Citrus Sinensis ID: 016696

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380----
MCSTFSLAAKPSIGESRGKIWSLQVINSAARSELNINIPREKNSIILPRLSTQGMLQSDVHICEIAERQSLANNLSDKGDAFRSKPQLDAMFLDEAYERCRKICAEYAKTYYLGTLLLTKERQKAIWAVYAWCKRTDELVDGPNAFCVSPAALDRWEERLQDIFNGHPNDILDAALTDTVSKFNLHIKPFRDMIKGMRMDTEKCRYANFQELYLYCYYAGGTVGLMSVPVMGMDPDSSASAQSIYNAALYLGIGNQLTNILRDVGEDASRGRIYLPQDELAKFGLRDEDIFSRKVSDEWREFMKEQITRARYFYKLAEEGASELDKASRWPVWTVLILYQKILDAIQDNDYDNLTKRAYVGNIKKLFLVRQAYYRAQSISTATD
ccccccccccccccccccccccccHHccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHccccHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHcccccHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHccccHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHcccccccc
ccccHHHccccccccccccEEEEEEccccccccccccccccEEccEcccccccccccHHHHHHHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHccccccHHHHHHHcccccccccccccHHHHHHHHHHHHHHHcHcEccEcccccccccccHHHHHHHHHHHHHHHHHHHHHHHcHHHccccEEccHHHHHHHcccHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHccccccHHccHHHHHHHHHHHHHHHHHHHcccccccEEEEccHHHHHHHHHHHHHHHcccccccc
mcstfslaakpsigesrgkiWSLQVINSAARselninipreknsiilprlstqgmlqsdVHICEIAERQSLAnnlsdkgdafrskpqlDAMFLDEAYERCRKICAEYAKTYYLGTLLLTKERQKAIWAVYAWCKRtdelvdgpnafcvspaALDRWEERLQDIFnghpndilDAALTDTVSkfnlhikpfRDMIKGMRMDTEKCRYANFQELYLYCYYAggtvglmsvpvmgmdpdssasAQSIYNAALYLGIGNQLTNILRDvgedasrgriylpqdelakfglrdedifsRKVSDEWREFMKEQITRARYFYKLAEEGaseldkasrwpvWTVLILYQKILDAiqdndydnltkrayVGNIKKLFLVRQAYYRAQSISTATD
mcstfslaakpsigesrgkiwSLQVINSAarselninipreknsiiLPRLSTQGMLQSDVHICEIAERQSLANNLSDKGDAFRSKPQLDAMFLDEAYERCRKICAEYAKTYYLGTLLLTKERQKAIWAVYAWCKRTDELVDGPNAFCVSPAALDRWEERLQDIFNGHPNDILDAALTDTVSKFNLHIKPFRDMIKGMRMDTEKCRYANFQELYLYCYYAGGTVGLMSVPVMGMDPDSSASAQSIYNAALYLGIGNQLTNILRDVGEDASRGRIylpqdelakfglrdedifSRKVSDEWREFMKEQITRARYFYKLAEEGaseldkasrwpVWTVLILYQKILDAIQDNDYDNLTKRAYVGNIKKLFLVRQAYYraqsistatd
MCSTFSLAAKPSIGESRGKIWSLQVINSAARSELNINIPREKNSIILPRLSTQGMLQSDVHICEIAERQSLANNLSDKGDAFRSKPQLDAMFLDEAYERCRKICAEYAKtyylgtllltKERQKAIWAVYAWCKRTDELVDGPNAFCVSPAALDRWEERLQDIFNGHPNDILDAALTDTVSKFNLHIKPFRDMIKGMRMDTEKCRYANFQELYLYCYYAGGTVGLMSVPVMGMDPDSSASAQSIYNAALYLGIGNQLTNILRDVGEDASRGRIYLPQDELAKFGLRDEDIFSRKVSDEWREFMKEQITRARYFYKLAEEGASELDKASRWPVWTVLILYQKILDAIQDNDYDNLTKRAYVGNIKKLFLVRQAYYRAQSISTATD
******************KIWSLQVINSAARSELNINIPREKNSIILPRLSTQGMLQSDVHICEIAE********************LDAMFLDEAYERCRKICAEYAKTYYLGTLLLTKERQKAIWAVYAWCKRTDELVDGPNAFCVSPAALDRWEERLQDIFNGHPNDILDAALTDTVSKFNLHIKPFRDMIKGMRMDTEKCRYANFQELYLYCYYAGGTVGLMSVPVMG*********QSIYNAALYLGIGNQLTNILRDVGEDASRGRIYLPQDELAKFGLRDEDIFSRKVSDEWREFMKEQITRARYFYKLAEEGASELDKASRWPVWTVLILYQKILDAIQDNDYDNLTKRAYVGNIKKLFLVRQAYYRA********
********************************************************************************************LDEAYERCRKICAEYAKTYYLGTLLLTKERQKAIWAVYAWCKRTDELVDGPNAFCVSPAALDRWEERLQDIFNGHPNDILDAALTDTVSKFNLHIKPFRDMIKGMRMDTEKCRYANFQELYLYCYYAGGTVGLMSVPVMGMDPDSSASAQSIYNAALYLGIGNQLTNILRDVGEDASRGRIYLPQDELAKFGLRDEDIFSRKVSDEWREFMKEQITRARYFYKLAEEGASELDKASRWPVWTVLILYQKILDAIQDNDYDNLTKRAYVGNIKKLFLVRQAYY***S******
********AKPSIGESRGKIWSLQVINSAARSELNINIPREKNSIILPRLSTQGMLQSDVHICEIAERQSLANNLSDKGDAFRSKPQLDAMFLDEAYERCRKICAEYAKTYYLGTLLLTKERQKAIWAVYAWCKRTDELVDGPNAFCVSPAALDRWEERLQDIFNGHPNDILDAALTDTVSKFNLHIKPFRDMIKGMRMDTEKCRYANFQELYLYCYYAGGTVGLMSVPVMGMDPDSSASAQSIYNAALYLGIGNQLTNILRDVGEDASRGRIYLPQDELAKFGLRDEDIFSRKVSDEWREFMKEQITRARYFYKLAEEGASELDKASRWPVWTVLILYQKILDAIQDNDYDNLTKRAYVGNIKKLFLVRQAYYRAQSISTATD
*****************GKIWSLQVINS************EKNSIILPRLSTQGMLQSDVHICEIAERQSLANNLSDKGDAFRSKPQLDAMFLDEAYERCRKICAEYAKTYYLGTLLLTKERQKAIWAVYAWCKRTDELVDGPNAFCVSPAALDRWEERLQDIFNGHPNDILDAALTDTVSKFNLHIKPFRDMIKGMRMDTEKCRYANFQELYLYCYYAGGTVGLMSVPVMGMDPDSSASAQSIYNAALYLGIGNQLTNILRDVGEDASRGRIYLPQDELAKFGLRDEDIFSRKVSDEWREFMKEQITRARYFYKLAEEGASELDKASRWPVWTVLILYQKILDAIQDNDYDNLTKRAYVGNIKKLFLVRQAYYRAQS******
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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MCSTFSLAAKPSIGESRGKIWSLQVINSAARSELNINIPREKNSIILPRLSTQGMLQSDVHICEIAERQSLANNLSDKGDAFRSKPQLDAMFLDEAYERCRKICAEYAKTYYLGTLLLTKERQKAIWAVYAWCKRTDELVDGPNAFCVSPAALDRWEERLQDIFNGHPNDILDAALTDTVSKFNLHIKPFRDMIKGMRMDTEKCRYANFQELYLYCYYAGGTVGLMSVPVMGMDPDSSASAQSIYNAALYLGIGNQLTNILRDVGEDASRGRIYLPQDELAKFGLRDEDIFSRKVSDEWREFMKEQITRARYFYKLAEEGASELDKASRWPVWTVLILYQKILDAIQDNDYDNLTKRAYVGNIKKLFLVRQAYYRAQSISTATD
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 ?
Query384 2.2.26 [Sep-21-2011]
P37271422 Phytoene synthase, chloro yes no 0.742 0.675 0.670 1e-118
P37272419 Phytoene synthase, chloro N/A no 0.760 0.696 0.667 1e-118
P08196412 Phytoene synthase 1, chlo N/A no 0.885 0.825 0.585 1e-117
P49293422 Phytoene synthase, chloro N/A no 0.742 0.675 0.678 1e-117
P53797423 Phytoene synthase, chloro N/A no 0.734 0.666 0.666 1e-115
P37273310 Phytoene synthase 2, chlo N/A no 0.742 0.919 0.670 1e-115
P49085410 Phytoene synthase, chloro N/A no 0.731 0.685 0.665 1e-113
Q9SSU8398 Phytoene synthase, chloro N/A no 0.742 0.716 0.659 1e-113
O07333309 Phytoene synthase OS=Spir N/A no 0.742 0.922 0.551 7e-87
P37269308 Phytoene synthase OS=Syne yes no 0.763 0.951 0.521 8e-87
>sp|P37271|PSY_ARATH Phytoene synthase, chloroplastic OS=Arabidopsis thaliana GN=PSY1 PE=2 SV=2 Back     alignment and function desciption
 Score =  425 bits (1092), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 191/285 (67%), Positives = 235/285 (82%)

Query: 92  FLDEAYERCRKICAEYAKTYYLGTLLLTKERQKAIWAVYAWCKRTDELVDGPNAFCVSPA 151
            L EAY+RC ++CAEYAKT+YLGTLL+T ER+KAIWA+Y WC+RTDELVDGPNA  ++P 
Sbjct: 127 LLGEAYDRCGEVCAEYAKTFYLGTLLMTPERRKAIWAIYVWCRRTDELVDGPNASHITPM 186

Query: 152 ALDRWEERLQDIFNGHPNDILDAALTDTVSKFNLHIKPFRDMIKGMRMDTEKCRYANFQE 211
           ALDRWE RL+D+F G P D+LDAAL DTV+++ + I+PFRDMI+GMRMD +K RY NF +
Sbjct: 187 ALDRWEARLEDLFRGRPFDMLDAALADTVARYPVDIQPFRDMIEGMRMDLKKSRYQNFDD 246

Query: 212 LYLYCYYAGGTVGLMSVPVMGMDPDSSASAQSIYNAALYLGIGNQLTNILRDVGEDASRG 271
           LYLYCYY  GTVGLMSVPVMG+DP S A+ +S+YNAAL LGI NQLTNILRDVGEDA RG
Sbjct: 247 LYLYCYYVAGTVGLMSVPVMGIDPKSKATTESVYNAALALGIANQLTNILRDVGEDARRG 306

Query: 272 RIYLPQDELAKFGLRDEDIFSRKVSDEWREFMKEQITRARYFYKLAEEGASELDKASRWP 331
           R+YLPQDELA+ GL DEDIF+ KV+D+WR FMK Q+ RAR F+  AE+G +EL  ASRWP
Sbjct: 307 RVYLPQDELAQAGLSDEDIFAGKVTDKWRNFMKMQLKRARMFFDEAEKGVTELSAASRWP 366

Query: 332 VWTVLILYQKILDAIQDNDYDNLTKRAYVGNIKKLFLVRQAYYRA 376
           VW  L+LY++ILD I+ NDY+N TKRAYVG +KK+  +  AY ++
Sbjct: 367 VWASLLLYRRILDEIEANDYNNFTKRAYVGKVKKIAALPLAYAKS 411
Catalyzes the reaction from prephytoene diphosphate to phytoene.
Arabidopsis thaliana (taxid: 3702)
EC: 2EC: .EC: 5EC: .EC: 1EC: .EC: 3EC: 2
>sp|P37272|PSY_CAPAN Phytoene synthase, chloroplastic OS=Capsicum annuum GN=PSY1 PE=2 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|P49293|PSY_CUCME Phytoene synthase, chloroplastic OS=Cucumis melo GN=PSY PE=2 SV=1 Back     alignment and function description
>sp|P53797|PSY_NARPS Phytoene synthase, chloroplastic OS=Narcissus pseudonarcissus GN=PSY PE=2 SV=1 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|P49085|PSY_MAIZE Phytoene synthase, chloroplastic OS=Zea mays GN=Y1 PE=3 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|O07333|CRTY_SPIPL Phytoene synthase OS=Spirulina platensis GN=crtB PE=3 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

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 ?
Query384
225435712419 PREDICTED: phytoene synthase 2, chloropl 0.966 0.885 0.682 1e-149
255572256385 Phytoene synthase, chloroplast precursor 0.979 0.976 0.666 1e-147
357462675387 Phytoene synthase [Medicago truncatula] 0.973 0.966 0.654 1e-140
449448822385 PREDICTED: phytoene synthase 1, chloropl 0.981 0.979 0.617 1e-135
334725693385 phytoene synthase [Cucumis melo] 0.955 0.953 0.636 1e-135
297746444357 unnamed protein product [Vitis vinifera] 0.755 0.812 0.775 1e-133
224052972284 predicted protein [Populus trichocarpa] 0.739 1.0 0.774 1e-130
356569141397 PREDICTED: phytoene synthase, chloroplas 0.908 0.879 0.626 1e-130
224073174298 predicted protein [Populus trichocarpa] 0.765 0.986 0.704 1e-124
255572258370 Phytoene synthase, chloroplast precursor 0.864 0.897 0.598 1e-123
>gi|225435712|ref|XP_002283501.1| PREDICTED: phytoene synthase 2, chloroplastic-like [Vitis vinifera] Back     alignment and taxonomy information
 Score =  534 bits (1376), Expect = e-149,   Method: Compositional matrix adjust.
 Identities = 258/378 (68%), Positives = 303/378 (80%), Gaps = 7/378 (1%)

Query: 1   MCSTFSLAAKPSIGESRGKIWSLQVINSAARSELNINIPREKNSIILPRLSTQGMLQSDV 60
           M S FSLA KPS+  S GK+ S +    AAR+E+ +   +  ++  +P LS QG+  +D+
Sbjct: 1   MSSAFSLAVKPSVAWSNGKLLSRKSTRRAARAEVIVAPKKRTSTHNVPELSKQGIPHTDL 60

Query: 61  HICEIAERQSLANNLSDKGDAFR--SKPQLDAMFLDEAYERCRKICAEYAKTYYLGTLLL 118
           H+ EI +RQS     +DK   F    KPQ   MFL+EAYERCR ICAEYAKT+YLGTLL+
Sbjct: 61  HVREIVKRQS-----TDKSSMFDVCQKPQFHPMFLEEAYERCRNICAEYAKTFYLGTLLM 115

Query: 119 TKERQKAIWAVYAWCKRTDELVDGPNAFCVSPAALDRWEERLQDIFNGHPNDILDAALTD 178
           T+ERQKAIWA+Y WC+RTDELVDGPNA  +S A LDRWEERL DIFNG P D+LDAALTD
Sbjct: 116 TEERQKAIWAIYVWCRRTDELVDGPNAAYMSSAVLDRWEERLHDIFNGRPYDMLDAALTD 175

Query: 179 TVSKFNLHIKPFRDMIKGMRMDTEKCRYANFQELYLYCYYAGGTVGLMSVPVMGMDPDSS 238
           T+ KF L IKPFRDMI+GMRMDT+  RY NFQELYLYCYY  GTVGLMSVPVMG+ P+S 
Sbjct: 176 TIYKFPLDIKPFRDMIEGMRMDTKNFRYENFQELYLYCYYVAGTVGLMSVPVMGIAPESP 235

Query: 239 ASAQSIYNAALYLGIGNQLTNILRDVGEDASRGRIYLPQDELAKFGLRDEDIFSRKVSDE 298
            SAQSIYN+ALYLGIGNQLTNILRDVGED+ RGR+YLPQDELA+FGL D DIFSRKV+D 
Sbjct: 236 VSAQSIYNSALYLGIGNQLTNILRDVGEDSLRGRVYLPQDELAQFGLCDRDIFSRKVNDG 295

Query: 299 WREFMKEQITRARYFYKLAEEGASELDKASRWPVWTVLILYQKILDAIQDNDYDNLTKRA 358
           WREFMK+QITRAR+++  AEEGAS+LDKASRWPVW+ L+LY+KILDAI++NDYDNLTKRA
Sbjct: 296 WREFMKQQITRARFYFNQAEEGASQLDKASRWPVWSSLLLYRKILDAIEENDYDNLTKRA 355

