Citrus Sinensis ID: 047640

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-
Protein Sequence
MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTYETYKKNEGGLHTCGAACGAILGGGSVEEIEKKFRGLIIKITKMMIRNSFC
Secondary Structure (PSIPRED)
ccccHHHHHHHHHHcccccccccHHHHHHHHHHHHHHccHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHcHHHHEEccccccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHcccccEEEEEEEEcccccccEEEHHHccccHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHcccc
Coil and Loop (DISEMBL)
MADAMLPFGLELLassdnpagnnsgRILRVMVEMTRAmgsqgvvegqynELQCSQYVEMTYETykknegglhtcgaacgailgggsVEEIEKKFRGLIIKITKMMIRNSFC
Flexible Loop (DISEMBL)
MADAMLPFGLELLassdnpagnnsGRILRVMVEMTRAMGsqgvvegqynELQCSQYVEMTYETYKKNEGGLHTCGAACGAILGGGSVEEIEKKFRGLIIKITKMMIRNSFC
Low Complexity Region (SEG)
MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTYETYKKNEGGLHTcgaacgailgggSVEEIEKKFRGLIIKITKMMIRNSFC
Disordered region (IsUnstruct)
**************************ILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTYETYKKNEGGLHTCGAACGAILGGGSVEEIEKKFRGLIIKITKMMIR****
Disordered Region (DISOPRED)
MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTYETYKKNEGGLHTCGAACGAILGGGSVEEIEKKFRGLIIKITKMMIRNSFC
Disordered Region (DISEMBL)
MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTYETYKKNEGGLHTCGAACGAILGGGSVEEIEKKFRGLIIKITKMMIRNSFC
Disordered Region (DISPRO)
*ADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTYETYKKNEGGLHTCGAACGAILGGGSVEEIEKKFRGLIIKITKMMIRNSFC
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTYETYKKNEGGLHTCGAACGAILGGGSVEEIEKKFRGLIIKITKMMIRNSFC
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	111	2.2.26 [Sep-21-2011]
Q39108	326	Heterodimeric geranylgera	yes	no	0.819	0.279	0.311	2e-07
P80042	369	Geranylgeranyl pyrophosph	N/A	no	0.828	0.249	0.306	1e-06
Q94ID7	370	Geranylgeranyl pyrophosph	N/A	no	0.801	0.240	0.336	1e-05
P34802	371	Heterodimeric geranylgera	no	no	0.747	0.223	0.314	1e-05
Q9ZU77	347	Geranylgeranyl pyrophosph	no	no	0.747	0.239	0.314	1e-05
Q43133	366	Geranylgeranyl pyrophosph	N/A	no	0.810	0.245	0.309	3e-05
Q9LRR0	361	Putative geranylgeranyl p	no	no	0.621	0.191	0.36	9e-05
Q42698	357	Geranylgeranyl pyrophosph	N/A	no	0.792	0.246	0.322	0.0004
Q9SLG2	372	Geranylgeranyl pyrophosph	no	no	0.765	0.228	0.294	0.0009

>sp|Q39108|GGR_ARATH Heterodimeric geranylgeranyl pyrophosphate synthase small subunit, chloroplastic OS=Arabidopsis thaliana GN=GGR PE=1 SV=2

 Score = 54.3 bits (129), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 29/93 (31%), Positives = 49/93 (52%), Gaps = 2/93 (2%)

Query: 3   DAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTYE 62
           DA+ P   + + S   P       ILR++ E+ R +GS G+  GQY +L+   +  +++ 
Sbjct: 158 DALFPLAFQHIVSHTPPDLVPRATILRLITEIARTVGSTGMAAGQYVDLEGGPF-PLSFV 216

Query: 63  TYKKNEGGLHTCGAACGAILGGGSVEEIEKKFR 95
             KK  G +  C A CG +LGG + +E++   R
Sbjct: 217 QEKKF-GAMGECSAVCGGLLGGATEDELQSLRR 248

Heterodimeric geranyl(geranyl)-diphosphate (GPP) synthase small subunit. The small subunit alone is inactive in vitro while the large subunit GGPPS1 catalyzes mainly the production of geranygeranyl-diphosphate in vitro. Upon association of the two subunits, the product profile changes and the production of gerany-diphosphate is strongly increased.
Arabidopsis thaliana (taxid: 3702)

>sp|P80042|GGPPS_CAPAN Geranylgeranyl pyrophosphate synthase, chloroplastic OS=Capsicum annuum GN=GGPS1 PE=3 SV=1

 Score = 51.6 bits (122), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 30/98 (30%), Positives = 52/98 (53%), Gaps = 6/98 (6%)

Query: 2   ADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTY 61
            D++L F  E + +S   AG    RI+  + E+ +++G++G+V GQ  +++C+    ++ 
Sbjct: 187 GDSLLAFAFEHIVNST--AGVTPSRIVGAVAELAKSIGTEGLVAGQVADIKCTGNASVSL 244

Query: 62  ETYK----KNEGGLHTCGAACGAILGGGSVEEIEKKFR 95
           ET +         L       GAILGGG+  E+EK  R
Sbjct: 245 ETLEFIHVHKTAALLESSVVLGAILGGGTNVEVEKLRR 282

Catalyzes the trans-addition of the three molecules of IPP onto DMAPP to form geranylgeranyl pyrophosphate.

Capsicum annuum (taxid: 4072)

EC: 2

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 1

EC: 0

>sp|Q94ID7|GGPPS_HEVBR Geranylgeranyl pyrophosphate synthase, chloroplastic OS=Hevea brasiliensis GN=GGPS PE=1 SV=1

 Score = 48.9 bits (115), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 32/95 (33%), Positives = 49/95 (51%), Gaps = 6/95 (6%)

Query: 2   ADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTY 61
            DA+L F  E +A S      +S RI+R + E+ +A+G++G+V GQ  ++      E+  
Sbjct: 188 GDALLAFAFEHIAVST--LNVSSARIVRAVGELAKAIGAEGLVAGQVVDINSEGSSEVDL 245

Query: 62  ETYK----KNEGGLHTCGAACGAILGGGSVEEIEK 92
           E  +         L       GAILGGG+ EE+EK
Sbjct: 246 EKLEFIHIHKTAKLLEGAVVLGAILGGGTDEEVEK 280

Catalyzes the trans-addition of the three molecules of IPP onto DMAPP to form geranylgeranyl pyrophosphate.

Hevea brasiliensis (taxid: 3981)

EC: 2

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 1

EC: 0

>sp|P34802|GGPP1_ARATH Heterodimeric geranylgeranyl pyrophosphate synthase large subunit 1, chloroplastic OS=Arabidopsis thaliana GN=GGPPS1 PE=1 SV=2

 Score = 48.5 bits (114), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 33/105 (31%), Positives = 53/105 (50%), Gaps = 22/105 (20%)

Query: 2   ADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTY 61
            DA+L F  E LAS+ +    +  R++R + E+ +A+G++G+V G        Q V+++ 
Sbjct: 185 GDALLSFAFEHLASATSSDVVSPVRVVRAVGELAKAIGTEGLVAG--------QVVDISS 236

Query: 62  ETYKKNEGGLH--------------TCGAACGAILGGGSVEEIEK 92
           E    N+ GL                  A  GAI+GGGS +EIE+
Sbjct: 237 EGLDLNDVGLEHLEFIHLHKTAALLEASAVLGAIVGGGSDDEIER 281

Heterodimeric geranyl(geranyl)-diphosphate (GPP) synthase large subunit. In vitro, the large subunit catalyzes mainly the trans-addition of the three molecules of IPP onto DMAPP to form geranylgeranyl pyrophosphate while the small subunit alone is inactive. Upon association of the two subunits, the product profile changes and the production of gerany-diphosphate is strongly increased.

Arabidopsis thaliana (taxid: 3702)

EC: 2

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 1

EC: 0

>sp|Q9ZU77|GGPP7_ARATH Geranylgeranyl pyrophosphate synthase 7, chloroplastic OS=Arabidopsis thaliana GN=At2g18620 PE=2 SV=1

 Score = 48.5 bits (114), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 34/108 (31%), Positives = 52/108 (48%), Gaps = 25/108 (23%)

Query: 2   ADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTY 61
            DA++ F  E LA+S      +  R++R + E+ +A+GS+G+V G        Q V++T 
Sbjct: 164 GDALISFAFEHLATS---TAVSPARVVRAIGELAKAIGSKGLVAG--------QVVDLTS 212

Query: 62  ETYKKNEGGLHT--------------CGAACGAILGGGSVEEIEKKFR 95
               +N+ GL                     GAI+GGGS EE+EK  R
Sbjct: 213 GGMDQNDVGLEVLEFIHVHKTAVLLEAATVLGAIVGGGSDEEVEKLRR 260

Catalyzes the trans-addition of the three molecules of IPP onto DMAPP to form geranylgeranyl pyrophosphate.

Arabidopsis thaliana (taxid: 3702)

EC: 2

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 1

EC: 0

>sp|Q43133|GGPPS_SINAL Geranylgeranyl pyrophosphate synthase, chloroplastic/chromoplastic OS=Sinapis alba GN=GGPS1 PE=1 SV=1

 Score = 47.0 bits (110), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 30/97 (30%), Positives = 50/97 (51%), Gaps = 7/97 (7%)

Query: 2   ADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQY----- 56
            DA+L F  E LAS+ + +  +  R++R + E+ +A+G++G+V GQ  ++          
Sbjct: 181 GDALLSFAFEHLASATS-SEVSPARVVRAVGELAKAIGTEGLVAGQVVDISSEGLDLNNV 239

Query: 57  -VEMTYETYKKNEGGLHTCGAACGAILGGGSVEEIEK 92
            +E     +      L    A  G I+GGGS EEIE+
Sbjct: 240 GLEHLKFIHLHKTAALLEASAVLGGIIGGGSDEEIER 276

Catalyzes the trans-addition of the three molecules of IPP onto DMAPP to form geranylgeranyl pyrophosphate.

Sinapis alba (taxid: 3728)

EC: 2

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 1

EC: 0

>sp|Q9LRR0|GGPP8_ARATH Putative geranylgeranyl pyrophosphate synthase 8, chloroplastic OS=Arabidopsis thaliana GN=At3g14510 PE=5 SV=2

 Score = 45.8 bits (107), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 27/75 (36%), Positives = 41/75 (54%), Gaps = 6/75 (8%)

Query: 24  SGRILRVMVEMTRAMGSQGVVEGQYNELQCSQY------VEMTYETYKKNEGGLHTCGAA 77
           S R++R +VE+ RA+G++G+V GQ  +L   +       +E     +      L    A 
Sbjct: 197 SERMIRAVVELARAIGTKGLVAGQVVDLSSERLNPHDVGLERLEFIHLHKTAALLEAAAV 256

Query: 78  CGAILGGGSVEEIEK 92
            GAI+GGG+ EEIEK
Sbjct: 257 IGAIMGGGTEEEIEK 271

Catalyzes the trans-addition of the three molecules of IPP onto DMAPP to form geranylgeranyl pyrophosphate.

Arabidopsis thaliana (taxid: 3702)

EC: 2

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 1

EC: 0

>sp|Q42698|GGPPS_CATRO Geranylgeranyl pyrophosphate synthase, chloroplastic OS=Catharanthus roseus GN=GGPS1 PE=3 SV=1

 Score = 43.5 bits (101), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 31/96 (32%), Positives = 51/96 (53%), Gaps = 8/96 (8%)

Query: 2   ADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYV---- 57
            DA+L F  E +A++    G +S RI+RV+ E+ + +GS+G+V GQ  ++ CS+ +    
Sbjct: 175 GDALLAFAFEHIATATK--GVSSERIVRVVGELAKCIGSEGLVAGQVVDV-CSEGIADVG 231

Query: 58  -EMTYETYKKNEGGLHTCGAACGAILGGGSVEEIEK 92
            E     +      L       GAI+GG + E+I K
Sbjct: 232 LEHLEFIHIHKTAALLEGSVVLGAIVGGANDEQISK 267

Catalyzes the trans-addition of the three molecules of IPP onto DMAPP to form geranylgeranyl pyrophosphate.

Catharanthus roseus (taxid: 4058)

EC: 2

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 1

EC: 0

>sp|Q9SLG2|GGPP4_ARATH Geranylgeranyl pyrophosphate synthase 4 OS=Arabidopsis thaliana GN=GGPP4 PE=2 SV=1

 Score = 42.4 bits (98), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 28/95 (29%), Positives = 49/95 (51%), Gaps = 10/95 (10%)

Query: 4   AMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNEL------QCSQYV 57
           A+L    E L  +D     +S +++R + E+ +++G++G+V GQ  +L      Q    +
Sbjct: 192 ALLALAFEHLTEADV----SSKKMVRAVKELAKSIGTKGLVAGQAKDLSSEGLEQNDVGL 247

Query: 58  EMTYETYKKNEGGLHTCGAACGAILGGGSVEEIEK 92
           E     +    G L    A  GA++GGG+ +EIEK
Sbjct: 248 EDLEYIHVHKTGSLLEASAVIGAVIGGGTEKEIEK 282

Catalyzes the trans-addition of the three molecules of IPP onto DMAPP to form geranylgeranyl pyrophosphate.

Arabidopsis thaliana (taxid: 3702)

EC: 2

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 1

EC: 0

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	111
255583629	308	geranyl geranyl pyrophosphate synthase,	0.837	0.301	0.58	8e-24
164605008	306	geranyl-diphosphate synthase [Hevea bras	0.855	0.310	0.529	2e-22
46241272	297	geranyl diphosphate synthase small subun	0.837	0.313	0.557	1e-21
224135433	236	predicted protein [Populus trichocarpa]	0.927	0.436	0.541	1e-21
323463187	273	Chain B, Crystal Structure Of Geranyl Di	0.837	0.340	0.557	1e-21
229915238	279	geranyl diphosphate synthase small subun	0.828	0.329	0.494	4e-18
225460953	298	PREDICTED: geranylgeranyl pyrophosphate	0.918	0.342	0.478	1e-17
147776970	298	hypothetical protein VITISV_007690 [Viti	0.918	0.342	0.478	2e-17
46241300	300	geranyl diphosphate synthase small subun	0.801	0.296	0.5	7e-17
449444204	300	PREDICTED: heterodimeric geranylgeranyl	0.909	0.336	0.449	5e-16

>gi|255583629|ref|XP_002532570.1| geranyl geranyl pyrophosphate synthase, putative [Ricinus communis] gi|223527725|gb|EEF29831.1| geranyl geranyl pyrophosphate synthase, putative [Ricinus communis]

 Score =  114 bits (285), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 58/100 (58%), Positives = 68/100 (68%), Gaps = 7/100 (7%)

Query: 3   DAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQ------- 55
           D M+PF  ELLA  +NPA +NS RILRVM+E++RAMGSQG+VEGQYNE Q  Q       
Sbjct: 154 DGMIPFAFELLAQLNNPAQDNSDRILRVMIEISRAMGSQGMVEGQYNEFQYDQSVGDELF 213

Query: 56  YVEMTYETYKKNEGGLHTCGAACGAILGGGSVEEIEKKFR 95
           +V    +  KK EG  H C  ACGAILGGG+ EEIEK  R
Sbjct: 214 HVAWLRDVCKKKEGASHACAGACGAILGGGNEEEIEKLRR 253

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|164605008|dbj|BAF98300.1| geranyl-diphosphate synthase [Hevea brasiliensis]

 Score =  109 bits (272), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 54/102 (52%), Positives = 69/102 (67%), Gaps = 7/102 (6%)

Query: 1   MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQ----- 55
           +AD ++P+G ELLA  D+ A NNS R+LR ++E++RAMGSQGV+EGQYNE Q  +     
Sbjct: 146 IADGIIPYGFELLARDDDAAENNSNRVLRAIIEISRAMGSQGVIEGQYNESQYEESEGEE 205

Query: 56  --YVEMTYETYKKNEGGLHTCGAACGAILGGGSVEEIEKKFR 95
             +V       +K EG LH C  ACGAILGGGS +EIEK  R
Sbjct: 206 IFHVGWLQNVCRKKEGTLHACAGACGAILGGGSEDEIEKLRR 247

Source: Hevea brasiliensis

Species: Hevea brasiliensis

Genus: Hevea

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|46241272|gb|AAS82859.1| geranyl diphosphate synthase small subunit [Antirrhinum majus]

 Score =  107 bits (266), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 53/95 (55%), Positives = 68/95 (71%), Gaps = 2/95 (2%)

Query: 3   DAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTYE 62
           D ++PFGLEL+A S +P  NN  RILR ++E+TR MGS+G+VEGQY+EL  +Q  ++   
Sbjct: 145 DGIIPFGLELMARSMDPTRNNPDRILRAIIELTRVMGSEGIVEGQYHELGLNQLNDLELI 204

Query: 63  TY--KKNEGGLHTCGAACGAILGGGSVEEIEKKFR 95
            Y  KK EG LH CGAACGAILGG   ++IEK  R
Sbjct: 205 EYVCKKKEGTLHACGAACGAILGGCDEDKIEKLRR 239

Source: Antirrhinum majus

Species: Antirrhinum majus

Genus: Antirrhinum

Family: Plantaginaceae

Order: Lamiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224135433|ref|XP_002322072.1| predicted protein [Populus trichocarpa] gi|222869068|gb|EEF06199.1| predicted protein [Populus trichocarpa]

 Score =  107 bits (266), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 59/109 (54%), Positives = 76/109 (69%), Gaps = 6/109 (5%)

Query: 3   DAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQ--YVEMT 60
           D M+PFGLELLA SD+   NNS RILRV++E+T+AMGSQG+  GQYN+ Q  Q  Y++  
Sbjct: 103 DGMVPFGLELLAKSDDLTQNNSERILRVIIEITQAMGSQGMALGQYNQFQHGQSDYID-- 160

Query: 61  YETYKKNEGGLHTCGAACGAILGGGSVEEIEKKFR-GLIIKITKMMIRN 108
               KK EG LH+C  A GAILGGG+ EEIEK  R GL + + + ++ N
Sbjct: 161 -HVCKKKEGELHSCAGAVGAILGGGTEEEIEKLRRYGLYVGLMQGVLSN 208

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|323463187|pdb|3QKC|B Chain B, Crystal Structure Of Geranyl Diphosphate Synthase Small Subunit From Antirrhinum Majus gi|323463188|pdb|3QKC|A Chain A, Crystal Structure Of Geranyl Diphosphate Synthase Small Subunit From Antirrhinum Majus

 Score =  106 bits (265), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 53/95 (55%), Positives = 68/95 (71%), Gaps = 2/95 (2%)

Query: 3   DAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTYE 62
           D ++PFGLEL+A S +P  NN  RILR ++E+TR MGS+G+VEGQY+EL  +Q  ++   
Sbjct: 113 DGIIPFGLELMARSMDPTRNNPDRILRAIIELTRVMGSEGIVEGQYHELGLNQLNDLELI 172

Query: 63  TY--KKNEGGLHTCGAACGAILGGGSVEEIEKKFR 95
            Y  KK EG LH CGAACGAILGG   ++IEK  R
Sbjct: 173 EYVCKKKEGTLHACGAACGAILGGCDEDKIEKLRR 207

Source: Antirrhinum majus

Species: Antirrhinum majus

Genus: Antirrhinum

Family: Plantaginaceae

Order: Lamiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|229915238|gb|ACQ90681.1| geranyl diphosphate synthase small subunit [Humulus lupulus]

 Score = 95.5 bits (236), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 49/99 (49%), Positives = 62/99 (62%), Gaps = 7/99 (7%)

Query: 1   MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS------ 54
           M DA+LP G ELLA S NPA NNS R+LRV+VE  RA GS+G+++GQY +   S      
Sbjct: 120 MPDAILPLGFELLAQSYNPAQNNSDRVLRVIVEFARAFGSKGILDGQYRQRVVSISNGDE 179

Query: 55  -QYVEMTYETYKKNEGGLHTCGAACGAILGGGSVEEIEK 92
               E    + ++ EG +H C AACGAILG  + EE EK
Sbjct: 180 VDNAERVDCSGREKEGKMHACAAACGAILGDANEEETEK 218

Source: Humulus lupulus

Species: Humulus lupulus

Genus: Humulus

Family: Cannabaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225460953|ref|XP_002278023.1| PREDICTED: geranylgeranyl pyrophosphate synthase-related protein, chloroplastic [Vitis vinifera]

 Score = 93.6 bits (231), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 55/115 (47%), Positives = 71/115 (61%), Gaps = 13/115 (11%)

Query: 3   DAMLPFGLELLASSDNPAGNN--SGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVE-- 58
           D M+PFGLELLA S+N   ++  S RIL+V++E+TR +GSQGVV GQY + QC +     
Sbjct: 146 DGMIPFGLELLAKSNNLDDDDEHSDRILQVIIELTRTIGSQGVVNGQYIQAQCDESSPSV 205

Query: 59  ----MTYETYKKNEGGLHTCGAACGAILGGGSVEEIEKK-----FRGLIIKITKM 104
                T     K    LH CGAACGAILGGG  +EIEK      + G I K++K+
Sbjct: 206 GKAGSTRIVTDKKGTELHACGAACGAILGGGKEKEIEKLRKYGFYAGTIQKMSKL 260

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147776970|emb|CAN63418.1| hypothetical protein VITISV_007690 [Vitis vinifera]

 Score = 93.2 bits (230), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 55/115 (47%), Positives = 71/115 (61%), Gaps = 13/115 (11%)

Query: 3   DAMLPFGLELLASSDNPAGNN--SGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVE-- 58
           D M+PFGLELLA S+N   ++  S RIL+V++E+TR +GSQGVV GQY + QC +     
Sbjct: 146 DGMIPFGLELLAKSNNLDDDDEHSDRILQVIIELTRXIGSQGVVNGQYIQAQCDESSPSV 205

Query: 59  ----MTYETYKKNEGGLHTCGAACGAILGGGSVEEIEKK-----FRGLIIKITKM 104
                T     K    LH CGAACGAILGGG  +EIEK      + G I K++K+
Sbjct: 206 GKAGSTRIVTDKKGTELHACGAACGAILGGGKEKEIEKLRKYGFYAGTIQKMSKL 260

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|46241300|gb|AAS82870.1| geranyl diphosphate synthase small subunit [Clarkia breweri]

 Score = 91.3 bits (225), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 51/102 (50%), Positives = 67/102 (65%), Gaps = 13/102 (12%)

Query: 3   DAMLPFGLELLASSDNPAGN--NSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMT 60
           D MLP   ELLA+S+  AG+   S RILRV+VE+++A GS+G+++G+YNELQ  +    T
Sbjct: 130 DGMLPLAFELLANSEG-AGDESRSRRILRVIVEISKAAGSEGLLKGEYNELQLGRLAGFT 188

Query: 61  YETYK----------KNEGGLHTCGAACGAILGGGSVEEIEK 92
              ++          K EGGLH C AACG ILGGG+ EEIEK
Sbjct: 189 GGDWRDAFWMDHVCGKKEGGLHACAAACGGILGGGTEEEIEK 230

Source: Clarkia breweri

Species: Clarkia breweri

Genus: Clarkia

Family: Onagraceae

Order: Myrtales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449444204|ref|XP_004139865.1| PREDICTED: heterodimeric geranylgeranyl pyrophosphate synthase small subunit, chloroplastic-like [Cucumis sativus] gi|449502924|ref|XP_004161781.1| PREDICTED: heterodimeric geranylgeranyl pyrophosphate synthase small subunit, chloroplastic-like [Cucumis sativus]

 Score = 88.2 bits (217), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 49/109 (44%), Positives = 69/109 (63%), Gaps = 8/109 (7%)

Query: 3   DAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTYE 62
           D + P G E+LA S + +   S R+ RVMVE+ RAMG++G + GQ+  L+    VE   E
Sbjct: 152 DGITPMGFEILAESCDWSERGSERVRRVMVEVARAMGTEGWIGGQFRGLEEEATVE---E 208

