Citrus Sinensis ID: 036976

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240---
ALLMTEERRKAIWAICVLDRWEERLQDIFYGRPYDMLDAALTDAVFKFPLDIKMRMDTRKFRYENLQELYLYCYYVAGTVGLMSVPVMGIAPDSSSSAQSIYNGALNLGVGNQLTNFLRDVGEDASRGRVYLPQDKLAQFVLCDKDVFARKVTDNWREFMKEQIKRARTFFNMAEEGASQLDKDSRWPVWSSLLIYREILDAIEENDYDNLTKRAYVGRMKKYLMLPQAYNRTQSKGSLIFPY
cccccHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHccccHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHccccHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHHccccccccc
cccccHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHcccccccEEcccccccccHHHHHHHHHHHHHHHcccEccEcccccccccccHHHHHHHHHHHHHHHHHHHHHHHcHHcccccEEccHHHHHHHcccHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHccccccHHccHHHHHHHHHHHHHHHHHHHccccccccEEEccHHHHHHHHHHHHHHHHccccccccc
ALLMTEERRKAIWAICVLDRWEERLQdifygrpydmlDAALTDAVFKFPLDIKMRMDTRKFRYENLQELYLYCYYVAGTvglmsvpvmgiapdssssaQSIYNGALNLGVGNQLTNFLRDvgedasrgrvylpqdklaQFVLCDKDVFARKVTDNWREFMKEQIKRARTFFNMAEEgasqldkdsrwpvwSSLLIYREILDAIeendydnltKRAYVGRMKKYLMlpqaynrtqskgslifpy
allmteerRKAIWAICVLDRWEERLQDIFYGRPYDMLDAALTDAVFKFPLDIKMRMDTRKFRYENLQELYLYCYYVAGTVGLMSVPVMGIAPDSSSSAQSIYNGALNLGVGNQLTNFLRDVGEDASRGRVYLPQDKLAQFVLCDKDVFARKVTDNWREFMKEQIKRARTFFNMAEEgasqldkdsrwpVWSSLLIYREILDaieendydnltKRAYVGRMKKYLMlpqaynrtqskgslifpy
ALLMTEERRKAIWAICVLDRWEERLQDIFYGRPYDMLDAALTDAVFKFPLDIKMRMDTRKFRYENLQELYLYCYYVAGTVGLMSVPVMGIAPDSSSSAQSIYNGALNLGVGNQLTNFLRDVGEDASRGRVYLPQDKLAQFVLCDKDVFARKVTDNWREFMKEQIKRARTFFNMAEEGASQLDKDSRWPVWSSLLIYREILDAIEENDYDNLTKRAYVGRMKKYLMLPQAYNRTQSKGSLIFPY
*********KAIWAICVLDRWEERLQDIFYGRPYDMLDAALTDAVFKFPLDIKMRMDTRKFRYENLQELYLYCYYVAGTVGLMSVPVMGIA********SIYNGALNLGVGNQLTNFLRDVGEDASRGRVYLPQDKLAQFVLCDKDVFARKVTDNWREFMKEQIKRARTFFNMAEEGASQLDKDSRWPVWSSLLIYREILDAIEENDYDNLTKRAYVGRMKKYLMLPQAY*************
ALLMTEERRKAIWAICVLDRWEERLQDIFYGRPYDMLDAALTDAVFKFPLDIKMRMDTRKFRYENLQELYLYCYYVAGTVGLMSVPVMGIAPDSSSSAQSIYNGALNLGVGNQLTNFLRDVGEDASRGRVYLPQDKLAQFVLCDKDVFARKVTDNWREFMKEQIKRARTFFNMAEEGASQLDKDSRWPVWSSLLIYREILDAIEENDYDNLTKRAYVGRMKKYLMLPQAYNRTQS*G******
ALLMTEERRKAIWAICVLDRWEERLQDIFYGRPYDMLDAALTDAVFKFPLDIKMRMDTRKFRYENLQELYLYCYYVAGTVGLMSVPVMGIAPDSSSSAQSIYNGALNLGVGNQLTNFLRDVGEDASRGRVYLPQDKLAQFVLCDKDVFARKVTDNWREFMKEQIKRARTFFNMAE*********SRWPVWSSLLIYREILDAIEENDYDNLTKRAYVGRMKKYLMLPQAYNRTQS********
*LLMTEERRKAIWAICVLDRWEERLQDIFYGRPYDMLDAALTDAVFKFPLDIKMRMDTRKFRYENLQELYLYCYYVAGTVGLMSVPVMGIAPDSSSSAQSIYNGALNLGVGNQLTNFLRDVGEDASRGRVYLPQDKLAQFVLCDKDVFARKVTDNWREFMKEQIKRARTFFNMAEEGASQLDKDSRWPVWSSLLIYREILDAIEENDYDNLTKRAYVGRMKKYLMLPQAYNRTQSKGSL****
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iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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ALLMTEERRKAIWAICVLDRWEERLQDIFYGRPYDMLDAALTDAVFKFPLDIKMRMDTRKFRYENLQELYLYCYYVAGTVGLMSVPVMGIAPDSSSSAQSIYNGALNLGVGNQLTNFLRDVGEDASRGRVYLPQDKLAQFVLCDKDVFARKVTDNWREFMKEQIKRARTFFNMAEEGASQLDKDSRWPVWSSLLIYREILDAIEENDYDNLTKRAYVGRMKKYLMLPQAYNRTQSKGSLIFPY
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query243 2.2.26 [Sep-21-2011]
P53797423 Phytoene synthase, chloro N/A no 0.971 0.557 0.607 1e-89
P37271422 Phytoene synthase, chloro yes no 0.975 0.561 0.609 4e-88
P49293422 Phytoene synthase, chloro N/A no 0.954 0.549 0.622 4e-88
P37272419 Phytoene synthase, chloro N/A no 0.954 0.553 0.613 2e-87
P49085410 Phytoene synthase, chloro N/A no 0.971 0.575 0.592 1e-86
P08196412 Phytoene synthase 1, chlo N/A no 0.958 0.565 0.595 2e-86
P37273310 Phytoene synthase 2, chlo N/A no 0.954 0.748 0.609 1e-85
Q9SSU8398 Phytoene synthase, chloro N/A no 0.950 0.580 0.584 4e-83
P37269308 Phytoene synthase OS=Syne yes no 0.954 0.753 0.479 4e-61
O07333309 Phytoene synthase OS=Spir N/A no 0.954 0.750 0.485 7e-60
>sp|P53797|PSY_NARPS Phytoene synthase, chloroplastic OS=Narcissus pseudonarcissus GN=PSY PE=2 SV=1 Back     alignment and function desciption
 Score =  329 bits (843), Expect = 1e-89,   Method: Compositional matrix adjust.
 Identities = 164/270 (60%), Positives = 195/270 (72%), Gaps = 34/270 (12%)

Query: 2   LLMTEERRKAIWAICV---------------------LDRWEERLQDIFYGRPYDMLDAA 40
           LLMT ERR+AIWAI V                     LDRWE RL+D+F GRPYDM DAA
Sbjct: 148 LLMTPERRRAIWAIYVWCRRTDELVDGHNASHITPSALDRWEARLEDLFAGRPYDMFDAA 207

Query: 41  LTDAVFKFPLDIK--------MRMDTRKFRYENLQELYLYCYYVAGTVGLMSVPVMGIAP 92
           L+D V +FP+DI+        MRMD +K RY+N  ELYLYCYYVAGTVGLMSVPVMGIAP
Sbjct: 208 LSDTVSRFPVDIQPFMDMVEGMRMDLKKSRYKNFDELYLYCYYVAGTVGLMSVPVMGIAP 267

Query: 93  DSSSSAQSIYNGALNLGVGNQLTNFLRDVGEDASRGRVYLPQDKLAQFVLCDKDVFARKV 152
           +S + A+S+YN AL LG+ NQLTN LRDVGEDA RGR+YLPQD+LA+  L D+DVF  KV
Sbjct: 268 ESLAEAESVYNAALALGIANQLTNILRDVGEDARRGRIYLPQDELAEAGLSDEDVFTGKV 327

Query: 153 TDNWREFMKEQIKRARTFFNMAEEGASQLDKDSRWPVWSSLLIYREILDAIEENDYDNLT 212
           TD WR FMK QIKRARTFF  AE+G ++L + SRWPVW+SLL+YR+ILD IE NDY+N T
Sbjct: 328 TDKWRSFMKRQIKRARTFFEQAEKGVTELSQASRWPVWASLLLYRQILDEIEANDYNNFT 387

