLAQILGWCVEIV------------------------------------------------  133 (255)
Q Consensus       102 ~lla~~~l~~~~~~~~~~~~~a~~lA~avEll------------------------------------------------  133 (255)
                      ++++++++++...++++.++.+..+|||+||+                                                
T Consensus        78 ~l~~~~~~~~~~~~~~~~~~~~~~~A~aiEliH~asLiHDDImD~s~~RRG~pt~h~~~g~~~~ai~dg~~l~~~a~~~l  157 (367)
T 1uby_A           78 VVAAYRELSGPGQKDAESLRCALAVGWCIELFQAASLVADDIMDQSLTRRGQLCWYKKEGVGLDAINDSFLLESSVYRVL  157 (367)
T ss_dssp             HHHHHHHHCCGGGCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEETTEECGGGSTTTTTHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCccCChhhHHHHHHHHHHHHHHHHHHHHhCcccCCCCCCCCCCChhhccCcHHHHHHHHHHHHHHHHHHH
Confidence            99999998752112355455678899999999                                                


Q ss_pred             --------------------HHHhhcccchhcccCCC----CCCCCHHHHHHHHhccccchhHHHHHHHHHHHhC-CCCH
Q psy9101         134 --------------------SLKTSMGQSLDLSTAND----LSKFTMDRYEAIVKYKTAFYSFQLPVALAMHMAG-MQDV  188 (255)
Q Consensus       134 --------------------~~~~~~GQ~lDl~~~~~----~~~~t~~~y~~i~~~KTa~Ltf~~~~~lga~lag-~~~~  188 (255)
                                          ...++.||.+|+.+..+    +..+++++|.+|+++|||+|||++||.+|++++| + ++
T Consensus       158 ~~~~~~~~~~~~~~~~~~~~~~~~~~GQ~lDl~~~~~~~~d~~~~t~~~y~~ii~~KTa~Lsf~~~~~~ga~lag~~-~~  236 (367)
T 1uby_A          158 KKYCRQRPYYVHLLELFLQTAYQTELGQMLDLITAPVSKVDLSHFSEERYKAIVKYKTAFYSFYLPVAAAMYMVGID-SK  236 (367)
T ss_dssp             HHHHTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHSCTTSCCCTTCCHHHHHHHHHHHTHHHHTHHHHHHHHHHHTCC-CH
T ss_pred             HHhccccccHHHHHHHHHHHHHHHHHHHHHHHhcccccccccccCCHHHHHHHHHhCchHHHHHHHHHHHHHHcCCc-cH
Confidence                                45679999999988642    2258999999999999999999999999999999 7 88