Query: 63  TYKKNEGGLHTCGAACGAILGGGSVEEIEK-----KFRGLIIKITKMMI 106
             +K EGGLH CG ACGAI+GGG+ EEIEK     K  G++  +T+++ 
Sbjct: 209 VIEKTEGGLHACGGACGAIMGGGNEEEIEKMRKYGKLVGIVKGLTQIVF 257

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

No hits with e-value below 0.001 by BLAST

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	111
cd00685	259	cd00685, Trans_IPPS_HT, Trans-Isoprenyl Diphosphat	3e-05

>gnl|CDD|173833 cd00685, Trans_IPPS_HT, Trans-Isoprenyl Diphosphate Synthases, head-to-tail

 Score = 40.6 bits (96), Expect = 3e-05
 Identities = 27/95 (28%), Positives = 35/95 (36%), Gaps = 12/95 (12%)

Query: 2   ADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTY 61
            D +L    ELLA   NP      R L +  E    +     VEGQ  +L      ++T 
Sbjct: 87  GDYLLARAFELLARLGNPYYP---RALELFSEAILEL-----VEGQLLDLLSEYDTDVTE 138

Query: 62  ETYKKNE----GGLHTCGAACGAILGGGSVEEIEK 92
           E Y +        L       GA+L G   EE E 
Sbjct: 139 EEYLRIIRLKTAALFAAAPLLGALLAGADEEEAEA 173

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	111
PRK10581	299	geranyltranstransferase; Provisional	99.93
COG0142	322	IspA Geranylgeranyl pyrophosphate synthase [Coenzy	99.92
TIGR02748	319	GerC3_HepT heptaprenyl diphosphate synthase compon	99.9
PLN02890	422	geranyl diphosphate synthase	99.9
PRK10888	323	octaprenyl diphosphate synthase; Provisional	99.9
TIGR02749	322	prenyl_cyano solanesyl diphosphate synthase. Membe	99.9
KOG0776	384	consensus Geranylgeranyl pyrophosphate synthase/Po	99.89
PLN02857	416	octaprenyl-diphosphate synthase	99.88
CHL00151	323	preA prenyl transferase; Reviewed	99.87
cd00685	259	Trans_IPPS_HT Trans-Isoprenyl Diphosphate Synthase	99.86
PF00348	260	polyprenyl_synt: Polyprenyl synthetase; InterPro:	99.84
cd00867	236	Trans_IPPS Trans-Isoprenyl Diphosphate Synthases.	99.74
cd00385	243	Isoprenoid_Biosyn_C1 Isoprenoid Biosynthesis enzym	98.9
KOG0777	322	consensus Geranylgeranyl pyrophosphate synthase/Po	98.73
KOG0711	347	consensus Polyprenyl synthetase [Coenzyme transpor	97.6
PLN02632	334	phytoene synthase	91.25
PF00494	267	SQS_PSY: Squalene/phytoene synthase; InterPro: IPR	88.2
cd00683	265	Trans_IPPS_HH Trans-Isoprenyl Diphosphate Synthase	87.26
PF07307	212	HEPPP_synt_1: Heptaprenyl diphosphate synthase (HE	84.41
TIGR03465	266	HpnD squalene synthase HpnD. The genes of this fam	82.05

>PRK10581 geranyltranstransferase; Provisional

Probab=99.93  E-value=4.1e-25  Score=168.01  Aligned_cols=107  Identities=15%  Similarity=0.200  Sum_probs=93.5

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc---CCHHHHHHHHHhhhHHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS---QYVEMTYETYKKNEGGLHTCGAA   77 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~---~~~~~~~~i~~~KTa~L~~~~~~   77 (111)
                      +||+|+++||+++++... ..+.+...+++++.++++.|..+||.||++|+.+.   .++++|++|+++|||+||++|+.
T Consensus       113 ~GD~L~~~a~~~l~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~GQ~ld~~~~~~~~~~~~y~~i~~~KTa~L~~~~~~  191 (299)
T PRK10581        113 AGDALQTLAFSILSDAPM-PEVSDRDRISMISELASASGIAGMCGGQALDLEAEGKQVPLDALERIHRHKTGALIRAAVR  191 (299)
T ss_pred             HHHHHHHHHHHHHHhCCC-ccCChHHHHHHHHHHHHhcccchhhHhhHHHHhccCCCCCHHHHHHHHHHhhHHHHHHHHH
Confidence            599999999999987642 12344567788888998878899999999999873   78899999999999999999999


Q ss_pred             HHHHhCCCCH-HHHHHHH-HhHHhhHhhhhhcC
Q 047640           78 CGAILGGGSV-EEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        78 ~Gai~~g~~~-e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      +|++++|+++ +.++.++ ||+++|+||||+||
T Consensus       192 ~gailag~~~~~~~~~l~~~g~~lG~aFQI~DD  224 (299)
T PRK10581        192 LGALSAGDKGRRALPVLDRYAESIGLAFQVQDD  224 (299)
T ss_pred             HHHHHcCCCcHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999864 5789999 99999999999998

>COG0142 IspA Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]

Probab=99.92  E-value=6.8e-25  Score=168.22  Aligned_cols=100  Identities=23%  Similarity=0.295  Sum_probs=91.5

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc---CCHHHHHHHHHhhhHHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS---QYVEMTYETYKKNEGGLHTCGAA   77 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~---~~~~~~~~i~~~KTa~L~~~~~~   77 (111)
                      +||+|+++||+++++.++     +  ..++++.++.++  .+||+||++|+.++   +|+++|.+|+++|||+||++|+.
T Consensus       113 aGD~L~~~Af~~l~~~~~-----~--~~~~~~~~~~~~--~~~~~GQ~lDl~~~~~~~t~e~y~~~i~~KTa~L~~~a~~  183 (322)
T COG0142         113 AGDALLAAAFELLSKLGS-----E--ALEAIKALAEAI--NGLCGGQALDLAFENKPVTLEEYLRVIELKTAALFAAAAV  183 (322)
T ss_pred             HHHHHHHHHHHHHHhCCc-----h--hHHHHHHHHHHH--HHHHHhHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            599999999999999853     1  456777788887  99999999999885   78999999999999999999999


Q ss_pred             HHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcCC
Q 047640           78 CGAILGGGSVEEIEKKF-RGLIIKITKMMIRNS  109 (111)
Q Consensus        78 ~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~~  109 (111)
                      +||++++++++..+.++ ||+++|+||||+||-
T Consensus       184 ~ga~la~~~~~~~~~l~~~g~~lGlaFQi~DDi  216 (322)
T COG0142         184 LGAILAGADEELLEALEDYGRNLGLAFQIQDDI  216 (322)
T ss_pred             HHHHHcCCCHHHHHHHHHHHHHhhHHHHHHHHh
Confidence            99999999999999999 999999999999984

>TIGR02748 GerC3_HepT heptaprenyl diphosphate synthase component II

Probab=99.90  E-value=2.3e-23  Score=159.50  Aligned_cols=97  Identities=15%  Similarity=0.256  Sum_probs=87.2

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc----CCHHHHHHHHHhhhHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS----QYVEMTYETYKKNEGGLHTCGA   76 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~----~~~~~~~~i~~~KTa~L~~~~~   76 (111)
                      +||+|+++||+++++.++         .++++.+++++  ..|+.||++|+...    .+++.|.+|+++|||+||++||
T Consensus       110 ~GD~L~~~a~~~l~~~~~---------~~~~~~~~~~~--~~~~~Gq~~~~~~~~~~~~~~~~Y~~~i~~KTa~L~~~~~  178 (319)
T TIGR02748       110 TGDYLFAKSLETMTEIKD---------PRAHQILSHTI--VEVCRGEIEQIKDKYNFDQNLRTYLRRIKRKTALLIAASC  178 (319)
T ss_pred             HHHHHHHHHHHHHHhCCc---------HHHHHHHHHHH--HHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            599999999999987631         24566778888  89999999999763    6789999999999999999999


Q ss_pred             HHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           77 ACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        77 ~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      .+|++++|++++.++.++ ||.++|++|||+||
T Consensus       179 ~~ga~~ag~~~~~~~~l~~~g~~lG~aFQI~DD  211 (319)
T TIGR02748       179 QLGAIASGANEAIVKKLYWFGYYVGMSYQITDD  211 (319)
T ss_pred             HHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999 99999999999998

Members of this family are component II of the heterodimeric heptaprenyl diphosphate synthase. The trusted cutoff was set such that all members identified are encoded near to a recognizable gene for component I (in Pfam family pfam07307). This enzyme acts in menaquinone-7 isoprenoid side chain biosynthesis.

>PLN02890 geranyl diphosphate synthase

Probab=99.90  E-value=2.6e-23  Score=164.21  Aligned_cols=97  Identities=20%  Similarity=0.224  Sum_probs=88.1

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc----CCHHHHHHHHHhhhHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS----QYVEMTYETYKKNEGGLHTCGA   76 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~----~~~~~~~~i~~~KTa~L~~~~~   76 (111)
                      +||+|+++|++.+++..+         .++++.+++++  ..|++||++|+.+.    .++++|.+|+.+|||+||++||
T Consensus       208 aGD~Lla~A~~~l~~~~~---------~~~~~~~s~a~--~~l~~Gq~ld~~~~~~~~~s~~~Yl~~i~~KTa~Lf~~s~  276 (422)
T PLN02890        208 AGDFLLSRACVALAALKN---------TEVVSLLATAV--EHLVTGETMQITSSREQRRSMDYYMQKTYYKTASLISNSC  276 (422)
T ss_pred             HHHHHHHHHHHHHHcCCc---------HHHHHHHHHHH--HHHHHHHHHHHHhccCCCCCHHHHHHHHHHhHHHHHHHHH
Confidence            599999999999987631         35667788888  99999999999763    7899999999999999999999


Q ss_pred             HHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           77 ACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        77 ~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      .+||+++|++++.++.++ ||+++|+||||+||
T Consensus       277 ~~gAilaga~~~~~~~l~~fG~~lGlAFQI~DD  309 (422)
T PLN02890        277 KAVAILAGQTAEVAVLAFEYGRNLGLAFQLIDD  309 (422)
T ss_pred             HHHHHHcCcCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999 99999999999998

>PRK10888 octaprenyl diphosphate synthase; Provisional

Probab=99.90  E-value=3.6e-23  Score=158.78  Aligned_cols=97  Identities=21%  Similarity=0.263  Sum_probs=87.2

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc----CCHHHHHHHHHhhhHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS----QYVEMTYETYKKNEGGLHTCGA   76 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~----~~~~~~~~i~~~KTa~L~~~~~   76 (111)
                      +||+|+++||+++++.+      .   .+++..+++++  ..|++||++|+...    .++++|.+|+.+|||+||++||
T Consensus       111 ~GD~L~~~a~~~l~~~~------~---~~~~~~~~~~~--~~~~~Gq~~d~~~~~~~~~s~~~y~~~i~~KTa~lf~~~~  179 (323)
T PRK10888        111 VGDFIYTRAFQMMTSLG------S---LKVLEVMSEAV--NVIAEGEVLQLMNVNDPDITEENYMRVIYSKTARLFEAAA  179 (323)
T ss_pred             HHHHHHHHHHHHHHhCC------C---HHHHHHHHHHH--HHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            59999999999998763      1   24566678888  89999999999752    7889999999999999999999


Q ss_pred             HHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           77 ACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        77 ~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      ++|++++|.++++++.++ ||+++|+||||+||
T Consensus       180 ~~ga~lag~~~~~~~~l~~~g~~lG~aFQi~DD  212 (323)
T PRK10888        180 QCSGILAGCTPEQEKGLQDYGRYLGTAFQLIDD  212 (323)
T ss_pred             HHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999 99999999999998

>TIGR02749 prenyl_cyano solanesyl diphosphate synthase

Probab=99.90  E-value=4.2e-23  Score=158.34  Aligned_cols=97  Identities=14%  Similarity=0.169  Sum_probs=86.9

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc----CCHHHHHHHHHhhhHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS----QYVEMTYETYKKNEGGLHTCGA   76 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~----~~~~~~~~i~~~KTa~L~~~~~   76 (111)
                      +||+|+++|++++++.++         .++++.+++++  ..|+.||++|+...    .++++|.+|+.+|||+||++||
T Consensus       114 ~GD~l~~~a~~~l~~~~~---------~~~~~~~~~~~--~~~~~Gq~~~~~~~~~~~~~~~~y~~~~~~KTa~L~~~~~  182 (322)
T TIGR02749       114 AGDFLFAQASWYLANLEN---------LEVVKLISKVI--TDFAEGEIKQGLNQFDSDLSLEDYLEKSFYKTASLVAASS  182 (322)
T ss_pred             HHHHHHHHHHHHHHhcCC---------HHHHHHHHHHH--HHHHHHHHHHHHcccCCCCCHHHHHHHHHccHHHHHHHHH
Confidence            599999999999987632         24566678887  88999999998652    7899999999999999999999


Q ss_pred             HHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           77 ACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        77 ~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      .+|++++|+++++++.++ ||.++|+||||+||
T Consensus       183 ~~ga~~ag~~~~~~~~l~~~G~~lG~aFQi~DD  215 (322)
T TIGR02749       183 KAAAVLSDVPSQVANDLYEYGKHLGLAFQVVDD  215 (322)
T ss_pred             HHHHHHcCcCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999 99999999999998

Members of this family all are from cyanobacteria or plastid-containing eukaryotes. A member from Arabidopsis (where both plastoquinone and ubiquinone contain the C(45) prenyl moiety) was characterized by heterologous expression as a solanesyl diphosphate synthase.

>KOG0776 consensus Geranylgeranyl pyrophosphate synthase/Polyprenyl synthetase [Coenzyme transport and metabolism]

Probab=99.89  E-value=8.3e-23  Score=158.63  Aligned_cols=105  Identities=27%  Similarity=0.295  Sum_probs=93.2

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhcccCCHHHHHHHHHhhhHHHHHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTYETYKKNEGGLHTCGAACGA   80 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~~~~~~~~~i~~~KTa~L~~~~~~~Ga   80 (111)
                      +||||+++|++.+++..+  ...++.+.++|..+++..+.+++..||.+|... ..+++|+.++.+|||+|+++||++|+
T Consensus       177 aGD~LLa~A~~~la~l~n--~~v~elm~~aI~dLv~ge~~~~~~~~~~~d~~~-~~~e~~e~~~~~KTAsLla~Sc~~~a  253 (384)
T KOG0776|consen  177 AGDALLALASEHLASLEN--PVVVELMASAIADLVRGEFTQGLVAGEGLDLDD-VGLEYLEFKTLLKTASLLAKSCVAAA  253 (384)
T ss_pred             hhHHHHHHHHHHHHhccC--chHHHHHHHHHHHHHHhhhhcccccccccccCC-cchHHHHHHHHHHHHHHHHHHHHHHH
Confidence            699999999999999875  244567788888888888888888887666643 57899999999999999999999999


Q ss_pred             HhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           81 ILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        81 i~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      |++|.++++++.++ ||+++|++||++||
T Consensus       254 ILgg~s~ev~e~~~~yGR~lGL~fQvvDD  282 (384)
T KOG0776|consen  254 ILGGGSEEVIEAAFEYGRCLGLAFQVVDD  282 (384)
T ss_pred             HHcCCCHHHHHHHHHHHHHHHHHHHHhhc
Confidence            99999999999999 99999999999998

>PLN02857 octaprenyl-diphosphate synthase

Probab=99.88  E-value=2.6e-22  Score=158.42  Aligned_cols=97  Identities=14%  Similarity=0.190  Sum_probs=86.5

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhcc----cCCHHHHHHHHHhhhHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQC----SQYVEMTYETYKKNEGGLHTCGA   76 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~----~~~~~~~~~i~~~KTa~L~~~~~   76 (111)
                      +||+|+++||+.+++.+      .   .++++.+++++  ..++.||+.|+..    +.++++|.+|+++|||+||++||
T Consensus       208 aGD~L~a~A~~~la~~~------~---~~~~~~~s~~~--~~l~~Gei~q~~~~~~~~~s~~~Yl~~i~~KTa~L~~~a~  276 (416)
T PLN02857        208 AGDFMFAQSSWYLANLD------N---LEVIKLISQVI--KDFASGEIKQASSLFDCDVTLDEYLLKSYYKTASLIAAST  276 (416)
T ss_pred             HHHHHHHHHHHHHHcCC------c---HHHHHHHHHHH--HHHHhhHHHHHhcccCCCCCHHHHHHHHHHhHHHHHHHHH
Confidence            69999999999998763      1   24556677777  8899999999875    27899999999999999999999


Q ss_pred             HHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           77 ACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        77 ~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      .+||+++|+++++++.++ ||+++|++|||+||
T Consensus       277 ~~gallaga~~~~~~~l~~fG~~LGiAFQI~DD  309 (416)
T PLN02857        277 KSAAIFSGVDSSVKEQMYEYGKNLGLAFQVVDD  309 (416)
T ss_pred             HHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999 99999999999998

>CHL00151 preA prenyl transferase; Reviewed

Probab=99.87  E-value=1e-21  Score=150.58  Aligned_cols=97  Identities=14%  Similarity=0.177  Sum_probs=85.4

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhcc----cCCHHHHHHHHHhhhHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQC----SQYVEMTYETYKKNEGGLHTCGA   76 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~----~~~~~~~~~i~~~KTa~L~~~~~   76 (111)
                      +||+|+++||+++++..+         .++++.+++++  ..++.||..|...    ..++++|.+|+.+|||+||++||
T Consensus       115 ~GD~l~~~a~~~l~~~~~---------~~~~~~~~~~~--~~l~~G~~~~~~~~~~~~~~~~~yl~~i~~KTa~L~~~~~  183 (323)
T CHL00151        115 AGDFLFAQSSWYLANLNN---------LEVVKLISKVI--TDFAEGEIRQGLVQFDTTLSILNYIEKSFYKTASLIAASC  183 (323)
T ss_pred             hHHHHHHHHHHHHHhCCC---------hHHHHHHHHHH--HHHHHHHHHHHhcCCCCCCCHHHHHHHHHhHHHHHHHHHH
Confidence            699999999999987631         13445567777  8899999999765    26788999999999999999999


Q ss_pred             HHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           77 ACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        77 ~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      .+||+++|.++++++.++ ||.++|+||||+||
T Consensus       184 ~~ga~lag~~~~~~~~l~~~G~~lG~aFQi~DD  216 (323)
T CHL00151        184 KAAALLSDADEKDHNDFYLYGKHLGLAFQIIDD  216 (323)
T ss_pred             HHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999 99999999999998

>cd00685 Trans_IPPS_HT Trans-Isoprenyl Diphosphate Synthases, head-to-tail

Probab=99.86  E-value=5e-21  Score=142.38  Aligned_cols=100  Identities=24%  Similarity=0.255  Sum_probs=90.6

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc----CCHHHHHHHHHhhhHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS----QYVEMTYETYKKNEGGLHTCGA   76 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~----~~~~~~~~i~~~KTa~L~~~~~   76 (111)
                      +||+|++++++++++..+     + ...++++.+++.+  ..++.||++|+.+.    .+++.|.+|+.+|||+||..++
T Consensus        86 ~gd~l~~~a~~~l~~~~~-----~-~~~~~~~~~~~~~--~~~~~GQ~~d~~~~~~~~~~~~~y~~~~~~KT~~l~~~~~  157 (259)
T cd00685          86 AGDYLLARAFELLARLGN-----P-YYPRALELFSEAI--LELVEGQLLDLLSEYDTDVTEEEYLRIIRLKTAALFAAAP  157 (259)
T ss_pred             HHHHHHHHHHHHHHhCCC-----c-cHHHHHHHHHHHH--HHHHHHHHHHHHccCCCCCCHHHHHHHHHHhHHHHHHHHH
Confidence            599999999999998742     1 3567788888888  99999999999873    6789999999999999999999


Q ss_pred             HHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           77 ACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        77 ~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      ++|++++++++++++.++ ||.++|++|||.||
T Consensus       158 ~~~a~l~~~~~~~~~~l~~~g~~lG~afQi~DD  190 (259)
T cd00685         158 LLGALLAGADEEEAEALKRFGRNLGLAFQIQDD  190 (259)
T ss_pred             HHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999 99999999999998

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

>PF00348 polyprenyl_synt: Polyprenyl synthetase; InterPro: IPR000092 A variety of isoprenoid compounds are synthesized by various organisms

Probab=99.84  E-value=2.8e-20  Score=138.48  Aligned_cols=103  Identities=26%  Similarity=0.285  Sum_probs=85.1

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCCh-HHHHHHHHHHHHhhchhHHHHhhHHHhccc---CCHHHHHHHHHhhhHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNS-GRILRVMVEMTRAMGSQGVVEGQYNELQCS---QYVEMTYETYKKNEGGLHTCGA   76 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~-~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~---~~~~~~~~i~~~KTa~L~~~~~   76 (111)
                      +||+|+++|++++++..   ..++ .....++..+...+  .....||..|+...   .++++|.+|+++|||+||++||
T Consensus        80 ~gd~ll~~a~~~l~~~~---~~~~~~~~~~i~~~~~~~~--~~~~~~q~~d~~~~~~~~~~~~y~~i~~~KTg~l~~~~~  154 (260)
T PF00348_consen   80 AGDYLLALAFELLARLG---HFDPSERVLRILELFIEAL--IEGEIGQALDLANEDKDPTEEEYLEIIRLKTGSLFALAC  154 (260)
T ss_dssp             HHHHHHHHHHHHHHHHC---HSHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHTTTSSTSHHHHHHHHHHHTHHHHHHHH
T ss_pred             hchHHHHHHHHHHHHhh---cccchHHHHHHHHHHHHhc--ccceeehhhccccccccccHHHHHHHHhhcchHHHHHHH
Confidence            59999999999999874   1123 34555555555444  33344599999774   7899999999999999999999


Q ss_pred             HHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           77 ACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        77 ~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      .+|++++|.+++..+.++ ||+++|++|||.||
T Consensus       155 ~~ga~lag~~~~~~~~l~~~g~~lG~afQi~DD  187 (260)
T PF00348_consen  155 QLGAILAGADEEQIEALREFGRHLGIAFQIRDD  187 (260)
T ss_dssp             HHHHHHTTSGHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhccchhHHHHHHHHHHHHHHHHHhhhhh
Confidence            999999999999999999 99999999999997

For example in eukaryotes the isoprenoid biosynthetic pathway is responsible for the synthesis of a variety of end products including cholesterol, dolichol, ubiquinone or coenzyme Q. In bacteria this pathway leads to the synthesis of isopentenyl tRNA, isoprenoid quinones, and sugar carrier lipids. Among the enzymes that participate in that pathway, are a number of polyprenyl synthetase enzymes which catalyze a 1'4-condensation between 5 carbon isoprene units. It has been shown [, , , , ] that all the above enzymes share some regions of sequence similarity. Two of these regions are rich in aspartic-acid residues and could be involved in the catalytic mechanism and/or the binding of the substrates.; GO: 0008299 isoprenoid biosynthetic process; PDB: 3AQC_B 3AQB_D 3Q1O_C 3LLW_B 3EFQ_A 3EGT_A 3DYG_A 2P1C_A 2OGD_A 2EWG_B ....