Query: 213 KRAYVGRMKKYLMLPQAYNRTQSKGSLIFP 242
           KRAYV ++K+   LP AY +     SL+ P
Sbjct: 388 KRAYVSKVKRLAALPLAYGK-----SLLIP 412
Catalyzes the reaction from prephytoene diphosphate to phytoene.
Narcissus pseudonarcissus (taxid: 39639)
EC: 2EC: .EC: 5EC: .EC: 1EC: .EC: 3EC: 2
>sp|P37271|PSY_ARATH Phytoene synthase, chloroplastic OS=Arabidopsis thaliana GN=PSY1 PE=2 SV=2 Back     alignment and function description
>sp|P49293|PSY_CUCME Phytoene synthase, chloroplastic OS=Cucumis melo GN=PSY PE=2 SV=1 Back     alignment and function description
>sp|P37272|PSY_CAPAN Phytoene synthase, chloroplastic OS=Capsicum annuum GN=PSY1 PE=2 SV=1 Back     alignment and function description
>sp|P49085|PSY_MAIZE Phytoene synthase, chloroplastic OS=Zea mays GN=Y1 PE=3 SV=1 Back     alignment and function description
>sp|P08196|PSY1_SOLLC Phytoene synthase 1, chloroplastic OS=Solanum lycopersicum GN=PSY1 PE=1 SV=2 Back     alignment and function description
>sp|P37273|PSY2_SOLLC Phytoene synthase 2, chloroplastic (Fragment) OS=Solanum lycopersicum GN=PSY2 PE=2 SV=1 Back     alignment and function description
>sp|Q9SSU8|PSY_DAUCA Phytoene synthase, chloroplastic OS=Daucus carota GN=PSY PE=2 SV=1 Back     alignment and function description
>sp|P37269|CRTB_SYNE7 Phytoene synthase OS=Synechococcus elongatus (strain PCC 7942) GN=crtB PE=3 SV=2 Back     alignment and function description
>sp|O07333|CRTY_SPIPL Phytoene synthase OS=Spirulina platensis GN=crtB PE=3 SV=1 Back     alignment and function description

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

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query243
297746444 357 unnamed protein product [Vitis vinifera] 0.967 0.658 0.734 1e-105
225435712 419 PREDICTED: phytoene synthase 2, chloropl 0.954 0.553 0.735 1e-105
255572256 385 Phytoene synthase, chloroplast precursor 1.0 0.631 0.705 1e-103
224052972284 predicted protein [Populus trichocarpa] 0.946 0.809 0.733 1e-102
224073174298 predicted protein [Populus trichocarpa] 0.991 0.808 0.688 1e-100
334725693 385 phytoene synthase [Cucumis melo] 0.991 0.625 0.670 4e-99
357462675 387 Phytoene synthase [Medicago truncatula] 0.967 0.607 0.689 6e-99
449448822 385 PREDICTED: phytoene synthase 1, chloropl 0.991 0.625 0.662 2e-98
356569141 397 PREDICTED: phytoene synthase, chloroplas 0.991 0.607 0.677 4e-97
148906078 418 unknown [Picea sitchensis] 0.954 0.555 0.639 5e-93
>gi|297746444|emb|CBI16500.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
 Score =  388 bits (997), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 194/264 (73%), Positives = 210/264 (79%), Gaps = 29/264 (10%)

Query: 1   ALLMTEERRKAIWAI---------------------CVLDRWEERLQDIFYGRPYDMLDA 39
            LLMTEER+KAIWAI                      VLDRWEERL DIF GRPYDMLDA
Sbjct: 25  TLLMTEERQKAIWAIYVWCRRTDELVDGPNAAYMSSAVLDRWEERLHDIFNGRPYDMLDA 84

Query: 40  ALTDAVFKFPLDIK--------MRMDTRKFRYENLQELYLYCYYVAGTVGLMSVPVMGIA 91
           ALTD ++KFPLDIK        MRMDT+ FRYEN QELYLYCYYVAGTVGLMSVPVMGIA
Sbjct: 85  ALTDTIYKFPLDIKPFRDMIEGMRMDTKNFRYENFQELYLYCYYVAGTVGLMSVPVMGIA 144

Query: 92  PDSSSSAQSIYNGALNLGVGNQLTNFLRDVGEDASRGRVYLPQDKLAQFVLCDKDVFARK 151
           P+S  SAQSIYN AL LG+GNQLTN LRDVGED+ RGRVYLPQD+LAQF LCD+D+F+RK
Sbjct: 145 PESPVSAQSIYNSALYLGIGNQLTNILRDVGEDSLRGRVYLPQDELAQFGLCDRDIFSRK 204

Query: 152 VTDNWREFMKEQIKRARTFFNMAEEGASQLDKDSRWPVWSSLLIYREILDAIEENDYDNL 211
           V D WREFMK+QI RAR +FN AEEGASQLDK SRWPVWSSLL+YR+ILDAIEENDYDNL
Sbjct: 205 VNDGWREFMKQQITRARFYFNQAEEGASQLDKASRWPVWSSLLLYRKILDAIEENDYDNL 264

Query: 212 TKRAYVGRMKKYLMLPQAYNRTQS 235
           TKRAYVGR KK L LP AY+R QS
Sbjct: 265 TKRAYVGRTKKLLTLPLAYSRAQS 288

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|225435712|ref|XP_002283501.1| PREDICTED: phytoene synthase 2, chloroplastic-like [Vitis vinifera] Back     alignment and taxonomy information
>gi|255572256|ref|XP_002527067.1| Phytoene synthase, chloroplast precursor, putative [Ricinus communis] gi|223533572|gb|EEF35311.1| Phytoene synthase, chloroplast precursor, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|224052972|ref|XP_002297643.1| predicted protein [Populus trichocarpa] gi|222844901|gb|EEE82448.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|224073174|ref|XP_002304008.1| predicted protein [Populus trichocarpa] gi|222841440|gb|EEE78987.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|334725693|gb|AEH03199.1| phytoene synthase [Cucumis melo] Back     alignment and taxonomy information
>gi|357462675|ref|XP_003601619.1| Phytoene synthase [Medicago truncatula] gi|355490667|gb|AES71870.1| Phytoene synthase [Medicago truncatula] Back     alignment and taxonomy information
>gi|449448822|ref|XP_004142164.1| PREDICTED: phytoene synthase 1, chloroplastic-like [Cucumis sativus] gi|449522422|ref|XP_004168225.1| PREDICTED: phytoene synthase 1, chloroplastic-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|356569141|ref|XP_003552764.1| PREDICTED: phytoene synthase, chloroplastic-like [Glycine max] Back     alignment and taxonomy information
>gi|148906078|gb|ABR16198.1| unknown [Picea sitchensis] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query243
UNIPROTKB|Q6ED64421 Q6ED64 "Phytoene synthase 1" [ 0.909 0.524 0.632 1.2e-81
TAIR|locus:2167225437 PSY "PHYTOENE SYNTHASE" [Arabi 0.909 0.505 0.646 9e-77
UNIPROTKB|Q8X0Z1612 carRA "Bifunctional lycopene c 0.790 0.313 0.246 9.4e-07
UNIPROTKB|Q60AN4362 sqs "Squalene synthase" [Methy 0.296 0.198 0.369 6e-06
UNIPROTKB|P37295602 al-2 "Bifunctional lycopene cy 0.691 0.279 0.258 8.8e-05
UNIPROTKB|Q9UUQ6614 CARRP "Bifunctional lycopene c 0.810 0.320 0.259 0.0002
UNIPROTKB|Q7Z859673 crtYB "Bifunctional lycopene c 0.769 0.277 0.264 0.00038
UNIPROTKB|Q6ED64 Q6ED64 "Phytoene synthase 1" [Oryza sativa Indica Group (taxid:39946)] Back     alignment and assigned GO terms
 Score = 768 (275.4 bits), Expect = 1.2e-81, Sum P(2) = 1.2e-81
 Identities = 148/234 (63%), Positives = 178/234 (76%)

Query:    18 LDRWEERLQDIFYGRPYDMLDAALTDAVFKFPLDIK--------MRMDTRKFRYENLQEL 69
             LDRWE+RL D+F GRPYDMLDAAL+D + K P+DI+        MR D RK RY+N  EL
Sbjct:   186 LDRWEKRLDDLFTGRPYDMLDAALSDTISKSPIDIQPFRDMIEGMRSDLRKTRYKNFDEL 245

Query:    70 YLYCYYVAGTVGLMSVPVMGIAPDSSSSAQSIYNGALNLGVGNQLTNFLRDVGEDASRGR 129
             Y+YCYYVAGTVGLMSVPVMGIAP+S ++ +S+Y+ AL LG+ NQLTN LRDVGEDA RGR
Sbjct:   246 YMYCYYVAGTVGLMSVPVMGIAPESKATTESVYSAALALGIANQLTNILRDVGEDARRGR 305

Query:   130 VYLPQDKLAQFVLCDKDVFARKVTDNWREFMKEQIKRARTFFNMAEEGASQLDKDSRWPV 189
             +YLPQD+LA+  L D+D+F   VT+ WR FMK QIKRAR FF  AE G ++L + SRWPV
Sbjct:   306 IYLPQDELAEAGLSDEDIFNGVVTNKWRSFMKRQIKRARMFFEEAERGVTELSQASRWPV 365