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhccCCCCCccCCccchHhcCCchHHHHHHHhhCCHHHHHHHHh
Q psy9101         189 EVHRQARTLLLEMGHFFQVQDDYLDCFGTPDVTGKIGTDIEDGKCSWLAVVALQRATPAQRKLMEV  254 (255)
Q Consensus       189 ~~~~~l~~~g~~iGiaFQI~DD~lD~~gd~~~~GK~g~Di~~gK~T~p~i~al~~a~~~~r~~l~~  254 (255)
                      +..+.+++||.++|+||||+|||+|++||++++||.|+|+++||+|||+++|++.+++++|+.|++
T Consensus       237 ~~~~~l~~~g~~lG~aFQI~DD~LD~~gd~~~~GK~g~Dl~egK~T~p~l~al~~~~~~~~~~l~~  302 (367)
T 1uby_A          237 EEHENAKAILLEMGEYFQIQDDYLDCFGDPALTGAVGTDIQDNKCSWLVVQCLQRVTPEQRQLLED  302 (367)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCTTCSSCCCCCSSSCCCCHHHHHHHHHCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhcCChhhcCCchhhHHcCCchHHHHHHHHhCCHHHHHHHHH
Confidence            899999999999999999999999999999999999999999999999999999999999988764
>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
>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
>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
>3oyr_A Trans-isoprenyl diphosphate synthase; isoprenyl synthase, PSI, protein structure initiative; HET: IPE; 2.00A {Caulobacter crescentus} Back     alignment and structure
>3mzv_A Decaprenyl diphosphate synthase; transferase, structural genomics, PSI-2, protein structure initiative; 1.90A {Rhodobacter capsulatus} Back     alignment and structure
>4dhd_A Polyprenyl synthetase; isoprenoid synthesis, isoprenoid diphosphate synthase, trans; 1.65A {Pyrobaculum calidifontis} PDB: 4gp1_A* 4gp2_A* 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
>1wy0_A Geranylgeranyl pyrophosphate synthetase; pyrococcus horikosh structural genomics, riken structural genomics/proteomics initiative, RSGI; 2.20A {Pyrococcus horikoshii} 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
>3aqb_B Component B of hexaprenyl diphosphate synthase; prenyltransferase, transferase; 2.40A {Micrococcus luteus} PDB: 3aqc_B* 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
>3nf2_A Putative polyprenyl synthetase; isoprenyl diphosphate synthase, structural genomics, PSI, PR structure initiative, nysgrc; 2.20A {Streptomyces coelicolor} Back     alignment and structure
>4f62_A Geranyltranstransferase; enzyme function initiative, structural genomics; 2.10A {Marinomonas SP} 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
>3uca_A Geranyltranstransferase; isoprenoid synthesis, isoprenoid diphosphate synthase; 2.00A {Clostridium perfringens} Back     alignment and structure
>3p8l_A Geranyltranstransferase; isoprenyl synthase, structural genomics, PSI, protein struct initiative, nysgrc; 2.00A {Enterococcus faecalis} 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
>3ts7_A Geranyltranstransferase; isoprenoid synthesis, farnesyl diphosphate synthase; 1.94A {Methylococcus capsulatus} 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
>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
>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
>1rtr_A Geranyltranstransferase; 2.50A {Staphylococcus aureus} SCOP: a.128.1.1 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
>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
>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
>3lk5_A Geranylgeranyl pyrophosphate synthase; structural genomics, protein structure initiative, geranylge pyrophosphate synthase; 1.90A {Corynebacterium glutamicum} PDB: 3qqv_A* Back     alignment and structure
>3tc1_A Octaprenyl pyrophosphate synthase; all alpha-helices fold, transferase; 2.00A {Helicobacter pylori} Back     alignment and structure
>3npk_A Geranyltranstransferase; isoprene biosynthesis, SGX, structural genomics protein structure initiative; 1.50A {Campylobacter jejuni} 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
>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
>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
>3ipi_A Geranyltranstransferase; isoprene biosynthesis, helical bundle, protein structure initiative II (PSI II), structural genomics, nysgxrc; 1.90A {Methanosarcina mazei} 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
>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
>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
>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
>3acx_A Dehydrosqualene synthase; CRTM, carotenoid biosynthesis, staphyloxanthin biosynthesis, transferase, head-TO-head condensation, inhibitor; HET: 673; 1.31A {Staphylococcus aureus} PDB: 2zcp_A* 2zcq_A* 2zcr_A* 2zcs_A* 2zy1_A* 3acw_A* 2zco_A* 3acy_A* 3npr_A* 3nri_A* 3tfn_A* 3tfp_A* 3tfv_A* 3adz_A* 3lgz_B* 3vjd_A* 3vje_A* 3ae0_A* 4ea2_A* 4e9u_A* ... Back     alignment and structure
>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 255
d1fpsa_ 348 a.128.1.1 (A:) Farnesyl diphosphate synthase (gera 6e-17
d1rqja_299 a.128.1.1 (A:) Farnesyl diphosphate synthase (gera 9e-10
d1v4ea_280 a.128.1.1 (A:) Octoprenyl-diphosphate synthase {Th 6e-09
d1rtra_290 a.128.1.1 (A:) Farnesyl diphosphate synthase (gera 6e-06
>d1fpsa_ a.128.1.1 (A:) Farnesyl diphosphate synthase (geranyltranstransferase) {Chicken (Gallus gallus) [TaxId: 9031]} Length = 348 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: Chicken (Gallus gallus) [TaxId: 9031]

 Score = 77.0 bits (188), Expect = 6e-17
 Identities = 37/109 (33%), Positives = 53/109 (48%), Gaps = 22/109 (20%)