>cd00867 Trans_IPPS Trans-Isoprenyl Diphosphate Synthases

Probab=99.74  E-value=3.1e-17  Score=119.34  Aligned_cols=97  Identities=22%  Similarity=0.247  Sum_probs=85.8

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc----CCHHHHHHHHHhhhHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS----QYVEMTYETYKKNEGGLHTCGA   76 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~----~~~~~~~~i~~~KTa~L~~~~~   76 (111)
                      +||++++.+|+.+++..         ..+.++.+++.+  ..|+.||.+|+...    .++++|.+++++|||++++.++
T Consensus        66 ~gd~l~~~a~~~l~~~~---------~~~~~~~~~~~~--~~~~~Gq~~Dl~~~~~~~~t~~~y~~~~~~Kta~l~~~~~  134 (236)
T cd00867          66 AGDYLLARAFQLLARLG---------YPRALELFAEAL--RELLEGQALDLEFERDTYETLDEYLEYCRYKTAGLVGLLC  134 (236)
T ss_pred             HHHHHHHHHHHHHHhCC---------hHHHHHHHHHHH--HHHHHHHHHHHHhccCCCCCHHHHHHHHHhccHHHHHHHH
Confidence            48999999999998762         234455567777  99999999999863    6789999999999999999999


Q ss_pred             HHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           77 ACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        77 ~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      ..++++++.+++..+.+. ||.++|++|||.||
T Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~lG~a~Qi~dd  167 (236)
T cd00867         135 LLGAGLSGADDEQAEALKDYGRALGLAFQLTDD  167 (236)
T ss_pred             HHHHHHcCcCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999 99999999999997

Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) of class 1 isoprenoid biosynthesis enzymes which either synthesis geranyl/farnesyl diphosphates (GPP/FPP) or longer chained products from isoprene precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), or use geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate as substrate. These enzymes produce a myriad of precursors for such end products as steroids, cholesterol, sesquiterpenes, heme, carotenoids, retinoids, diterpenes, ubiquinone, and archaeal ether linked lipids; and are widely distributed among archaea, bacteria, and eukareya. The enzymes in this family share the same 'isoprenoid synthase fold' and include the head-to-tail (HT) IPPS which catalyze the successive 1'-4 condensation of the 5-carbon IPP to the growing isoprene chain to form linear, all-trans, C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid diphosphates

>cd00385 Isoprenoid_Biosyn_C1 Isoprenoid Biosynthesis enzymes, Class 1

Probab=98.90  E-value=4.9e-08  Score=68.74  Aligned_cols=96  Identities=23%  Similarity=0.267  Sum_probs=80.2

Q ss_pred             hhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc----CCHHHHHHHHHhhhHHHHHHHHH
Q 047640            2 ADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS----QYVEMTYETYKKNEGGLHTCGAA   77 (111)
Q Consensus         2 GD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~----~~~~~~~~i~~~KTa~L~~~~~~   77 (111)
                      ||.++..+++.+....     +    ......+.+.+  ..++.||..|+.+.    .+.++|.++.+.|||.++..++.
T Consensus        61 ~~~~~~~~~~~~~~~~-----~----~~~~~~~~~~~--~~~~~g~~~d~~~~~~~~~t~~ey~~~~~~~t~~~~~~~~~  129 (243)
T cd00385          61 GDLLLADAFEELAREG-----S----PEALEILAEAL--LDLLEGQLLDLKWRREYVPTLEEYLEYCRYKTAGLVGALCL  129 (243)
T ss_pred             HHHHHHHHHHHHHhCC-----C----HHHHHHHHHHH--HHHHHHHHHHHHhccCCCCCHHHHHHHHHHhHHHHHHHHHH
Confidence            6778888888887653     1    24445566777  89999999999873    77899999999999999999999


Q ss_pred             HHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           78 CGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        78 ~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      .++.....+.+....+. ++.++|+++|+.||
T Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~g~~~ql~nD  161 (243)
T cd00385         130 LGAGLSGGEAELLEALRKLGRALGLAFQLTND  161 (243)
T ss_pred             HHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99998887777778888 99999999999987

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 monoter

>KOG0777 consensus Geranylgeranyl pyrophosphate synthase/Polyprenyl synthetase [Coenzyme transport and metabolism]

Probab=98.73  E-value=4.5e-08  Score=72.78  Aligned_cols=92  Identities=14%  Similarity=0.105  Sum_probs=74.7

Q ss_pred             hhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc-----CCHHHHHHHHHhhhHHHHHHHH
Q 047640            2 ADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS-----QYVEMTYETYKKNEGGLHTCGA   76 (111)
Q Consensus         2 GD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~-----~~~~~~~~i~~~KTa~L~~~~~   76 (111)
                      .+|++-+|++.+++...     |    .++..+.+..  ..+..||-+|+.|.     .+++.|..|..+|||-||..+.
T Consensus       103 ANY~yFlalekV~qLdh-----P----~a~kifteqL--leLHrGQGldIYWRD~~tcPtee~Yk~Mv~~KTGGLF~La~  171 (322)
T KOG0777|consen  103 ANYMYFLALEKVSQLDH-----P----NAIKIFTEQL--LELHRGQGLDIYWRDFLTCPTEEMYKNMVMNKTGGLFRLAL  171 (322)
T ss_pred             hHHHHHHHHHHHHhcCC-----c----hHHHHHHHHH--HHHhcCCCcceeeeccCcCCCHHHHHHHHHHhcccHHHHHH
Confidence            57889999999998753     2    4556677777  88999999999984     6789999999999999999999


Q ss_pred             HHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           77 ACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        77 ~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      ++--.++.-.+    .+. +=--+|+.|||+||
T Consensus       172 rLMqlfS~~ke----dl~pl~n~LGl~fQIRDD  200 (322)
T KOG0777|consen  172 RLMQLFSHHKE----DLVPLINLLGLIFQIRDD  200 (322)
T ss_pred             HHHHHHHhcch----hHHHHHHHHhHhhhhhhh
Confidence            98877774333    344 66678899999987

>KOG0711 consensus Polyprenyl synthetase [Coenzyme transport and metabolism]

Probab=97.60  E-value=0.00023  Score=55.06  Aligned_cols=68  Identities=10%  Similarity=-0.101  Sum_probs=55.8

Q ss_pred             hHHHHhhHHHhcc------cCCHHHHHHHHHhhhHHH-HHHHHHHHHHhCCCC-HHHHHHHH-HhHHhhHhhhhhcC
Q 047640           41 QGVVEGQYNELQC------SQYVEMTYETYKKNEGGL-HTCGAACGAILGGGS-VEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        41 ~~m~~GQ~lDl~~------~~~~~~~~~i~~~KTa~L-~~~~~~~Gai~~g~~-~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      ...+.||.++-..      +.|++.|..|...|||.+ |-.|..++-+++|.+ .+...... +-..+|..||+.||
T Consensus       160 f~T~lGdllt~~~~~~~ls~fsl~~y~~Iv~~KTa~YsFYLPialAl~~ag~~~~k~~~~~k~v~~~lg~~FQvQDD  236 (347)
T KOG0711|consen  160 FQTELGDLLTTPEGNKDLSKFSLEKYVFIVEYKTAYYSFYLPVALALLLAGIANLKEHACEKKVLLLLGEYFQVQDD  236 (347)
T ss_pred             HHHhhhccccCcccchhHhhhhHHHHHHHhhccccceeeecHHHHHHHHhhhhhHHHhhhHHHHHHHHHHHHhcchH
Confidence            5567777766543      167899999999999999 999999999999854 55556666 99999999999997

>PLN02632 phytoene synthase

Probab=91.25  E-value=1.1  Score=34.73  Aligned_cols=64  Identities=16%  Similarity=0.206  Sum_probs=43.1

Q ss_pred             hHHHHhhHHHhccc--CCHHHHHHHHHhhhHHHHHHHHHHHHHhCCCC--HHHHHHHH-HhHHhhHhhhhhc
Q 047640           41 QGVVEGQYNELQCS--QYVEMTYETYKKNEGGLHTCGAACGAILGGGS--VEEIEKKF-RGLIIKITKMMIR  107 (111)
Q Consensus        41 ~~m~~GQ~lDl~~~--~~~~~~~~i~~~KTa~L~~~~~~~Gai~~g~~--~e~~~~l~-~G~~~GiafQi~D  107 (111)
                      ..|+.|...|+...  .|.++++...+.--|.+...++.+   ++..+  +...+.+. .+.++|+|+|+.+
T Consensus       143 ~~li~g~~~Dl~~~~~~t~~eL~~Ycy~vAgtVG~l~l~v---lg~~~~~~~~~~~~~~~A~~lG~AlQltN  211 (334)
T PLN02632        143 RDMIEGMRMDLVKSRYENFDELYLYCYYVAGTVGLMSVPV---MGIAPESKASTESVYNAALALGIANQLTN  211 (334)
T ss_pred             HHHHHHHHHHhccCCCCCHHHHHHHHHHhhHHHHHHHHHH---hCCCCccccchHHHHHHHHHHHHHHHHHH
Confidence            77899999999764  578888887766556666555544   33222  22234455 8888899988763

>PF00494 SQS_PSY: Squalene/phytoene synthase; InterPro: IPR002060 Squalene synthase 2

Probab=88.20  E-value=2  Score=31.62  Aligned_cols=61  Identities=7%  Similarity=-0.088  Sum_probs=41.0

Q ss_pred             hHHHHhhHHHhccc--CCHHHHHHHHHhhhHHHHHHHHHHHHHhCCCCHHHHHHHH-HhHHhhHhhhhh
Q 047640           41 QGVVEGQYNELQCS--QYVEMTYETYKKNEGGLHTCGAACGAILGGGSVEEIEKKF-RGLIIKITKMMI  106 (111)
Q Consensus        41 ~~m~~GQ~lDl~~~--~~~~~~~~i~~~KTa~L~~~~~~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~  106 (111)
                      ..|+.|...|+...  .|.+++....+.-.|++....+.+-..-  .+.   .... ...++|.++|+.
T Consensus        94 ~~li~~~~~dl~~~~~~t~~~L~~Y~~~vag~vg~l~~~~~~~~--~~~---~~~~~~a~~lG~alql~  157 (267)
T PF00494_consen   94 LELIDGMEMDLEFTPYETFADLERYCYYVAGSVGLLLLQLLGAH--DPD---EAARDAARALGRALQLT  157 (267)
T ss_dssp             HHHHHHHHHCTT-S--SSHHHHHHHHHHHTHHHHHHHHHHHHSS--TSH---HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhcccccCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccc--cch---hhHHHHHHHHHHHHHHH
Confidence            78999999999864  6889998888888888887777665442  222   2233 555555555554

5.1.21 from EC (farnesyl-diphosphate farnesyltransferase) (SQS) and Phytoene synthase 2.5.1.32 from EC (PSY) share a number of functional similarities. These similarities are also reflected at the level of their primary structure [, , ]. In particular three well conserved regions are shared by SQS and PSY; they could be involved in substrate binding and/or the catalytic mechanism. SQS catalyzes the conversion of two molecules of farnesyl diphosphate (FPP) into squalene. It is the first committed step in the cholesterol biosynthetic pathway. The reaction carried out by SQS is catalyzed in two separate steps: the first is a head-to-head condensation of the two molecules of FPP to form presqualene diphosphate; this intermediate is then rearranged in a NADP-dependent reduction, to form squalene: 2 FPP -> presqualene diphosphate + NADP -> squalene SQS is found in eukaryotes. In yeast it is encoded by the ERG9 gene, in mammals by the FDFT1 gene. SQS seems to be membrane-bound. PSY catalyzes the conversion of two molecules of geranylgeranyl diphosphate (GGPP) into phytoene. It is the second step in the biosynthesis of carotenoids from isopentenyl diphosphate. The reaction carried out by PSY is catalyzed in two separate steps: the first is a head-to-head condensation of the two molecules of GGPP to form prephytoene diphosphate; this intermediate is then rearranged to form phytoene. 2 GGPP -> prephytoene diphosphate -> phytoene PSY is found in all organisms that synthesize carotenoids: plants and photosynthetic bacteria as well as some non- photosynthetic bacteria and fungi. In bacteria PSY is encoded by the gene crtB. In plants PSY is localized in the chloroplast.; GO: 0016740 transferase activity, 0009058 biosynthetic process; PDB: 3NRI_A 3NPR_A 2ZCR_A 2ZCP_B 4F6V_A 4EA0_A 3ACW_A 4F6X_A 3VJE_B 3ACX_A ....

>cd00683 Trans_IPPS_HH Trans-Isoprenyl Diphosphate Synthases, head-to-head

Probab=87.26  E-value=2.1  Score=31.75  Aligned_cols=60  Identities=13%  Similarity=0.109  Sum_probs=39.1

Q ss_pred             hHHHHhhHHHhccc--CCHHHHHHHHHhhhHHHHHHHHHHHHHhCCCCHHHHHHHH-HhHHhhHhhhhh
Q 047640           41 QGVVEGQYNELQCS--QYVEMTYETYKKNEGGLHTCGAACGAILGGGSVEEIEKKF-RGLIIKITKMMI  106 (111)
Q Consensus        41 ~~m~~GQ~lDl~~~--~~~~~~~~i~~~KTa~L~~~~~~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~  106 (111)
                      ..|+.|...|+...  .|.+++......--|++...++.+   ++....   +... ++.++|+|+|+.
T Consensus        96 ~~li~g~~~Dl~~~~~~t~~eL~~Y~~~vAg~vg~l~~~i---~~~~~~---~~~~~~A~~lG~Alqlt  158 (265)
T cd00683          96 RDLLAGMAMDLDKRRYETLDELDEYCYYVAGVVGLMLLRV---FGASSD---EAALERARALGLALQLT  158 (265)
T ss_pred             HHHHHHHHHhCCCCCCCCHHHHHHHHHHhHHHHHHHHHHH---hCCCCC---hHHHHHHHHHHHHHHHH
Confidence            78999999999874  677888887766556665555543   332111   2234 677777777765

These trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) catalyze a head-to-head (HH) (1'-1) condensation reaction. This CD includes squalene and phytoene synthases which catalyze the 1'-1 condensation of two 15-carbon (farnesyl) and 20-carbon (geranylgeranyl) isoprenyl diphosphates, respectively. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions (DXXXD) located on opposite walls. These residues mediate binding of prenyl phosphates. A two-step reaction has been proposed for squalene synthase (farnesyl-diphosphate farnesyltransferase) in which, two molecules of FPP react to form a stable cyclopropylcarbinyl diphosphate intermediate, and then the intermediate undergoes heterolysis, isomerization, and reduction with NADPH to form squalene, a precursor of cholestrol. The carotenoid biosynthesis enzyme, phytoene synthase (CrtB), catalyzes

>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

Probab=84.41  E-value=11  Score=27.75  Aligned_cols=64  Identities=14%  Similarity=0.137  Sum_probs=41.8

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc-CCHH-HHHHHHHhhhHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS-QYVE-MTYETYKKNEGGLHTCG   75 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~-~~~~-~~~~i~~~KTa~L~~~~   75 (111)
                      |||+.-++-+.+|++.++         +.+++.+|.++  ..+.+..+.=-... .+.+ .+..+..-+|+.+...+
T Consensus        75 AGDy~S~~yY~lLA~~~~---------i~li~~ls~aI--~eiNE~K~~ly~~~~~~~e~~~~~~~~ies~l~~~~~  140 (212)
T PF07307_consen   75 AGDYYSGLYYQLLAESGD---------ISLIRALSEAI--KEINELKMSLYQKKKETAEEYLESVVTIESALFQSFA  140 (212)
T ss_pred             hHHHHHHHHHHHHHhCCC---------HHHHHHHHHHH--HHHHHHHHHHHHhhhCCHHHHHHHHHHHHHHHHHHHH
Confidence            799999999999999863         47777888887  77777765433222 3444 34444444555444433

5.1.30 from EC) (approximately 230 residues long). The enzyme consists of two subunits, both of which are required for catalysis of heptaprenyl diphosphate synthesis, the precursor for the side chain of the isoprenoid quinone menaquinone-7 (MQ-7) [, ].

>TIGR03465 HpnD squalene synthase HpnD

Probab=82.05  E-value=13  Score=27.56  Aligned_cols=59  Identities=10%  Similarity=0.078  Sum_probs=39.8

Q ss_pred             hHHHHhhHHHhccc--CCHHHHHHHHHhhhHHHHHHHHHHHHHhCCCCHHHHHHHH-HhHHhhHhhhhh
Q 047640           41 QGVVEGQYNELQCS--QYVEMTYETYKKNEGGLHTCGAACGAILGGGSVEEIEKKF-RGLIIKITKMMI  106 (111)
Q Consensus        41 ~~m~~GQ~lDl~~~--~~~~~~~~i~~~KTa~L~~~~~~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~  106 (111)
                      ..|++|...|+...  .|.+++....+.--|.+...++.+   ++..++.    .. .+.++|+|+|+.
T Consensus        88 ~~li~g~~~Dl~~~~~~t~~dL~~Y~~~vAg~vg~l~~~l---lg~~~~~----~~~~a~~lG~Alqlt  149 (266)
T TIGR03465        88 LEVIDGMEMDLEQTRYPDFAELDLYCDRVAGAVGRLSARI---FGATDAR----TLEYAHHLGRALQLT  149 (266)
T ss_pred             HHHHHHHHHHcCCCCCCCHHHHHHHHHHhHHHHHHHHHHH---hCCCChh----HHHHHHHHHHHHHHH
Confidence            78999999999864  678888887766666666666654   3433322    23 666667776664

The genes of this family are often found in the same genetic locus with squalene-hopene cyclase genes, and are never associated with genes for the metabolism of phytoene. In the organisms Zymomonas mobilis and Bradyrhizobium japonicum these genes have been characterized as squalene synthases (farnesyl-pyrophosphate ligases). Often, these genes appear in tandem with the HpnC gene which appears to have resulted from an ancient gene duplication event. Presumably these proteins form a heteromeric complex, but this has not yet been experimentally demonstrated.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	111
3qkc_B	273	Crystal Structure Of Geranyl Diphosphate Synthase S		8e-16
3kra_B	274	Mint Heterotetrameric Geranyl Pyrophosphate Synthas		1e-07
3oab_B	264	Mint Deletion Mutant Of Heterotetrameric Geranyl Py		1e-07

>pdb|3QKC|B Chain B, Crystal Structure Of Geranyl Diphosphate Synthase Small Subunit From Antirrhinum Majus Length = 273

Iteration: 1
 Score = 78.6 bits (192), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 38/74 (51%), Positives = 51/74 (68%), Gaps = 2/74 (2%)
Query: 2   ADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTY 61
            D ++PFGLEL+A S +P  NN  RILR ++E+TR MGS+G+VEGQY+EL  +Q  ++  
Sbjct: 112 GDGIIPFGLELMARSMDPTRNNPDRILRAIIELTRVMGSEGIVEGQYHELGLNQLNDLEL 171
Query: 62  ETY--KKNEGGLHT 73
             Y  KK EG LH 
Sbjct: 172 IEYVCKKKEGTLHA 185

>pdb|3KRA|B Chain B, Mint Heterotetrameric Geranyl Pyrophosphate Synthase In Complex With Magnesium Length = 274

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 31/94 (32%), Positives = 51/94 (54%), Gaps = 4/94 (4%)
Query: 3   DAMLPFGLELLASSDNPA-GNNSGRILRVMVEMTRAMGSQGVVEGQYNE---LQCSQYVE 58
           D ++PFG ELLA S +PA  ++  RILRV++E++RA G +G++ G + E   +  +  ++
Sbjct: 110 DGIVPFGFELLAGSVDPARTDDPDRILRVIIEISRAGGPEGMISGLHREEEIVDGNTSLD 169
Query: 59  MTYETYKKNEGGLHTXXXXXXXXXXXXSVEEIEK 92
                 KK  G +H             + EEI+K
Sbjct: 170 FIEYVCKKKYGEMHACGAACGAILGGAAEEEIQK 203

>pdb|3OAB|B Chain B, Mint Deletion Mutant Of Heterotetrameric Geranyl Pyrophosphate Synthase In Complex With Ligands Length = 264

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 31/94 (32%), Positives = 51/94 (54%), Gaps = 4/94 (4%)
Query: 3   DAMLPFGLELLASSDNPA-GNNSGRILRVMVEMTRAMGSQGVVEGQYNE---LQCSQYVE 58
           D ++PFG ELLA S +PA  ++  RILRV++E++RA G +G++ G + E   +  +  ++
Sbjct: 100 DGIVPFGFELLAGSVDPARTDDPDRILRVIIEISRAGGPEGMISGLHREEEIVDGNTSLD 159
Query: 59  MTYETYKKNEGGLHTXXXXXXXXXXXXSVEEIEK 92
                 KK  G +H             + EEI+K
Sbjct: 160 FIEYVCKKKYGEMHACGAACGAILGGAAEEEIQK 193

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	111
3qkc_B	273	Geranyl diphosphate synthase small subunit; struct	8e-23
3kra_B	274	Geranyl diphosphate synthase small subunit; prenyl	1e-19
3uca_A	324	Geranyltranstransferase; isoprenoid synthesis, iso	2e-08
2j1p_A	293	Geranylgeranyl pyrophosphate synthetase; transfera	3e-08
3lom_A	313	Geranyltranstransferase; geranyltransferase, struc	2e-07
2h8o_A	335	Geranyltranstransferase; geranyltransferase,agroba	2e-07
1rtr_A	301	Geranyltranstransferase; 2.50A {Staphylococcus aur	1e-06
3m0g_A	297	Farnesyl diphosphate synthase; structural genomics	1e-06
3nf2_A	352	Putative polyprenyl synthetase; isoprenyl diphosph	1e-06
3pde_A	309	Farnesyl-diphosphate synthase; isoprenyl diphospha	2e-06
1rqj_A	299	Geranyltranstransferase; bisphosphonate, isoprenyl	2e-06
3llw_A	311	Geranyltranstransferase (ISPA); structural genomic	3e-06
3p8l_A	302	Geranyltranstransferase; isoprenyl synthase, struc	3e-06
3p8r_A	302	Geranyltranstransferase; isoprenyl synthase, struc	4e-06
3npk_A	291	Geranyltranstransferase; isoprene biosynthesis, SG	5e-06
3ts7_A	324	Geranyltranstransferase; isoprenoid synthesis, far	5e-06
3lsn_A	304	Geranyltranstransferase; structural genomics, prot	8e-06
4f62_A	317	Geranyltranstransferase; enzyme function initiativ	1e-05
3lk5_A	380	Geranylgeranyl pyrophosphate synthase; structural	2e-05
1wy0_A	342	Geranylgeranyl pyrophosphate synthetase; pyrococcu	3e-05
1wmw_A	330	Geranylgeranyl diphosphate synthetase; GGPP, preny	8e-04

>3qkc_B Geranyl diphosphate synthase small subunit; structural genomics, protein structure initiative, NEW YORK structural genomix research consortium; 2.20A {Antirrhinum majus} Length = 273

 Score = 88.1 bits (219), Expect = 8e-23
 Identities = 52/92 (56%), Positives = 67/92 (72%), Gaps = 2/92 (2%)

Query: 3   DAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTYE 62
           D ++PFGLEL+A S +P  NN  RILR ++E+TR MGS+G+VEGQY+EL  +Q  ++   
Sbjct: 113 DGIIPFGLELMARSMDPTRNNPDRILRAIIELTRVMGSEGIVEGQYHELGLNQLNDLELI 172

Query: 63  TY--KKNEGGLHTCGAACGAILGGGSVEEIEK 92
            Y  KK EG LH CGAACGAILGG   ++IEK
Sbjct: 173 EYVCKKKEGTLHACGAACGAILGGCDEDKIEK 204

>3kra_B Geranyl diphosphate synthase small subunit; prenyltransferase, isoprene biosynthesis, isoprenyl pyrophosphate synthase, transferase; 1.90A {Mentha x piperita} PDB: 3krc_B* 3krf_B* 3kro_B* 3krp_B* 3oab_B* 3oac_B* Length = 274

 Score = 79.6 bits (197), Expect = 1e-19
 Identities = 42/95 (44%), Positives = 61/95 (64%), Gaps = 6/95 (6%)

Query: 3   DAMLPFGLELLASSDNPA-GNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTY 61
           D ++PFG ELLA S +PA  ++  RILRV++E++RA G +G++ G + E +       + 
Sbjct: 110 DGIVPFGFELLAGSVDPARTDDPDRILRVIIEISRAGGPEGMISGLHREEEIVD-GNTSL 168