Query:   190 WSSLLIYREILDAIEENDYDNLTKRAYVGRMKKYLMLPQAYNRTQSKGSLIFPY 243
             W+SLL+YR+ILD IE NDY+N TKR YVG+ KK L LP AY R     SL+ PY
Sbjct:   366 WASLLLYRQILDEIEANDYNNFTKRTYVGKAKKLLALPVAYGR-----SLLMPY 414
GO:0009536 "plastid" evidence=IC
TAIR|locus:2167225 PSY "PHYTOENE SYNTHASE" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|Q8X0Z1 carRA "Bifunctional lycopene cyclase/phytoene synthase" [Fusarium fujikuroi (taxid:5127)] Back     alignment and assigned GO terms
UNIPROTKB|Q60AN4 sqs "Squalene synthase" [Methylococcus capsulatus str. Bath (taxid:243233)] Back     alignment and assigned GO terms
UNIPROTKB|P37295 al-2 "Bifunctional lycopene cyclase/phytoene synthase" [Neurospora crassa OR74A (taxid:367110)] Back     alignment and assigned GO terms
UNIPROTKB|Q9UUQ6 CARRP "Bifunctional lycopene cyclase/phytoene synthase" [Mucor circinelloides f. lusitanicus (taxid:29924)] Back     alignment and assigned GO terms
UNIPROTKB|Q7Z859 crtYB "Bifunctional lycopene cyclase/phytoene synthase" [Xanthophyllomyces dendrorhous (taxid:5421)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

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

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

Prediction LevelEC numberConfidence of Prediction
3rd Layer2.5.1.320.914
3rd Layer2.5.10.921

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query243
PLN02632334 PLN02632, PLN02632, phytoene synthase 1e-147
cd00683265 cd00683, Trans_IPPS_HH, Trans-Isoprenyl Diphosphat 3e-68
pfam00494262 pfam00494, SQS_PSY, Squalene/phytoene synthase 7e-57
COG1562288 COG1562, ERG9, Phytoene/squalene synthetase [Lipid 4e-47
TIGR03465266 TIGR03465, HpnD, squalene synthase HpnD 2e-42
TIGR03464266 TIGR03464, HpnC, squalene synthase HpnC 3e-26
cd00385243 cd00385, Isoprenoid_Biosyn_C1, Isoprenoid Biosynth 2e-21
cd00867236 cd00867, Trans_IPPS, Trans-Isoprenyl Diphosphate S 3e-20
TIGR01559337 TIGR01559, squal_synth, farnesyl-diphosphate farne 4e-04
>gnl|CDD|215339 PLN02632, PLN02632, phytoene synthase Back     alignment and domain information 
 Score =  414 bits (1066), Expect = e-147
 Identities = 177/266 (66%), Positives = 194/266 (72%), Gaps = 29/266 (10%)

Query: 2   LLMTEERRKAIWAICV---------------------LDRWEERLQDIFYGRPYDMLDAA 40
           LLMT ERRKAIWAI V                     LDRWE RL+D+F GRPYDMLDAA
Sbjct: 68  LLMTPERRKAIWAIYVWCRRTDELVDGPNASHITPAALDRWEARLEDLFDGRPYDMLDAA 127

Query: 41  LTDAVFKFPLDIK--------MRMDTRKFRYENLQELYLYCYYVAGTVGLMSVPVMGIAP 92
           L D V KFPLDI+        MRMD  K RYEN  ELYLYCYYVAGTVGLMSVPVMGIAP
Sbjct: 128 LADTVSKFPLDIQPFRDMIEGMRMDLVKSRYENFDELYLYCYYVAGTVGLMSVPVMGIAP 187

Query: 93  DSSSSAQSIYNGALNLGVGNQLTNFLRDVGEDASRGRVYLPQDKLAQFVLCDKDVFARKV 152
           +S +S +S+YN AL LG+ NQLTN LRDVGEDA RGRVYLPQD+LAQF L D+D+FA KV
Sbjct: 188 ESKASTESVYNAALALGIANQLTNILRDVGEDARRGRVYLPQDELAQFGLTDEDIFAGKV 247

Query: 153 TDNWREFMKEQIKRARTFFNMAEEGASQLDKDSRWPVWSSLLIYREILDAIEENDYDNLT 212
           TD WR FMK QIKRAR +F  AEEG S+LD  SRWPVW+SLL+YR+ILDAIE NDYDN T
Sbjct: 248 TDKWRAFMKFQIKRARMYFAEAEEGVSELDPASRWPVWASLLLYRQILDAIEANDYDNFT 307

Query: 213 KRAYVGRMKKYLMLPQAYNRTQSKGS 238
           KRAYVG+ KK L LP AY R     S
Sbjct: 308 KRAYVGKWKKLLALPLAYARALFPPS 333

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

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 243
TIGR03464266 HpnC squalene synthase HpnC. This family of genes 100.0
PLN02632334 phytoene synthase 100.0
TIGR03465266 HpnD squalene synthase HpnD. The genes of this fam 100.0
cd00683265 Trans_IPPS_HH Trans-Isoprenyl Diphosphate Synthase 100.0
PF00494267 SQS_PSY: Squalene/phytoene synthase; InterPro: IPR 100.0
COG1562288 ERG9 Phytoene/squalene synthetase [Lipid metabolis 100.0
TIGR01559336 squal_synth farnesyl-diphosphate farnesyltransfera 100.0
KOG4411292 consensus Phytoene/squalene synthetase [Lipid tran 100.0
cd00867236 Trans_IPPS Trans-Isoprenyl Diphosphate Synthases. 99.61
cd00385243 Isoprenoid_Biosyn_C1 Isoprenoid Biosynthesis enzym 99.48
KOG1459413 consensus Squalene synthetase [Lipid transport and 99.48
KOG1459413 consensus Squalene synthetase [Lipid transport and 99.08
PLN02890422 geranyl diphosphate synthase 95.66
TIGR02749322 prenyl_cyano solanesyl diphosphate synthase. Membe 95.47
PLN02857416 octaprenyl-diphosphate synthase 95.23
CHL00151323 preA prenyl transferase; Reviewed 95.1
PRK10888323 octaprenyl diphosphate synthase; Provisional 94.87
TIGR02748319 GerC3_HepT heptaprenyl diphosphate synthase compon 94.54
cd00685259 Trans_IPPS_HT Trans-Isoprenyl Diphosphate Synthase 94.18
PRK10581299 geranyltranstransferase; Provisional 93.94
COG0142322 IspA Geranylgeranyl pyrophosphate synthase [Coenzy 89.02
PF00348260 polyprenyl_synt: Polyprenyl synthetase; InterPro: 87.36
KOG0776384 consensus Geranylgeranyl pyrophosphate synthase/Po 81.98
>TIGR03464 HpnC squalene synthase HpnC Back     alignment and domain information 
Probab=100.00  E-value=8.4e-56  Score=382.51  Aligned_cols=225  Identities=30%  Similarity=0.429  Sum_probs=215.4

Q ss_pred             CCCCChhhhHHHHHHH----------------------HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhCCCCHH-----
Q 036976            1 ALLMTEERRKAIWAIC----------------------VLDRWEERLQDIFYGRPYDMLDAALTDAVFKFPLDIK-----   53 (243)
Q Consensus         1 ~lllp~~~R~~~~aly----------------------~L~~w~~~l~~~~~g~~~~pv~~aL~~~i~~~~l~~~-----   53 (243)
                      ++|+|+++|+++++||                      +|+||+++++++++|.+.|||..+|.+++++++||.+     
T Consensus        12 ~~~lp~~~R~~~~alYAf~R~~Ddi~D~~~~~~~~~~~~L~~wr~~l~~~~~g~~~~pv~~aL~~~~~~~~l~~~~~~~l   91 (266)
T TIGR03464        12 SLLLPARLRAPIHAVYAFARTADDIADEGDGSAEERLALLDDFRAELDAIYSGEPAAPVFVALARTVQRHGLPIEPFLDL   91 (266)
T ss_pred             HHhCCHHHHHHHHHHHHHHHHHHHhccCCCCChHHHHHHHHHHHHHHHHHhCCCCCChHHHHHHHHHHHcCCChHHHHHH
Confidence            4689999999999999                      5999999999999998899999999999999999987     


Q ss_pred             ---hhccCCCCCCCCHHHHHHHHHHhhhHHHHHHHhhhCCCCCCCchhhhhHHHHHHHHHHHHHHHHHHhhhhhhhCCCc
Q 036976           54 ---MRMDTRKFRYENLQELYLYCYYVAGTVGLMSVPVMGIAPDSSSSAQSIYNGALNLGVGNQLTNFLRDVGEDASRGRV  130 (243)
Q Consensus        54 ---~~~Dl~~~~~~t~~dL~~Y~~~~Ag~vg~l~~~l~g~~~~~~~~~~~~~~~a~~lG~alql~nilRDi~~D~~~gR~  130 (243)
                         |++|+.+.+|+|++||+.|||+|||+||+|+++++|..+..      ..++|.++|.|+|+|||||||++|+++|||
T Consensus        92 i~~~~~Dl~~~~~~t~~eL~~Y~~~vAg~vg~l~~~i~g~~~~~------~~~~A~~lG~AlQltniLRDl~eD~~~gR~  165 (266)
T TIGR03464        92 LDAFRQDVVVTRYATWAELLDYCRYSANPVGRLVLDLYGASDPE------NVALSDAICTALQLINFWQDVGVDYRKGRV  165 (266)
T ss_pred             HHHHHHhccCCCCCCHHHHHHHHHHhHHHHHHHHHHHcCCCChh------HHHHHHHHHHHHHHHHHHHhhHHHHhcCCc
Confidence               89999999999999999999999999999999999975432      468899999999999999999999999999


Q ss_pred             ccCHhhHHhCCCChHhhhhccCCHHHHHHHHHHHHHHHHHHHHHHHchhhcCccCChHHHHHHHHHHHHHHHHHHCCCCC
Q 036976          131 YLPQDKLAQFVLCDKDVFARKVTDNWREFMKEQIKRARTFFNMAEEGASQLDKDSRWPVWSSLLIYREILDAIEENDYDN  210 (243)
Q Consensus       131 YlP~~~l~~~gv~~~~l~~~~~~~~~~~l~~~~~~~A~~~~~~a~~~~~~lp~~~~~~~~~~~~~~~~iL~~l~~~~~~~  210 (243)
                      |||.|+|++||++++++.++..++++++++++++++|+++|.+|+.+++.+|+++++++.+++.+|+.+|++|+++||++
T Consensus       166 YLP~~~l~~~Gv~~edl~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~lp~~~~~~~~~~~~~y~~iL~~l~~~~~~~  245 (266)
T TIGR03464       166 YLPRDDLARFGVSEEDLAAGRATPALRELMAFEVSRTRALLDRGAPLAARVDGRLGLELALIVRGGLRILEKIERQGYDV  245 (266)
T ss_pred             cCCHHHHHHcCCCHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHhHHhCCHhhhHHHHHHHHHHHHHHHHHHHcCCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCcccChHHHHHHHHHHHH
Q 036976          211 LTKRAYVGRMKKYLMLPQAYN  231 (243)
Q Consensus       211 ~~~r~~ls~~~k~~~~~~a~~  231 (243)
                      |++|+++|+++|+|++++++|
T Consensus       246 ~~~r~~~~~~~kl~~~~~a~~  266 (266)
T TIGR03464       246 LRERPKLGKFDWAGLLLRALW  266 (266)
T ss_pred             CCCCCcCCHHHHHHHHHHHhC
Confidence            999999999999999999874

This family of genes are members of a superfamily (pfam00494) of phytoene and squalene synthases which catalyze the head-t0-head condensation of polyisoprene pyrophosphates. 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 HpnD 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.
>PLN02632 phytoene synthase Back     alignment and domain information
>TIGR03465 HpnD squalene synthase HpnD Back     alignment and domain information
>cd00683 Trans_IPPS_HH Trans-Isoprenyl Diphosphate Synthases, head-to-head Back     alignment and domain information
>PF00494 SQS_PSY: Squalene/phytoene synthase; InterPro: IPR002060 Squalene synthase 2 Back     alignment and domain information
>COG1562 ERG9 Phytoene/squalene synthetase [Lipid metabolism] Back     alignment and domain information
>TIGR01559 squal_synth farnesyl-diphosphate farnesyltransferase Back     alignment and domain information
>KOG4411 consensus Phytoene/squalene synthetase [Lipid transport and metabolism] Back     alignment and domain information
>cd00867 Trans_IPPS Trans-Isoprenyl Diphosphate Synthases Back     alignment and domain information
>cd00385 Isoprenoid_Biosyn_C1 Isoprenoid Biosynthesis enzymes, Class 1 Back     alignment and domain information
>KOG1459 consensus Squalene synthetase [Lipid transport and metabolism] Back     alignment and domain information
>KOG1459 consensus Squalene synthetase [Lipid transport and metabolism] Back     alignment and domain information
>PLN02890 geranyl diphosphate synthase Back     alignment and domain information
>TIGR02749 prenyl_cyano solanesyl diphosphate synthase Back     alignment and domain information
>PLN02857 octaprenyl-diphosphate synthase Back     alignment and domain information
>CHL00151 preA prenyl transferase; Reviewed Back     alignment and domain information
>PRK10888 octaprenyl diphosphate synthase; Provisional Back     alignment and domain information
>TIGR02748 GerC3_HepT heptaprenyl diphosphate synthase component II Back     alignment and domain information
>cd00685 Trans_IPPS_HT Trans-Isoprenyl Diphosphate Synthases, head-to-tail Back     alignment and domain information
>PRK10581 geranyltranstransferase; Provisional Back     alignment and domain information
>COG0142 IspA Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism] Back     alignment and domain information
>PF00348 polyprenyl_synt: Polyprenyl synthetase; InterPro: IPR000092 A variety of isoprenoid compounds are synthesized by various organisms Back     alignment and domain information
>KOG0776 consensus Geranylgeranyl pyrophosphate synthase/Polyprenyl synthetase [Coenzyme transport and metabolism] Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query243
3ae0_A293 Crystal Structure Of The C(30) Carotenoid Dehydrosq 8e-13
4f6v_A292 Crystal Structure Of Dehydrosqualene Synthase (Crtm 9e-13
2zco_A293 Crystal Structure Of The C(30) Carotenoid Dehydrosq 9e-13
4e9u_A287 Crystal Structure Of Dehydrosqualene Synthase (Crtm 9e-13
4hd1_A294 Crystal Structure Of Squalene Synthase Hpnc From Al 8e-12
3vjd_A293 Crystal Structure Of The Y248a Mutant Of C(30) Caro 9e-12
3adz_A293 Crystal Structure Of The C(30) Carotenoid Dehydrosq 9e-12
>pdb|3AE0|A Chain A, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Complexed With Geranylgeranyl Thiopyrophosphate Length = 293 Back     alignment and structure 
Iteration: 1

 Score = 70.5 bits (171), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 48/160 (30%), Positives = 78/160 (48%), Gaps = 6/160 (3%)
Query: 63  YENLQELYLYCYYVAGTVGLMSVPVMGIAPDSSSSAQSIYNGALNLGVGNQLTNFLRDVG 122
           +E   EL+ YCY VAGTVG +  P++     S       Y+ A  LG   QL N LRDVG
Sbjct: 126 FETDAELFGYCYGVAGTVGEVLTPIL-----SDHETHQTYDVARRLGESLQLINILRDVG 180
Query: 123 EDASRGRVYLPQDKLAQFVLCDKDVFARKVTDNWREFMKEQIKRARTFFNMAEEGASQLD 182
           ED    R+Y  + +L Q+ +   +V+   V +++ +  +     A   F    +      
Sbjct: 181 EDFENERIYFSKQRLKQYEVDIAEVYQNGVNNHYIDLWEYYAAIAEKDFRDVMDQIKVFS 240
Query: 183 KDSRWPVWSSLLIYREILDAIEENDYDNLTKRAYVGRMKK 222
            +++  +  +  IY EILD + + +Y  L +R +V + KK
Sbjct: 241 IEAQPIIELAARIYIEILDEVRQANY-TLHERVFVEKRKK 279
>pdb|4F6V|A Chain A, Crystal Structure Of Dehydrosqualene Synthase (Crtm) From S. Aureus Complexed With Bph-1034, Mg2+ And Fmp. Length = 292 Back     alignment and structure
>pdb|2ZCO|A Chain A, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Length = 293 Back     alignment and structure
>pdb|4E9U|A Chain A, Crystal Structure Of Dehydrosqualene Synthase (Crtm) From S. Aureus Complexed With A Thiocyanate Inhibitor Length = 287 Back     alignment and structure
>pdb|4HD1|A Chain A, Crystal Structure Of Squalene Synthase Hpnc From Alicyclobacillus Acidocaldarius Length = 294 Back     alignment and structure
>pdb|3VJD|A Chain A, Crystal Structure Of The Y248a Mutant Of C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Length = 293 Back     alignment and structure
>pdb|3ADZ|A Chain A, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Complexed With Intermediate Pspp Length = 293 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query243
3acx_A293 Dehydrosqualene synthase; CRTM, carotenoid biosynt 6e-88
3vj8_A343 Squalene synthase; farnesyl-diphosphate farnesyltr 4e-51
>3acx_A Dehydrosqualene synthase; CRTM, carotenoid biosynthesis, staphyloxanthin biosynthesis, transferase, head-TO-head condensation, inhibitor; HET: 673; 1.31A {Staphylococcus aureus} PDB: 2zcp_A* 2zcq_A* 2zcr_A* 2zcs_A* 2zy1_A* 3acw_A* 2zco_A* 3acy_A* 3npr_A* 3nri_A* 3tfn_A* 3tfp_A* 3tfv_A* 3adz_A* 3lgz_B* 3vjd_A* 3vje_A* 3ae0_A* 4ea2_A* 4e9u_A* ... Length = 293 Back     alignment and structure
 Score =  261 bits (669), Expect = 6e-88
 Identities = 59/265 (22%), Positives = 107/265 (40%), Gaps = 38/265 (14%)

Query: 2   LLMTEERRKAIWAI------------------------CVLDRWEERLQDIFYGRPYDML 37
            L+ E++RKA+WAI                          +   E+   +  + +    +
Sbjct: 33  DLLPEDQRKAVWAIYAVCRKIDDSIDVYGDIQFLNQIKEDIQSIEKYPYEYHHFQSDRRI 92

Query: 38  DAALTDAVFKFPLDIK--------MRMDTRKFRYENLQELYLYCYYVAGTVGLMSVPVMG 89
             AL        +  +        +  D     +E   EL+ YCY VAGTVG +  P++ 
Sbjct: 93  MMALQHVAQHKNIAFQSFYNLIDTVYKDQHFTMFETDAELFGYCYGVAGTVGEVLTPILS 152

Query: 90  IAPDSSSSAQSIYNGALNLGVGNQLTNFLRDVGEDASRGRVYLPQDKLAQFVLCDKDVFA 149
                 +     Y+ A  LG   QL N LRDVGED    R+Y  + +L Q+ +   +V+ 
Sbjct: 153 DHETHQT-----YDVARRLGESLQLINILRDVGEDFENERIYFSKQRLKQYEVDIAEVYQ 207

Query: 150 RKVTDNWREFMKEQIKRARTFFNMAEEGASQLDKDSRWPVWSSLLIYREILDAIEENDYD 209
             V +++ +  +     A   F    +       +++  +  +  IY EILD + + +Y 
Sbjct: 208 NGVNNHYIDLWEYYAAIAEKDFRDVMDQIKVFSIEAQPIIELAARIYIEILDEVRQANY- 266

Query: 210 NLTKRAYVGRMKKYLMLPQAYNRTQ 234
            L +R +V + KK  +  +  ++  
Sbjct: 267 TLHERVFVEKRKKAKLFHEINSKYH 291
>3vj8_A Squalene synthase; farnesyl-diphosphate farnesyltransferase, head-TO-head synth cholesterol biosynthesis, oxidoreductase, transferase; 1.52A {Homo sapiens} PDB: 3vj9_A 3vja_A 3vjb_A 3vjc_A* 3asx_A* 3lee_A* 3q2z_A* 3q30_A* 1ezf_A* Length = 343 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query243
4hd1_A294 Squalene synthase HPNC; MCSG, structural genomics, 100.0
3acx_A293 Dehydrosqualene synthase; CRTM, carotenoid biosynt 100.0
3vj8_A343 Squalene synthase; farnesyl-diphosphate farnesyltr 100.0
4f62_A317 Geranyltranstransferase; enzyme function initiativ 95.95
3ts7_A324 Geranyltranstransferase; isoprenoid synthesis, far 95.81
3rmg_A334 Octaprenyl-diphosphate synthase; structural genomi 95.67
4dhd_A358 Polyprenyl synthetase; isoprenoid synthesis, isopr 95.66
3lmd_A360 Geranylgeranyl pyrophosphate synthase; isoprenyl d 95.6
3p8r_A302 Geranyltranstransferase; isoprenyl synthase, struc 95.55
3lsn_A304 Geranyltranstransferase; structural genomics, prot 95.52
3apz_A348 Geranyl diphosphate synthase; prenyltransferase, a 95.46
3uca_A324 Geranyltranstransferase; isoprenoid synthesis, iso 95.38
3lom_A313 Geranyltranstransferase; geranyltransferase, struc 95.37
3mzv_A341 Decaprenyl diphosphate synthase; transferase, stru 95.33
1rtr_A301 Geranyltranstransferase; 2.50A {Staphylococcus aur 95.23
3pko_A334 Geranylgeranyl pyrophosphate synthase; isoprenyl d 95.2
3nf2_A352 Putative polyprenyl synthetase; isoprenyl diphosph 95.18
2h8o_A335 Geranyltranstransferase; geranyltransferase,agroba 94.88
3p8l_A302 Geranyltranstransferase; isoprenyl synthase, struc 94.84
3oyr_A345 Trans-isoprenyl diphosphate synthase; isoprenyl sy 94.58
3aqb_B325 Component B of hexaprenyl diphosphate synthase; pr 94.38
3tc1_A315 Octaprenyl pyrophosphate synthase; all alpha-helic 94.27
3ipi_A295 Geranyltranstransferase; isoprene biosynthesis, he 94.19
2q80_A301 Geranylgeranyl pyrophosphate synthetase; isoprenoi 94.15
2j1p_A293 Geranylgeranyl pyrophosphate synthetase; transfera 94.1
2qis_A374 Farnesyl pyrophosphate synthetase; trans-prenyltra 93.98
1uby_A367 FPS, farnesyl diphosphate synthase; transferase, i 93.87
1yhl_A362 Farnesyl pyrophosphate synthase; farnesyl diphosph 93.78
2her_A368 Fragment, farnesyl pyrophosphate synthase; farnesy 93.58
1wy0_A342 Geranylgeranyl pyrophosphate synthetase; pyrococcu 93.58
2e8v_A340 Geranylgeranyl pyrophosphate synthetase; prenyltra 93.56
1v4e_A299 Octoprenyl-diphosphate synthase; trans-type prenyl 93.53
3pde_A309 Farnesyl-diphosphate synthase; isoprenyl diphospha 93.06
3lk5_A380 Geranylgeranyl pyrophosphate synthase; structural 93.02
2ihi_A395 Pyrophosphate synthase; PV092040, structural genom 92.88
3m0g_A297 Farnesyl diphosphate synthase; structural genomics 92.59
1wmw_A330 Geranylgeranyl diphosphate synthetase; GGPP, preny 92.35
1rqj_A299 Geranyltranstransferase; bisphosphonate, isoprenyl 91.53
3kb9_A382 EPI-isozizaene synthase; terpenoid cyclase, alpha- 91.43
2azj_A289 Geranylgeranyl pyrophosphate synthetase; hexpps, t 90.84
3dyh_A390 Farnesyl pyrophosphate synthase; protein-bisphosph 90.25
3npk_A291 Geranyltranstransferase; isoprene biosynthesis, SG 89.7
1ps1_A337 Pentalenene synthase; antibiotic biosynthesis, ses 89.21
2ftz_A284 Geranyltranstransferase; TM0161, structural GE joi 88.96
3llw_A311 Geranyltranstransferase (ISPA); structural genomic 86.66
1n1b_A549 (+)-bornyl diphosphate synthase; terpene synthase 83.83
3mav_A395 Farnesyl pyrophosphate synthase; PV092040, structu 83.62
2q58_A368 Fragment, farnesyl pyrophosphate synthase; farnesy 82.39
1di1_A300 Aristolochene synthase; sesquiterpene cyclase, iso 80.99
>4hd1_A Squalene synthase HPNC; MCSG, structural genomics, PSI-biology, midwest center for S genomics, transferase; 2.40A {Alicyclobacillus acidocaldarius subsp} Back     alignment and structure
Probab=100.00  E-value=4e-57  Score=394.59  Aligned_cols=230  Identities=24%  Similarity=0.338  Sum_probs=198.1

Q ss_pred             CCCCChhhhHHHHHHH-------------------HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhCCCCHH--------
Q 036976            1 ALLMTEERRKAIWAIC-------------------VLDRWEERLQDIFYGRPYDMLDAALTDAVFKFPLDIK--------   53 (243)
Q Consensus         1 ~lllp~~~R~~~~aly-------------------~L~~w~~~l~~~~~g~~~~pv~~aL~~~i~~~~l~~~--------   53 (243)
                      ++|+|+++|+++++||                   +|+||+++++.++.|.|.||++.+|.+++++|+||.+        
T Consensus        33 ~~~lp~~~R~~~~alYaf~R~~Ddi~D~~~~~~~~~L~~~~~~l~~~~~g~~~~pv~~al~~~~~~~~l~~~~~~~li~g  112 (294)
T 4hd1_A           33 SLFVPRHLRPHFYSVYAFCRGVDDLGDEFAGDRMAALDAYEEELRRAFAGEATTPAFRALQFTIATCNLPMEPFLRLIEA  112 (294)
T ss_dssp             TTTCCTTTHHHHHHHHHHHHHHHHTSTTCCSCHHHHHHHHHHHHHHHHHTCCCSHHHHHHHHHHHHHTCCSHHHHHHHHH
T ss_pred             HHHCCHHHHHHHHHHHHHHHHHHHhccCCChhHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            5799999999999999                   8999999999999999999999999999999999987        


Q ss_pred             hhccCCCCCCCCHHHHHHHHHHhhhHHHHHHHhhhCCCCCCCchhhhhHHHHHHHHHHHHHHHHHHhhhhhhhCCCcccC
Q 036976           54 MRMDTRKFRYENLQELYLYCYYVAGTVGLMSVPVMGIAPDSSSSAQSIYNGALNLGVGNQLTNFLRDVGEDASRGRVYLP  133 (243)
Q Consensus        54 ~~~Dl~~~~~~t~~dL~~Y~~~~Ag~vg~l~~~l~g~~~~~~~~~~~~~~~a~~lG~alql~nilRDi~~D~~~gR~YlP  133 (243)
                      |++|+.+.+|+|++||+.||++|||+||+|+++|+|..++      +..+.|.++|.|+|+|||||||++|+++||||||
T Consensus       113 ~~~Dl~~~~~~t~~dL~~Y~~~vAg~VG~m~~~i~g~~~~------~~~~~A~~lG~AlQltNilRDv~eD~~~gR~YlP  186 (294)
T 4hd1_A          113 NRRDQRKHTYDTWEDLRDYCRYSADPVGRLVLGIFGCLDD------ERARLSDATCTALQVANHMQDIDRDLALGRIYVP  186 (294)
T ss_dssp             HHHHHHCSBCCSHHHHHHHHHHHTHHHHHHHHHHTTCCSH------HHHHHHHHHHHHHHHHHHHHTHHHHHHTTCBCSC
T ss_pred             HHhccccCCCCCHHHHHHHHHhccchHHHHHHHHhCCCCH------HHHHHHHHHHHHHHHHHHHHhchhhhccCceeCC
Confidence            9999999999999999999999999999999999998542      3578999999999999999999999999999999


Q ss_pred             HhhHHhCCCChHhhhhccCCHHHHHHHHHHHHHHHHHHHHHHHchhhcCccCChHHHHHHHHHHHHHHHHHHCCCCCCCC
Q 036976          134 QDKLAQFVLCDKDVFARKVTDNWREFMKEQIKRARTFFNMAEEGASQLDKDSRWPVWSSLLIYREILDAIEENDYDNLTK  213 (243)
Q Consensus       134 ~~~l~~~gv~~~~l~~~~~~~~~~~l~~~~~~~A~~~~~~a~~~~~~lp~~~~~~~~~~~~~~~~iL~~l~~~~~~~~~~  213 (243)
                      .|+|++||++++++.+++.+++++.++++++++|+.+|++|..++..+|+++++++.+++.+|+.||++|+++||++|++
T Consensus       187 ~~~l~~~gv~~~dl~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~lp~~~r~~~~~~~~~y~~il~~i~~~~~~~~~~  266 (294)
T 4hd1_A          187 RADLEQFGATLDDIRARRATDGVRRCIALEVDRAQALFDEGRRLESLVPPRLARQLKLYRLGGEAILAAIRRQGYNPFAG  266 (294)
T ss_dssp             HHHHHTTTCCHHHHHTTCCCHHHHHHHHHHHHHHHHHHHHHGGGGGSSCHHHHHHHHHHHHHHHHHHHHHHTTTTCCC--
T ss_pred             HHHHHHcCCCHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CcccChHHHHHHHHHHHHhhccC
Q 036976          214 RAYVGRMKKYLMLPQAYNRTQSK  236 (243)
Q Consensus       214 r~~ls~~~k~~~~~~a~~~~~~~  236 (243)
                      |+++|+++|+|++|+++..+.+.
T Consensus       267 R~~vs~~~Kl~l~~~al~~~~~~  289 (294)
T 4hd1_A          267 RPVVSGKQKLRIALSVLAGGAKG  289 (294)
T ss_dssp             -----------------------
T ss_pred             CCccCHHHHHHHHHHHHHHhhcc
Confidence            99999999999999999886544
>3acx_A Dehydrosqualene synthase; CRTM, carotenoid biosynthesis, staphyloxanthin biosynthesis, transferase, head-TO-head condensation, inhibitor; HET: 673; 1.31A {Staphylococcus aureus} PDB: 2zcp_A* 2zcq_A* 2zcr_A* 2zcs_A* 2zy1_A* 3acw_A* 2zco_A* 3acy_A* 3npr_A* 3nri_A* 3tfn_A* 3tfp_A* 3tfv_A* 3adz_A* 3lgz_B* 3vjd_A* 3vje_A* 3ae0_A* 4ea2_A* 4e9u_A* ... Back     alignment and structure
>3vj8_A Squalene synthase; farnesyl-diphosphate farnesyltransferase, head-TO-head synth cholesterol biosynthesis, oxidoreductase, transferase; 1.52A {Homo sapiens} PDB: 3vj9_A 3vja_A 3vjb_A 3vjc_A* 3v66_A* 3lee_A* 3q2z_A* 3q30_A* 3asx_A* 1ezf_A* Back     alignment and structure
>4f62_A Geranyltranstransferase; enzyme function initiative, structural genomics; 2.10A {Marinomonas SP} Back     alignment and structure
>3ts7_A Geranyltranstransferase; isoprenoid synthesis, farnesyl diphosphate synthase; 1.94A {Methylococcus capsulatus} Back     alignment and structure
>3rmg_A Octaprenyl-diphosphate synthase; structural genomics, protein structure initiative, isoprene biosynthesis, transferase; 2.30A {Bacteroides thetaiotaomicron} Back     alignment and structure
>4dhd_A Polyprenyl synthetase; isoprenoid synthesis, isoprenoid diphosphate synthase, trans; 1.65A {Pyrobaculum calidifontis} PDB: 4gp1_A* 4gp2_A* Back     alignment and structure
>3lmd_A Geranylgeranyl pyrophosphate synthase; isoprenyl diphosphate synthase, structural genomics, PSI, protein structure initiative, nysgrc; 1.90A {Corynebacterium glutamicum} PDB: 3q2q_A* Back     alignment and structure
>3p8r_A Geranyltranstransferase; isoprenyl synthase, structural genomics, PSI, protein struct initiative, nysgrc; 2.50A {Vibrio cholerae} SCOP: a.128.1.1 Back     alignment and structure
>3lsn_A Geranyltranstransferase; structural genomics, protein structure initiative, NEW YORK structural genomix research consortium, nysgxrc; HET: MSE; 1.35A {Pseudomonas fluorescens} PDB: 3lji_A* 3p41_A* Back     alignment and structure
>3apz_A Geranyl diphosphate synthase; prenyltransferase, all alpha-helices fold, chroloplast, TRAN isoprenoid biosynthetic process; 2.60A {Arabidopsis thaliana} PDB: 3aq0_A* Back     alignment and structure
>3uca_A Geranyltranstransferase; isoprenoid synthesis, isoprenoid diphosphate synthase; 2.00A {Clostridium perfringens} Back     alignment and structure
>3lom_A Geranyltranstransferase; geranyltransferase, structural genomics, PSI, protein structure initiative, nysgrc; 2.30A {Legionella pneumophila subsp} Back     alignment and structure
>3mzv_A Decaprenyl diphosphate synthase; transferase, structural genomics, PSI-2, protein structure initiative; 1.90A {Rhodobacter capsulatus} Back     alignment and structure
>1rtr_A Geranyltranstransferase; 2.50A {Staphylococcus aureus} SCOP: a.128.1.1 Back     alignment and structure
>3pko_A Geranylgeranyl pyrophosphate synthase; isoprenyl diphosphate synthase, structural genomics, PSI, PR structure initiative, nysgrc; HET: CIT; 1.98A {Lactobacillus brevis} PDB: 3n3d_A Back     alignment and structure
>3nf2_A Putative polyprenyl synthetase; isoprenyl diphosphate synthase, structural genomics, PSI, PR structure initiative, nysgrc; 2.20A {Streptomyces coelicolor} Back     alignment and structure
>2h8o_A Geranyltranstransferase; geranyltransferase,agrobacterium tumefaciens, structural GEN PSI-2, protein structure initiative; 1.60A {Agrobacterium tumefaciens} Back     alignment and structure
>3p8l_A Geranyltranstransferase; isoprenyl synthase, structural genomics, PSI, protein struct initiative, nysgrc; 2.00A {Enterococcus faecalis} Back     alignment and structure
>3oyr_A Trans-isoprenyl diphosphate synthase; isoprenyl synthase, PSI, protein structure initiative; HET: IPE; 2.00A {Caulobacter crescentus} Back     alignment and structure
>3aqb_B Component B of hexaprenyl diphosphate synthase; prenyltransferase, transferase; 2.40A {Micrococcus luteus} PDB: 3aqc_B* Back     alignment and structure
>3tc1_A Octaprenyl pyrophosphate synthase; all alpha-helices fold, transferase; 2.00A {Helicobacter pylori} Back     alignment and structure
>3ipi_A Geranyltranstransferase; isoprene biosynthesis, helical bundle, protein structure initiative II (PSI II), structural genomics, nysgxrc; 1.90A {Methanosarcina mazei} Back     alignment and structure
>2q80_A Geranylgeranyl pyrophosphate synthetase; isoprenoid pathway, isopentenyl transferase, structural GENO structural genomics consortium, SGC; HET: GRG; 2.70A {Homo sapiens} SCOP: a.128.1.1 Back     alignment and structure
>2j1p_A Geranylgeranyl pyrophosphate synthetase; transferase, isoprene biosynthesis, multifunctional enzyme, carotenoid biosynthesis; HET: GRG; 1.8A {Sinapis alba} PDB: 2j1o_A 3kra_A 3krc_A* 3krf_A* 3kro_A* 3krp_A* 3oab_A* 3oac_A* Back     alignment and structure
>2qis_A Farnesyl pyrophosphate synthetase; trans-prenyltransferase, structural genomics, structural GEN consortium, SGC, transferase; HET: RIS; 1.80A {Homo sapiens} PDB: 4dem_F* 1yv5_A* 1yq7_A* 2opm_A* 2opn_A* 3cp6_A* 2rah_A* 2vf6_A* 1zw5_A* 3b7l_A* 3s4j_A* 3rye_A* 3n45_F* 2f89_F* 2f7m_F* 2f8z_F* 2f8c_F* 2f92_F* 2f9k_F* 3n1v_F* ... Back     alignment and structure
>1uby_A FPS, farnesyl diphosphate synthase; transferase, isoprene biosynthesis, cholesterol biosynthesis; HET: DMA; 2.40A {Gallus gallus} SCOP: a.128.1.1 PDB: 1ubw_A* 1ubv_A* 1ubx_A* 1fps_A Back     alignment and structure
>1yhl_A Farnesyl pyrophosphate synthase; farnesyl diphosphate synthase, bisphosphonate, dimethyl ALLY pyrophosphate sulfate, FPPS, transferase; HET: DMA RIS; 1.95A {Trypanosoma cruzi} PDB: 1yhk_A* 1yhm_A* 3iba_A* 3ick_A* 3icm_A* 3icn_A* 3icz_A* 3id0_A* Back     alignment and structure
>1wy0_A Geranylgeranyl pyrophosphate synthetase; pyrococcus horikosh structural genomics, riken structural genomics/proteomics initiative, RSGI; 2.20A {Pyrococcus horikoshii} Back     alignment and structure
>2e8v_A Geranylgeranyl pyrophosphate synthetase; prenyltransferase, farnesyl pyrophosphate, bisphosphonate; HET: GRG; 1.80A {Saccharomyces cerevisiae} PDB: 2e8t_A* 2e8u_A* 2dh4_A* 2e8w_A* 2e8x_A* 2e90_A* 2e91_A* 2e92_A* 2e93_A* 2e94_A* 2e95_A* 2z4v_A* 2z4w_A* 2z4x_A* 2z4y_A* 2z4z_A* 2z50_A* 2z52_A* 2z78_A* 2z7h_A* ... Back     alignment and structure
>1v4e_A Octoprenyl-diphosphate synthase; trans-type prenyltransferase, thermophilic; 2.28A {Thermotoga maritima} SCOP: a.128.1.1 PDB: 1v4j_A 1wkz_A 1vg2_A 1wl3_A 1wl0_A 1wl2_A 1v4h_A 1v4i_A 1v4k_A 2azl_A 1wl1_A 1vg4_A 1vg3_A 1vg6_A 1vg7_A Back     alignment and structure
>3pde_A Farnesyl-diphosphate synthase; isoprenyl diphosphate synthase, structural genomics, PSI, PR structure initiative; HET: IPE; 1.75A {Lactobacillus brevis} PDB: 3m9u_A* Back     alignment and structure
>3lk5_A Geranylgeranyl pyrophosphate synthase; structural genomics, protein structure initiative, geranylge pyrophosphate synthase; 1.90A {Corynebacterium glutamicum} PDB: 3qqv_A* Back     alignment and structure
>3m0g_A Farnesyl diphosphate synthase; structural genomics, protein structure initiative, NYSGXRC, biosynthesis, transferase, PSI-2; 1.90A {Rhodobacter capsulatus} PDB: 3lvs_A Back     alignment and structure
>1wmw_A Geranylgeranyl diphosphate synthetase; GGPP, prenyl diphosphate synthase, structural genom riken structural genomics/proteomics initiative; 1.55A {Thermus thermophilus} Back     alignment and structure
>1rqj_A Geranyltranstransferase; bisphosphonate, isoprenyl synthase; HET: IPR RIS; 1.95A {Escherichia coli} SCOP: a.128.1.1 PDB: 1rqi_A* 2for_A* Back     alignment and structure
>3kb9_A EPI-isozizaene synthase; terpenoid cyclase, alpha-helical fold, farnesyl diphosphate, metal-binding, lyase, magnesium; HET: BTM; 1.60A {Streptomyces coelicolor} PDB: 3kbk_A 3lgk_A 3lg5_A* Back     alignment and structure
>2azj_A Geranylgeranyl pyrophosphate synthetase; hexpps, trans-prenyltransferase; 2.40A {Sulfolobus solfataricus} PDB: 2azk_A Back     alignment and structure
>3dyh_A Farnesyl pyrophosphate synthase; protein-bisphosphonate complex, isoprene biosynthesis, transferase; HET: 721; 1.94A {Trypanosoma brucei} PDB: 2ewg_A* 2i19_A* 2p1c_A* 3dyf_A* 3dyg_A* 2ogd_A* 3efq_A* 3egt_A* Back     alignment and structure
>3npk_A Geranyltranstransferase; isoprene biosynthesis, SGX, structural genomics protein structure initiative; 1.50A {Campylobacter jejuni} Back     alignment and structure
>1ps1_A Pentalenene synthase; antibiotic biosynthesis, sesquiterpene cyclase, lyase; 2.60A {Streptomyces SP} SCOP: a.128.1.4 PDB: 1hm7_A 1hm4_A Back     alignment and structure
>2ftz_A Geranyltranstransferase; TM0161, structural GE joint center for structural genomics, JCSG, protein structu initiative, PSI; HET: MLY; 1.90A {Thermotoga maritima} Back     alignment and structure
>3llw_A Geranyltranstransferase (ISPA); structural genomics, PSI, protein structure initiative, nysgrc; 2.30A {Helicobacter pylori} PDB: 3q1o_A* Back     alignment and structure
>1n1b_A (+)-bornyl diphosphate synthase; terpene synthase fold, isomerase; 2.00A {Salvia officinalis} SCOP: a.102.4.1 a.128.1.3 PDB: 1n1z_A* 1n20_A* 1n21_A* 1n22_A* 1n23_A* 1n24_A* Back     alignment and structure
>3mav_A Farnesyl pyrophosphate synthase; PV092040, structural genomics, structural genomics consortium, SGC, transferase, isoprene biosynthesis; 2.10A {Plasmodium vivax} PDB: 3cc9_A* 3ez3_A* 3ldw_A* 3mys_A* 3ph7_A* 3rbm_A* 3ryw_A* Back     alignment and structure
>2q58_A Fragment, farnesyl pyrophosphate synthase; farnesyl diphosphate synthase, structural genomics, structur genomics consortium, SGC; HET: ZOL; 2.37A {Cryptosporidium parvum} PDB: 2o1o_A* Back     alignment and structure
>1di1_A Aristolochene synthase; sesquiterpene cyclase, isoprenoid biosynthesis, lyase; 2.50A {Penicillium roqueforti} SCOP: a.128.1.4 PDB: 1dgp_A Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

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

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 243
d1ezfa_333 a.128.1.2 (A:) Squalene synthase {Human (Homo sapi 5e-35
>d1ezfa_ a.128.1.2 (A:) Squalene synthase {Human (Homo sapiens) [TaxId: 9606]} Length = 333 Back     information, alignment and structure

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

 Score =  125 bits (315), Expect = 5e-35
 Identities = 46/284 (16%), Positives = 86/284 (30%), Gaps = 43/284 (15%)

Query: 2   LLMTEERRKAIWAI---C-------------------VLDRWEERLQDIFYGRP------ 33
             +  E R A+                          +L  +   L    +         
Sbjct: 22  QALDGEMRNAVCIFYLVLRALDTLEDDMTISVEKKVPLLHNFHSFLYQPDWRFMESKEKD 81