Query: 26  VLSKDESRDFMAIFPDLVRDLT-DAGRHSDIPDVTKWYAKVLQYNKAISNNVYLGTYFIV 84
           V+ + E  +F+  FP +VRDLT D   H ++ D      +VLQYN               
Sbjct: 3   VVVEREREEFVGFFPQIVRDLTEDGIGHPEVGDAVARLKEVLQYN--------------- 47

Query: 85  QVLQYNVPSGKKNRGLALVVAYKMLAQPSELTPENLHLAQILGWCVEIV 133
                  P GK NRGL +V AY+ L+ P +   E+L  A  +GWC+E+ 
Sbjct: 48  ------APGGKCNRGLTVVAAYRELSGPGQKDAESLRCALAVGWCIELF 90
>d1rqja_ a.128.1.1 (A:) Farnesyl diphosphate synthase (geranyltranstransferase) {Escherichia coli [TaxId: 562]} Length = 299 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
>d1rtra_ a.128.1.1 (A:) Farnesyl diphosphate synthase (geranyltranstransferase) {Staphylococcus aureus [TaxId: 1280]} Length = 290 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 ?
Query255
d1fpsa_348 Farnesyl diphosphate synthase (geranyltranstransfe 100.0
d1rtra_290 Farnesyl diphosphate synthase (geranyltranstransfe 100.0
d1rqja_299 Farnesyl diphosphate synthase (geranyltranstransfe 100.0
d2q80a1291 Geranylgeranyl pyrophosphate synthetase {Human (Ho 100.0
d1v4ea_280 Octoprenyl-diphosphate synthase {Thermotoga mariti 100.0
d1ezfa_ 333 Squalene synthase {Human (Homo sapiens) [TaxId: 96 83.66
>d1fpsa_ a.128.1.1 (A:) Farnesyl diphosphate synthase (geranyltranstransferase) {Chicken (Gallus gallus) [TaxId: 9031]} 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: Chicken (Gallus gallus) [TaxId: 9031]

Probab=100.00  E-value=6e-42  Score=314.84  Aligned_cols=208  Identities=54%  Similarity=0.954  Sum_probs=181.1

Q ss_pred             hchHHHHHHHHHHhhHHHHHHHhccCC-CCCchHHHHHHHHHhHHHHHHhhhhcchhhHHHHhhcccCCCCccchHHHHH
Q psy9101          26 VLSKDESRDFMAIFPDLVRDLTDAGRH-SDIPDVTKWYAKVLQYNKAISNNVYLGTYFIVQVLQYNVPSGKKNRGLALVV  104 (255)
Q Consensus        26 ~~~~~~~~~f~~~~~~l~~~l~~~~~~-~~~~~~~~~~~~~l~~~~~l~~~~~~~~~~i~~a~~y~~~gGKr~Rpll~ll  104 (255)
                      +...+++++|+..|+++.+++.+.... ++.+++.+|+.+++                     +|+++||||+||+++++
T Consensus         3 ~~v~~~~~~f~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~~---------------------~y~~~GGKrlRp~l~l~   61 (348)
T d1fpsa_           3 VVVEREREEFVGFFPQIVRDLTEDGIGHPEVGDAVARLKEVL---------------------QYNAPGGKCNRGLTVVA   61 (348)
T ss_dssp             HHHHHHHHHHHTTHHHHHHHHHTTTTTCTTTHHHHHHHHHHH---------------------HHHSSCSCCHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHHHHH---------------------HhccCCcccHhHHHHHH
Confidence            455789999999999999999887644 34447888999988                     99999999999999999