Query: 359 YVGNIKKLFLVRQAYYRA 376
           YVG  KKL  +  AY RA
Sbjct: 356 YVGRTKKLLTLPLAYSRA 373

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>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|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|334725693|gb|AEH03199.1| phytoene synthase [Cucumis melo] Back     alignment and taxonomy information
>gi|297746444|emb|CBI16500.3| unnamed protein product [Vitis vinifera] 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|356569141|ref|XP_003552764.1| PREDICTED: phytoene synthase, chloroplastic-like [Glycine max] 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|255572258|ref|XP_002527068.1| Phytoene synthase, chloroplast precursor, putative [Ricinus communis] gi|223533573|gb|EEF35312.1| Phytoene synthase, chloroplast precursor, putative [Ricinus communis] 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 ?
Query384
UNIPROTKB|Q6ED64421 Q6ED64 "Phytoene synthase 1" [ 0.739 0.674 0.630 3.5e-98
TAIR|locus:2167225437 PSY "PHYTOENE SYNTHASE" [Arabi 0.739 0.649 0.612 1.5e-97
UNIPROTKB|Q9UUQ6614 CARRP "Bifunctional lycopene c 0.593 0.371 0.243 3.4e-07
UNIPROTKB|P37295602 al-2 "Bifunctional lycopene cy 0.486 0.310 0.265 1.7e-06
UNIPROTKB|Q7Z859673 crtYB "Bifunctional lycopene c 0.476 0.271 0.239 1.8e-06
MGI|MGI:1924197333 Ndufaf6 "NADH dehydrogenase (u 0.585 0.675 0.210 1.9e-05
UNIPROTKB|Q60AN4362 sqs "Squalene synthase" [Methy 0.268 0.284 0.315 2.9e-05
UNIPROTKB|A7YVD7333 NDUFAF6 "NADH dehydrogenase (u 0.583 0.672 0.213 4.2e-05
UNIPROTKB|Q9P854602 carRA "Bifunctional lycopene c 0.643 0.410 0.232 5.2e-05
RGD|1309085333 Ndufaf6 "NADH dehydrogenase (u 0.585 0.675 0.206 7e-05
UNIPROTKB|Q6ED64 Q6ED64 "Phytoene synthase 1" [Oryza sativa Indica Group (taxid:39946)] Back     alignment and assigned GO terms
 Score = 975 (348.3 bits), Expect = 3.5e-98, P = 3.5e-98
 Identities = 179/284 (63%), Positives = 221/284 (77%)

Query:    93 LDEAYERCRKICAEYAKXXXXXXXXXXKERQKAIWAVYAWCKRTDELVDGPNAFCVSPAA 152
             L +AY RC +IC EYAK          ++R++AIWA+Y WC+RTDELVDGPNA  ++P+A
Sbjct:   126 LKQAYHRCGEICEEYAKTFYLGTMLMTEDRRRAIWAIYVWCRRTDELVDGPNASHITPSA 185

Query:   153 LDRWEERLQDIFNGHPNDILDAALTDTVSKFNLHIKPFRDMIKGMRMDTEKCRYANFQEL 212
             LDRWE+RL D+F G P D+LDAAL+DT+SK  + I+PFRDMI+GMR D  K RY NF EL
Sbjct:   186 LDRWEKRLDDLFTGRPYDMLDAALSDTISKSPIDIQPFRDMIEGMRSDLRKTRYKNFDEL 245

Query:   213 YLYCYYAGGTVGLMSVPVMGMDPDSSASAQSIYNAALYLGIGNQLTNILRDVGEDASRGR 272
             Y+YCYY  GTVGLMSVPVMG+ P+S A+ +S+Y+AAL LGI NQLTNILRDVGEDA RGR
Sbjct:   246 YMYCYYVAGTVGLMSVPVMGIAPESKATTESVYSAALALGIANQLTNILRDVGEDARRGR 305

Query:   273 IYLPQDELAKFGLRDEDIFSRKVSDEWREFMKEQITRARYFYKLAEEGASELDKASRWPV 332
             IYLPQDELA+ GL DEDIF+  V+++WR FMK QI RAR F++ AE G +EL +ASRWPV
Sbjct:   306 IYLPQDELAEAGLSDEDIFNGVVTNKWRSFMKRQIKRARMFFEEAERGVTELSQASRWPV 365

Query:   333 WTVLILYQKILDAIQDNDYDNLTKRAYVGNIKKLFLVRQAYYRA 376
             W  L+LY++ILD I+ NDY+N TKR YVG  KKL  +  AY R+
Sbjct:   366 WASLLLYRQILDEIEANDYNNFTKRTYVGKAKKLLALPVAYGRS 409
GO:0009536 "plastid" evidence=IC
TAIR|locus:2167225 PSY "PHYTOENE SYNTHASE" [Arabidopsis thaliana (taxid:3702)] 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|P37295 al-2 "Bifunctional lycopene cyclase/phytoene synthase" [Neurospora crassa OR74A (taxid:367110)] Back     alignment and assigned GO terms
UNIPROTKB|Q7Z859 crtYB "Bifunctional lycopene cyclase/phytoene synthase" [Xanthophyllomyces dendrorhous (taxid:5421)] Back     alignment and assigned GO terms
MGI|MGI:1924197 Ndufaf6 "NADH dehydrogenase (ubiquinone) complex I, assembly factor 6" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
UNIPROTKB|Q60AN4 sqs "Squalene synthase" [Methylococcus capsulatus str. Bath (taxid:243233)] Back     alignment and assigned GO terms
UNIPROTKB|A7YVD7 NDUFAF6 "NADH dehydrogenase (ubiquinone) complex I, assembly factor 6" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|Q9P854 carRA "Bifunctional lycopene cyclase/phytoene synthase" [Phycomyces blakesleeanus NRRL 1555(-) (taxid:763407)] Back     alignment and assigned GO terms
RGD|1309085 Ndufaf6 "NADH dehydrogenase (ubiquinone) complex I, assembly factor 6" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

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

Original result of BLAST against SWISS-PROT

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
P37269CRTB_SYNE72, ., 5, ., 1, ., 3, 20.52170.76300.9512yesno
P08196PSY1_SOLLC2, ., 5, ., 1, ., 3, 20.58550.88540.8252N/Ano
P37271PSY_ARATH2, ., 5, ., 1, ., 3, 20.67010.74210.6753yesno

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 Layer2.5.1.320.946
3rd Layer2.5.10.963

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 ?
Query384
PLN02632334 PLN02632, PLN02632, phytoene synthase 0.0
cd00683265 cd00683, Trans_IPPS_HH, Trans-Isoprenyl Diphosphat 8e-94
pfam00494262 pfam00494, SQS_PSY, Squalene/phytoene synthase 3e-77
COG1562288 COG1562, ERG9, Phytoene/squalene synthetase [Lipid 5e-77
TIGR03465266 TIGR03465, HpnD, squalene synthase HpnD 1e-65
TIGR03464266 TIGR03464, HpnC, squalene synthase HpnC 5e-41
cd00385243 cd00385, Isoprenoid_Biosyn_C1, Isoprenoid Biosynth 1e-29
cd00867236 cd00867, Trans_IPPS, Trans-Isoprenyl Diphosphate S 2e-26
TIGR01559337 TIGR01559, squal_synth, farnesyl-diphosphate farne 0.002
>gnl|CDD|215339 PLN02632, PLN02632, phytoene synthase Back     alignment and domain information 
 Score =  538 bits (1388), Expect = 0.0
 Identities = 209/319 (65%), Positives = 249/319 (78%)

Query: 64  EIAERQSLANNLSDKGDAFRSKPQLDAMFLDEAYERCRKICAEYAKTYYLGTLLLTKERQ 123
           E+  +Q+     + +         L    L+EAY+RC ++CAEYAKT+YLGTLL+T ER+
Sbjct: 16  EVVLKQAALVRKAARRSVRPRATSLSPALLEEAYDRCGEVCAEYAKTFYLGTLLMTPERR 75

Query: 124 KAIWAVYAWCKRTDELVDGPNAFCVSPAALDRWEERLQDIFNGHPNDILDAALTDTVSKF 183
           KAIWA+Y WC+RTDELVDGPNA  ++PAALDRWE RL+D+F+G P D+LDAAL DTVSKF
Sbjct: 76  KAIWAIYVWCRRTDELVDGPNASHITPAALDRWEARLEDLFDGRPYDMLDAALADTVSKF 135

Query: 184 NLHIKPFRDMIKGMRMDTEKCRYANFQELYLYCYYAGGTVGLMSVPVMGMDPDSSASAQS 243
            L I+PFRDMI+GMRMD  K RY NF ELYLYCYY  GTVGLMSVPVMG+ P+S AS +S
Sbjct: 136 PLDIQPFRDMIEGMRMDLVKSRYENFDELYLYCYYVAGTVGLMSVPVMGIAPESKASTES 195

Query: 244 IYNAALYLGIGNQLTNILRDVGEDASRGRIYLPQDELAKFGLRDEDIFSRKVSDEWREFM 303
           +YNAAL LGI NQLTNILRDVGEDA RGR+YLPQDELA+FGL DEDIF+ KV+D+WR FM
Sbjct: 196 VYNAALALGIANQLTNILRDVGEDARRGRVYLPQDELAQFGLTDEDIFAGKVTDKWRAFM 255

Query: 304 KEQITRARYFYKLAEEGASELDKASRWPVWTVLILYQKILDAIQDNDYDNLTKRAYVGNI 363
           K QI RAR ++  AEEG SELD ASRWPVW  L+LY++ILDAI+ NDYDN TKRAYVG  
Sbjct: 256 KFQIKRARMYFAEAEEGVSELDPASRWPVWASLLLYRQILDAIEANDYDNFTKRAYVGKW 315

Query: 364 KKLFLVRQAYYRAQSISTA 382
           KKL  +  AY RA    ++
Sbjct: 316 KKLLALPLAYARALFPPSS 334

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 384
PLN02632334 phytoene synthase 100.0
TIGR03464266 HpnC squalene synthase HpnC. This family of genes 100.0
TIGR03465266 HpnD squalene synthase HpnD. The genes of this fam 100.0
cd00683265 Trans_IPPS_HH Trans-Isoprenyl Diphosphate Synthase 100.0
COG1562288 ERG9 Phytoene/squalene synthetase [Lipid metabolis 100.0
PF00494267 SQS_PSY: Squalene/phytoene synthase; InterPro: IPR 100.0
TIGR01559336 squal_synth farnesyl-diphosphate farnesyltransfera 100.0
KOG4411292 consensus Phytoene/squalene synthetase [Lipid tran 100.0
KOG1459413 consensus Squalene synthetase [Lipid transport and 99.94
cd00867236 Trans_IPPS Trans-Isoprenyl Diphosphate Synthases. 99.87
cd00385243 Isoprenoid_Biosyn_C1 Isoprenoid Biosynthesis enzym 99.82
KOG1459413 consensus Squalene synthetase [Lipid transport and 99.74
cd00685259 Trans_IPPS_HT Trans-Isoprenyl Diphosphate Synthase 96.5
PLN02890422 geranyl diphosphate synthase 95.94
TIGR02749322 prenyl_cyano solanesyl diphosphate synthase. Membe 95.79
PRK10888323 octaprenyl diphosphate synthase; Provisional 95.51
TIGR02748319 GerC3_HepT heptaprenyl diphosphate synthase compon 95.42
PRK10581299 geranyltranstransferase; Provisional 94.71
PLN02857416 octaprenyl-diphosphate synthase 94.16
cd00868284 Terpene_cyclase_C1 Terpene cyclases, Class 1. Terp 93.42
PF03936270 Terpene_synth_C: Terpene synthase family, metal bi 92.91
cd00687303 Terpene_cyclase_nonplant_C1 Non-plant Terpene Cycl 92.79
CHL00151323 preA prenyl transferase; Reviewed 92.26
COG0142322 IspA Geranylgeranyl pyrophosphate synthase [Coenzy 92.26
PF00348260 polyprenyl_synt: Polyprenyl synthetase; InterPro: 91.88
cd00684542 Terpene_cyclase_plant_C1 Plant Terpene Cyclases, C 91.6
PF06330376 TRI5: Trichodiene synthase (TRI5); InterPro: IPR02 85.73
>PLN02632 phytoene synthase Back     alignment and domain information 
Probab=100.00  E-value=2.4e-70  Score=540.56  Aligned_cols=328  Identities=64%  Similarity=1.083  Sum_probs=302.8

Q ss_pred             cccchhhHHHHHHhhhhhhhcccCCCCCCCCCCccchhhHHHHHHHHHHHHHhcCcchhHHHhcCChhhhHHHHHHHHHH
Q 016696           54 GMLQSDVHICEIAERQSLANNLSDKGDAFRSKPQLDAMFLDEAYERCRKICAEYAKTYYLGTLLLTKERQKAIWAVYAWC  133 (384)
Q Consensus        54 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~C~~i~r~~s~sfyla~~~lP~~~R~al~ALYAf~  133 (384)
                      -..+++++|++++.+++.............+++..+...++++|++|.++++++|+|||++++|||++.|+++++||+||
T Consensus         6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~c~~i~r~~s~sFyla~~lLP~~~R~ai~alYAf~   85 (334)
T PLN02632          6 AAASSEEKVYEVVLKQAALVRKAARRSVRPRATSLSPALLEEAYDRCGEVCAEYAKTFYLGTLLMTPERRKAIWAIYVWC   85 (334)
T ss_pred             CCCccHhHHHHHHHHHHHHHHHhcccccCCCCCCCCcccchHHHHHHHHHHhhcCchHHHHHHhCCHHHHHHHHHHHHHH
Confidence            45678999999999999998885543222334456667899999999999999999999999999999999999999999


Q ss_pred             HHHhhhcCCCCCCCChHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCChHHHHHHHHHHHhhccCCCCCCHHHHH
Q 016696          134 KRTDELVDGPNAFCVSPAALDRWEERLQDIFNGHPNDILDAALTDTVSKFNLHIKPFRDMIKGMRMDTEKCRYANFQELY  213 (384)
Q Consensus       134 R~~DdivD~~~~~~~~~~rL~~Wr~~L~~~~~g~p~~Pv~~aL~~~v~~~~L~~~~~~~lI~g~~~DL~~~~~~t~~dL~  213 (384)
                      |++|||+|+++.+.+++++|+||++.|++++.|.|.||+..+|.+++.+|+|+.++|.+||+||++|+...+|+|++||+
T Consensus        86 R~~DdI~D~~~~~~~~~~~L~~w~~~l~~~~~g~~~~pv~~aL~~~~~~~~L~~~~~~~li~g~~~Dl~~~~~~t~~eL~  165 (334)
T PLN02632         86 RRTDELVDGPNASHITPAALDRWEARLEDLFDGRPYDMLDAALADTVSKFPLDIQPFRDMIEGMRMDLVKSRYENFDELY  165 (334)
T ss_pred             HHHhHHhcCCCCChhhHHHHHHHHHHHHHHhCCCCCChHHHHHHHHHHHCCCChHHHHHHHHHHHHHhccCCCCCHHHHH
Confidence            99999999988877778999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhchHHHHHHHhhhCCCCCCchhHHhHHHHHHHHHHHHHHHHHHHhHHHHHhcCCCCCCHHHHHhcCCChhhhhcc
Q 016696          214 LYCYYAGGTVGLMSVPVMGMDPDSSASAQSIYNAALYLGIGNQLTNILRDVGEDASRGRIYLPQDELAKFGLRDEDIFSR  293 (384)
Q Consensus       214 ~Yc~~vAGtVG~l~l~ilg~~~~~~~~~~~~~~~A~~LG~AlQLtNILRDv~eD~~~GR~YLP~d~L~~~Gvs~edl~~~  293 (384)
                      .|||+|||+||+|+++++|..+......+.+.+.|.++|+|+|||||||||+||+++||||||.|+|++||++++|++.+
T Consensus       166 ~Ycy~vAgtVG~l~l~vlg~~~~~~~~~~~~~~~A~~lG~AlQltNILRDv~eD~~~GRvYLP~e~L~~~Gv~~edl~~~  245 (334)
T PLN02632        166 LYCYYVAGTVGLMSVPVMGIAPESKASTESVYNAALALGIANQLTNILRDVGEDARRGRVYLPQDELAQFGLTDEDIFAG  245 (334)
T ss_pred             HHHHHhhHHHHHHHHHHhCCCCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCceeCCHHHHHHcCCCHHHHhcC
Confidence            99999999999999999997652222234567899999999999999999999999999999999999999999999999


Q ss_pred             cCCHHHHHHHHHHHHHHHHHHHHHHHhhhhccccCcHHHHHHHHHHHHHHHHHHhCCCCCCCCCcccChHHHHHHHHHHH
Q 016696          294 KVSDEWREFMKEQITRARYFYKLAEEGASELDKASRWPVWTVLILYQKILDAIQDNDYDNLTKRAYVGNIKKLFLVRQAY  373 (384)
Q Consensus       294 ~~~~~~~~li~~~~~~A~~~l~~A~~~~~~Lp~~~r~~v~~~~~ly~~iL~~Ie~~~y~vf~~r~~v~~~~kl~~l~~a~  373 (384)
                      ..+++++.++.+++++|+.||++|+.++..||+++++++++++.+|+.||++|+++||++|++|+++++++|+|+++++|
T Consensus       246 ~~~~~~~~l~~~~~~~Ar~~~~~a~~~l~~lp~~~r~~v~~a~~~y~~iL~~i~~~~~~v~~~R~~l~~~~Kl~~~~~~~  325 (334)
T PLN02632        246 KVTDKWRAFMKFQIKRARMYFAEAEEGVSELDPASRWPVWASLLLYRQILDAIEANDYDNFTKRAYVGKWKKLLALPLAY  325 (334)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHhHhhCCHHhHHHHHHHHHHHHHHHHHHHHcCCCcCCCCCccCHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhcccCC
Q 016696          374 YRAQSIST  381 (384)
Q Consensus       374 ~~~~~~~~  381 (384)
                      ++..-+++
T Consensus       326 ~~~~~~~~  333 (334)
T PLN02632        326 ARALFPPS  333 (334)
T ss_pred             HhhcccCC
Confidence            88765543

>TIGR03464 HpnC squalene synthase HpnC 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
>COG1562 ERG9 Phytoene/squalene synthetase [Lipid metabolism] Back     alignment and domain information
>PF00494 SQS_PSY: Squalene/phytoene synthase; InterPro: IPR002060 Squalene synthase 2 Back     alignment and domain information
>TIGR01559 squal_synth farnesyl-diphosphate farnesyltransferase Back     alignment and domain information
>KOG4411 consensus Phytoene/squalene synthetase [Lipid transport and metabolism] Back     alignment and domain information
>KOG1459 consensus 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
>cd00685 Trans_IPPS_HT Trans-Isoprenyl Diphosphate Synthases, head-to-tail 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
>PRK10888 octaprenyl diphosphate synthase; Provisional Back     alignment and domain information
>TIGR02748 GerC3_HepT heptaprenyl diphosphate synthase component II Back     alignment and domain information
>PRK10581 geranyltranstransferase; Provisional Back     alignment and domain information
>PLN02857 octaprenyl-diphosphate synthase Back     alignment and domain information
>cd00868 Terpene_cyclase_C1 Terpene cyclases, Class 1 Back     alignment and domain information
>PF03936 Terpene_synth_C: Terpene synthase family, metal binding domain; InterPro: IPR005630 Sequences containing this domain belong to the terpene synthase family Back     alignment and domain information
>cd00687 Terpene_cyclase_nonplant_C1 Non-plant Terpene Cyclases, Class 1 Back     alignment and domain information
>CHL00151 preA prenyl transferase; Reviewed 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
>cd00684 Terpene_cyclase_plant_C1 Plant Terpene Cyclases, Class 1 Back     alignment and domain information
>PF06330 TRI5: Trichodiene synthase (TRI5); InterPro: IPR024652 This family consists of several fungal trichodiene synthase proteins (EC:4 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 ?
Query384
4hd1_A294 Crystal Structure Of Squalene Synthase Hpnc From Al 5e-20
2zco_A293 Crystal Structure Of The C(30) Carotenoid Dehydrosq 6e-18
4e9u_A287 Crystal Structure Of Dehydrosqualene Synthase (Crtm 6e-18
3ae0_A293 Crystal Structure Of The C(30) Carotenoid Dehydrosq 6e-18
4f6v_A292 Crystal Structure Of Dehydrosqualene Synthase (Crtm 2e-17
3vjd_A293 Crystal Structure Of The Y248a Mutant Of C(30) Caro 2e-17
3adz_A293 Crystal Structure Of The C(30) Carotenoid Dehydrosq 8e-17
>pdb|4HD1|A Chain A, Crystal Structure Of Squalene Synthase Hpnc From Alicyclobacillus Acidocaldarius Length = 294 Back     alignment and structure 
Iteration: 1

 Score = 95.1 bits (235), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 76/274 (27%), Positives = 126/274 (45%), Gaps = 16/274 (5%)
Query: 97  YERCRKICAEYAKXXXXXXXXXXKERQKAIWAVYAWCKRTDELVDGPNAFCVSPAALDRW 156
           +E CR++   + +          +  +   ++VYA+C+  D+L  G        AALD +
Sbjct: 15  FEVCRRLTRSHYENFSVVSLFVPRHLRPHFYSVYAFCRGVDDL--GDEFAGDRXAALDAY 72
Query: 157 EERLQDIFNGHPNDILDAALTDTVSKFNLHIKPFRDMIKGMRMDTEKCRYANFQELYLYC 216
           EE L+  F G        AL  T++  NL  +PF  +I+  R D  K  Y  +++L  YC
Sbjct: 73  EEELRRAFAGEATTPAFRALQFTIATCNLPXEPFLRLIEANRRDQRKHTYDTWEDLRDYC 132
Query: 217 YYAGGTVGLMSVPVMGMDPDSSASAQSIYNAALYLGIGNQLTNILRDVGEDASRGRIYLP 276
            Y+   VG + + + G   D  A        AL      Q+ N  +D+  D + GRIY+P
Sbjct: 133 RYSADPVGRLVLGIFGCLDDERARLSDATCTAL------QVANHXQDIDRDLALGRIYVP 186
Query: 277 QDELAKFGLRDEDIFSRKVSDEWREFMKEQITRARYFYKLAEEGASELDKASRWPVWTVL 336
           + +L +FG   +DI +R+ +D  R  +  ++ RA+  +   +EG   L+      +   L
Sbjct: 187 RADLEQFGATLDDIRARRATDGVRRCIALEVDRAQALF---DEG-RRLESLVPPRLARQL 242
Query: 337 ILY----QKILDAIQDNDYDNLTKRAYVGNIKKL 366
            LY    + IL AI+   Y+    R  V   +KL
Sbjct: 243 KLYRLGGEAILAAIRRQGYNPFAGRPVVSGKQKL 276
>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|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
>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|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 ?
Query384
3acx_A293 Dehydrosqualene synthase; CRTM, carotenoid biosynt 1e-125
3vj8_A343 Squalene synthase; farnesyl-diphosphate farnesyltr 8e-82
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 4e-06
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 5e-05
>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 =  360 bits (926), Expect = e-125
 Identities = 66/290 (22%), Positives = 128/290 (44%), Gaps = 9/290 (3%)

Query: 93  LDEAYERCRKICAEYAKTYYLGTLLLTKERQKAIWAVYAWCKRTDELVDGPN---AFCVS 149
           +D  ++ C KI  +++K++     LL ++++KA+WA+YA C++ D+ +D           
Sbjct: 10  MDMNFKYCHKIMKKHSKSFSYAFDLLPEDQRKAVWAIYAVCRKIDDSIDVYGDIQFLNQI 69

Query: 150 PAALDRWEERLQDIFNGHPNDILDAALTDTVSKFNLHIKPFRDMIKGMRMDTEKCRYANF 209
              +   E+   +  +   +  +  AL       N+  + F ++I  +  D     +   
Sbjct: 70  KEDIQSIEKYPYEYHHFQSDRRIMMALQHVAQHKNIAFQSFYNLIDTVYKDQHFTMFETD 129

Query: 210 QELYLYCYYAGGTVGLMSVPVMGMDPDSSASAQSIYNAALYLGIGNQLTNILRDVGEDAS 269
            EL+ YCY   GTVG +  P++             Y+ A  LG   QL NILRDVGED  
Sbjct: 130 AELFGYCYGVAGTVGEVLTPILSDHETHQT-----YDVARRLGESLQLINILRDVGEDFE 184

Query: 270 RGRIYLPQDELAKFGLRDEDIFSRKVSDEWREFMKEQITRARYFYKLAEEGASELDKASR 329
             RIY  +  L ++ +   +++   V++ + +  +     A   ++   +        ++
Sbjct: 185 NERIYFSKQRLKQYEVDIAEVYQNGVNNHYIDLWEYYAAIAEKDFRDVMDQIKVFSIEAQ 244

Query: 330 WPVWTVLILYQKILDAIQDNDYDNLTKRAYVGNIKKLFLVRQAYYRAQSI 379
             +     +Y +ILD ++  +Y  L +R +V   KK  L  +   +   I
Sbjct: 245 PIIELAARIYIEILDEVRQANY-TLHERVFVEKRKKAKLFHEINSKYHRI 293
>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
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query384
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
3rmg_A334 Octaprenyl-diphosphate synthase; structural genomi 96.59
3nf2_A352 Putative polyprenyl synthetase; isoprenyl diphosph 96.55
3kb9_A382 EPI-isozizaene synthase; terpenoid cyclase, alpha- 96.29
3apz_A348 Geranyl diphosphate synthase; prenyltransferase, a 96.17
4f62_A317 Geranyltranstransferase; enzyme function initiativ 96.08
2her_A368 Fragment, farnesyl pyrophosphate synthase; farnesy 96.07
2qis_A374 Farnesyl pyrophosphate synthetase; trans-prenyltra 96.0
3lk5_A380 Geranylgeranyl pyrophosphate synthase; structural 95.98
3lom_A313 Geranyltranstransferase; geranyltransferase, struc 95.98
1wmw_A330 Geranylgeranyl diphosphate synthetase; GGPP, preny 95.97
1wy0_A342 Geranylgeranyl pyrophosphate synthetase; pyrococcu 95.96
2q80_A301 Geranylgeranyl pyrophosphate synthetase; isoprenoi 95.94
3ts7_A324 Geranyltranstransferase; isoprenoid synthesis, far 95.9
2e8v_A340 Geranylgeranyl pyrophosphate synthetase; prenyltra 95.79
3p8l_A302 Geranyltranstransferase; isoprenyl synthase, struc 95.74
3p8r_A302 Geranyltranstransferase; isoprenyl synthase, struc 95.74
3uca_A324 Geranyltranstransferase; isoprenoid synthesis, iso 95.64
1uby_A367 FPS, farnesyl diphosphate synthase; transferase, i 95.63
1v4e_A299 Octoprenyl-diphosphate synthase; trans-type prenyl 95.62
3lmd_A360 Geranylgeranyl pyrophosphate synthase; isoprenyl d 95.6
3mzv_A341 Decaprenyl diphosphate synthase; transferase, stru 95.48
3lsn_A304 Geranyltranstransferase; structural genomics, prot 95.46
1ps1_A337 Pentalenene synthase; antibiotic biosynthesis, ses 95.41
3pko_A334 Geranylgeranyl pyrophosphate synthase; isoprenyl d 95.37
3aqb_B325 Component B of hexaprenyl diphosphate synthase; pr 95.35
2ihi_A395 Pyrophosphate synthase; PV092040, structural genom 95.31
1rtr_A301 Geranyltranstransferase; 2.50A {Staphylococcus aur 95.31
3oyr_A345 Trans-isoprenyl diphosphate synthase; isoprenyl sy 95.28
1di1_A300 Aristolochene synthase; sesquiterpene cyclase, iso 95.13
4dhd_A358 Polyprenyl synthetase; isoprenoid synthesis, isopr 94.99
3tc1_A315 Octaprenyl pyrophosphate synthase; all alpha-helic 94.78
1yhl_A362 Farnesyl pyrophosphate synthase; farnesyl diphosph 94.69
3ipi_A295 Geranyltranstransferase; isoprene biosynthesis, he 94.63
2h8o_A335 Geranyltranstransferase; geranyltransferase,agroba 94.58
3dyh_A390 Farnesyl pyrophosphate synthase; protein-bisphosph 94.24
1rqj_A299 Geranyltranstransferase; bisphosphonate, isoprenyl 93.17
1n1b_A549 (+)-bornyl diphosphate synthase; terpene synthase 93.14
3m0g_A297 Farnesyl diphosphate synthase; structural genomics 93.08
2j1p_A293 Geranylgeranyl pyrophosphate synthetase; transfera 93.01
3pde_A309 Farnesyl-diphosphate synthase; isoprenyl diphospha 92.59
3npk_A291 Geranyltranstransferase; isoprene biosynthesis, SG 92.23
2ftz_A284 Geranyltranstransferase; TM0161, structural GE joi 91.48
2azj_A289 Geranylgeranyl pyrophosphate synthetase; hexpps, t 91.45
3bny_A320 Aristolochene synthase; sesquiterpene cyclase, iso 91.01
2ong_A543 4S-limonene synthase; monoterpene synthase, monote 90.93
3kra_B274 Geranyl diphosphate synthase small subunit; prenyl 90.02
3mav_A395 Farnesyl pyrophosphate synthase; PV092040, structu 89.34
3llw_A311 Geranyltranstransferase (ISPA); structural genomic 88.58
3n0f_A555 Isoprene synthase; terpene cyclase fold, hemiterpe 88.18
2j5c_A569 1,8-cineole synthase; terpene synthases, 1, monote 88.17
3m00_A550 Aristolochene synthase; plant terpenoid cyclase, l 87.64
3v1v_A433 2-MIB synthase, 2-methylisoborneol synthase; class 87.53
2q58_A368 Fragment, farnesyl pyrophosphate synthase; farnesy 86.38
3g4d_A554 (+)-delta-cadinene synthase isozyme XC1; cyclase, 85.78
>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=4.2e-68  Score=515.45  Aligned_cols=281  Identities=25%  Similarity=0.392  Sum_probs=247.3

Q ss_pred             hhhHHHHHHHHHHHHHhcCcchhHHHhcCChhhhHHHHHHHHHHHHHhhhcCCCCCCCChHHHHHHHHHHHHHHHcCCCC
Q 016696           90 AMFLDEAYERCRKICAEYAKTYYLGTLLLTKERQKAIWAVYAWCKRTDELVDGPNAFCVSPAALDRWEERLQDIFNGHPN  169 (384)
Q Consensus        90 ~~~l~~a~~~C~~i~r~~s~sfyla~~~lP~~~R~al~ALYAf~R~~DdivD~~~~~~~~~~rL~~Wr~~L~~~~~g~p~  169 (384)
                      +..|+++|++|+++++++++|||++++|||++.|+++++||+|||++|||+|++..+  ...+|+||++.|++++.|.|.
T Consensus         8 p~~l~~~y~~C~~i~~~~~~sF~~a~~~lp~~~R~~~~alYaf~R~~Ddi~D~~~~~--~~~~L~~~~~~l~~~~~g~~~   85 (294)
T 4hd1_A            8 PVELRGDFEVCRRLTRSHYENFSVVSLFVPRHLRPHFYSVYAFCRGVDDLGDEFAGD--RMAALDAYEEELRRAFAGEAT   85 (294)
T ss_dssp             CGGGHHHHHHHHHHHHHHCTTHHHHTTTCCTTTHHHHHHHHHHHHHHHHTSTTCCSC--HHHHHHHHHHHHHHHHHTCCC
T ss_pred             CHHHHHHHHHHHHHHHHhCCcHHHHHHHCCHHHHHHHHHHHHHHHHHHHhccCCChh--HHHHHHHHHHHHHHHhcCCCC
Confidence            467899999999999999999999999999999999999999999999999997653  567999999999999999999


Q ss_pred             CHHHHHHHHHHHhcCCChHHHHHHHHHHHhhccCCCCCCHHHHHHHHHHhchHHHHHHHhhhCCCCCCchhHHhHHHHHH
Q 016696          170 DILDAALTDTVSKFNLHIKPFRDMIKGMRMDTEKCRYANFQELYLYCYYAGGTVGLMSVPVMGMDPDSSASAQSIYNAAL  249 (384)
Q Consensus       170 ~Pv~~aL~~~v~~~~L~~~~~~~lI~g~~~DL~~~~~~t~~dL~~Yc~~vAGtVG~l~l~ilg~~~~~~~~~~~~~~~A~  249 (384)
                      ||+..+|.+++++|+||.++|.+||+||++|+.+.+|+|++||+.|||+|||+||+|+++|+|..++      +..+.|.
T Consensus        86 ~pv~~al~~~~~~~~l~~~~~~~li~g~~~Dl~~~~~~t~~dL~~Y~~~vAg~VG~m~~~i~g~~~~------~~~~~A~  159 (294)
T 4hd1_A           86 TPAFRALQFTIATCNLPMEPFLRLIEANRRDQRKHTYDTWEDLRDYCRYSADPVGRLVLGIFGCLDD------ERARLSD  159 (294)
T ss_dssp             SHHHHHHHHHHHHHTCCSHHHHHHHHHHHHHHHCSBCCSHHHHHHHHHHHTHHHHHHHHHHTTCCSH------HHHHHHH
T ss_pred             CHHHHHHHHHHHHcCCCHHHHHHHHHHHHhccccCCCCCHHHHHHHHHhccchHHHHHHHHhCCCCH------HHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999999997542      3567899


Q ss_pred             HHHHHHHHHHHHHhHHHHHhcCCCCCCHHHHHhcCCChhhhhcccCCHHHHHHHHHHHHHHHHHHHHHHHhhhhccccCc
Q 016696          250 YLGIGNQLTNILRDVGEDASRGRIYLPQDELAKFGLRDEDIFSRKVSDEWREFMKEQITRARYFYKLAEEGASELDKASR  329 (384)
Q Consensus       250 ~LG~AlQLtNILRDv~eD~~~GR~YLP~d~L~~~Gvs~edl~~~~~~~~~~~li~~~~~~A~~~l~~A~~~~~~Lp~~~r  329 (384)
                      ++|+|+|||||||||+||+++||||||.|+|++||++++|+.++..+++++.++.+++++|+.||++|..++..||++++
T Consensus       160 ~lG~AlQltNilRDv~eD~~~gR~YlP~~~l~~~gv~~~dl~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~lp~~~r  239 (294)
T 4hd1_A          160 ATCTALQVANHMQDIDRDLALGRIYVPRADLEQFGATLDDIRARRATDGVRRCIALEVDRAQALFDEGRRLESLVPPRLA  239 (294)
T ss_dssp             HHHHHHHHHHHHHTHHHHHHTTCBCSCHHHHHTTTCCHHHHHTTCCCHHHHHHHHHHHHHHHHHHHHHGGGGGSSCHHHH
T ss_pred             HHHHHHHHHHHHHhchhhhccCceeCCHHHHHHcCCCHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCCCCCcccChHHHHHHHHHHHHHhcc
Q 016696          330 WPVWTVLILYQKILDAIQDNDYDNLTKRAYVGNIKKLFLVRQAYYRAQS  378 (384)
Q Consensus       330 ~~v~~~~~ly~~iL~~Ie~~~y~vf~~r~~v~~~~kl~~l~~a~~~~~~  378 (384)
                      +++.++..+|+.||++|+++||++|++|+++++++|+|++|+++.....
T Consensus       240 ~~~~~~~~~y~~il~~i~~~~~~~~~~R~~vs~~~Kl~l~~~al~~~~~  288 (294)
T 4hd1_A          240 RQLKLYRLGGEAILAAIRRQGYNPFAGRPVVSGKQKLRIALSVLAGGAK  288 (294)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTTTCCC------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCCCCCCccCHHHHHHHHHHHHHHhhc
Confidence            9999999999999999999999999999999999999999999887543
>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
>3rmg_A Octaprenyl-diphosphate synthase; structural genomics, protein structure initiative, isoprene biosynthesis, transferase; 2.30A {Bacteroides thetaiotaomicron} 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
>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
>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
>4f62_A Geranyltranstransferase; enzyme function initiative, structural genomics; 2.10A {Marinomonas SP} 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
>3lk5_A Geranylgeranyl pyrophosphate synthase; structural genomics, protein structure initiative, geranylge pyrophosphate synthase; 1.90A {Corynebacterium glutamicum} PDB: 3qqv_A* Back     alignment and structure
>3lom_A Geranyltranstransferase; geranyltransferase, structural genomics, PSI, protein structure initiative, nysgrc; 2.30A {Legionella pneumophila subsp} Back     alignment and structure
>1wmw_A Geranylgeranyl diphosphate synthetase; GGPP, prenyl diphosphate synthase, structural genom riken structural genomics/proteomics initiative; 1.55A {Thermus thermophilus} 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
>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
>3ts7_A Geranyltranstransferase; isoprenoid synthesis, farnesyl diphosphate synthase; 1.94A {Methylococcus capsulatus} 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
>3p8l_A Geranyltranstransferase; isoprenyl synthase, structural genomics, PSI, protein struct initiative, nysgrc; 2.00A {Enterococcus faecalis} Back     alignment and structure
>3p8r_A Geranyltranstransferase; isoprenyl synthase, structural genomics, PSI, protein struct initiative, nysgrc; 2.50A {Vibrio cholerae} SCOP: a.128.1.1 Back     alignment and structure
>3uca_A Geranyltranstransferase; isoprenoid synthesis, isoprenoid diphosphate synthase; 2.00A {Clostridium perfringens} Back     alignment and structure
>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
>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
>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
>3mzv_A Decaprenyl diphosphate synthase; transferase, structural genomics, PSI-2, protein structure initiative; 1.90A {Rhodobacter capsulatus} 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
>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
>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
>3aqb_B Component B of hexaprenyl diphosphate synthase; prenyltransferase, transferase; 2.40A {Micrococcus luteus} PDB: 3aqc_B* Back     alignment and structure
>1rtr_A Geranyltranstransferase; 2.50A {Staphylococcus aureus} SCOP: a.128.1.1 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
>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
>4dhd_A Polyprenyl synthetase; isoprenoid synthesis, isoprenoid diphosphate synthase, trans; 1.65A {Pyrobaculum calidifontis} PDB: 4gp1_A* 4gp2_A* Back     alignment and structure
>3tc1_A Octaprenyl pyrophosphate synthase; all alpha-helices fold, transferase; 2.00A {Helicobacter pylori} 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
>3ipi_A Geranyltranstransferase; isoprene biosynthesis, helical bundle, protein structure initiative II (PSI II), structural genomics, nysgxrc; 1.90A {Methanosarcina mazei} 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
>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
>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
>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
>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
>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
>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
>3npk_A Geranyltranstransferase; isoprene biosynthesis, SGX, structural genomics protein structure initiative; 1.50A {Campylobacter jejuni} 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
>2azj_A Geranylgeranyl pyrophosphate synthetase; hexpps, trans-prenyltransferase; 2.40A {Sulfolobus solfataricus} PDB: 2azk_A Back     alignment and structure
>3bny_A Aristolochene synthase; sesquiterpene cyclase, isoprenoid, farnesyl diphosphate, magnesium, cyclization, lyase; HET: FPF; 1.89A {Aspergillus terreus} PDB: 2e4o_A 2oa6_A* 3bnx_A* 3cke_A* Back     alignment and structure
>2ong_A 4S-limonene synthase; monoterpene synthase, monoterpene cyclase, geranyl diphosphate, 2 fluorogeranyl diphosphate linalyl diphosphate; HET: FPG BTB; 2.70A {Mentha spicata} PDB: 2onh_A* Back     alignment and structure
>3kra_B Geranyl diphosphate synthase small subunit; prenyltransferase, isoprene biosynthesis, isoprenyl pyrophosphate synthase, transferase; 1.90A {Mentha x piperita} PDB: 3krc_B* 3krf_B* 3kro_B* 3krp_B* 3oab_B* 3oac_B* Back     alignment and structure
>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
>3llw_A Geranyltranstransferase (ISPA); structural genomics, PSI, protein structure initiative, nysgrc; 2.30A {Helicobacter pylori} PDB: 3q1o_A* Back     alignment and structure
>3n0f_A Isoprene synthase; terpene cyclase fold, hemiterpene synthase, DDXXD motif, NSE motif, lyase; 2.70A {Populus tremula x populus alba} PDB: 3n0g_A* Back     alignment and structure
>2j5c_A 1,8-cineole synthase; terpene synthases, 1, monoterpene, lyase; 1.95A {Salvia fruticosa} Back     alignment and structure
>3m00_A Aristolochene synthase; plant terpenoid cyclase, lyase binding domain, (2-CIS, 6-trans)-2-fluorofarnesyl diphospha magnesium, metal-binding; HET: 2CF; 2.10A {Nicotiana tabacum} PDB: 3lz9_A* 3m02_A* 3m01_A* 5eau_A* 1hxa_A* 1hx9_A* 1hxc_A* 5eas_A 1hxg_A 4di5_A* 5eat_A* Back     alignment and structure
>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid cyclase fold, DDXXXXD motif, NDXXSXXXE MOT methylisoborneol biosynthesis; HET: GST; 1.80A {Streptomyces coelicolor} PDB: 3v1x_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
>3g4d_A (+)-delta-cadinene synthase isozyme XC1; cyclase, lyase, magnesium, metal-binding; 2.40A {Gossypium arboreum} PDB: 3g4f_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 384
d1ezfa_333 a.128.1.2 (A:) Squalene synthase {Human (Homo sapi 8e-60
>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 =  194 bits (495), Expect = 8e-60
 Identities = 48/290 (16%), Positives = 89/290 (30%), Gaps = 13/290 (4%)

Query: 96  AYERCRKICAEYAKTYYLGTLLLTKERQKAIWAVYAWCKRTDELVDGPNAFC-VSPAALD 154
           + + C K   + ++++      L  E + A+   Y   +  D L D            L 
Sbjct: 2   SLKTCYKYLNQTSRSFAAVIQALDGEMRNAVCIFYLVLRALDTLEDDMTISVEKKVPLLH 61

Query: 155 RWEERLQDIFNGHPN------------DILDAALTDTVSKFNLHIKPFRDMIKGMRMDTE 202
            +   L                       +     +   K+   I      +     +  
Sbjct: 62  NFHSFLYQPDWRFMESKEKDRQVLEDFPTISLEFRNLAEKYQTVIADICRRMGIGMAEFL 121

Query: 203 KCRYANFQELYLYCYYAGGTVGLMSVPVMGMDPDSSASAQSIYNAALYLGIGNQLTNILR 262
                + QE   YC+Y  G VG+    +                 A  +G+  Q TNI+R
Sbjct: 122 DKHVTSEQEWDKYCHYVAGLVGIGLSRLFSASEFEDPLVGEDTERANSMGLFLQKTNIIR 181

Query: 263 DVGEDASRGRIYLPQDELAKFGLRDEDIFSRKVSDEWREFMKEQITRARYFYKLAEEGAS 322
           D  ED   GR + PQ+  +++  +  D    +  D   + + E IT A +         S
Sbjct: 182 DYLEDQQGGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELITNALHHIPDVITYLS 241

Query: 323 ELDKASRWPVWTVLILYQKILDAIQDNDYDNLTKRAYVGNIKKLFLVRQA 372
            L   S +    +  +      A   N+         +   + + L+  A
Sbjct: 242 RLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGAVKIRKGQAVTLMMDA 291

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query384
d1ezfa_333 Squalene synthase {Human (Homo sapiens) [TaxId: 96 100.0
d1ps1a_311 Pentalenene synthase {Streptomyces sp., UC5319 [Ta 96.77
d2q80a1291 Geranylgeranyl pyrophosphate synthetase {Human (Ho 94.79
d1fpsa_348 Farnesyl diphosphate synthase (geranyltranstransfe 94.73
d1di1a_300 Aristolochene synthase {Fungus (Penicillium roquef 93.99
d1rqja_299 Farnesyl diphosphate synthase (geranyltranstransfe 93.64
d1n1ba2328 (+)-bornyl diphosphate synthase {Garden sage (Salv 93.53
d5easa2328 5-Epi-aristolochene synthase {Tobacco (Nicotiana t 91.99
d1kiya_354 Trichodiene synthase {Fusarium sporotrichioides [T 91.85
d1v4ea_280 Octoprenyl-diphosphate synthase {Thermotoga mariti 90.93
d1rtra_290 Farnesyl diphosphate synthase (geranyltranstransfe 89.77
>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=6.5e-54  Score=420.15  Aligned_cols=276  Identities=17%  Similarity=0.110  Sum_probs=227.8

Q ss_pred             HHHHHHHHHHHhcCcchhHHHhcCChhhhHHHHHHHHHHHHHhhhcCCCCCCC-ChHHHHHHHHHHHHHHHcCC-----C
Q 016696           95 EAYERCRKICAEYAKTYYLGTLLLTKERQKAIWAVYAWCKRTDELVDGPNAFC-VSPAALDRWEERLQDIFNGH-----P  168 (384)
Q Consensus        95 ~a~~~C~~i~r~~s~sfyla~~~lP~~~R~al~ALYAf~R~~DdivD~~~~~~-~~~~rL~~Wr~~L~~~~~g~-----p  168 (384)
                      +++++|.++++++|+|||+++++||++.|++++++|+|||.+|||+|++..+. .....|++|++.+.+...+.     +
T Consensus         1 ~sl~~C~~~l~~~SrSF~~a~~~Lp~~~R~~v~~lYafcR~~DdI~D~~~~~~~~k~~~L~~~~~~l~~~~~~~~~~~~~   80 (333)
T d1ezfa_           1 NSLKTCYKYLNQTSRSFAAVIQALDGEMRNAVCIFYLVLRALDTLEDDMTISVEKKVPLLHNFHSFLYQPDWRFMESKEK   80 (333)
T ss_dssp             CHHHHHHHHHHHHCSSHHHHHHTSCTHHHHHHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHHTTCTTCCCCCCCST
T ss_pred             ChHHHHHHHHHhhCccHHHHHHHCCHHHHHHHHHHHHHHHHhhhhHhCCCCCHHHHHHHHHHHHHHHHHhhhcccccCcc
Confidence            37899999999999999999999999999999999999999999999976542 34567889998887654332     2


Q ss_pred             CCHHHHHHHHHH-------HhcCCChHHHHHHHHHHHhhccCCCCCCHHHHHHHHHHhchHHHHHHHhhhCCCCCCchhH
Q 016696          169 NDILDAALTDTV-------SKFNLHIKPFRDMIKGMRMDTEKCRYANFQELYLYCYYAGGTVGLMSVPVMGMDPDSSASA  241 (384)
Q Consensus       169 ~~Pv~~aL~~~v-------~~~~L~~~~~~~lI~g~~~DL~~~~~~t~~dL~~Yc~~vAGtVG~l~l~ilg~~~~~~~~~  241 (384)
                      .+++...+..++       ..+..+...+.+.+.++.+|+.+.+|+|++||+.|||+|||+||+|+++++|..+......
T Consensus        81 ~~~ll~~~~~v~~~~~~l~~~~~~~i~~~~~~m~~gm~d~~~~~~~t~~dL~~Ycy~VAG~VG~~l~~l~~~~~~~~~~~  160 (333)
T d1ezfa_          81 DRQVLEDFPTISLEFRNLAEKYQTVIADICRRMGIGMAEFLDKHVTSEQEWDKYCHYVAGLVGIGLSRLFSASEFEDPLV  160 (333)
T ss_dssp             THHHHHTHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTSCCCSHHHHHHHHHHHTHHHHHHHHHHHHHHTSSCHHH
T ss_pred             hHHHHhhccHHHHHHHHHHHHhccchHHHHHHHhccHHHHccCcCCCHHHHHHHHHHHHHHHHHHHHHHhCcCCCccccH
Confidence            345555444444       4444555556666666666666678999999999999999999999999999765444444


Q ss_pred             HhHHHHHHHHHHHHHHHHHHHhHHHHHhcCCCCCCHHHHHhcCCChhhhhcccCCHHHHHHHHHHHHHHHHHHHHHHHhh
Q 016696          242 QSIYNAALYLGIGNQLTNILRDVGEDASRGRIYLPQDELAKFGLRDEDIFSRKVSDEWREFMKEQITRARYFYKLAEEGA  321 (384)
Q Consensus       242 ~~~~~~A~~LG~AlQLtNILRDv~eD~~~GR~YLP~d~L~~~Gvs~edl~~~~~~~~~~~li~~~~~~A~~~l~~A~~~~  321 (384)
                      ++..+.|.+||+|+|+||||||++||+++||||||.|+|.+||++++++.+++.++++..++.+++++|+.||++|..++
T Consensus       161 ~~~~~~A~~lG~AlQltNIlRDi~eD~~~gR~YlP~e~l~~~g~~~~dl~~~~~~~~~~~~~~~l~~~A~~~~~~a~~y~  240 (333)
T d1ezfa_         161 GEDTERANSMGLFLQKTNIIRDYLEDQQGGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELITNALHHIPDVITYL  240 (333)
T ss_dssp             HHCHHHHHHHHHHHHHHHHHHTHHHHHHHTCCCSCHHHHTTTCSSGGGGGSGGGHHHHHHHHHHHHHHHHTTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhHHHHhCCcEECCHHHHHHcCCCHHHHHhccchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            56678899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhccccCcHHHHHHHHHHHHHHHHHHhCCCCCCCCCcccChHHHHHHHH
Q 016696          322 SELDKASRWPVWTVLILYQKILDAIQDNDYDNLTKRAYVGNIKKLFLVR  370 (384)
Q Consensus       322 ~~Lp~~~r~~v~~~~~ly~~iL~~Ie~~~y~vf~~r~~v~~~~kl~~l~  370 (384)
                      ..||..+++.+.+...+|..+.-++.++|+++|++++++++.++..++.
T Consensus       241 ~~lp~~~~~~~~~~~~~~a~~tl~~~~~~~~~~~~~vkisr~~~~~l~~  289 (333)
T d1ezfa_         241 SRLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGAVKIRKGQAVTLMM  289 (333)
T ss_dssp             HTCCCHHHHHHHHHHHHHHHHHHHHHTTCGGGGTSCCCC----------
T ss_pred             HHCCchhHHHHHHHHHHHHHHHHHHHHcCchhcCCCeEeeHHHHHHHHH
Confidence            9999998887777778888888888889999999999999999887653
>d1ps1a_ a.128.1.4 (A:) Pentalenene synthase {Streptomyces sp., UC5319 [TaxId: 1931]} Back     information, alignment and structure
>d2q80a1 a.128.1.1 (A:6-296) Geranylgeranyl pyrophosphate synthetase {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1fpsa_ a.128.1.1 (A:) Farnesyl diphosphate synthase (geranyltranstransferase) {Chicken (Gallus gallus) [TaxId: 9031]} Back     information, alignment and structure
>d1di1a_ a.128.1.4 (A:) Aristolochene synthase {Fungus (Penicillium roqueforti) [TaxId: 5082]} Back     information, alignment and structure
>d1rqja_ a.128.1.1 (A:) Farnesyl diphosphate synthase (geranyltranstransferase) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1n1ba2 a.128.1.3 (A:271-598) (+)-bornyl diphosphate synthase {Garden sage (Salvia officinalis) [TaxId: 38868]} Back     information, alignment and structure
>d5easa2 a.128.1.3 (A:221-548) 5-Epi-aristolochene synthase {Tobacco (Nicotiana tabacum) [TaxId: 4097]} Back     information, alignment and structure
>d1kiya_ a.128.1.5 (A:) Trichodiene synthase {Fusarium sporotrichioides [TaxId: 5514]} Back     information, alignment and structure
>d1v4ea_ a.128.1.1 (A:) Octoprenyl-diphosphate synthase {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1rtra_ a.128.1.1 (A:) Farnesyl diphosphate synthase (geranyltranstransferase) {Staphylococcus aureus [TaxId: 1280]} Back     information, alignment and structure