Query: 62  ET----YKKNEGGLHTCGAACGAILGGGSVEEIEK 92
           +      KK  G +H CGAACGAILGG + EEI+K
Sbjct: 169 DFIEYVCKKKYGEMHACGAACGAILGGAAEEEIQK 203

>3uca_A Geranyltranstransferase; isoprenoid synthesis, isoprenoid diphosphate synthase; 2.00A {Clostridium perfringens} Length = 324

 Score = 49.6 bits (119), Expect = 2e-08
 Identities = 21/94 (22%), Positives = 40/94 (42%), Gaps = 7/94 (7%)

Query: 3   DAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTYE 62
           DA+L   +++L    + +       L+    +  A GS G++ GQ  ++      E++ +
Sbjct: 145 DALLNEAMKILV---DYSLEEGKSALKATKIIADAAGSDGMIGGQIVDIINEDKEEISLK 201

Query: 63  T----YKKNEGGLHTCGAACGAILGGGSVEEIEK 92
                + K  G L       GA+L   S  +I+K
Sbjct: 202 ELDYMHLKKTGELIKASIMSGAVLAEASEGDIKK 235

>2j1p_A Geranylgeranyl pyrophosphate synthetase; transferase, isoprene biosynthesis, multifunctional enzyme, carotenoid biosynthesis; HET: GRG; 1.8A {Sinapis alba} PDB: 2j1o_A 3kra_A 3krc_A* 3krf_A* 3kro_A* 3krp_A* 3oab_A* 3oac_A* Length = 293

 Score = 48.7 bits (117), Expect = 3e-08
 Identities = 33/104 (31%), Positives = 51/104 (49%), Gaps = 23/104 (22%)

Query: 3   DAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTYE 62
           DA+L F  E LAS+ +    +  R++R + E+ +A+G++G+V G        Q V+++ E
Sbjct: 123 DALLSFAFEHLASATSS-EVSPARVVRAVGELAKAIGTEGLVAG--------QVVDISSE 173

Query: 63  TYKKNEGGLHT--------------CGAACGAILGGGSVEEIEK 92
               N  GL                  A  G I+GGGS EEIE+
Sbjct: 174 GLDLNNVGLEHLKFIHLHKTAALLEASAVLGGIIGGGSDEEIER 217

>3lom_A Geranyltranstransferase; geranyltransferase, structural genomics, PSI, protein structure initiative, nysgrc; 2.30A {Legionella pneumophila subsp} Length = 313

 Score = 46.8 bits (112), Expect = 2e-07
 Identities = 19/97 (19%), Positives = 34/97 (35%), Gaps = 5/97 (5%)

Query: 3   DAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTYE 62
           D M    +E+L    +P    + +++ +   +  A G  G+V GQ  +L       +T E
Sbjct: 121 DGMQALAIEVLLMRLSP-LLPAAQVVAITQVLVNASGISGMVSGQSLDLSELAKSSVTEE 179

Query: 63  T----YKKNEGGLHTCGAACGAILGGGSVEEIEKKFR 95
                +    G L                E+I+   R
Sbjct: 180 QLREIHLLKTGKLILACFEMVLAAQHEVSEQIKSALR 216

>2h8o_A Geranyltranstransferase; geranyltransferase,agrobacterium tumefaciens, structural GEN PSI-2, protein structure initiative; 1.60A {Agrobacterium tumefaciens} Length = 335

 Score = 46.5 bits (111), Expect = 2e-07
 Identities = 23/95 (24%), Positives = 42/95 (44%), Gaps = 9/95 (9%)

Query: 3   DAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTYE 62
           D++L    +++AS DNP    + R   +++ + RA G  G+  GQ  +L  ++      +
Sbjct: 156 DSLLTLAFDIIASDDNPL--AAERKAALVISLARAAGIGGMAGGQALDLA-AEKKAPDED 212

Query: 63  T-----YKKNEGGLHTCGAACGAILGGGSVEEIEK 92
                   K  G L       GAI+ G +  E ++
Sbjct: 213 GIITLQAMKT-GALLRFACEAGAIIAGSNQAERQR 246

>1rtr_A Geranyltranstransferase; 2.50A {Staphylococcus aureus} SCOP: a.128.1.1 Length = 301

 Score = 44.5 bits (106), Expect = 1e-06
 Identities = 22/94 (23%), Positives = 38/94 (40%), Gaps = 8/94 (8%)

Query: 3   DAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTYE 62
           DA+L    EL++   +         ++V+  ++ A G  G+V GQ  ++Q S+   +  E
Sbjct: 113 DALLTKAFELIS---SDDRLTDEVKIKVLQRLSIASGHVGMVGGQMLDMQ-SEGQPIDLE 168

Query: 63  T----YKKNEGGLHTCGAACGAILGGGSVEEIEK 92
           T    +K   G L T      A +        E 
Sbjct: 169 TLEMIHKTKTGALLTFAVMSAADIANVDDTTKEH 202

>3m0g_A Farnesyl diphosphate synthase; structural genomics, protein structure initiative, NYSGXRC, biosynthesis, transferase, PSI-2; 1.90A {Rhodobacter capsulatus} PDB: 3lvs_A Length = 297

 Score = 44.1 bits (105), Expect = 1e-06
 Identities = 21/95 (22%), Positives = 40/95 (42%), Gaps = 8/95 (8%)

Query: 3   DAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQC-SQYVEMTY 61
           DA+     EL     +P   ++   + ++  + +A G++G+V GQ  ++   +  V +T 
Sbjct: 112 DALQTLAFELCT---DPVLGSAENRVALVAALAQASGAEGMVYGQALDIAAETAAVPLTL 168

Query: 62  ET----YKKNEGGLHTCGAACGAILGGGSVEEIEK 92
           +          G L +  A  GAIL G     +  
Sbjct: 169 DEIIRLQAGKTGALISFAAQAGAILAGADRGPLTA 203

>3nf2_A Putative polyprenyl synthetase; isoprenyl diphosphate synthase, structural genomics, PSI, PR structure initiative, nysgrc; 2.20A {Streptomyces coelicolor} Length = 352

 Score = 44.2 bits (105), Expect = 1e-06
 Identities = 20/94 (21%), Positives = 37/94 (39%), Gaps = 14/94 (14%)

Query: 3   DAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTYE 62
           DA+     E+L          +GR  R + + +R      +++GQ  ++       ++ E
Sbjct: 123 DALFALANEVLLELGTVE---AGRATRRLTKASR-----SLIDGQAQDISYEHRDRVSVE 174

Query: 63  TY-----KKNEGGLHTCGAACGAILGGGSVEEIE 91
                   K  G L  C ++ GA+LGG      +
Sbjct: 175 ECLEMEGNKT-GALLACASSIGAVLGGADERTAD 207

>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

 Score = 43.8 bits (104), Expect = 2e-06
 Identities = 22/95 (23%), Positives = 37/95 (38%), Gaps = 11/95 (11%)

Query: 3   DAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTYE 62
           D +L    + L ++D PA         ++  +  A G  G+V GQ  ++Q S++V +   
Sbjct: 121 DGLLTLAFQWLTATDLPAT----MQAALVQALATAAGPSGMVAGQAKDIQ-SEHVNLPLS 175

Query: 63  T-----YKKNEGGLHTCGAACGAILGGGSVEEIEK 92
                  +K  G L       G ILG     +   
Sbjct: 176 QLRVLHKEKT-GALLHYAVQAGLILGQAPEAQWPA 209

>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

 Score = 43.7 bits (104), Expect = 2e-06
 Identities = 17/97 (17%), Positives = 35/97 (36%), Gaps = 6/97 (6%)

Query: 3   DAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTYE 62
           DA+      +L+ +D P   +    + ++ E+  A G  G+  GQ  +L  ++   +  +
Sbjct: 115 DALQTLAFSILSDADMP-EVSDRDRISMISELASASGIAGMCGGQALDLD-AEGKHVPLD 172

Query: 63  T----YKKNEGGLHTCGAACGAILGGGSVEEIEKKFR 95
                ++   G L       GA+  G           
Sbjct: 173 ALERIHRHKTGALIRAAVRLGALSAGDKGRRALPVLD 209

>3llw_A Geranyltranstransferase (ISPA); structural genomics, PSI, protein structure initiative, nysgrc; 2.30A {Helicobacter pylori} PDB: 3q1o_A* Length = 311

 Score = 43.4 bits (103), Expect = 3e-06
 Identities = 17/97 (17%), Positives = 40/97 (41%), Gaps = 9/97 (9%)

Query: 3   DAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTYE 62
           DA+  +  ELL+++   +      I+ ++  ++   G +G++ GQ  +    +   +  E
Sbjct: 125 DALNTYSFELLSNALLESH----IIVELIKILSANGGIKGMILGQALDCY-FENTPLNLE 179

Query: 63  T----YKKNEGGLHTCGAACGAILGGGSVEEIEKKFR 95
                ++     L +     G +  G   EE+ K  +
Sbjct: 180 QLTFLHEHKTAKLISASLIMGLVASGIKDEELFKWLQ 216

>3p8l_A Geranyltranstransferase; isoprenyl synthase, structural genomics, PSI, protein struct initiative, nysgrc; 2.00A {Enterococcus faecalis} Length = 302

 Score = 43.4 bits (103), Expect = 3e-06
 Identities = 23/94 (24%), Positives = 42/94 (44%), Gaps = 9/94 (9%)

Query: 3   DAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTYE 62
           D +L    +LL+ S           + +M ++ +A G+QG+V GQ  +++  + V +T E
Sbjct: 122 DGLLTGAFQLLSLSQLGLS----EKVLLMQQLAKAAGNQGMVSGQMGDIE-GEKVSLTLE 176

Query: 63  T----YKKNEGGLHTCGAACGAILGGGSVEEIEK 92
                ++K  G L       G +L   + E I  
Sbjct: 177 ELAAVHEKKTGALIEFALIAGGVLANQTEEVIGL 210

>3p8r_A Geranyltranstransferase; isoprenyl synthase, structural genomics, PSI, protein struct initiative, nysgrc; 2.50A {Vibrio cholerae} Length = 302

 Score = 43.0 bits (102), Expect = 4e-06
 Identities = 20/97 (20%), Positives = 39/97 (40%), Gaps = 6/97 (6%)

Query: 3   DAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTYE 62
           DA+      +LA  D  A   + + + ++  +  A G+QG+  GQ  +L  ++   ++ E
Sbjct: 121 DALQTLAFTILAEGDLSAAGET-QRVAMLQALAEASGAQGMCLGQALDLA-AENRLISLE 178

Query: 63  T----YKKNEGGLHTCGAACGAILGGGSVEEIEKKFR 95
                ++   G L  C    GA+  G     +     
Sbjct: 179 ELETIHRNKTGALMRCAIRLGALAAGEKGRAMLPHLD 215

>3npk_A Geranyltranstransferase; isoprene biosynthesis, SGX, structural genomics protein structure initiative; 1.50A {Campylobacter jejuni} Length = 291

 Score = 42.6 bits (101), Expect = 5e-06
 Identities = 12/94 (12%), Positives = 30/94 (31%), Gaps = 9/94 (9%)

Query: 3   DAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTYE 62
           DA+      +L+ +           ++++  +    G  G+V GQ  +    +   ++  
Sbjct: 111 DALNTEAFLVLSHAHLKDE----IKIKLIKTLAFNAGLNGMVIGQAIDCF-FEDKRLSLN 165

Query: 63  T----YKKNEGGLHTCGAACGAILGGGSVEEIEK 92
                +      L       G  +   + EE  +
Sbjct: 166 ELEFLHTHKTARLIAAALKMGCEICELNNEESNQ 199

>3ts7_A Geranyltranstransferase; isoprenoid synthesis, farnesyl diphosphate synthase; 1.94A {Methylococcus capsulatus} Length = 324

 Score = 42.6 bits (101), Expect = 5e-06
 Identities = 15/97 (15%), Positives = 32/97 (32%), Gaps = 6/97 (6%)

Query: 3   DAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTYE 62
           D +      +LA   +     +   + ++  + +A G  G+V GQ  +L  S   ++   
Sbjct: 121 DGLQALAFHVLAQDPSI-AVPAENRIAMIETLAKASGPAGMVGGQAIDLA-SVGKKLDLP 178

Query: 63  T----YKKNEGGLHTCGAACGAILGGGSVEEIEKKFR 95
                + +  G L         +   G   E   +  
Sbjct: 179 GLENMHIRKTGALIRASVRLACLARPGLPAEQFDRLD 215

>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

 Score = 41.8 bits (99), Expect = 8e-06
 Identities = 17/91 (18%), Positives = 35/91 (38%), Gaps = 6/91 (6%)

Query: 3   DAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTYE 62
           D +       L         ++   LR++  + +A G  G+V GQ  +L  S  +++  +
Sbjct: 115 DGLQSLAFSALLDPALS-DASAEIRLRMVTTLAQAAGPAGMVGGQAIDLG-SVGLKLDQQ 172

Query: 63  T----YKKNEGGLHTCGAACGAILGGGSVEE 89
                ++   G L       GA+  G + + 
Sbjct: 173 ALEYMHRHKTGALIEASVILGALASGRAEKG 203

>4f62_A Geranyltranstransferase; enzyme function initiative, structural genomics; 2.10A {Marinomonas SP} Length = 317

 Score = 41.4 bits (98), Expect = 1e-05
 Identities = 23/97 (23%), Positives = 38/97 (39%), Gaps = 8/97 (8%)

Query: 3   DAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTYE 62
           DA+  F  ELL+   NP        ++++ E+  A G  G++ GQ  +L  S+   ++  
Sbjct: 116 DALQTFAFELLS---NPTSAQPELAIKLIQELVVASGRNGMITGQMIDLS-SENKNISLA 171

Query: 63  T----YKKNEGGLHTCGAACGAILGGGSVEEIEKKFR 95
                +    G L       GA+  G    E   K  
Sbjct: 172 ELEQMHVHKTGALIKASVRMGALSTGQVKPEQLAKLD 208

>3lk5_A Geranylgeranyl pyrophosphate synthase; structural genomics, protein structure initiative, geranylge pyrophosphate synthase; 1.90A {Corynebacterium glutamicum} PDB: 3qqv_A* Length = 380

 Score = 40.9 bits (96), Expect = 2e-05
 Identities = 19/97 (19%), Positives = 32/97 (32%), Gaps = 17/97 (17%)

Query: 3   DAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTYE 62
           D  L +  ++L  S   A   + R       M        V+ GQ  ++    +   + E
Sbjct: 153 DMALVWAEDMLQDSGLSAEALA-RTRDAWRGMRTE-----VIGGQLLDIYLESHANESVE 206

Query: 63  TY------KKNEGGLHTCGAAC--GAILGGGSVEEIE 91
                   K      +T       GA + GGS + I+
Sbjct: 207 LADSVNRFKT---AAYTIARPLHLGASIAGGSPQLID 240

>1wy0_A Geranylgeranyl pyrophosphate synthetase; pyrococcus horikosh structural genomics, riken structural genomics/proteomics initiative, RSGI; 2.20A {Pyrococcus horikoshii} Length = 342

 Score = 40.4 bits (95), Expect = 3e-05
 Identities = 23/93 (24%), Positives = 38/93 (40%), Gaps = 10/93 (10%)

Query: 3   DAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTYE 62
           D +     E +A ++ P         RV+  + +A  S  + EGQ  +L+  +   +T E
Sbjct: 115 DLLFSKAFEAVARAEIPPEKK----ARVLEVIVKA--SNELCEGQARDLEFEKKSTVTIE 168

Query: 63  TY----KKNEGGLHTCGAACGAILGGGSVEEIE 91
            Y        G L    A  G I+G  + E I+
Sbjct: 169 EYMEMISGKTGALFEASAKVGGIIGTDNEEYIK 201

>1wmw_A Geranylgeranyl diphosphate synthetase; GGPP, prenyl diphosphate synthase, structural genom riken structural genomics/proteomics initiative; 1.55A {Thermus thermophilus} Length = 330

 Score = 36.1 bits (84), Expect = 8e-04
 Identities = 21/97 (21%), Positives = 30/97 (30%), Gaps = 19/97 (19%)

Query: 3   DAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNEL--QCSQYVEMT 60
           DAM      LLA            +L    E+ R         GQ+ +L        ++ 
Sbjct: 108 DAMHAEMWGLLAEGLARGLFPP-EVLLEFHEVVRR-----TAYGQHLDLLWTLGGTFDLR 161

Query: 61  YETY------KKNEGGLHTCGAAC--GAILGGGSVEE 89
            E Y      K      +T  A    GA+L G +   
Sbjct: 162 PEDYFRMVAHKA---AYYTAVAPLRLGALLAGKTPPA 195

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	111
3qkc_B	273	Geranyl diphosphate synthase small subunit; struct	99.94
4f62_A	317	Geranyltranstransferase; enzyme function initiativ	99.94
3p8l_A	302	Geranyltranstransferase; isoprenyl synthase, struc	99.94
3kra_B	274	Geranyl diphosphate synthase small subunit; prenyl	99.94
3ts7_A	324	Geranyltranstransferase; isoprenoid synthesis, far	99.94
3pde_A	309	Farnesyl-diphosphate synthase; isoprenyl diphospha	99.94
3npk_A	291	Geranyltranstransferase; isoprene biosynthesis, SG	99.94
3lsn_A	304	Geranyltranstransferase; structural genomics, prot	99.94
1rtr_A	301	Geranyltranstransferase; 2.50A {Staphylococcus aur	99.94
3llw_A	311	Geranyltranstransferase (ISPA); structural genomic	99.94
2h8o_A	335	Geranyltranstransferase; geranyltransferase,agroba	99.93
3uca_A	324	Geranyltranstransferase; isoprenoid synthesis, iso	99.93
1rqj_A	299	Geranyltranstransferase; bisphosphonate, isoprenyl	99.93
3p8r_A	302	Geranyltranstransferase; isoprenyl synthase, struc	99.93
3lom_A	313	Geranyltranstransferase; geranyltransferase, struc	99.92
2j1p_A	293	Geranylgeranyl pyrophosphate synthetase; transfera	99.92
1wy0_A	342	Geranylgeranyl pyrophosphate synthetase; pyrococcu	99.92
3m0g_A	297	Farnesyl diphosphate synthase; structural genomics	99.92
3ipi_A	295	Geranyltranstransferase; isoprene biosynthesis, he	99.91
3nf2_A	352	Putative polyprenyl synthetase; isoprenyl diphosph	99.91
3oyr_A	345	Trans-isoprenyl diphosphate synthase; isoprenyl sy	99.91
3lk5_A	380	Geranylgeranyl pyrophosphate synthase; structural	99.91
3mzv_A	341	Decaprenyl diphosphate synthase; transferase, stru	99.91
3aqb_B	325	Component B of hexaprenyl diphosphate synthase; pr	99.91
3rmg_A	334	Octaprenyl-diphosphate synthase; structural genomi	99.91
3apz_A	348	Geranyl diphosphate synthase; prenyltransferase, a	99.91
3lmd_A	360	Geranylgeranyl pyrophosphate synthase; isoprenyl d	99.9
4dhd_A	358	Polyprenyl synthetase; isoprenoid synthesis, isopr	99.9
3pko_A	334	Geranylgeranyl pyrophosphate synthase; isoprenyl d	99.9
2ftz_A	284	Geranyltranstransferase; TM0161, structural GE joi	99.89
1v4e_A	299	Octoprenyl-diphosphate synthase; trans-type prenyl	99.89
2e8v_A	340	Geranylgeranyl pyrophosphate synthetase; prenyltra	99.89
3tc1_A	315	Octaprenyl pyrophosphate synthase; all alpha-helic	99.88
1yhl_A	362	Farnesyl pyrophosphate synthase; farnesyl diphosph	99.88
2azj_A	289	Geranylgeranyl pyrophosphate synthetase; hexpps, t	99.88
1wmw_A	330	Geranylgeranyl diphosphate synthetase; GGPP, preny	99.88
2qis_A	374	Farnesyl pyrophosphate synthetase; trans-prenyltra	99.86
4fp4_A	285	Polyprenyl synthetase; isoprenoid synthesis, isopr	99.86
1uby_A	367	FPS, farnesyl diphosphate synthase; transferase, i	99.86
2q80_A	301	Geranylgeranyl pyrophosphate synthetase; isoprenoi	99.85
3dyh_A	390	Farnesyl pyrophosphate synthase; protein-bisphosph	99.85
2her_A	368	Fragment, farnesyl pyrophosphate synthase; farnesy	99.84
2ihi_A	395	Pyrophosphate synthase; PV092040, structural genom	99.84
2q58_A	368	Fragment, farnesyl pyrophosphate synthase; farnesy	99.84
3mav_A	395	Farnesyl pyrophosphate synthase; PV092040, structu	99.83

>3qkc_B Geranyl diphosphate synthase small subunit; structural genomics, protein structure initiative, NEW YORK structural genomix research consortium; 2.20A {Antirrhinum majus}

Probab=99.94  E-value=8.8e-27  Score=174.10  Aligned_cols=109  Identities=49%  Similarity=0.816  Sum_probs=96.4

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc--CCHHHHHHHHHhhhHHHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS--QYVEMTYETYKKNEGGLHTCGAAC   78 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~--~~~~~~~~i~~~KTa~L~~~~~~~   78 (111)
                      +||+|+++||+++++..++...++.+.++++..+++++|..+|+.||++|+.++  .+++++..|+++|||+||++||++
T Consensus       111 aGD~Ll~~Af~~l~~~~~~~~~~~~~~~~~~~~l~~a~g~~~~~~GQ~lDl~~~~~~~~eyl~~I~~~KTa~L~~~a~~l  190 (273)
T 3qkc_B          111 TGDGIIPFGLELMARSMDPTRNNPDRILRAIIELTRVMGSEGIVEGQYHELGLNQLNDLELIEYVCKKKEGTLHACGAAC  190 (273)
T ss_dssp             HHHHHHHHHHHHHHHHSCSSCCCHHHHHHHHHHHHHHHTTTTHHHHHHHHTTCCSSCCHHHHHHHHHHTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCcccccHHHHHHHHHHHHHHhchhHHHHHHHHHHhcCCCCCHHHHHHHHHhhHHHHHHHHHHH
Confidence            599999999999998643112345677899999999999999999999999874  567788889999999999999999


Q ss_pred             HHHhCCCCHHHHHHHH-HhHHhhHhhhhhcCC
Q 047640           79 GAILGGGSVEEIEKKF-RGLIIKITKMMIRNS  109 (111)
Q Consensus        79 Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~~  109 (111)
                      ||+++|+++++++.++ ||.++|++|||+||-
T Consensus       191 Gailaga~~~~~~~l~~~G~~lGlaFQI~DD~  222 (273)
T 3qkc_B          191 GAILGGCDEDKIEKLRRFGLYVGTVQGLLGKN  222 (273)
T ss_dssp             HHHHHCCCHHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999 999999999999984

>4f62_A Geranyltranstransferase; enzyme function initiative, structural genomics; 2.10A {Marinomonas SP}

Probab=99.94  E-value=1.3e-26  Score=176.39  Aligned_cols=105  Identities=20%  Similarity=0.281  Sum_probs=96.6

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc---CCHHHHHHHHHhhhHHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS---QYVEMTYETYKKNEGGLHTCGAA   77 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~---~~~~~~~~i~~~KTa~L~~~~~~   77 (111)
                      +||+|+++||+++++.+   ++++...+++++.+++++|..+|+.||++|+.++   .++++|.+|+++|||+||++||+
T Consensus       114 aGD~Ll~~Af~~l~~~~---~~~~~~~~~~i~~la~a~g~~~m~~GQ~lDl~~~~~~~t~~~y~~i~~~KTg~L~~~a~~  190 (317)
T 4f62_A          114 AGDALQTFAFELLSNPT---SAQPELAIKLIQELVVASGRNGMITGQMIDLSSENKNISLAELEQMHVHKTGALIKASVR  190 (317)
T ss_dssp             HHHHHHHHHHHHHTCTT---CCCHHHHHHHHHHHHHHHSTTTHHHHHHHHHHTSSSCCCHHHHHHHHHHHTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcc---CCCHHHHHHHHHHHHHHHhhhhHHHhHHHHHhccCCCCCHHHHHHHHHhchHHHHHHHHH
Confidence            59999999999999863   3456678899999999999889999999999874   78999999999999999999999


Q ss_pred             HHHHhCC-CCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           78 CGAILGG-GSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        78 ~Gai~~g-~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      +|++++| +++++++.++ ||.++|++|||+||
T Consensus       191 ~Ga~lag~a~~~~~~~l~~~g~~lGlAFQI~DD  223 (317)
T 4f62_A          191 MGALSTGQVKPEQLAKLDAYAHAIGLAFQVQDD  223 (317)
T ss_dssp             HHHHTTTCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999 8999999999 99999999999997

>3p8l_A Geranyltranstransferase; isoprenyl synthase, structural genomics, PSI, protein struct initiative, nysgrc; 2.00A {Enterococcus faecalis}

Probab=99.94  E-value=1.5e-26  Score=175.08  Aligned_cols=104  Identities=20%  Similarity=0.247  Sum_probs=96.2

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc---CCHHHHHHHHHhhhHHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS---QYVEMTYETYKKNEGGLHTCGAA   77 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~---~~~~~~~~i~~~KTa~L~~~~~~   77 (111)
                      +||+|+++||+++++..    +++...+++++.+++++|..+|+.||++|+.++   .++++|.+|+++|||+||++||+
T Consensus       120 aGD~Ll~~A~~~l~~~~----~~~~~~~~~~~~l~~a~g~~~~~~GQ~lDl~~~~~~~t~~~y~~i~~~KTg~L~~~~~~  195 (302)
T 3p8l_A          120 AGDGLLTGAFQLLSLSQ----LGLSEKVLLMQQLAKAAGNQGMVSGQMGDIEGEKVSLTLEELAAVHEKKTGALIEFALI  195 (302)
T ss_dssp             HHHHHHHHHHHHHHTSS----CCHHHHHHHHHHHHHHHSTTTHHHHHHHHHHTTTSCCCHHHHHHHHHHHTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcC----CChHHHHHHHHHHHHHhhhhHHHHHHHHHHHccCCCCCHHHHHHHHHcCcHHHHHHHHH
Confidence            59999999999999862    356677899999999999899999999999874   78999999999999999999999


Q ss_pred             HHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           78 CGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        78 ~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      +|++++|+++++.+.++ ||.++|++|||+||
T Consensus       196 ~ga~laga~~~~~~~l~~~g~~lGlaFQI~DD  227 (302)
T 3p8l_A          196 AGGVLANQTEEVIGLLTQFAHHYGLAFQIRDD  227 (302)
T ss_dssp             HHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999 99999999999997

>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*

Probab=99.94  E-value=1.5e-26  Score=172.97  Aligned_cols=110  Identities=41%  Similarity=0.664  Sum_probs=97.6

Q ss_pred             ChhhHHHHHHHHHHcCCCCC-CCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc---CCHHHHHHHHHhhhHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPA-GNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS---QYVEMTYETYKKNEGGLHTCGA   76 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~-~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~---~~~~~~~~i~~~KTa~L~~~~~   76 (111)
                      +||+|+++||+++++..++. ..++.+.++++..+++++|..+|+.||++|+.++   .++++|.+|+++|||+||++||
T Consensus       108 aGD~Ll~~Af~~l~~~~~~~~~~~~~~~~~~~~~l~~a~G~~~~~~GQ~lDl~~~~~~~t~~~y~~~i~~KTa~L~~~a~  187 (274)
T 3kra_B          108 TGDGIVPFGFELLAGSVDPARTDDPDRILRVIIEISRAGGPEGMISGLHREEEIVDGNTSLDFIEYVCKKKYGEMHACGA  187 (274)
T ss_dssp             HHHHHHHHHHHHHHHTCCTTCTTHHHHHHHHHHHHHHHTSTTTHHHHHHHHTTCCTTSSCHHHHHHHHHHHTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcCCccccccHHHHHHHHHHHHHHHhHHHHHHhHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            59999999999999875310 1234567889999999999999999999999874   7889999999999999999999


Q ss_pred             HHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcCCC
Q 047640           77 ACGAILGGGSVEEIEKKF-RGLIIKITKMMIRNSF  110 (111)
Q Consensus        77 ~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~~~  110 (111)
                      ++|++++|+++++++.++ ||.++|++|||+||-+
T Consensus       188 ~lGailaga~~~~~~~l~~~G~~lG~aFQI~DD~~  222 (274)
T 3kra_B          188 ACGAILGGAAEEEIQKLRNFGLYQGTLRGMMEMKN  222 (274)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            999999999999999999 9999999999999853

>3ts7_A Geranyltranstransferase; isoprenoid synthesis, farnesyl diphosphate synthase; 1.94A {Methylococcus capsulatus}

Probab=99.94  E-value=1.8e-26  Score=176.02  Aligned_cols=107  Identities=13%  Similarity=0.163  Sum_probs=97.2

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc---CCHHHHHHHHHhhhHHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS---QYVEMTYETYKKNEGGLHTCGAA   77 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~---~~~~~~~~i~~~KTa~L~~~~~~   77 (111)
                      +||+|+++||+++++... .+.++...+++++.+++++|+.+|+.||++|+.++   .++++|.+|+++|||+||++||+
T Consensus       119 aGD~L~~~Af~~l~~~~~-~~~~~~~~~~~i~~la~a~g~~~m~~GQ~lDl~~~~~~~t~~~y~~i~~~KTg~L~~~a~~  197 (324)
T 3ts7_A          119 AGDGLQALAFHVLAQDPS-IAVPAENRIAMIETLAKASGPAGMVGGQAIDLASVGKKLDLPGLENMHIRKTGALIRASVR  197 (324)
T ss_dssp             HHHHHHHHHHHHHHHCTT-SCCCHHHHHHHHHHHHHHHSTTTHHHHHHHHHHTTTCCCCHHHHHHHHHHHTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccc-cCCCHHHHHHHHHHHHHHHhhhHHHHhHHHHHHccCCCCCHHHHHHHHHhhHHHHHHHHHH
Confidence            599999999999998731 13456668899999999999899999999999874   78999999999999999999999


Q ss_pred             HHHHhCC-CCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           78 CGAILGG-GSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        78 ~Gai~~g-~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      +|++++| +++++.+.++ ||.++|+||||+||
T Consensus       198 ~Ga~lag~a~~~~~~~l~~~g~~lGlAFQI~DD  230 (324)
T 3ts7_A          198 LACLARPGLPAEQFDRLDHYAKCIGLAFQIQDD  230 (324)
T ss_dssp             HHHTTSTTCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999 9999999999 99999999999997

>3pde_A Farnesyl-diphosphate synthase; isoprenyl diphosphate synthase, structural genomics, PSI, PR structure initiative; HET: IPE; 1.75A {Lactobacillus brevis} PDB: 3m9u_A*

Probab=99.94  E-value=1.3e-26  Score=175.89  Aligned_cols=104  Identities=17%  Similarity=0.246  Sum_probs=96.3

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc---CCHHHHHHHHHhhhHHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS---QYVEMTYETYKKNEGGLHTCGAA   77 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~---~~~~~~~~i~~~KTa~L~~~~~~   77 (111)
                      +||+|+++||+++++..    .++...+++++.+++++|+.+|+.||++|+.++   +++++|.+|+++|||+||++||+
T Consensus       119 aGD~Ll~~Af~~l~~~~----~~~~~~~~~~~~l~~a~g~~~m~~GQ~lDl~~~~~~~t~~~y~~i~~~KTg~L~~~a~~  194 (309)
T 3pde_A          119 AGDGLLTLAFQWLTATD----LPATMQAALVQALATAAGPSGMVAGQAKDIQSEHVNLPLSQLRVLHKEKTGALLHYAVQ  194 (309)
T ss_dssp             HHHHHHHHHHHHHTSSS----CCHHHHHHHHHHHHHHHSTTTHHHHHHHHHHTTTCCCCHHHHHHHHHHHTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcC----CChHHHHHHHHHHHHHhhHhHHHHhHHHHHHccCCCCCHHHHHHHHHhccHHHHHHHHH
Confidence            59999999999999863    356677899999999999899999999999874   78999999999999999999999


Q ss_pred             HHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           78 CGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        78 ~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      +|++++|+++++.+.++ ||.++|++|||+||
T Consensus       195 ~ga~laga~~~~~~~l~~~g~~lGlaFQI~DD  226 (309)
T 3pde_A          195 AGLILGQAPEAQWPAYLQFADAFGLAFQIYDD  226 (309)
T ss_dssp             HHHHHTTCCGGGHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999 99999999999997

>3npk_A Geranyltranstransferase; isoprene biosynthesis, SGX, structural genomics protein structure initiative; 1.50A {Campylobacter jejuni}

Probab=99.94  E-value=2.3e-26  Score=173.32  Aligned_cols=104  Identities=13%  Similarity=0.112  Sum_probs=95.4

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc---CCHHHHHHHHHhhhHHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS---QYVEMTYETYKKNEGGLHTCGAA   77 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~---~~~~~~~~i~~~KTa~L~~~~~~   77 (111)
                      +||+|+++||+++++..    +++....++++.++++.|+.+|+.||.+|+.++   .++++|.+|+++|||+||++||+
T Consensus       109 aGD~Ll~~A~~~l~~~~----~~~~~~~~~~~~l~~~~g~~~~~~GQ~lDl~~~~~~~~~~~y~~i~~~KTg~L~~~a~~  184 (291)
T 3npk_A          109 VGDALNTEAFLVLSHAH----LKDEIKIKLIKTLAFNAGLNGMVIGQAIDCFFEDKRLSLNELEFLHTHKTARLIAAALK  184 (291)
T ss_dssp             HHHHHHHHHHHHHHTSS----SCHHHHHHHHHHHHHHHSTTTHHHHHHHHHHTTTSCCCHHHHHHHHHHHTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcC----CChHHHHHHHHHHHHHHhHHHHHHHHHHHHhccCCCCCHHHHHHHHHcccHHHHHHHHH
Confidence            59999999999998752    356667889999999978899999999999863   78999999999999999999999


Q ss_pred             HHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           78 CGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        78 ~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      +||+++|+++++.+.++ ||.++|++|||+||
T Consensus       185 ~ga~laga~~~~~~~l~~~g~~lGlaFQI~DD  216 (291)
T 3npk_A          185 MGCEICELNNEESNQIYKLGLKLGLIFQINDD  216 (291)
T ss_dssp             HHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999 99999999999997

>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*

Probab=99.94  E-value=2.9e-26  Score=173.63  Aligned_cols=107  Identities=17%  Similarity=0.210  Sum_probs=97.0

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc---CCHHHHHHHHHhhhHHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS---QYVEMTYETYKKNEGGLHTCGAA   77 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~---~~~~~~~~i~~~KTa~L~~~~~~   77 (111)
                      +||+|+++||+++++... +++++...+++++.+++++|..+|+.||++|+.++   .++++|++|+++|||+||++||+
T Consensus       113 aGD~Ll~~a~~~l~~~~~-~~~~~~~~~~~~~~l~~a~~~~~~~~GQ~lDl~~~~~~~s~~~y~~i~~~KTg~L~~~~~~  191 (304)
T 3lsn_A          113 AGDGLQSLAFSALLDPAL-SDASAEIRLRMVTTLAQAAGPAGMVGGQAIDLGSVGLKLDQQALEYMHRHKTGALIEASVI  191 (304)
T ss_dssp             HHHHHHHHHHHHHHCTTS-CCCCHHHHHHHHHHHHHHHSTTTHHHHHHHHHHTTTCCCCHHHHHHHHHHHTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcc-cCCChHHHHHHHHHHHHHHchhhHhHhHHHHHHccCCCCCHHHHHHHHHhhhHHHHHHHHH
Confidence            599999999999998632 13456678899999999998889999999999874   78999999999999999999999


Q ss_pred             HHHHhCCC-CHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           78 CGAILGGG-SVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        78 ~Gai~~g~-~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      +|++++|+ +++..+.++ ||.++|++|||+||
T Consensus       192 ~ga~lag~~~~~~~~~l~~~g~~lGlaFQI~DD  224 (304)
T 3lsn_A          192 LGALASGRAEKGELKALQTYAQAIGLAFQVQDD  224 (304)
T ss_dssp             HHHHHTTCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999 898999999 99999999999997

>1rtr_A Geranyltranstransferase; 2.50A {Staphylococcus aureus} SCOP: a.128.1.1

Probab=99.94  E-value=2.8e-26  Score=173.43  Aligned_cols=105  Identities=21%  Similarity=0.208  Sum_probs=96.6

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc---CCHHHHHHHHHhhhHHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS---QYVEMTYETYKKNEGGLHTCGAA   77 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~---~~~~~~~~i~~~KTa~L~~~~~~   77 (111)
                      +||+|+++||+++++..   .++++...++++.+++++|..+|+.||++|+.++   .++++|.+|+++|||+||++||+
T Consensus       111 aGD~Ll~~A~~~l~~~~---~~~~~~~~~~~~~ls~~~g~~~~~~GQ~~Dl~~~~~~~~~~~y~~i~~~KTa~L~~~~~~  187 (301)
T 1rtr_A          111 AGDALLTKAFELISSDD---RLTDEVKIKVLQRLSIASGHVGMVGGQMLDMQSEGQPIDLETLEMIHKTKTGALLTFAVM  187 (301)
T ss_dssp             HHHHHHHHHHHHHHTCT---TSCHHHHHHHHHHHHHHHSTTTHHHHHHHHHHTTTSCCCHHHHHHHHHHHTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhc---cCCchHHHHHHHHHHHHHhHhHHHHHHHHHHHccCCCCCHHHHHHHHHhchHHHHHHHHH
Confidence            59999999999999862   2355677889999999999999999999999873   78999999999999999999999


Q ss_pred             HHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           78 CGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        78 ~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      +|++++|+++++.+.++ ||.++|++|||+||
T Consensus       188 ~ga~lag~~~~~~~~l~~~g~~lG~aFQI~DD  219 (301)
T 1rtr_A          188 SAADIANVDDTTKEHLESYSYHLGMMFQIKDD  219 (301)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999 99999999999997

>3llw_A Geranyltranstransferase (ISPA); structural genomics, PSI, protein structure initiative, nysgrc; 2.30A {Helicobacter pylori} PDB: 3q1o_A*

Probab=99.94  E-value=2.4e-26  Score=174.55  Aligned_cols=104  Identities=18%  Similarity=0.203  Sum_probs=95.5

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc---CCHHHHHHHHHhhhHHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS---QYVEMTYETYKKNEGGLHTCGAA   77 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~---~~~~~~~~i~~~KTa~L~~~~~~   77 (111)
                      +||+|+++||+++++.    .+++...+++++.+++++|+.+|+.||++|+.++   .++++|.+|+++|||+||++||+
T Consensus       123 aGD~Ll~~Af~~l~~~----~~~~~~~~~~i~~la~a~g~~~m~~GQ~lDl~~~~~~~t~~~y~~i~~~KTg~L~~~a~~  198 (311)
T 3llw_A          123 IGDALNTYSFELLSNA----LLESHIIVELIKILSANGGIKGMILGQALDCYFENTPLNLEQLTFLHEHKTAKLISASLI  198 (311)
T ss_dssp             HHHHHHHHHHHHHHHS----CSCHHHHHHHHHHHHHHHSTTTHHHHHHHHHHTTTSCCCHHHHHHHHHHHTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhc----CCChHHHHHHHHHHHHHHHHHHHHHhHHHHHHhcCCCCCHHHHHHHHHHhHHHHHHHHHH
Confidence            5999999999999984    2356667899999999988899999999999873   78999999999999999999999


Q ss_pred             HHHHhCCCCHHHH-HHHH-HhHHhhHhhhhhcC
Q 047640           78 CGAILGGGSVEEI-EKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        78 ~Gai~~g~~~e~~-~~l~-~G~~~GiafQi~D~  108 (111)
                      +|++++|++++++ +.++ ||.++|++|||+||
T Consensus       199 lga~laga~~~~~~~~l~~~g~~lGlaFQI~DD  231 (311)
T 3llw_A          199 MGLVASGIKDEELFKWLQAFGLKMGLCFQVLDD  231 (311)
T ss_dssp             HHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999988 9999 99999999999997

>2h8o_A Geranyltranstransferase; geranyltransferase,agrobacterium tumefaciens, structural GEN PSI-2, protein structure initiative; 1.60A {Agrobacterium tumefaciens}

Probab=99.93  E-value=4e-26  Score=174.81  Aligned_cols=106  Identities=22%  Similarity=0.319  Sum_probs=97.0

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc---CCHHHHHHHHHhhhHHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS---QYVEMTYETYKKNEGGLHTCGAA   77 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~---~~~~~~~~i~~~KTa~L~~~~~~   77 (111)
                      +||+|+++||+++++...  +++++...++++.+++++|..+|+.||++|+.++   .++++|.+|+++|||+||++||+
T Consensus       154 aGD~Ll~~A~~~l~~~~~--~~~~~~~~~~~~~ls~a~g~~~~~~GQ~lDl~~~~~~~~~~~y~~i~~~KTa~L~~~a~~  231 (335)
T 2h8o_A          154 AGDSLLTLAFDIIASDDN--PLAAERKAALVISLARAAGIGGMAGGQALDLAAEKKAPDEDGIITLQAMKTGALLRFACE  231 (335)
T ss_dssp             HHHHHHHHHHHHHHSTTS--CSCHHHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHSCCCHHHHHHHHHHHTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcc--cCCchHHHHHHHHHHHHhhhhHHHHHHHHHHHccCCCCCHHHHHHHHHhchHHHHHHHHH
Confidence            599999999999998621  3456677889999999999999999999999873   78999999999999999999999


Q ss_pred             HHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           78 CGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        78 ~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      +|++++|+++++++.++ ||.++|++|||+||
T Consensus       232 ~Ga~laga~~~~~~~l~~~g~~lGlAFQI~DD  263 (335)
T 2h8o_A          232 AGAIIAGSNQAERQRLRLFGEKIGLSFQLADD  263 (335)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999 99999999999997

>3uca_A Geranyltranstransferase; isoprenoid synthesis, isoprenoid diphosphate synthase; 2.00A {Clostridium perfringens}

Probab=99.93  E-value=2.1e-26  Score=175.76  Aligned_cols=104  Identities=21%  Similarity=0.264  Sum_probs=93.8

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHH-HHHHHHHHHhhchhHHHHhhHHHhccc----CCHHHHHHHHHhhhHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRI-LRVMVEMTRAMGSQGVVEGQYNELQCS----QYVEMTYETYKKNEGGLHTCG   75 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~-~~~i~~~~~~~G~~~m~~GQ~lDl~~~----~~~~~~~~i~~~KTa~L~~~~   75 (111)
                      +||+|+++||+++++..    +++... +++++.+++++|..+|+.||++|+.++    .++++|.+|+++|||+||++|
T Consensus       143 aGD~Ll~~A~~~l~~~~----~~~~~~~~~~i~~la~a~g~~~m~~GQ~lDl~~~~~~~~t~~~y~~i~~~KTa~L~~~a  218 (324)
T 3uca_A          143 AGDALLNEAMKILVDYS----LEEGKSALKATKIIADAAGSDGMIGGQIVDIINEDKEEISLKELDYMHLKKTGELIKAS  218 (324)
T ss_dssp             HHHHHHHHHHHHHHHHH----HHHCHHHHHHHHHHHHHHSTTTHHHHHHHHHHTSSCSSCCHHHHHHHHHHHTHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcC----CChhhHHHHHHHHHHHHHhHhHHHHhHHHHHHcCCCCCCCHHHHHHHHhcchHHHHHHH
Confidence            59999999999999852    123334 789999999998899999999999873    789999999999999999999


Q ss_pred             HHHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           76 AACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        76 ~~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      |++|++++|+++++.+.++ ||.++|++|||+||
T Consensus       219 ~~~Ga~laga~~~~~~~l~~~g~~lGlAFQI~DD  252 (324)
T 3uca_A          219 IMSGAVLAEASEGDIKKLEGFGYKLGLAFQIKDD  252 (324)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999 99999999999997

>1rqj_A Geranyltranstransferase; bisphosphonate, isoprenyl synthase; HET: IPR RIS; 1.95A {Escherichia coli} SCOP: a.128.1.1 PDB: 1rqi_A* 2for_A*

Probab=99.93  E-value=6.7e-26  Score=171.09  Aligned_cols=107  Identities=16%  Similarity=0.214  Sum_probs=96.5

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc---CCHHHHHHHHHhhhHHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS---QYVEMTYETYKKNEGGLHTCGAA   77 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~---~~~~~~~~i~~~KTa~L~~~~~~   77 (111)
                      +||+|+++||+++++... .++++....++++.+++++|..+|+.||++|+.++   .++++|.+|+++|||+||++||+
T Consensus       113 ~GD~L~~~a~~~l~~~~~-~~~~~~~~~~~~~~l~~~~g~~~~~~GQ~~dl~~~~~~~~~~~y~~i~~~KTa~L~~~~~~  191 (299)
T 1rqj_A          113 AGDALQTLAFSILSDADM-PEVSDRDRISMISELASASGIAGMCGGQALDLDAEGKHVPLDALERIHRHKTGALIRAAVR  191 (299)
T ss_dssp             HHHHHHHHHHHHHHHSCC-TTCCHHHHHHHHHHHHHHHSTTTHHHHHHHHHHTTTTCCCHHHHHHHHHHHTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhhc-ccCChHHHHHHHHHHHHHhhhhHHHHhHHHHHhccCCCCCHHHHHHHHHhhhHHHHHHHHH
Confidence            599999999999998521 13456678899999999998899999999999874   78999999999999999999999


Q ss_pred             HHHHh-CCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           78 CGAIL-GGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        78 ~Gai~-~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      +|+++ +|+++++.+.++ ||.++|++|||+||
T Consensus       192 ~ga~l~ag~~~~~~~~l~~~g~~lG~aFQi~DD  224 (299)
T 1rqj_A          192 LGALSAGDKGRRALPVLDKYAESIGLAFQVQDD  224 (299)
T ss_dssp             HHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999 998899999999 99999999999997

>3p8r_A Geranyltranstransferase; isoprenyl synthase, structural genomics, PSI, protein struct initiative, nysgrc; 2.50A {Vibrio cholerae} SCOP: a.128.1.1

Probab=99.93  E-value=3.6e-26  Score=172.93  Aligned_cols=107  Identities=18%  Similarity=0.260  Sum_probs=94.5

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc---CCHHHHHHHHHhhhHHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS---QYVEMTYETYKKNEGGLHTCGAA   77 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~---~~~~~~~~i~~~KTa~L~~~~~~   77 (111)
                      +||+|+++||+++++... .++++...+++++.+++++|+.+|+.||++|+.+.   .++++|.+|+++|||+||++||+
T Consensus       119 aGD~L~~~a~~~l~~~~~-~~~~~~~~~~~~~~l~~a~g~~~~~~GQ~lDl~~~~~~~s~~~y~~i~~~KTa~L~~~~~~  197 (302)
T 3p8r_A          119 TGDALQTLAFTILAEGDL-SAAGETQRVAMLQALAEASGAQGMCLGQALDLAAENRLISLEELETIHRNKTGALMRCAIR  197 (302)
T ss_dssp             HHHHHHHHHHHHHHHSCC-CHHHHTTHHHHHHHHHHHHSTTTHHHHHHHHHHTTTSCCCHHHHHHHHHHHTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccc-cCCCHHHHHHHHHHHHHHHhHhHHHHhHHHHHHccCCCCCHHHHHHHhccCcHHHHHHHHH
Confidence            599999999999998731 01123346788999999998899999999999873   78999999999999999999999