Q ss_pred             HHHHhcCCCCCCHHHHHHHHHHHHHHHHH---------------------------------------------------
Q psy9101         105 AYKMLAQPSELTPENLHLAQILGWCVEIV---------------------------------------------------  133 (255)
Q Consensus       105 a~~~l~~~~~~~~~~~~~a~~lA~avEll---------------------------------------------------  133 (255)
                      +++++++....+.+.++.+..+|||+|++                                                   
T Consensus        62 ~~~~~~~~~~~~~~~~~~~~~~A~avEliH~asLihDDi~D~~~~RRG~pt~~~~~g~~~ail~gd~ll~~~~~~~l~~~  141 (348)
T d1fpsa_          62 AYRELSGPGQKDAESLRCALAVGWCIELFQAFFLVADDIMDQSLTRRGQLCWYKKEGVGLDAINDSFLLESSVYRVLKKY  141 (348)
T ss_dssp             HHHHHCCTTSCSHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCCEETTEECTTTSTTTTTTHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhCCCcccchHHHHHHHHHHHHHHHHHHHHHHhCccccCCccccccchhhhhccccHHHHHHHHHHHHHHHHHHHhh
Confidence            99999876555677788899999999999                                                   


Q ss_pred             -----------------HHHhhcccchhcccCC----CCCCCCHHHHHHHHhccccchhHHHHHHHHHHHhCCCCHHHHH
Q psy9101         134 -----------------SLKTSMGQSLDLSTAN----DLSKFTMDRYEAIVKYKTAFYSFQLPVALAMHMAGMQDVEVHR  192 (255)
Q Consensus       134 -----------------~~~~~~GQ~lDl~~~~----~~~~~t~~~y~~i~~~KTa~Ltf~~~~~lga~lag~~~~~~~~  192 (255)
                                       ...++.||.+|+.+..    +...+++++|++|+++|||+|||..|+.+|+.+++..+++..+
T Consensus       142 ~~~~~~~~~~~~~~~~~~~~~~~GQ~ldl~~~~~~~~~~~~~t~~~Y~~~i~~KTa~l~~~~~~~~~~~~~~~~~~~~~~  221 (348)
T d1fpsa_         142 CRQRPYYVHLLELFLQTAYQTELGQMLDLITAPVSKVDLSHFSEERYKAIVKYKTAFYSFYLPVAAAMYMVGIDSKEEHE  221 (348)
T ss_dssp             HTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHSCTTTCCSSSCCHHHHHHHHHHHTHHHHTHHHHHHHHHHTTCCCHHHHH
T ss_pred             ccchHHHHHHHHhhhhhhhHHHHHHHHHHhhhccccccccccCHHHHHHHHHHHhhhhhHHHHHHHHHHhhhhccccchh
Confidence                             5577899999997654    2234689999999999999997777777776555443788899


Q ss_pred             HHHHHHHHHHHHHHHHhhhhccCCCCCccCCccchHhcCCchHHHHHHHhhCCHHHHHHHHh
Q psy9101         193 QARTLLLEMGHFFQVQDDYLDCFGTPDVTGKIGTDIEDGKCSWLAVVALQRATPAQRKLMEV  254 (255)
Q Consensus       193 ~l~~~g~~iGiaFQI~DD~lD~~gd~~~~GK~g~Di~~gK~T~p~i~al~~a~~~~r~~l~~  254 (255)
                      .+.+||.++|+||||+||++|++||++.+||.|+||++||+|||++++++.+++++|+.|.+
T Consensus       222 ~l~~~g~~lGiaFQI~DDilD~~gd~~~~GK~g~Dl~egK~Tlpii~al~~~~~~~r~~l~~  283 (348)
T d1fpsa_         222 NAKAILLEMGEYFQIQDDYLDCFGDPALTGKVGTDIQDNKCSWLVVQCLQRVTPEQRQLLED  283 (348)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSCCSSCCSSCSCCCSSCCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             hccccccccchHHHHHHHHhhhhcchhccCcccccccCCccHHHHHHHHHhCCHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999998865
>d1rtra_ a.128.1.1 (A:) Farnesyl diphosphate synthase (geranyltranstransferase) {Staphylococcus aureus [TaxId: 1280]} Back     information, alignment and structure
>d1rqja_ a.128.1.1 (A:) Farnesyl diphosphate synthase (geranyltranstransferase) {Escherichia coli [TaxId: 562]} 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
>d1v4ea_ a.128.1.1 (A:) Octoprenyl-diphosphate synthase {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1ezfa_ a.128.1.2 (A:) Squalene synthase {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure