Citrus Sinensis ID: 019466

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
MGSLAAVLRHPDDLYPLLKLKMASRQAEKQIPPEPHWAFCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGTKEYKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFICKEVESIDDYDEYCYYVAGLVGLGLSKLFYASGTEDLAPDSLSNSMGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGMILILNMYFFKGETRVTSDMQHKK
cHHHHHHHHccHHHHHHHHcHHHcccccccccccHHHHHHHHHHHHHcccHHHHHHHccHHHHHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHccccHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHcccHHHHHHHHHccc
ccHHHHHHccHHHHHHHHHHHHHcccHHccccccHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHcccccccccccHHccHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHcHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccEEHHHHHHHHHHHHHHHccHHHHcccEEEccHHHHHHHHHHcHcHHEEHHHHHccc
mgslaavlrhpddlypLLKLKMASrqaekqippephwAFCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRAldtveddtsiptdvkvPILIAFHRHvydrewhfscgtkEYKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFICKEvesiddydeyCYYVAGLVGLGLSKLFyasgtedlapdslsnsmglflqKTNIIRDYLEDineipkcrmfwprEIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGMILILNMYFfkgetrvtsdmqhkk
mgslaavlrhpddlyPLLKLKMASRQAEKQIPPEPHWAFCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDtveddtsiptdvkVPILIAFHRHVYDREWHFSCGTKEYKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFICKEVESIDDYDEYCYYVAGLVGLGLSKLFYASGTEDLAPDSLSNSMGLFLQKTNIIRDYLEDINEIpkcrmfwprEIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGMILILNMyffkgetrvtsdmqhkk
MGSLAAVLRHPDDLYPLLKLKMASRQAEKQIPPEPHWAFCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGTKEYKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFICKEVESIDDYDEYCYYVAGLVGLGLSKLFYASGTEDLAPDSLSNSMGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGMILILNMYFFKGETRVTSDMQHKK
************DLYPLLKL**************PHWAFCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGTKEYKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFICKEVESIDDYDEYCYYVAGLVGLGLSKLFYASGTEDLAPDSLSNSMGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGMILILNMYFFKGE***********
*GSLAAVLRHPDDLYPLLKLK*****************FCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGTKEYKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFICKEVESIDDYDEYCYYVAGLVGLGLSKLFYASGTEDLAPDSLSNSMGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGMILILNMYFFKGETRVTSDM****
MGSLAAVLRHPDDLYPLLKLKMASRQAEKQIPPEPHWAFCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGTKEYKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFICKEVESIDDYDEYCYYVAGLVGLGLSKLFYASGTEDLAPDSLSNSMGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGMILILNMYFFKGET**********
*GSLAAVLRHPDDLYPLLKLKMASRQAEKQIPPEPHWAFCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGTKEYKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFICKEVESIDDYDEYCYYVAGLVGLGLSKLFYASGTEDLAPDSLSNSMGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGMILILNMYFFKGETRVTSDMQHKK
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MGSLAAVLRHPDDLYPLLKLKMASRQAEKQIPPEPHWAFCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGTKEYKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFICKEVESIDDYDEYCYYVAGLVGLGLSKLFYASGTEDLAPDSLSNSMGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGMILILNMYFFKGETRVTSDMQHKK
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 ?
Query340 2.2.26 [Sep-21-2011]
P53800411 Squalene synthase OS=Nico N/A no 0.932 0.771 0.870 1e-168
P53799410 Squalene synthase OS=Arab yes no 0.932 0.773 0.824 1e-163
G0Y287 465 Botryococcus squalene syn N/A no 0.994 0.726 0.507 8e-97
P53798416 Squalene synthase OS=Mus yes no 0.920 0.752 0.520 2e-92
Q9SDW9 461 Squalene synthase OS=Botr N/A no 0.905 0.668 0.545 6e-92
Q02769416 Squalene synthase OS=Ratt yes no 0.914 0.747 0.516 8e-92
Q32KR6417 Squalene synthase OS=Bos yes no 0.914 0.745 0.513 1e-88
Q5R6U3417 Squalene synthase OS=Pong yes no 0.914 0.745 0.501 2e-87
P37268417 Squalene synthase OS=Homo yes no 0.914 0.745 0.501 2e-87
Q54DR1416 Squalene synthase OS=Dict yes no 0.967 0.790 0.475 5e-82
>sp|P53800|FDFT_NICBE Squalene synthase OS=Nicotiana benthamiana PE=2 SV=1 Back     alignment and function desciption
 Score =  590 bits (1521), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 276/317 (87%), Positives = 299/317 (94%)

Query: 1   MGSLAAVLRHPDDLYPLLKLKMASRQAEKQIPPEPHWAFCYSMLHKVSRSFALVIQQLGT 60
           MGSL A+L++P+DLYPL+KLK+A+R AEKQIPP P+W FCYSMLHKVSRSFALVIQQL  
Sbjct: 1   MGSLRAILKNPEDLYPLVKLKLAARHAEKQIPPSPNWGFCYSMLHKVSRSFALVIQQLPV 60

Query: 61  DLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGTKEYKVLMD 120
           +LR+AVCIFYLVLRALDTVEDDTSIPTDVKVPILI+FH+HVYDREWHFSCGTKEYKVLMD
Sbjct: 61  ELRDAVCIFYLVLRALDTVEDDTSIPTDVKVPILISFHQHVYDREWHFSCGTKEYKVLMD 120

Query: 121 QFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFICKEVESIDDYDEYCYYVAGLVGLGL 180
           QFHHVSTAFLEL K YQ AIEDIT RMGAGMAKFICKEVE+ DDYDEYC+YVAGLVGLGL
Sbjct: 121 QFHHVSTAFLELRKHYQQAIEDITMRMGAGMAKFICKEVETTDDYDEYCHYVAGLVGLGL 180

Query: 181 SKLFYASGTEDLAPDSLSNSMGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKL 240
           SKLF+AS  EDLA DSLSNSMGLFLQKTNIIRDYLEDINE+PKCRMFWPREIWSKYVNKL
Sbjct: 181 SKLFHASEKEDLASDSLSNSMGLFLQKTNIIRDYLEDINEVPKCRMFWPREIWSKYVNKL 240

Query: 241 EDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALC 300
           E+LKYE+NS KAVQCLNDMVTNAL HVEDCL YMSALRD +IFRFCAIPQ+MAIGTLA+C
Sbjct: 241 EELKYEDNSAKAVQCLNDMVTNALPHVEDCLTYMSALRDPSIFRFCAIPQVMAIGTLAMC 300

Query: 301 YNNIEVFRGVVKMRRGM 317
           Y+NIEVFRGVVKMRRG+
Sbjct: 301 YDNIEVFRGVVKMRRGL 317

Nicotiana benthamiana (taxid: 4100)
EC: 2EC: .EC: 5EC: .EC: 1EC: .EC: 2EC: 1
>sp|P53799|FDFT_ARATH Squalene synthase OS=Arabidopsis thaliana GN=SQS1 PE=2 SV=1 Back     alignment and function description
>sp|G0Y287|BOSS_BOTBR Botryococcus squalene synthase OS=Botryococcus braunii GN=SSL-2 PE=1 SV=1 Back     alignment and function description
>sp|P53798|FDFT_MOUSE Squalene synthase OS=Mus musculus GN=Fdft1 PE=2 SV=2 Back     alignment and function description
>sp|Q9SDW9|BSS_BOTBR Squalene synthase OS=Botryococcus braunii GN=BSS PE=1 SV=1 Back     alignment and function description
>sp|Q02769|FDFT_RAT Squalene synthase OS=Rattus norvegicus GN=Fdft1 PE=2 SV=1 Back     alignment and function description
>sp|Q32KR6|FDFT_BOVIN Squalene synthase OS=Bos taurus GN=FDFT1 PE=2 SV=1 Back     alignment and function description
>sp|Q5R6U3|FDFT_PONAB Squalene synthase OS=Pongo abelii GN=FDFT1 PE=2 SV=1 Back     alignment and function description
>sp|P37268|FDFT_HUMAN Squalene synthase OS=Homo sapiens GN=FDFT1 PE=1 SV=1 Back     alignment and function description
>sp|Q54DR1|FDFT_DICDI Squalene synthase OS=Dictyostelium discoideum GN=fdfT 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 ?
Query340
356538706413 PREDICTED: squalene synthase-like [Glyci 0.932 0.767 0.911 1e-175
351726622413 squalene synthase [Glycine max] gi|24635 0.932 0.767 0.911 1e-175
255641455413 unknown [Glycine max] 0.932 0.767 0.911 1e-175
223972398411 squalene synthetase [Euphorbia tirucalli 0.932 0.771 0.905 1e-174
295822131412 squalene synthase 2 [Glycyrrhiza uralens 0.932 0.769 0.905 1e-174
224924202415 squalene synthase [Diospyros kaki] 0.932 0.763 0.902 1e-174
253993200412 squalene synthase 2 [Glycyrrhiza uralens 0.932 0.769 0.902 1e-173
241062156412 squalene synthase [Glycyrrhiza uralensis 0.932 0.769 0.902 1e-173
133917969412 squalene synthase 2 [Glycyrrhiza eurycar 0.932 0.769 0.902 1e-173
133917208412 squalene synthase 2 [Glycyrrhiza uralens 0.932 0.769 0.899 1e-173
>gi|356538706|ref|XP_003537842.1| PREDICTED: squalene synthase-like [Glycine max] Back     alignment and taxonomy information
 Score =  621 bits (1601), Expect = e-175,   Method: Compositional matrix adjust.
 Identities = 289/317 (91%), Positives = 305/317 (96%)

Query: 1   MGSLAAVLRHPDDLYPLLKLKMASRQAEKQIPPEPHWAFCYSMLHKVSRSFALVIQQLGT 60
           MGSL A+L++PDD YPLLKLKMA+R AEKQIPPEPHWAFCY+MLHKVSRSFALVIQQLGT
Sbjct: 1   MGSLGAILKNPDDFYPLLKLKMAARNAEKQIPPEPHWAFCYTMLHKVSRSFALVIQQLGT 60

Query: 61  DLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGTKEYKVLMD 120
           +LRNAVCIFYLVLRALDTVEDDTSI TDVKVPILIAFHRH+YDR+WHFSCGTKEYKVLMD
Sbjct: 61  ELRNAVCIFYLVLRALDTVEDDTSIETDVKVPILIAFHRHIYDRDWHFSCGTKEYKVLMD 120

Query: 121 QFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFICKEVESIDDYDEYCYYVAGLVGLGL 180
           QFHHVSTAFLELGK YQ+AIEDITKRMGAGMAKFICKEVE+IDDYDEYC+YVAGLVGLGL
Sbjct: 121 QFHHVSTAFLELGKNYQEAIEDITKRMGAGMAKFICKEVETIDDYDEYCHYVAGLVGLGL 180

Query: 181 SKLFYASGTEDLAPDSLSNSMGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKL 240
           SKLF+ASG+EDLAPD LSNSMGLFLQKTNIIRDYLEDINEIPK RMFWPR+IWSKYVNKL
Sbjct: 181 SKLFHASGSEDLAPDDLSNSMGLFLQKTNIIRDYLEDINEIPKSRMFWPRQIWSKYVNKL 240

Query: 241 EDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALC 300
           EDLKYEENS KAVQCLNDMVTNALMH EDCL YM+ALRD  IFRFCAIPQIMAIGTLALC
Sbjct: 241 EDLKYEENSVKAVQCLNDMVTNALMHAEDCLTYMAALRDPPIFRFCAIPQIMAIGTLALC 300

Query: 301 YNNIEVFRGVVKMRRGM 317
           YNNIEVFRGVVKMRRG+
Sbjct: 301 YNNIEVFRGVVKMRRGL 317

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|351726622|ref|NP_001236365.1| squalene synthase [Glycine max] gi|2463569|dbj|BAA22559.1| squalene synthase [Glycine max] Back     alignment and taxonomy information
>gi|255641455|gb|ACU21003.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|223972398|dbj|BAH23428.1| squalene synthetase [Euphorbia tirucalli] gi|223972400|dbj|BAH23429.1| squalene synthetase [Euphorbia tirucalli] Back     alignment and taxonomy information
>gi|295822131|gb|ADG36719.1| squalene synthase 2 [Glycyrrhiza uralensis] gi|295822135|gb|ADG36721.1| squalene synthase 2 [Glycyrrhiza uralensis] Back     alignment and taxonomy information
>gi|224924202|gb|ACN69082.1| squalene synthase [Diospyros kaki] Back     alignment and taxonomy information
>gi|253993200|gb|ACT52825.1| squalene synthase 2 [Glycyrrhiza uralensis] gi|295822121|gb|ADG36714.1| squalene synthase 2 [Glycyrrhiza uralensis] Back     alignment and taxonomy information
>gi|241062156|gb|ACS66749.1| squalene synthase [Glycyrrhiza uralensis] gi|295822123|gb|ADG36715.1| squalene synthase 2 [Glycyrrhiza uralensis] gi|295822125|gb|ADG36716.1| squalene synthase 2 [Glycyrrhiza uralensis] gi|295822133|gb|ADG36720.1| squalene synthase 2 [Glycyrrhiza uralensis] gi|295822137|gb|ADG36722.1| squalene synthase 2 [Glycyrrhiza uralensis] gi|295822139|gb|ADG36723.1| squalene synthase 2 [Glycyrrhiza uralensis] gi|295822141|gb|ADG36724.1| squalene synthase 2 [Glycyrrhiza uralensis] Back     alignment and taxonomy information
>gi|133917969|emb|CAJ77655.1| squalene synthase 2 [Glycyrrhiza eurycarpa] Back     alignment and taxonomy information
>gi|133917208|emb|CAJ77653.1| squalene synthase 2 [Glycyrrhiza uralensis] 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 ?
Query340
TAIR|locus:2139514410 SQS1 "squalene synthase 1" [Ar 0.932 0.773 0.824 1.2e-147
TAIR|locus:2139534413 SQS2 "squalene synthase 2" [Ar 0.935 0.769 0.787 1e-139
UNIPROTKB|F1NFJ9418 FDFT1 "Uncharacterized protein 0.920 0.748 0.541 1.8e-87
MGI|MGI:102706416 Fdft1 "farnesyl diphosphate fa 0.920 0.752 0.523 6.2e-85
RGD|61834416 Fdft1 "farnesyl diphosphate fa 0.914 0.747 0.516 1.7e-84
UNIPROTKB|Q6IE76417 fdft1 "FDFT1 protein" [Bos tau 0.914 0.745 0.513 2e-81
UNIPROTKB|I3LFX7417 FDFT1 "Uncharacterized protein 0.914 0.745 0.510 2e-81
UNIPROTKB|Q32KR6417 FDFT1 "Squalene synthase" [Bos 0.914 0.745 0.513 2.5e-81
UNIPROTKB|E9PNM1410 FDFT1 "Squalene synthase" [Hom 0.911 0.756 0.504 1.1e-80
UNIPROTKB|E2R6N6417 FDFT1 "Uncharacterized protein 0.914 0.745 0.498 3.7e-80
TAIR|locus:2139514 SQS1 "squalene synthase 1" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 1442 (512.7 bits), Expect = 1.2e-147, P = 1.2e-147
 Identities = 263/319 (82%), Positives = 297/319 (93%)

Query:     1 MGSLAAVLRHPDDLYPLLKLKMASRQAEKQIPPEPHWAFCYSMLHKVSRSFALVIQQLGT 60
             MGSL  +LR+PDD+YPLLK+K A  +AEKQIPPEPHW FCYSMLHKVSRSF+LVIQQL T
Sbjct:     1 MGSLGTMLRYPDDIYPLLKMKRAIEKAEKQIPPEPHWGFCYSMLHKVSRSFSLVIQQLNT 60