Q ss_pred             HHHHhCC-CCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           78 CGAILGG-GSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        78 ~Gai~~g-~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      +|++++| +++++.+.++ ||.++|++|||+||
T Consensus       198 ~ga~lag~~~~~~~~~l~~~g~~lG~aFQI~DD  230 (302)
T 3p8r_A          198 LGALAAGEKGRAMLPHLDRYAEAVGLAFQVQDD  230 (302)
T ss_dssp             HHHHTTTHHHHTTHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999 8888899999 99999999999997

>3lom_A Geranyltranstransferase; geranyltransferase, structural genomics, PSI, protein structure initiative, nysgrc; 2.30A {Legionella pneumophila subsp}

Probab=99.92  E-value=2e-25  Score=169.64  Aligned_cols=105  Identities=18%  Similarity=0.107  Sum_probs=94.7

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCCh-HHHHHHHHHHHHhhchhHHHHhhHHHhccc----CCHHHHHHHHHhhhHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNS-GRILRVMVEMTRAMGSQGVVEGQYNELQCS----QYVEMTYETYKKNEGGLHTCG   75 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~-~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~----~~~~~~~~i~~~KTa~L~~~~   75 (111)
                      +||+|+++||+++++...  +.++ ...+++++.+++++|+.+|+.||++|+.++    .++++|.+|+++|||+||++|
T Consensus       119 aGD~Ll~~a~~~l~~~~~--~~~~~~~~~~~i~~la~a~g~~~m~~GQ~lDl~~~~~~~~t~~~y~~i~~~KTg~L~~~a  196 (313)
T 3lom_A          119 VGDGMQALAIEVLLMRLS--PLLPAAQVVAITQVLVNASGISGMVSGQSLDLSELAKSSVTEEQLREIHLLKTGKLILAC  196 (313)
T ss_dssp             HHHHHHHHHHHHHHHHHT--TTSCHHHHHHHHHHHHHHHSTTTHHHHHHHHHHTTTSSCCCHHHHHHHHHHHTHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcc--CCCcHHHHHHHHHHHHHHHhHhHHHHhHHHHHHccCCCCCCHHHHHHHHHcCcHHHHHHH
Confidence            599999999999998621  2334 567899999999999899999999999873    789999999999999999999


Q ss_pred             HHHHHHhCC--CCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           76 AACGAILGG--GSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        76 ~~~Gai~~g--~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      |++ |+++|  +++++++.++ ||.++|++|||+||
T Consensus       197 ~~~-a~lag~~a~~~~~~~l~~~g~~lGlaFQI~DD  231 (313)
T 3lom_A          197 FEM-VLAAQHEVSEQIKSALRTYGKHIGLVFQMQDD  231 (313)
T ss_dssp             HHH-HHTTCSSCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHH-HHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999 99999  8999999999 99999999999997

>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*

Probab=99.92  E-value=1.7e-25  Score=168.46  Aligned_cols=107  Identities=29%  Similarity=0.422  Sum_probs=94.0

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc------CCHHHHHHHHHhhhHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS------QYVEMTYETYKKNEGGLHTC   74 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~------~~~~~~~~i~~~KTa~L~~~   74 (111)
                      +||+|+++||+++++..+ ..+++...++++..+++++|+.+|+.||++|+.++      .++++|..|+++|||+||++
T Consensus       121 aGD~Ll~~A~~~l~~~~~-~~~~~~~~~~~~~~l~~~~g~~~~~~GQ~~Dl~~~~~~~~~~~~~~y~~i~~~KTa~L~~~  199 (293)
T 2j1p_A          121 AGDALLSFAFEHLASATS-SEVSPARVVRAVGELAKAIGTEGLVAGQVVDISSEGLDLNNVGLEHLKFIHLHKTAALLEA  199 (293)
T ss_dssp             HHHHHHHHHHHHHHHHSC-TTSCHHHHHHHHHHHHHHHSTTTHHHHHHHTTC---CCHHHHHHHHHHHHHHHHTHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcc-ccCChHHHHHHHHHHHHHHhHhHHHHHHHHHHHHccCCCCCCCHHHHHHHHHcccHHHHHH
Confidence            599999999999998631 11346678889999999988889999999999763      45688999999999999999


Q ss_pred             HHHHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           75 GAACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        75 ~~~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      ||++|++++|+++++.+.++ ||.++|++|||+||
T Consensus       200 a~~~ga~lag~~~~~~~~l~~~g~~lG~aFQI~DD  234 (293)
T 2j1p_A          200 SAVLGGIIGGGSDEEIERLRKFARCIGLLFQVVDD  234 (293)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999 99999999999997

>1wy0_A Geranylgeranyl pyrophosphate synthetase; pyrococcus horikosh structural genomics, riken structural genomics/proteomics initiative, RSGI; 2.20A {Pyrococcus horikoshii}

Probab=99.92  E-value=7.2e-25  Score=167.83  Aligned_cols=102  Identities=22%  Similarity=0.283  Sum_probs=93.7

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc----CCHHHHHHHHHhhhHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS----QYVEMTYETYKKNEGGLHTCGA   76 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~----~~~~~~~~i~~~KTa~L~~~~~   76 (111)
                      +||+|+++||+++++..    .+++...++++.+++++  .+|+.||++|+.+.    .++++|.+|+++|||+||++||
T Consensus       113 ~GD~L~~~a~~~l~~~~----~~~~~~~~~~~~~~~~~--~~~~~GQ~~dl~~~~~~~~~~~~y~~~i~~KTa~L~~~~~  186 (342)
T 1wy0_A          113 AGDLLFSKAFEAVARAE----IPPEKKARVLEVIVKAS--NELCEGQARDLEFEKKSTVTIEEYMEMISGKTGALFEASA  186 (342)
T ss_dssp             HHHHHHHHHHHHHHTCC----SCHHHHHHHHHHHHHHH--HHHHHHHHHHHHHTTCSCCCHHHHHHHHHHHTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcc----cCcccHHHHHHHHHHHH--HHHHHHHHHHHHcccCCCCCHHHHHHHHHHhhHHHHHHHH
Confidence            59999999999999873    34556778999999998  99999999999863    7899999999999999999999


Q ss_pred             HHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           77 ACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        77 ~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      ++|++++|++++..+.++ ||.++|++|||+||
T Consensus       187 ~~ga~lag~~~~~~~~l~~~g~~lG~aFQI~DD  219 (342)
T 1wy0_A          187 KVGGIIGTDNEEYIKALSSWGRNVGIAFQIWDD  219 (342)
T ss_dssp             HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999 99999999999997

>3m0g_A Farnesyl diphosphate synthase; structural genomics, protein structure initiative, NYSGXRC, biosynthesis, transferase, PSI-2; 1.90A {Rhodobacter capsulatus} PDB: 3lvs_A

Probab=99.92  E-value=4.1e-25  Score=166.86  Aligned_cols=103  Identities=17%  Similarity=0.250  Sum_probs=92.0

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc-----CCHHHHHHHHHhhhHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS-----QYVEMTYETYKKNEGGLHTCG   75 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~-----~~~~~~~~i~~~KTa~L~~~~   75 (111)
                      +||+|+++||+++++...   .++...+++++.+++++|..+|+.||++|+.++     .++++|.+|+++|||+||++|
T Consensus       110 aGD~Ll~~a~~~l~~~~~---~~~~~~~~~~~~l~~~~g~~~~~~GQ~lDl~~~~~~~~~~~~~y~~i~~~KTg~L~~~~  186 (297)
T 3m0g_A          110 AGDALQTLAFELCTDPVL---GSAENRVALVAALAQASGAEGMVYGQALDIAAETAAVPLTLDEIIRLQAGKTGALISFA  186 (297)
T ss_dssp             HHHHHHHHHHHHTTCGGG---CCHHHHHHHHHHHHHHHSTTTHHHHHHHHHHHTTSSSCCCHHHHHHHHHHHTHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcc---CChHHHHHHHHHHHHHHhHhHHHHhHHHHHHhhhcCCCCCHHHHHHHHccchHHHHHHH
Confidence            599999999999998631   135567889999999999999999999999763     789999999999999999999


Q ss_pred             HHHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcCC
Q 047640           76 AACGAILGGGSVEEIEKKF-RGLIIKITKMMIRNS  109 (111)
Q Consensus        76 ~~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~~  109 (111)
                      |++|++++|++++   .++ ||.++|++|||+||=
T Consensus       187 ~~~ga~lag~~~~---~l~~~g~~lG~aFQI~DDi  218 (297)
T 3m0g_A          187 AQAGAILAGADRG---PLTAYATALGLAFQIADDI  218 (297)
T ss_dssp             HHHHHHHHTCCCH---HHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHcCCCHH---HHHHHHHHHHHHHHHHHHH
Confidence            9999999998876   788 999999999999983

>3ipi_A Geranyltranstransferase; isoprene biosynthesis, helical bundle, protein structure initiative II (PSI II), structural genomics, nysgxrc; 1.90A {Methanosarcina mazei}

Probab=99.91  E-value=1e-24  Score=164.49  Aligned_cols=96  Identities=17%  Similarity=0.232  Sum_probs=84.7

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc---CCHHHHHHHHHhhhHHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS---QYVEMTYETYKKNEGGLHTCGAA   77 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~---~~~~~~~~i~~~KTa~L~~~~~~   77 (111)
                      +||+|+++||+++++..      +    ++++.+++++  .+|+.||++|+.+.   .++++|.+|+++|||+||++||+
T Consensus       109 aGD~Ll~~a~~ll~~~~------~----~~~~~~~~~~--~~~~~GQ~~dl~~~~~~~t~~~y~~~i~~KTg~L~~~a~~  176 (295)
T 3ipi_A          109 CGDYLIAKSIAFISPYG------E----KVIQDFGKAG--MDMAEGEVLDLKLEDESFGENDYFKCIYKKTASLFAISAS  176 (295)
T ss_dssp             HHHHHHHHHHHHHGGGC------H----HHHHHHHHHH--HHHHHHHHHHHC-------CHHHHHHHHHHTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHch------H----HHHHHHHHHH--HHHHccchHHHHccCCCCCHHHHHHHHHhhhHHHHHHHHH
Confidence            59999999999998762      2    5667778887  88999999999874   67789999999999999999999


Q ss_pred             HHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           78 CGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        78 ~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      +|++++|+++++++.++ ||+++|++|||+||
T Consensus       177 ~ga~lag~~~~~~~~l~~~g~~lGlaFQI~DD  208 (295)
T 3ipi_A          177 IGAYTGGAEEELAERFSHFGNALGTAYQIVDD  208 (295)
T ss_dssp             HHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999 99999999999997

>3nf2_A Putative polyprenyl synthetase; isoprenyl diphosphate synthase, structural genomics, PSI, PR structure initiative, nysgrc; 2.20A {Streptomyces coelicolor}

Probab=99.91  E-value=2.5e-24  Score=165.77  Aligned_cols=100  Identities=21%  Similarity=0.356  Sum_probs=90.9

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc----CCHHHHHHHHHhhhHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS----QYVEMTYETYKKNEGGLHTCGA   76 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~----~~~~~~~~i~~~KTa~L~~~~~   76 (111)
                      +||+|+++||+++++.++     + ...++++.+++++  .+|+.||++|+.+.    .++++|.+|+++|||+||++||
T Consensus       121 ~GD~L~~~a~~~l~~~~~-----~-~~~~~~~~~~~~~--~~l~~GQ~~dl~~~~~~~~t~~~y~~~i~~KTa~L~~~~~  192 (352)
T 3nf2_A          121 VGDALFALANEVLLELGT-----V-EAGRATRRLTKAS--RSLIDGQAQDISYEHRDRVSVEECLEMEGNKTGALLACAS  192 (352)
T ss_dssp             HHHHHHHHHHHHHHTTCS-----H-HHHHHHHHHHHHH--HHHHHHHHHHHHHTTCSCCCHHHHHHHHHHHTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCC-----c-hHHHHHHHHHHHH--HHHHHHHHHHHHcccCCCCCHHHHHHHHHcccHHHHHHHH
Confidence            599999999999998742     2 2457788889988  99999999999863    7899999999999999999999


Q ss_pred             HHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           77 ACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        77 ~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      .+|++++|++++..+.++ ||+++|++|||+||
T Consensus       193 ~~ga~lag~~~~~~~~l~~~g~~lG~aFQi~DD  225 (352)
T 3nf2_A          193 SIGAVLGGADERTADTLEKYGYHLGLAFQAVDD  225 (352)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999 99999999999997

>3oyr_A Trans-isoprenyl diphosphate synthase; isoprenyl synthase, PSI, protein structure initiative; HET: IPE; 2.00A {Caulobacter crescentus}

Probab=99.91  E-value=3e-24  Score=164.92  Aligned_cols=97  Identities=19%  Similarity=0.284  Sum_probs=88.9

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc----CCHHHHHHHHHhhhHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS----QYVEMTYETYKKNEGGLHTCGA   76 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~----~~~~~~~~i~~~KTa~L~~~~~   76 (111)
                      +||+|+++||+++++..+         .++++.+++++  .+|+.||++|+.+.    .++++|.+|+++|||+||++||
T Consensus       132 ~GD~Ll~~a~~~l~~~~~---------~~~~~~~~~~~--~~~~~GQ~~dl~~~~~~~~~~~~y~~~i~~KTa~L~~~~~  200 (345)
T 3oyr_A          132 VGDFLFARAFELMVETNS---------MKALEILARAS--RVIAEGEVLQLMRSHDLNLSQAVYLEIIQAKTAELFAAAS  200 (345)
T ss_dssp             HHHHHHHHHHHHHHTTTC---------HHHHHHHHHHH--HHHHHHHHHHHHTSSCSSCCHHHHHHHHHHHTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCc---------HHHHHHHHHHH--HHHHHHHHHHHHcCCCCCCCHHHHHHHHHcchHHHHHHHH
Confidence            599999999999998742         36677788888  89999999999873    7899999999999999999999


Q ss_pred             HHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           77 ACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        77 ~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      ++|++++|++++..+.++ ||.++|++|||+||
T Consensus       201 ~~ga~lag~~~~~~~~l~~~g~~lG~aFQi~DD  233 (345)
T 3oyr_A          201 EAGAVSAGVDVAKSEALRDYGLNLGLAFQLADD  233 (345)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999 99999999999997

>3lk5_A Geranylgeranyl pyrophosphate synthase; structural genomics, protein structure initiative, geranylge pyrophosphate synthase; 1.90A {Corynebacterium glutamicum} PDB: 3qqv_A*

Probab=99.91  E-value=3.9e-24  Score=166.09  Aligned_cols=102  Identities=19%  Similarity=0.196  Sum_probs=91.9

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc----CCHHHHHHHHHhhhHHH-HHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS----QYVEMTYETYKKNEGGL-HTCG   75 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~----~~~~~~~~i~~~KTa~L-~~~~   75 (111)
                      +||+|+++||+++++..    +++....++++.++.+.  .+|+.||++|+.++    .+++.|.+|+++|||+| |++|
T Consensus       151 ~GD~Ll~~A~~~l~~~~----~~~~~~~~~~~~~~~~~--~~~~~GQ~lDl~~~~~~~~s~~~y~~ii~~KTa~L~~~~~  224 (380)
T 3lk5_A          151 AGDMALVWAEDMLQDSG----LSAEALARTRDAWRGMR--TEVIGGQLLDIYLESHANESVELADSVNRFKTAAYTIARP  224 (380)
T ss_dssp             HHHHHHHHHHHHHHTSC----CCHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHTHHHHTHHH
T ss_pred             HHHHHHHHHHHHHHHcC----CCHHHHHHHHHHHHHHH--HHHHHHHHHHHHhccCCCCCHHHHHHHHHhhchHHHHHHH
Confidence            59999999999999863    35566677788888776  89999999999873    68999999999999999 8999


Q ss_pred             HHHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           76 AACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        76 ~~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      |.+|++++|++++.++.++ ||+++|+||||+||
T Consensus       225 ~~~Ga~laga~~~~~~~l~~~G~~lG~AFQI~DD  258 (380)
T 3lk5_A          225 LHLGASIAGGSPQLIDALLHYGHDIGIAFQLRDD  258 (380)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999 99999999999997

>3mzv_A Decaprenyl diphosphate synthase; transferase, structural genomics, PSI-2, protein structure initiative; 1.90A {Rhodobacter capsulatus}

Probab=99.91  E-value=5.6e-24  Score=163.18  Aligned_cols=97  Identities=19%  Similarity=0.389  Sum_probs=88.5

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc----CCHHHHHHHHHhhhHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS----QYVEMTYETYKKNEGGLHTCGA   76 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~----~~~~~~~~i~~~KTa~L~~~~~   76 (111)
                      +||+|+++||+++++..+         .++++.+++++  .+|+.||++|+.+.    .++++|.+|+++|||+||++||
T Consensus       120 ~GD~L~~~a~~~l~~~~~---------~~~~~~~~~~~--~~~~~GQ~~dl~~~~~~~~t~~~y~~~i~~KTa~L~~~~~  188 (341)
T 3mzv_A          120 VGDYLFARSFQLMTDTGN---------MRVMEILANAS--AVIAEGEVLQLTAAQNLATTEDIYLRVIRGKTAALFSAAT  188 (341)
T ss_dssp             HHHHHHHHHHHHHGGGCC---------HHHHHHHHHHH--HHHHHHHHHHHHHTTCTTCCHHHHHHHHHHHTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCc---------HHHHHHHHHHH--HHHHHHHHHHHHhccCCCCCHHHHHHHHHcchHHHHHHHH
Confidence            599999999999998741         35667788888  89999999999863    7899999999999999999999


Q ss_pred             HHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           77 ACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        77 ~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      ++|++++|++++..+.++ ||.++|++|||+||
T Consensus       189 ~~ga~lag~~~~~~~~l~~~g~~lG~aFQI~DD  221 (341)
T 3mzv_A          189 EVGGIIGGAPEDQVQALFDYGDALGIAFQIVDD  221 (341)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999 99999999999997

>3aqb_B Component B of hexaprenyl diphosphate synthase; prenyltransferase, transferase; 2.40A {Micrococcus luteus} PDB: 3aqc_B*

Probab=99.91  E-value=5.8e-24  Score=161.94  Aligned_cols=97  Identities=12%  Similarity=0.132  Sum_probs=88.7

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc----CCHHHHHHHHHhhhHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS----QYVEMTYETYKKNEGGLHTCGA   76 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~----~~~~~~~~i~~~KTa~L~~~~~   76 (111)
                      +||+|+++||+++++..+         .++++.+++++  .+|+.||++|+.+.    .++++|.+|+++|||+||++||
T Consensus       111 ~GD~L~~~a~~~l~~~~~---------~~~~~~~~~~~--~~~~~GQ~~dl~~~~~~~~~~~~y~~~i~~KTa~L~~~~~  179 (325)
T 3aqb_B          111 TGHFLLARALQNIATINN---------SKFHQIFSKTI--LEVCFGEFDQMADRFNYPVSFTAYLRRINRKTAILIEASC  179 (325)
T ss_dssp             HHHHHHHHHHHHTTTCCC---------HHHHHHHHHHH--HHHHHHHHHHHHTTTCCCCCHHHHHHHHHHHTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCh---------HHHHHHHHHHH--HHHHHHHHHHHHcccCCCCCHHHHHHHHHhhHHHHHHHHH
Confidence            599999999999998631         35677788888  89999999999863    7899999999999999999999


Q ss_pred             HHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           77 ACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        77 ~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      ++|++++|++++..+.++ ||.++|++|||+||
T Consensus       180 ~~ga~lag~~~~~~~~l~~~g~~lG~afQi~DD  212 (325)
T 3aqb_B          180 HLGALSSQLDEQSTYHIKQFGHCIGMSYQIIDD  212 (325)
T ss_dssp             HHHHHTTTCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999 99999999999997

>3rmg_A Octaprenyl-diphosphate synthase; structural genomics, protein structure initiative, isoprene biosynthesis, transferase; 2.30A {Bacteroides thetaiotaomicron}

Probab=99.91  E-value=8e-24  Score=161.87  Aligned_cols=97  Identities=19%  Similarity=0.173  Sum_probs=88.3

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc----CCHHHHHHHHHhhhHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS----QYVEMTYETYKKNEGGLHTCGA   76 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~----~~~~~~~~i~~~KTa~L~~~~~   76 (111)
                      +||+|+++||+++++..+         .++++.+++++  .+|+.||++|+.+.    .++++|.+|+++|||+||++||
T Consensus       114 ~GD~L~~~a~~~l~~~~~---------~~~~~~~~~~~--~~~~~GQ~ldl~~~~~~~~t~~~y~~~i~~KTa~L~~~~~  182 (334)
T 3rmg_A          114 AGDYLLATSLVHAEQTNN---------YEIIRLVSSLG--QKLAEGELLQLSNVSNHSFSEEVYFDVIRKKTAALFAACA  182 (334)
T ss_dssp             HHHHHHHHHHHHHHHTTC---------HHHHHHHHHHH--HHHHHHHHHHHHCCCC--CCHHHHHHHHHHTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCc---------HHHHHHHHHHH--HHHHHHHHHHHHhCCCCCCCHHHHHHHHcCChHHHHHHHH
Confidence            599999999999998631         25667778888  99999999999873    7899999999999999999999


Q ss_pred             HHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           77 ACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        77 ~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      ++|++++|++++..+.++ ||.++|++|||+||
T Consensus       183 ~~ga~lag~~~~~~~~l~~~g~~lG~aFQi~DD  215 (334)
T 3rmg_A          183 EAAALSVQVGEEEVAFARLLGEYIGICFQIKDD  215 (334)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999 99999999999997

>3apz_A Geranyl diphosphate synthase; prenyltransferase, all alpha-helices fold, chroloplast, TRAN isoprenoid biosynthetic process; 2.60A {Arabidopsis thaliana} PDB: 3aq0_A*

Probab=99.91  E-value=7.8e-24  Score=162.44  Aligned_cols=97  Identities=20%  Similarity=0.219  Sum_probs=88.5

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc----CCHHHHHHHHHhhhHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS----QYVEMTYETYKKNEGGLHTCGA   76 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~----~~~~~~~~i~~~KTa~L~~~~~   76 (111)
                      +||+|+++||+++++..+         .++++.+++++  .+|+.||++|+.+.    .++++|.+|+++|||+||++||
T Consensus       134 ~GD~L~~~a~~~l~~~~~---------~~~~~~~~~~~--~~~~~GQ~~dl~~~~~~~~~~~~y~~~i~~KTa~L~~~~~  202 (348)
T 3apz_A          134 AGDFLLSRACGALAALKN---------TEVVALLATAV--EHLVTGETMEITSSTEQRYSMDYYMQKTYYKTASLISNSC  202 (348)
T ss_dssp             HHHHHHHHHHHHHHHTTC---------HHHHHHHHHHH--HHHHHHHHHHHTCCHHHHTCHHHHHHHHHHHHTHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCC---------HHHHHHHHHHH--HHHHHHHHHHHHhccCCCCCHHHHHHHHHcchHHHHHHHH
Confidence            599999999999998631         25667788888  99999999999873    7899999999999999999999


Q ss_pred             HHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           77 ACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        77 ~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      ++|++++|++++..+.++ ||.++|++|||+||
T Consensus       203 ~~ga~lag~~~~~~~~l~~~g~~lG~aFQi~DD  235 (348)
T 3apz_A          203 KAVAVLTGQTAEVAVLAFEYGRNLGLAFQLIDD  235 (348)
T ss_dssp             HHHHHTTTCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCcCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999 99999999999997

>3lmd_A Geranylgeranyl pyrophosphate synthase; isoprenyl diphosphate synthase, structural genomics, PSI, protein structure initiative, nysgrc; 1.90A {Corynebacterium glutamicum} PDB: 3q2q_A*

Probab=99.90  E-value=8.9e-24  Score=163.11  Aligned_cols=96  Identities=17%  Similarity=0.250  Sum_probs=88.2

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc---CCHHHHHHHHHhhhHHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS---QYVEMTYETYKKNEGGLHTCGAA   77 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~---~~~~~~~~i~~~KTa~L~~~~~~   77 (111)
                      +||+|+++||+++++.+      +    ++++.+++++  .+|+.||++|+.+.   .++++|.+|+++|||+||++||+
T Consensus       142 aGD~Ll~~A~~~l~~~~------~----~~~~~~~~~~--~~~~~GQ~ldl~~~~~~~t~~~y~~~i~~KTg~L~~~a~~  209 (360)
T 3lmd_A          142 AGDILLAHASGLMSQLG------T----DTVAHFAETF--GELVTGQMRETVGPRDTDPIEHYTNVIREKTGVLIASAGY  209 (360)
T ss_dssp             HHHHHHHHHHHHHHHHC------H----HHHHHHHHHH--HHHHHHHHHHHHCCTTSCHHHHHHHHHHHHTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCC------H----HHHHHHHHHH--HHHHHHHHHHHhccCCCCCHHHHHHHHHhhhHHHHHHHHH
Confidence            59999999999999862      2    5677788888  89999999999874   67899999999999999999999


Q ss_pred             HHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           78 CGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        78 ~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      +|++++|++++..+.++ ||.++|++|||+||
T Consensus       210 lga~laga~~~~~~~l~~~g~~lG~aFQI~DD  241 (360)
T 3lmd_A          210 LGAMHAGAAPEHIDALKNFGAAVGMIFQIVDD  241 (360)
T ss_dssp             HHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999 99999999999997

>4dhd_A Polyprenyl synthetase; isoprenoid synthesis, isoprenoid diphosphate synthase, trans; 1.65A {Pyrobaculum calidifontis} PDB: 4gp1_A* 4gp2_A*

Probab=99.90  E-value=1.9e-23  Score=161.13  Aligned_cols=98  Identities=11%  Similarity=0.083  Sum_probs=88.4

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc----------------CCHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS----------------QYVEMTYETY   64 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~----------------~~~~~~~~i~   64 (111)
                      +||+|+++||+++++.+        ...++++.+++++  ..|+.||++|+.+.                .++++|.+|+
T Consensus       112 ~GD~L~~~a~~~l~~~~--------~~~~~~~~~~~~~--~~~~~GQ~ldl~~~~~~~~dp~~~~~~~~~~t~~~y~~~i  181 (358)
T 4dhd_A          112 VGIWYREAIEEAVLDTP--------KPTLFAKEVAEVI--KAIDEGERLDILFEAAGRSDPYFVQARWREVTLDDYIKMV  181 (358)
T ss_dssp             HHHHHHHHHHHHHHTSS--------SHHHHHHHHHHHH--HHHHHHHHHHHHTBSSCCCCHHHHHTCCSCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCc--------cHHHHHHHHHHHH--HHHHHHHHHHHHccccccccccccccCCCCCCHHHHHHHH
Confidence            59999999999997552        2357778888988  89999999999753                4789999999


Q ss_pred             HhhhHHHHHHHHHHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           65 KKNEGGLHTCGAACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        65 ~~KTa~L~~~~~~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      ++|||+||++||++|++++|++++..+.++ ||.++|++|||+||
T Consensus       182 ~~KTa~L~~~~~~~ga~lag~~~~~~~~l~~~g~~lG~aFQI~DD  226 (358)
T 4dhd_A          182 SLKTGALIAAAAKWGVLSVSDDRGLAEAAWNFGMAAGVAFQIIDD  226 (358)
T ss_dssp             HHHTHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HcchHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999 99999999999997

>3pko_A Geranylgeranyl pyrophosphate synthase; isoprenyl diphosphate synthase, structural genomics, PSI, PR structure initiative, nysgrc; HET: CIT; 1.98A {Lactobacillus brevis} PDB: 3n3d_A

Probab=99.90  E-value=2.5e-23  Score=159.14  Aligned_cols=98  Identities=15%  Similarity=0.258  Sum_probs=87.8

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc----CCHHHHHHHHHhhhHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS----QYVEMTYETYKKNEGGLHTCGA   76 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~----~~~~~~~~i~~~KTa~L~~~~~   76 (111)
                      +||+|+++||+++++..+    ++    ++++.+++++  .+|+.||++|+...    .++++|.+|+++|||+||++||
T Consensus       123 ~GD~L~~~a~~~l~~~~~----~~----~~~~~~~~~~--~~~~~Gq~~dl~~~~~~~~~~~~yl~~i~~KTa~L~~~~~  192 (334)
T 3pko_A          123 AGDFMFTVYFDQVLKSTT----DR----SLIQNHIDAM--HRILQGELHQMDLNYREDITLDAYLNEIAGKTAELFALSC  192 (334)
T ss_dssp             HHHHHHHHHHHHHHHHCC----CH----HHHHHHHHHH--HHHHHHHHHHHHTTTCTTCCHHHHHHHHHHTTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcCC----CH----HHHHHHHHHH--HHHHHHHHHHHHhccCCCCCHHHHHHHHHcchHHHHHHHH
Confidence            599999999999998742    22    4566678887  99999999999863    7889999999999999999999


Q ss_pred             HHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           77 ACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        77 ~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      ++|++++|++++..+.++ ||.++|++|||+||
T Consensus       193 ~~ga~lag~~~~~~~~l~~~g~~lG~aFQi~DD  225 (334)
T 3pko_A          193 YQGAQLAGAPQSVIDRTRDIGIAIGCAYQMLDD  225 (334)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999 99999999999997

>2ftz_A Geranyltranstransferase; TM0161, structural GE joint center for structural genomics, JCSG, protein structu initiative, PSI; HET: MLY; 1.90A {Thermotoga maritima}

Probab=99.89  E-value=1.8e-23  Score=157.02  Aligned_cols=94  Identities=13%  Similarity=0.185  Sum_probs=84.8

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhcc-----cCCHHHHHHHHHhhhHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQC-----SQYVEMTYETYKKNEGGLHTCG   75 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~-----~~~~~~~~~i~~~KTa~L~~~~   75 (111)
                      +||+|+++||+++++.+      +.   ++++.+++++  .+|+.||++|+.+     ..++++|.+|+++|||+||++|
T Consensus       115 ~GD~Ll~~a~~~l~~~~------~~---~~~~~l~~~~--~~~~~GQ~ldl~~~~~~~~~~~~~y~~i~~~KTa~L~~~~  183 (284)
T 2ftz_A          115 AGDGLFFLAFSQISXIG------NS---XIFEEFSETA--YXLLLGEAMDVEFERRXMEVSQEMVERMYAFXTGALFAFC  183 (284)
T ss_dssp             HHHHHHHHHHHHHHTTC------CH---HHHHHHHHHH--HHHHHHHHHHHHHHHSCCCCCHHHHHHHHHHHTHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCC------hH---HHHHHHHHHH--HHHhhhhHHHHHhccCcCCCCHHHHHHHHHhhhHHHHHHH
Confidence            59999999999999873      22   6777888888  9999999999976     3688999999999999999999


Q ss_pred             HHHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           76 AACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        76 ~~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      |++|++++|++++   .++ ||.++|++|||+||
T Consensus       184 ~~~ga~lag~~~~---~l~~~g~~lG~aFQI~DD  214 (284)
T 2ftz_A          184 FSAPFILXGXDHT---XMXLLGEXFGVAFQIYDD  214 (284)
T ss_dssp             HHHHHHHHTCCCH---HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCChh---HHHHHHHHHHHHHHHHHh
Confidence            9999999998876   888 99999999999997

>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

Probab=99.89  E-value=2e-23  Score=157.65  Aligned_cols=94  Identities=16%  Similarity=0.139  Sum_probs=85.1

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc---CCHHHHHHHHHhhhHHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS---QYVEMTYETYKKNEGGLHTCGAA   77 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~---~~~~~~~~i~~~KTa~L~~~~~~   77 (111)
                      +||+|+++||+++++..+         .++++.+++++  .+|+.||++|+.+.   .++++|.+|+++|||+||++||+
T Consensus       108 ~GD~L~~~a~~~l~~~~~---------~~~~~~~~~~~--~~~~~GQ~~dl~~~~~~~~~~~y~~~i~~KTa~L~~~~~~  176 (299)
T 1v4e_A          108 AGDLVLVSAFHTVEEIGN---------NKLRRAFLNVI--GKMSEAELIEQLSRYKPITKEEYLRIVEGKSGALFGLALQ  176 (299)
T ss_dssp             HHHHHHHHHHHHHHHHCC---------HHHHHHHHHHH--HHHHHHHHHHHHHTTSCCCHHHHHHHHHHHTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCh---------HHHHHHHHHHH--HHHhhhHHHHHHccCCCCCHHHHHHHHHhccHHHHHHHHH
Confidence            599999999999998731         36677788888  99999999999864   68999999999999999999999


Q ss_pred             HHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           78 CGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        78 ~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      +|++++|+++   +.++ ||.++|++|||+||
T Consensus       177 ~ga~lag~~~---~~l~~~g~~lG~aFQi~DD  205 (299)
T 1v4e_A          177 LPALLEGELG---EDLYNLGVTIGTIYQMFDD  205 (299)
T ss_dssp             HHHHHHTCCC---HHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHcCCCH---HHHHHHHHHHHHHHHHHHH
Confidence            9999999877   8888 99999999999997

>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* ...

Probab=99.89  E-value=6.2e-23  Score=157.18  Aligned_cols=101  Identities=13%  Similarity=0.054  Sum_probs=84.8

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhcc-------cCCHHHHHHHHHhhhHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQC-------SQYVEMTYETYKKNEGGLHT   73 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~-------~~~~~~~~~i~~~KTa~L~~   73 (111)
                      +||+|+++||+++++..+    +.....++++.+++++  ..|+.||++|+.+       ..+++.|.+|+++|||+||+
T Consensus       107 ~GD~L~~~a~~~l~~~~~----~~~~~~~~~~~~~~~~--~~~~~GQ~ldl~~~~~~~~~~~t~~~y~~~i~~KTa~L~~  180 (340)
T 2e8v_A          107 TANYMYFRAMQLVSQLTT----KEPLYHNLITIFNEEL--INLHRGQGLDIYWRDFLPEIIPTQEMYLNMVMNKTGGLFR  180 (340)
T ss_dssp             HHHHHHHHHHHHGGGGCC----CHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHSTTSCCCCHHHHHHHHHHHTHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCC----chhhHHHHHHHHHHHH--HHHHHHHHHHHHhhcccccCCCCHHHHHHHHHhhhHHHHH
Confidence            599999999999998742    3445667888889988  9999999999974       24889999999999999999


Q ss_pred             HHHHHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           74 CGAACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        74 ~~~~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      +||.+|++++|+++ +.+.++ ||.++|++|||+||
T Consensus       181 ~~~~~ga~lag~~~-~~~~l~~~g~~lG~aFQi~DD  215 (340)
T 2e8v_A          181 LTLRLMEALSPSSH-HGHSLVPFINLLGIIYQIRDD  215 (340)
T ss_dssp             HHHHHHHHHCCC-------CHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCcH-HHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999987 578889 99999999999997

>3tc1_A Octaprenyl pyrophosphate synthase; all alpha-helices fold, transferase; 2.00A {Helicobacter pylori}

Probab=99.88  E-value=9.1e-23  Score=155.05  Aligned_cols=93  Identities=11%  Similarity=0.099  Sum_probs=84.2

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc----CCHHHHHHHHHhhhHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS----QYVEMTYETYKKNEGGLHTCGA   76 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~----~~~~~~~~i~~~KTa~L~~~~~   76 (111)
                      +||+|+++||+++++.+          .++++.+++++  .+|+.||++|+.+.    .++++|.+|+++|||+||++||
T Consensus       104 ~GD~L~~~a~~~l~~~~----------~~~~~~~~~~~--~~~~~GQ~~dl~~~~~~~~~~~~y~~~i~~KTa~L~~~~~  171 (315)
T 3tc1_A          104 LGDVFYSKAFFELSKMG----------ELIAQALSNAV--LRLSRGEIEDVFVGECFNSDKQKYWRILEDKTAHFIEASL  171 (315)
T ss_dssp             HHHHHHHHHHHHHTTSC----------HHHHHHHHHHH--HHHHHHHHHHHHHTTSCCCCHHHHHHHHHHHTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCc----------HHHHHHHHHHH--HHHHHHHHHHHHcCCCCCCCHHHHHHHHhcchHHHHHHHH
Confidence            59999999999998762          25667788888  99999999999863    7899999999999999999999


Q ss_pred             HHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           77 ACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        77 ~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      ++|++++|++   .+.++ ||.++|++|||+||
T Consensus       172 ~~ga~lag~~---~~~l~~~g~~lG~aFQI~DD  201 (315)
T 3tc1_A          172 KSMAILLNKD---AKIYADFGLNFGMAFQIIDD  201 (315)
T ss_dssp             HHHHHHTTSC---HHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCC---HHHHHHHHHHHHHHHHHHHH
Confidence            9999999998   67889 99999999999997

>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*

Probab=99.88  E-value=3.6e-23  Score=159.44  Aligned_cols=102  Identities=6%  Similarity=-0.093  Sum_probs=89.5

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc--------------------CCHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS--------------------QYVEMT   60 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~--------------------~~~~~~   60 (111)
                      +||+|+++||+++++...    ++....++++.+++++  ..|+.||++|+.+.                    .++++|
T Consensus       127 ~Gd~L~~~a~~~l~~~~~----~~~~~~~~~~~~~~~~--~~~~~GQ~ldl~~~~~~~~~~~~~~~~~~~~~~~~~~~~y  200 (362)
T 1yhl_A          127 DGIILKSWTQIMAWHYFA----DRPFLKDLLCLFQKVD--YATAVGQMYDVTSMCDSNKLDPEVAQPMTTDFAEFTPAIY  200 (362)
T ss_dssp             HHHHHHHHHHHHHHHHST----TCTTHHHHHHHHHHHH--HHHHHHHHHHHTTTBCGGGCCTTSCCCBCSSCTTCSHHHH
T ss_pred             HHHHHHHHHHHHHHHhcc----cchhHHHHHHHHHHHH--HHHHHHHHHHHHccccccccccccccccccccccCCHHHH
Confidence            499999999999998631    1223457788888888  99999999999754                    478999


Q ss_pred             HHHHHhhhHHH-HHHHHHHHHHhCC-CCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           61 YETYKKNEGGL-HTCGAACGAILGG-GSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        61 ~~i~~~KTa~L-~~~~~~~Gai~~g-~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      .+|+++|||+| |++||++|++++| ++++..+.++ ||.++|++|||+||
T Consensus       201 ~~~~~~KTa~Ls~~~~~~~ga~lag~~~~~~~~~l~~~g~~lG~aFQi~DD  251 (362)
T 1yhl_A          201 KRIVKYKTTFYTYLLPLVMGLFVSEAAASVEMNLVERVAHLIGEYFQVQDD  251 (362)
T ss_dssp             HHHHHHHTHHHHTHHHHHHHHHHTTCGGGSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhcCcHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999 9999999999999 8888899999 99999999999997

>2azj_A Geranylgeranyl pyrophosphate synthetase; hexpps, trans-prenyltransferase; 2.40A {Sulfolobus solfataricus} PDB: 2azk_A

Probab=99.88  E-value=4.7e-23  Score=155.04  Aligned_cols=92  Identities=12%  Similarity=0.164  Sum_probs=83.5

Q ss_pred             ChhhHHHHHHHHH-HcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhcccCCHHHHHHHHHhhhHHHHHHHHHHH
Q 047640            1 MADAMLPFGLELL-ASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTYETYKKNEGGLHTCGAACG   79 (111)
Q Consensus         1 aGD~Ll~~A~~~l-~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~~~~~~~~~i~~~KTa~L~~~~~~~G   79 (111)
                      +||+|+++||+++ ++.+      +    ++++.+++++  .+|+.||++|+..   +++|.+|+++|||+||++||++|
T Consensus       116 aGD~Ll~~a~~~l~~~~~------~----~~~~~~~~~~--~~~~~GQ~~dl~~---~~~y~~~i~~KTa~L~~~a~~~g  180 (289)
T 2azj_A          116 ITNYLIPTALRIIQTSYG------D----DALNTSIELW--KDTSVGALRDMYD---NSDYIRTIELKTGSLFKLSTVLS  180 (289)
T ss_dssp             HHHHHHHHHHHHHHHHHC------H----HHHHHHHHHH--HHHHHHHHHTTTT---TSCHHHHHHHHTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcCc------H----HHHHHHHHHH--HHHHHHHHHHHhh---HHHHHHHHHcchHHHHHHHHHHH
Confidence            5999999999999 8762      2    4667788888  9999999999975   67789999999999999999999


Q ss_pred             HHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           80 AILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        80 ai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      ++++ ++++..+.++ ||.++|++|||+||
T Consensus       181 a~la-~~~~~~~~l~~~g~~lG~aFQi~DD  209 (289)
T 2azj_A          181 AYAS-KHYNTKQQMLDVGKYLGIIYQVIDD  209 (289)
T ss_dssp             HHHT-TCGGGHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHc-CCHHHHHHHHHHHHHHHHHHHHHHh
Confidence            9999 9999999999 99999999999997

>1wmw_A Geranylgeranyl diphosphate synthetase; GGPP, prenyl diphosphate synthase, structural genom riken structural genomics/proteomics initiative; 1.55A {Thermus thermophilus}

Probab=99.88  E-value=1e-22  Score=155.37  Aligned_cols=100  Identities=19%  Similarity=0.149  Sum_probs=86.3

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhcc------cCCHHHHHHHHHhhhHHH-HH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQC------SQYVEMTYETYKKNEGGL-HT   73 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~------~~~~~~~~~i~~~KTa~L-~~   73 (111)
                      +||+|+++||+++++..+ .++++.   ++++.+++++  .+|+.||++|+.+      ..++++|.+|+++|||+| |+
T Consensus       106 ~GD~L~~~a~~~l~~~~~-~~~~~~---~~~~~~~~~~--~~~~~GQ~~dl~~~~~~~~~~~~~~y~~~i~~KTa~Ls~~  179 (330)
T 1wmw_A          106 AGDAMHAEMWGLLAEGLA-RGLFPP---EVLLEFHEVV--RRTAYGQHLDLLWTLGGTFDLRPEDYFRMVAHKAAYYTAV  179 (330)
T ss_dssp             HHHHHHHHHHHHHHHHHH-TTSSCH---HHHHHHHHHH--HHHHHHHHHHHHHHHSSSCCCCHHHHHHHHHHHTHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccc-ccccHH---HHHHHHHHHH--HHHHHHHHHHHHhcccCCCCCCHHHHHHHHHccccHHHHH
Confidence            599999999999998521 012222   6677788888  9999999999976      368999999999999999 99


Q ss_pred             HHHHHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           74 CGAACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        74 ~~~~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      +||++|++++|+++++.  ++ ||.++|++|||+||
T Consensus       180 ~~~~~ga~lag~~~~~~--l~~~g~~lG~aFQi~DD  213 (330)
T 1wmw_A          180 APLRLGALLAGKTPPAA--YEEGGLRLGTAFQIVDD  213 (330)
T ss_dssp             HHHHHHHHHTTCCCCHH--HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHH--HHHHHHHHHHHHHHHHc
Confidence            99999999999988776  88 99999999999997

>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* ...

Probab=99.86  E-value=5.7e-22  Score=153.55  Aligned_cols=102  Identities=12%  Similarity=-0.062  Sum_probs=88.2

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc---------CCHHHHHHHHHhhhHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS---------QYVEMTYETYKKNEGGL   71 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~---------~~~~~~~~i~~~KTa~L   71 (111)
                      +||+|++.+|+++++...    ++....++++.+++++  ..++.||++|+.+.         .+++.|.+|+++|||+|
T Consensus       152 ~g~~l~~~a~~~l~~~~~----~~~~~~~~~~~~~~~~--~~~~~GQ~lDl~~~~~~~~d~~~~t~~~y~~i~~~KTa~L  225 (374)
T 2qis_A          152 DANLLEACIYRLLKLYCR----EQPYYLNLIELFLQSS--YQTEIGQTLDLLTAPQGNVDLVRFTEKRYKSIVKYKSAFY  225 (374)
T ss_dssp             HHHHHHHHHHHHHHHHHT----TSTTHHHHHHHHHHHH--HHHHHHHHHHHHHSCTTCCCGGGCCHHHHHHHHHHHTHHH
T ss_pred             HHHHHHHHHHHHHHHhhc----ccccHHHHHHHHHHHH--HHHHHHHHHHHHcccccccccccCCHHHHHHHHHcCccHH
Confidence            489999999999987521    1112346777788888  99999999999752         57899999999999999


Q ss_pred             -HHHHHHHHHHhCC-CCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           72 -HTCGAACGAILGG-GSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        72 -~~~~~~~Gai~~g-~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                       |++||.+|++++| +++++.+.++ ||.++|++|||+||
T Consensus       226 sf~~~~~~ga~lag~a~~~~~~~l~~~g~~lG~aFQI~DD  265 (374)
T 2qis_A          226 SFYLPIAAAMYMAGIDGEKEHANAKKILLEMGEFFQIQDD  265 (374)
T ss_dssp             HTHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHHHHHHHHHH
Confidence             9999999999999 9999999999 99999999999997

>4fp4_A Polyprenyl synthetase; isoprenoid synthesis, isoprenoid diphosphate synthase, trans; HET: GER UNL; 2.00A {Pyrobaculum calidifontis}

Probab=99.86  E-value=4.9e-22  Score=149.32  Aligned_cols=90  Identities=14%  Similarity=0.114  Sum_probs=78.8

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhcccCCHHHHHHHHHhhhHHHHHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTYETYKKNEGGLHTCGAACGA   80 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~~~~~~~~~i~~~KTa~L~~~~~~~Ga   80 (111)
                      +||+|+++||+++++.+      +    ++++.+++++  .+|+.||++|+.+..+.     |+++|||+||++||++|+
T Consensus       115 aGD~Ll~~A~~~l~~~~------~----~~~~~ls~~~--~~~~~GQ~lDl~~~~~~-----~i~~KTg~Lf~~a~~lGa  177 (285)
T 4fp4_A          115 ASDWLIAESIKMAVNLG------A----DVVTYLADVA--QRLSVGQALDLEGERDK-----AAEFKTAPLIEAALVMPL  177 (285)
T ss_dssp             HHHHHHHHHHHHHHTTC------H----HHHHHHHHHH--HHHHHHHHHHHTTCHHH-----HHHHHTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhh------H----HHHHHHHHHH--HHHHHhHHHHHhccccc-----hhhcCcHHHHHHHHHHHH
Confidence            59999999999999862      2    6677788888  89999999999875221     899999999999999999


Q ss_pred             HhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           81 ILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        81 i~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      +++|++ ++.+.++ ||.++|++|||+||
T Consensus       178 ~lag~~-~~~~~l~~~G~~lGlAFQI~DD  205 (285)
T 4fp4_A          178 VILGRR-ELIETAKKLGTKLGILYQYSDD  205 (285)
T ss_dssp             HHHTCG-GGHHHHHHHHHHHHHHTTCC--
T ss_pred             HHcCCh-HHHHHHHHHHHHHHHHHHHHHH
Confidence            999999 8889999 99999999999998

>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

Probab=99.86  E-value=1.1e-21  Score=151.68  Aligned_cols=101  Identities=13%  Similarity=-0.064  Sum_probs=85.7