Query: 34  ------YDMLDAALTDAVFKFPLDIK--------MRMDTRKFRYENLQELYLYCYYVAGT 79
                 +  +     +   K+   I            +       + QE   YC+YVAG 
Sbjct: 82  RQVLEDFPTISLEFRNLAEKYQTVIADICRRMGIGMAEFLDKHVTSEQEWDKYCHYVAGL 141

Query: 80  VGLMSVPVMGIAPDSSSSAQSIYNGALNLGVGNQLTNFLRDVGEDASRGRVYLPQDKLAQ 139
           VG+    +   +             A ++G+  Q TN +RD  ED   GR + PQ+  ++
Sbjct: 142 VGIGLSRLFSASEFEDPLVGEDTERANSMGLFLQKTNIIRDYLEDQQGGREFWPQEVWSR 201

Query: 140 FVLCDKDVFARKVTDNWREFMKEQIKRARTFFNMAEEGASQLDKDSRWPVWSSLLIYREI 199
           +V    D    +  D   + + E I  A           S+L   S +   +   +    
Sbjct: 202 YVKKLGDFAKPENIDLAVQCLNELITNALHHIPDVITYLSRLRNQSVFNFCAIPQVMAIA 261

Query: 200 LDAIEENDYDNLTKRAYVGRMKKYLMLPQAYNRTQSKGSLIFPY 243
             A   N+         + + +   ++  A N    K ++I+ Y
Sbjct: 262 TLAACYNNQQVFKGAVKIRKGQAVTLMMDATNMPAVK-AIIYQY 304

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query243
d1ezfa_333 Squalene synthase {Human (Homo sapiens) [TaxId: 96 100.0
d2q80a1291 Geranylgeranyl pyrophosphate synthetase {Human (Ho 95.14
d1ps1a_311 Pentalenene synthase {Streptomyces sp., UC5319 [Ta 92.58
d1fpsa_348 Farnesyl diphosphate synthase (geranyltranstransfe 91.77
d1v4ea_280 Octoprenyl-diphosphate synthase {Thermotoga mariti 89.67
d1rqja_299 Farnesyl diphosphate synthase (geranyltranstransfe 89.36
d1rtra_290 Farnesyl diphosphate synthase (geranyltranstransfe 89.15
>d1ezfa_ a.128.1.2 (A:) Squalene synthase {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
class: All alpha proteins
fold: Terpenoid synthases
superfamily: Terpenoid synthases
family: Squalene synthase
domain: Squalene synthase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.1e-43  Score=312.38  Aligned_cols=228  Identities=18%  Similarity=0.133  Sum_probs=182.0

Q ss_pred             CCCChhhhHHHHHHHHH----------------------HHHHHHHHHHHcCC-----CCCHHHHHHHHHHHhCC-CCHH
Q 036976            2 LLMTEERRKAIWAICVL----------------------DRWEERLQDIFYGR-----PYDMLDAALTDAVFKFP-LDIK   53 (243)
Q Consensus         2 lllp~~~R~~~~aly~L----------------------~~w~~~l~~~~~g~-----~~~pv~~aL~~~i~~~~-l~~~   53 (243)
                      ++||++.|++++++|.+                      ++|++.+.....+.     +.+|+...+..++..+. ++..
T Consensus        22 ~~Lp~~~R~~v~~lYafcR~~DdI~D~~~~~~~~k~~~L~~~~~~l~~~~~~~~~~~~~~~~ll~~~~~v~~~~~~l~~~  101 (333)
T d1ezfa_          22 QALDGEMRNAVCIFYLVLRALDTLEDDMTISVEKKVPLLHNFHSFLYQPDWRFMESKEKDRQVLEDFPTISLEFRNLAEK  101 (333)
T ss_dssp             HTSCTHHHHHHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHHTTCTTCCCCCCCSTTHHHHHTHHHHHHHHHTSCHH
T ss_pred             HHCCHHHHHHHHHHHHHHHHhhhhHhCCCCCHHHHHHHHHHHHHHHHHhhhcccccCcchHHHHhhccHHHHHHHHHHHH
Confidence            68999999999999944                      44444444332221     22466666666665542 3321


Q ss_pred             --------------hhccCCCCCCCCHHHHHHHHHHhhhHHHHHHHhhhCCCCCCCchhhhhHHHHHHHHHHHHHHHHHH
Q 036976           54 --------------MRMDTRKFRYENLQELYLYCYYVAGTVGLMSVPVMGIAPDSSSSAQSIYNGALNLGVGNQLTNFLR  119 (243)
Q Consensus        54 --------------~~~Dl~~~~~~t~~dL~~Y~~~~Ag~vg~l~~~l~g~~~~~~~~~~~~~~~a~~lG~alql~nilR  119 (243)
                                    ..+|....+|+|++||+.|||+|||+||+|+++++|..+......++..+.|.++|.|+|+|||||
T Consensus       102 ~~~~i~~~~~~m~~gm~d~~~~~~~t~~dL~~Ycy~VAG~VG~~l~~l~~~~~~~~~~~~~~~~~A~~lG~AlQltNIlR  181 (333)
T d1ezfa_         102 YQTVIADICRRMGIGMAEFLDKHVTSEQEWDKYCHYVAGLVGIGLSRLFSASEFEDPLVGEDTERANSMGLFLQKTNIIR  181 (333)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTSCCCSHHHHHHHHHHHTHHHHHHHHHHHHHHTSSCHHHHHCHHHHHHHHHHHHHHHHHH
T ss_pred             hccchHHHHHHHhccHHHHccCcCCCHHHHHHHHHHHHHHHHHHHHHHhCcCCCccccHHHHHHHHHHHHHHHHHHHHHH
Confidence                          345666788999999999999999999999999999854333334456789999999999999999


Q ss_pred             hhhhhhhCCCcccCHhhHHhCCCChHhhhhccCCHHHHHHHHHHHHHHHHHHHHHHHchhhcCccCChHHHHHHHHHHHH
Q 036976          120 DVGEDASRGRVYLPQDKLAQFVLCDKDVFARKVTDNWREFMKEQIKRARTFFNMAEEGASQLDKDSRWPVWSSLLIYREI  199 (243)
Q Consensus       120 Di~~D~~~gR~YlP~~~l~~~gv~~~~l~~~~~~~~~~~l~~~~~~~A~~~~~~a~~~~~~lp~~~~~~~~~~~~~~~~i  199 (243)
                      |+++|+++||||||.|+|.+||++++++.+++.++++..++.+++++|+.||++|.+++..||.++++.+.++..+|..+
T Consensus       182 Di~eD~~~gR~YlP~e~l~~~g~~~~dl~~~~~~~~~~~~~~~l~~~A~~~~~~a~~y~~~lp~~~~~~~~~~~~~~a~~  261 (333)
T d1ezfa_         182 DYLEDQQGGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELITNALHHIPDVITYLSRLRNQSVFNFCAIPQVMAIA  261 (333)
T ss_dssp             THHHHHHHTCCCSCHHHHTTTCSSGGGGGSGGGHHHHHHHHHHHHHHHHTTHHHHHHHHHTCCCHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHhCCcEECCHHHHHHcCCCHHHHHhccchHHHHHHHHHHHHHHHHHHHHHHHHHHHCCchhHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999888887787889988


Q ss_pred             HHHHHHCCCCCCCCCcccChHHHHHHHHHH
Q 036976          200 LDAIEENDYDNLTKRAYVGRMKKYLMLPQA  229 (243)
Q Consensus       200 L~~l~~~~~~~~~~r~~ls~~~k~~~~~~a  229 (243)
                      .-++.++|+++|++|+++|+.++..++.++
T Consensus       262 tl~~~~~~~~~~~~~vkisr~~~~~l~~~~  291 (333)
T d1ezfa_         262 TLAACYNNQQVFKGAVKIRKGQAVTLMMDA  291 (333)
T ss_dssp             HHHHHTTCGGGGTSCCCC----------CT
T ss_pred             HHHHHHcCchhcCCCeEeeHHHHHHHHHHh
Confidence            888889999999999999999998776443
>d2q80a1 a.128.1.1 (A:6-296) Geranylgeranyl pyrophosphate synthetase {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1ps1a_ a.128.1.4 (A:) Pentalenene synthase {Streptomyces sp., UC5319 [TaxId: 1931]} Back     information, alignment and structure
>d1fpsa_ a.128.1.1 (A:) Farnesyl diphosphate synthase (geranyltranstransferase) {Chicken (Gallus gallus) [TaxId: 9031]} Back     information, alignment and structure
>d1v4ea_ a.128.1.1 (A:) Octoprenyl-diphosphate synthase {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1rqja_ a.128.1.1 (A:) Farnesyl diphosphate synthase (geranyltranstransferase) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1rtra_ a.128.1.1 (A:) Farnesyl diphosphate synthase (geranyltranstransferase) {Staphylococcus aureus [TaxId: 1280]} Back     information, alignment and structure