Q ss_pred             hhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhcc---------cCCHHHHHHHHHhhhHHH-
Q 047640            2 ADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQC---------SQYVEMTYETYKKNEGGL-   71 (111)
Q Consensus         2 GD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~---------~~~~~~~~~i~~~KTa~L-   71 (111)
                      ||+++++||+++++...    ++....++++.+++++  ..|+.||++|+.+         ..+++.|.+|+++|||+| 
T Consensus       146 g~~l~~~a~~~l~~~~~----~~~~~~~~~~~~~~~~--~~~~~GQ~lDl~~~~~~~~d~~~~t~~~y~~ii~~KTa~Ls  219 (367)
T 1uby_A          146 SFLLESSVYRVLKKYCR----QRPYYVHLLELFLQTA--YQTELGQMLDLITAPVSKVDLSHFSEERYKAIVKYKTAFYS  219 (367)
T ss_dssp             HHHHHHHHHHHHHHHHT----TSTTHHHHHHHHHHHH--HHHHHHHHHHHHHSCTTSCCCTTCCHHHHHHHHHHHTHHHH
T ss_pred             HHHHHHHHHHHHHHhcc----ccccHHHHHHHHHHHH--HHHHHHHHHHHhcccccccccccCCHHHHHHHHHhCchHHH
Confidence            45556889999998521    1112356777788888  8999999999975         257899999999999999 


Q ss_pred             HHHHHHHHHHhCC-CCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           72 HTCGAACGAILGG-GSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        72 ~~~~~~~Gai~~g-~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      |++||.+|++++| ++++..+.++ ||.++|++|||+||
T Consensus       220 f~~~~~~ga~lag~~~~~~~~~l~~~g~~lG~aFQI~DD  258 (367)
T 1uby_A          220 FYLPVAAAMYMVGIDSKEEHENAKAILLEMGEYFQIQDD  258 (367)
T ss_dssp             THHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999 8999999999 99999999999997

>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

Probab=99.85  E-value=1.5e-21  Score=147.49  Aligned_cols=93  Identities=14%  Similarity=0.069  Sum_probs=80.5

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhcc-----cCCHHHHHHHHHhhhHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQC-----SQYVEMTYETYKKNEGGLHTCG   75 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~-----~~~~~~~~~i~~~KTa~L~~~~   75 (111)
                      +||+|+++||+++++.++     +    ++++.+++++  ..|+.||++|+.+     ..++++|.+|+++|||+||++|
T Consensus        92 ~GD~l~~~a~~~l~~~~~-----~----~~~~~~~~~~--~~~~~GQ~~dl~~~~~~~~~~~~~y~~~i~~KTa~L~~~~  160 (301)
T 2q80_A           92 SANYVYFLGLEKVLTLDH-----P----DAVKLFTRQL--LELHQGQGLDIYWRDNYTCPTEEEYKAMVLQKTGGLFGLA  160 (301)
T ss_dssp             HHHHHHHHHHHHHHTTCC-----T----THHHHHHHHH--HHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCC-----H----HHHHHHHHHH--HHHHHHHHHHHHhccCCCCCCHHHHHHHHHcccHHHHHHH
Confidence            599999999999998742     2    2344567777  8999999999975     2679999999999999999999


Q ss_pred             HHHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           76 AACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        76 ~~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      |.+|+++++.++    .++ ||.++|++|||+||
T Consensus       161 ~~~ga~~a~~~~----~l~~~g~~lG~aFQi~DD  190 (301)
T 2q80_A          161 VGLMQLFSDYKE----DLKPLLNTLGLFFQIRDD  190 (301)
T ss_dssp             HHHHHHTCCCCS----CCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCChH----HHHHHHHHHHHHHHHHHH
Confidence            999999999873    478 99999999999997

>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*

Probab=99.85  E-value=2.7e-21  Score=150.53  Aligned_cols=102  Identities=8%  Similarity=-0.003  Sum_probs=84.7

Q ss_pred             ChhhHHH--HHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhcc--------------------cCCHH
Q 047640            1 MADAMLP--FGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQC--------------------SQYVE   58 (111)
Q Consensus         1 aGD~Ll~--~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~--------------------~~~~~   58 (111)
                      +||+|++  ++|+++++...  . ++ ...++++.+++++  ..++.||++|+.+                    ..+++
T Consensus       153 ~gD~ll~~a~a~~ll~~~~~--~-~~-~~~~~~~~~~~~~--~~~~~GQ~lDl~~~~e~~~~d~~~~~~~~~~~~~~t~~  226 (390)
T 3dyh_A          153 INDGLLLKSWTHMMAMHFFA--D-RP-FLQDLLCRFNRVD--YTTAVGQLYDVTSMFDSNKLDPDVSQPTTTDFAEFTLS  226 (390)
T ss_dssp             HHHHHHHHHHHHHHHHHHST--T-CT-THHHHHHHHHHHH--HHHHHHHHHHHTTTSCGGGCCTTSCCCCCSSCTTCCHH
T ss_pred             HHHHHHHHHHHHHHHHHhcc--C-ch-hHHHHHHHHHHHH--HHHHHHHHHHHhhcccccccccccccccccccCCCCHH
Confidence            4899986  55788887421  0 12 2346677778887  8999999999975                    26789


Q ss_pred             HHHHHHHhhhHHH-HHHHHHHHHHhCCCCHHH-HHHHH-HhHHhhHhhhhhcC
Q 047640           59 MTYETYKKNEGGL-HTCGAACGAILGGGSVEE-IEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        59 ~~~~i~~~KTa~L-~~~~~~~Gai~~g~~~e~-~~~l~-~G~~~GiafQi~D~  108 (111)
                      +|.+|+++|||+| |++||++|++++|+++++ .+.++ ||+++|++|||+||
T Consensus       227 ~y~~i~~~KTa~L~~~~~~~~ga~laga~~~~~~~~l~~~g~~lGlaFQI~DD  279 (390)
T 3dyh_A          227 NYKRIVKYKTAYYTYLLPLVMGLIVSEALPTVDMGVTEELAMLMGEYFQVQDD  279 (390)
T ss_dssp             HHHHHHHHHTHHHHTHHHHHHHHHHTTCGGGSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhhhHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999 999999999999998875 78899 99999999999997

>2q58_A Fragment, farnesyl pyrophosphate synthase; farnesyl diphosphate synthase, structural genomics, structur genomics consortium, SGC; HET: ZOL; 2.37A {Cryptosporidium parvum} PDB: 2o1o_A*

Probab=99.84  E-value=1.1e-21  Score=151.74  Aligned_cols=104  Identities=10%  Similarity=-0.036  Sum_probs=88.9

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc------CCHHHHHHHHHhhhHHH-HH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS------QYVEMTYETYKKNEGGL-HT   73 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~------~~~~~~~~i~~~KTa~L-~~   73 (111)
                      +||+|+++||+++.+..+  ..+++...++++.+++++  ..++.||.+|+.+.      .+++.|.+|++.|||.| |.
T Consensus       142 ~Gd~L~~~a~~~l~~~~~--~~~~~~~~~~~~~~~~~~--~~~~~GQ~lDl~~~~~~~~~~~~e~y~~ii~~KTa~l~~~  217 (368)
T 2q58_A          142 DIFFLKMLSLSLIFELSS--VFGNDIVMKIQKIYNESI--FFTVLGQHLDLSYFDLSKADKISERYFSMVEMKTSRYTFY  217 (368)
T ss_dssp             HHHHHHHHHHHHHTTTHH--HHCHHHHHHHHHHHHHHH--HHHHHHHHHHHCSCCCSSCSSHHHHHHHHHHHHTHHHHTH
T ss_pred             HHHHHHHHHHHHHHHhcc--ccChHHHHHHHHHHHHHH--HHhhhhHHHHHHhhhcccCCchHHHHHHHHHHHhccccch
Confidence            599999999999987531  123455678888899988  89999999999752      45788999999999998 89


Q ss_pred             HHHHHHHHhCC--CCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           74 CGAACGAILGG--GSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        74 ~~~~~Gai~~g--~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      +|+.+|++++|  +++++++.++ ||.++|+||||+||
T Consensus       218 ~~~~~g~~~ag~~~~~~~~~~l~~~g~~lG~aFQI~DD  255 (368)
T 2q58_A          218 MPVFFGLTLSEIQVSSAQLNLIEAILYKLGEFYQVHND  255 (368)
T ss_dssp             HHHHHHHHHSCCCCCCSSTTTHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCcccchHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999998  5677888999 99999999999998

>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*

Probab=99.83  E-value=9.3e-21  Score=147.52  Aligned_cols=102  Identities=14%  Similarity=0.076  Sum_probs=84.4

Q ss_pred             ChhhHH--HHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhcc-------------------------
Q 047640            1 MADAML--PFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQC-------------------------   53 (111)
Q Consensus         1 aGD~Ll--~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~-------------------------   53 (111)
                      +||+|+  +.+|+++.....    ++....++++.+++++  ..||.||.+|+.+                         
T Consensus       152 ~GD~ll~~~~~~~ll~~~~~----~~~~~~~~~~~~~~~~--~~~~~GQ~lDl~~~~~~~~~~~~~~~~~~~~~~e~~~~  225 (395)
T 3mav_A          152 VNDVLLLYNSIYKLIEIYLR----NESCYVDVIATFRDAT--LKTIIGQHLDTNIFSDKYSDAHREIDVNNINVPEQPVI  225 (395)
T ss_dssp             HHHHHHHHHHHHHHHHHHHT----TSTTHHHHHHHHHHHH--HHHHHHHHHHHHTTSHHHHCC-CCCCSSCSSSCCCCCC
T ss_pred             hhhHHHHHHHHHHHHHHhcc----ChhHHHHHHHHHHHHH--HHHHHHHHHHHHHHhccchhHHHHhhhcccccchhccc
Confidence            599877  567888876421    2234567888889988  9999999999953                         


Q ss_pred             ---cCCHHHHHHHHHhhhHHH-HHHHHHHHHHhCCCCH--HHHHHHH-HhHHhhHhhhhhcC
Q 047640           54 ---SQYVEMTYETYKKNEGGL-HTCGAACGAILGGGSV--EEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        54 ---~~~~~~~~~i~~~KTa~L-~~~~~~~Gai~~g~~~--e~~~~l~-~G~~~GiafQi~D~  108 (111)
                         .++++.|.+|+++|||+| |.+|+.+|++++|++.  +.++.++ ||.++|+||||+||
T Consensus       226 ~~~~~t~~~Y~~ii~~KTa~L~~~~~~~~ga~~ag~~~d~~~~~~l~~~g~~lG~aFQI~DD  287 (395)
T 3mav_A          226 DINMINFGVYKNIVIHKTAYYSFFLPIVCGMLLAGIAVDNLIYKKIEDISMLMGEYFQIHDD  287 (395)
T ss_dssp             CGGGCSHHHHHHHHHHHTHHHHTHHHHHHHHHHTTCCTTCTHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccCCHHHHHHHHHHhhhHHHHHHHHHHHHHhcCCcchhHHHHHHHHHHHHHHHHHHHHHH
Confidence               147899999999999999 9999999999999864  3578899 99999999999998

---

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	Length	Definition	Probability
Query	111
d1rqja_	299	Farnesyl diphosphate synthase (geranyltranstransfe	99.88
d1rtra_	290	Farnesyl diphosphate synthase (geranyltranstransfe	99.86
d2q80a1	291	Geranylgeranyl pyrophosphate synthetase {Human (Ho	99.8
d1v4ea_	280	Octoprenyl-diphosphate synthase {Thermotoga mariti	99.79
d1fpsa_	348	Farnesyl diphosphate synthase (geranyltranstransfe	99.77
d1ezfa_	333	Squalene synthase {Human (Homo sapiens) [TaxId: 96	83.0

>d1rqja_ a.128.1.1 (A:) Farnesyl diphosphate synthase (geranyltranstransferase) {Escherichia coli [TaxId: 562]}

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

Probab=99.88  E-value=1.2e-22  Score=151.03  Aligned_cols=107  Identities=15%  Similarity=0.195  Sum_probs=92.7

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc---CCHHHHHHHHHhhhHHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS---QYVEMTYETYKKNEGGLHTCGAA   77 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~---~~~~~~~~i~~~KTa~L~~~~~~   77 (111)
                      +||+|+++||+++++..+ ........++++..++.+.|..+||+||.+|+.++   .++++|.+|+.+|||+||.+|+.
T Consensus       113 ~Gd~l~~~a~~~l~~~~~-~~~~~~~~~~~~~~l~~~~~~~~l~~GQ~ldl~~~~~~~~~~~~~~i~~~KT~~l~~~~~~  191 (299)
T d1rqja_         113 AGDALQTLAFSILSDADM-PEVSDRDRISMISELASASGIAGMCGGQALDLDAEGKHVPLDALERIHRHKTGALIRAAVR  191 (299)
T ss_dssp             HHHHHHHHHHHHHHHSCC-TTCCHHHHHHHHHHHHHHHSTTTHHHHHHHHHHTTTTCCCHHHHHHHHHHHTHHHHHHHHH
T ss_pred             hcchHHHHHHHHHHhCCC-ccccHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhccCcccHHHHHHHHHHHHhhHHHHHHH
Confidence            599999999999998754 23455677888899999988899999999999763   77899999999999999999999


Q ss_pred             HHHHhC-CCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           78 CGAILG-GGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        78 ~Gai~~-g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      +|+++. +.++++.+.++ ||.++|++|||+||
T Consensus       192 ~~a~~~~~~~~~~~~~l~~~g~~lGiaFQi~DD  224 (299)
T d1rqja_         192 LGALSAGDKGRRALPVLDKYAESIGLAFQVQDD  224 (299)
T ss_dssp             HHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhcchhhHHHHHHHHHHHHHHHHHHHHHH
Confidence            988765 45566678899 99999999999997

>d1rtra_ a.128.1.1 (A:) Farnesyl diphosphate synthase (geranyltranstransferase) {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: Terpenoid synthases
superfamily: Terpenoid synthases
family: Isoprenyl diphosphate synthases
domain: Farnesyl diphosphate synthase (geranyltranstransferase)
species: Staphylococcus aureus [TaxId: 1280]

Probab=99.86  E-value=8e-22  Score=146.02  Aligned_cols=105  Identities=21%  Similarity=0.212  Sum_probs=93.0

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc---CCHHHHHHHHHhhhHHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS---QYVEMTYETYKKNEGGLHTCGAA   77 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~---~~~~~~~~i~~~KTa~L~~~~~~   77 (111)
                      +||+++++|+++++....   ............++.+.|..+++.||.+|+.+.   .++++|..|+++|||+||.+|+.
T Consensus       110 ~Gd~l~~~a~~l~~~~~~---~~~~~~~~~~~~l~~~~~~~~~~~GQ~~Dl~~~~~~~~~~~~~~i~~~KT~~l~~~~~~  186 (290)
T d1rtra_         110 AGDALLTKAFELISSDDR---LTDEVKIKVLQRLSIASGHVGMVGGQMLDMQSEGQPIDLETLEMIHKTKTGALLTFAVM  186 (290)
T ss_dssp             HHHHHHHHHHHHHHTCTT---SCHHHHHHHHHHHHHHHSTTTHHHHHHHHHHTTTSCCCHHHHHHHHHHHTHHHHHHHHH
T ss_pred             cCcchhHHHHHHHHhCCC---cchhhHhHHHHHHHHHHhHHHHHHhHHHHHHhcccCCCHHHHHHHHHHHHHHHHHhhhh
Confidence            599999999999998742   234455667777777777789999999999773   78999999999999999999999


Q ss_pred             HHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           78 CGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        78 ~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      +|++++++++++.+.++ ||.++|++|||+||
T Consensus       187 ~~a~~~~~~~~~~~~l~~~g~~lG~aFQi~DD  218 (290)
T d1rtra_         187 SAADIANVDDTTKEHLESYSYHLGMMFQIKDD  218 (290)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999 99999999999998

>d2q80a1 a.128.1.1 (A:6-296) Geranylgeranyl pyrophosphate synthetase {Human (Homo sapiens) [TaxId: 9606]}

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=99.80  E-value=4.1e-20  Score=136.76  Aligned_cols=93  Identities=14%  Similarity=0.068  Sum_probs=80.2

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc-----CCHHHHHHHHHhhhHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS-----QYVEMTYETYKKNEGGLHTCG   75 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~-----~~~~~~~~i~~~KTa~L~~~~   75 (111)
                      +||+|++.|++.+++.++     +    +++..+++++  ..++.||.+|+.+.     .++++|.+|+++|||+||++|
T Consensus        86 ~gd~l~~~a~~~l~~~~~-----~----~~~~~~~~~~--~~~~~gq~~d~~~~~~~~~~s~~~y~~ii~~KT~~Lf~~~  154 (291)
T d2q80a1          86 SANYVYFLGLEKVLTLDH-----P----DAVKLFTRQL--LELHQGQGLDIYWRDNYTCPTEEEYKAMVLQKTGGLFGLA  154 (291)
T ss_dssp             HHHHHHHHHHHHHHTTCC-----T----THHHHHHHHH--HHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhhhh-----h----HHHHHHHHHH--HHhHhccccccccccccccCCHHHHHHHHHhccchhhHhh
Confidence            499999999999998753     2    3445567777  88999999999752     578999999999999999999


Q ss_pred             HHHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           76 AACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        76 ~~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      |.+|+++++.++    .++ ||+++|++|||.||
T Consensus       155 ~~~ga~~~~~~~----~l~~~g~~lG~afQi~DD  184 (291)
T d2q80a1         155 VGLMQLFSDYKE----DLKPLLNTLGLFFQIRDD  184 (291)
T ss_dssp             HHHHHHTCCCCS----CCHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhhcccch----hhHHHHHHHHHHHHHHHH
Confidence            999999999874    378 99999999999997

>d1v4ea_ a.128.1.1 (A:) Octoprenyl-diphosphate synthase {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: Terpenoid synthases
superfamily: Terpenoid synthases
family: Isoprenyl diphosphate synthases
domain: Octoprenyl-diphosphate synthase
species: Thermotoga maritima [TaxId: 2336]

Probab=99.79  E-value=1e-19  Score=134.11  Aligned_cols=94  Identities=16%  Similarity=0.152  Sum_probs=80.5

Q ss_pred             ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc---CCHHHHHHHHHhhhHHHHHHHHH
Q 047640            1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS---QYVEMTYETYKKNEGGLHTCGAA   77 (111)
Q Consensus         1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~---~~~~~~~~i~~~KTa~L~~~~~~   77 (111)
                      +||+|++.+++.+++..+     +    ++...+++++  ..++.||.+|+...   +++++|.+|+.+|||+||++|+.
T Consensus       100 ~gd~l~~~a~~~l~~~~~-----~----~~~~~l~~~~--~~~~~Gq~~d~~~~~~~~t~~~y~~~i~~KT~~lf~~~~~  168 (280)
T d1v4ea_         100 AGDLVLVSAFHTVEEIGN-----N----KLRRAFLNVI--GKMSEAELIEQLSRYKPITKEEYLRIVEGKSGALFGLALQ  168 (280)
T ss_dssp             HHHHHHHHHHHHHHHHCC-----H----HHHHHHHHHH--HHHHHHHHHHHHHTTSCCCHHHHHHHHHHHTHHHHHHHHH
T ss_pred             hHHHHHHhhhhccccccc-----c----cccccchhhc--ccchhHHHHHHHhccCCCCHHHHHHHHHhccccHHHHHHH
Confidence            499999999999998742     2    3344566777  78999999998763   78999999999999999999999


Q ss_pred             HHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           78 CGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        78 ~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      +|++++|...+   .++ ||+++|++|||+||
T Consensus       169 ~ga~l~g~~~~---~l~~~g~~lG~afQi~DD  197 (280)
T d1v4ea_         169 LPALLEGELGE---DLYNLGVTIGTIYQMFDD  197 (280)
T ss_dssp             HHHHHHTCCCH---HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHccccHH---HHHHHHHHHHHHHHHHHh
Confidence            99999986654   578 99999999999997

>d1fpsa_ a.128.1.1 (A:) Farnesyl diphosphate synthase (geranyltranstransferase) {Chicken (Gallus gallus) [TaxId: 9031]}

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=99.77  E-value=4.2e-19  Score=134.01  Aligned_cols=102  Identities=15%  Similarity=-0.044  Sum_probs=83.3

Q ss_pred             ChhhHHHHHH-HHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc---------CCHHHHHHHHHhhhHH
Q 047640            1 MADAMLPFGL-ELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS---------QYVEMTYETYKKNEGG   70 (111)
Q Consensus         1 aGD~Ll~~A~-~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~---------~~~~~~~~i~~~KTa~   70 (111)
                      +||+|++.++ +++....    .++....++++.+++++  ..++.||.+|+.+.         .++++|.+|+++|||+
T Consensus       125 ~gd~ll~~~~~~~l~~~~----~~~~~~~~~~~~~~~~~--~~~~~GQ~ldl~~~~~~~~~~~~~t~~~Y~~~i~~KTa~  198 (348)
T d1fpsa_         125 NDSFLLESSVYRVLKKYC----RQRPYYVHLLELFLQTA--YQTELGQMLDLITAPVSKVDLSHFSEERYKAIVKYKTAF  198 (348)
T ss_dssp             HHHHHHHHHHHHHHHHHH----TTSTTHHHHHHHHHHHH--HHHHHHHHHHHHHSCTTTCCSSSCCHHHHHHHHHHHTHH
T ss_pred             HHHHHHHHHHHHHHHhhc----cchHHHHHHHHhhhhhh--hHHHHHHHHHHhhhccccccccccCHHHHHHHHHHHhhh
Confidence            4899997765 4444332    12334568888899998  89999999999642         4789999999999998


Q ss_pred             H--HHHHHHHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640           71 L--HTCGAACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN  108 (111)
Q Consensus        71 L--~~~~~~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~  108 (111)
                      |  |..++..+++.++.+++.++.++ ||.++|+||||.||
T Consensus       199 l~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~lGiaFQI~DD  239 (348)
T d1fpsa_         199 YSFYLPVAAAMYMVGIDSKEEHENAKAILLEMGEYFQIQDD  239 (348)
T ss_dssp             HHTHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHhhhhccccchhhccccccccchHHHHHHH
Confidence            8  66777778888888999999999 99999999999998

>d1ezfa_ a.128.1.2 (A:) Squalene synthase {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=83.00  E-value=4.9  Score=28.16  Aligned_cols=66  Identities=6%  Similarity=-0.213  Sum_probs=40.5

Q ss_pred             hHHHHhhHHHhccc-CCHHHHHHHHHhhhHHHHHHHHHHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhc
Q 047640           41 QGVVEGQYNELQCS-QYVEMTYETYKKNEGGLHTCGAACGAILGGGSVEEIEKKF-RGLIIKITKMMIR  107 (111)
Q Consensus        41 ~~m~~GQ~lDl~~~-~~~~~~~~i~~~KTa~L~~~~~~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D  107 (111)
                      ..|..|+..+.... .|.+++......=-|+.-...+.+=..-... ....+... ++.++|+|+|+..
T Consensus       111 ~~m~~gm~d~~~~~~~t~~dL~~Ycy~VAG~VG~~l~~l~~~~~~~-~~~~~~~~~~A~~lG~AlQltN  178 (333)
T d1ezfa_         111 RRMGIGMAEFLDKHVTSEQEWDKYCHYVAGLVGIGLSRLFSASEFE-DPLVGEDTERANSMGLFLQKTN  178 (333)
T ss_dssp             HHHHHHHHHHHTSCCCSHHHHHHHHHHHTHHHHHHHHHHHHHHTSS-CHHHHHCHHHHHHHHHHHHHHH
T ss_pred             HHHhccHHHHccCcCCCHHHHHHHHHHHHHHHHHHHHHHhCcCCCc-cccHHHHHHHHHHHHHHHHHHH
Confidence            55677777776554 6788887766444455555555553332222 23334455 8888999998753