Query:    61 DLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGTKEYKVLMD 120
             +LRNAVC+FYLVLRALDTVEDDTSIPTD KVPILIAFHRH+YD +WH+SCGTKEYK+LMD
Sbjct:    61 ELRNAVCVFYLVLRALDTVEDDTSIPTDEKVPILIAFHRHIYDTDWHYSCGTKEYKILMD 120

Query:   121 QFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFICKEVESIDDYDEYCYYVAGLVGLGL 180
             QFHHVS AFLEL KGYQ+AIE+IT+RMGAGMAKFIC+EVE++DDYDEYC+YVAGLVGLGL
Sbjct:   121 QFHHVSAAFLELEKGYQEAIEEITRRMGAGMAKFICQEVETVDDYDEYCHYVAGLVGLGL 180

Query:   181 SKLFYASGTEDLAPD--SLSNSMGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVN 238
             SKLF A+G+E L PD  ++SNSMGLFLQKTNIIRDYLEDINEIPK RMFWPREIW KY +
Sbjct:   181 SKLFLAAGSEVLTPDWEAISNSMGLFLQKTNIIRDYLEDINEIPKSRMFWPREIWGKYAD 240

Query:   239 KLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLA 298
             KLEDLKYEEN++K+VQCLN+MVTNALMH+EDCLKYM +LRD +IFRFCAIPQIMAIGTLA
Sbjct:   241 KLEDLKYEENTNKSVQCLNEMVTNALMHIEDCLKYMVSLRDPSIFRFCAIPQIMAIGTLA 300

Query:   299 LCYNNIEVFRGVVKMRRGM 317
             LCYNN +VFRGVVK+RRG+
Sbjct:   301 LCYNNEQVFRGVVKLRRGL 319
GO:0004310 "farnesyl-diphosphate farnesyltransferase activity" evidence=IEA;ISS;IDA
GO:0008610 "lipid biosynthetic process" evidence=IEA
GO:0009058 "biosynthetic process" evidence=IEA
GO:0016021 "integral to membrane" evidence=IEA
GO:0016740 "transferase activity" evidence=IEA
GO:0016765 "transferase activity, transferring alkyl or aryl (other than methyl) groups" evidence=IEA
GO:0005783 "endoplasmic reticulum" evidence=IDA
GO:0005886 "plasma membrane" evidence=IDA
GO:0006084 "acetyl-CoA metabolic process" evidence=RCA
GO:0006598 "polyamine catabolic process" evidence=RCA
GO:0009698 "phenylpropanoid metabolic process" evidence=RCA
GO:0016126 "sterol biosynthetic process" evidence=RCA;TAS
GO:0016132 "brassinosteroid biosynthetic process" evidence=RCA
GO:0042398 "cellular modified amino acid biosynthetic process" evidence=RCA
GO:0005789 "endoplasmic reticulum membrane" evidence=TAS
TAIR|locus:2139534 SQS2 "squalene synthase 2" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|F1NFJ9 FDFT1 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
MGI|MGI:102706 Fdft1 "farnesyl diphosphate farnesyl transferase 1" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
RGD|61834 Fdft1 "farnesyl diphosphate farnesyl transferase 1" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|Q6IE76 fdft1 "FDFT1 protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|I3LFX7 FDFT1 "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|Q32KR6 FDFT1 "Squalene synthase" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|E9PNM1 FDFT1 "Squalene synthase" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|E2R6N6 FDFT1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] 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) ?
P53800FDFT_NICBE2, ., 5, ., 1, ., 2, 10.87060.93230.7712N/Ano
P37268FDFT_HUMAN2, ., 5, ., 1, ., 2, 10.50150.91470.7458yesno
Q5R6U3FDFT_PONAB2, ., 5, ., 1, ., 2, 10.50150.91470.7458yesno
Q02769FDFT_RAT2, ., 5, ., 1, ., 2, 10.51690.91470.7475yesno
P53798FDFT_MOUSE2, ., 5, ., 1, ., 2, 10.52010.92050.7524yesno
P53799FDFT_ARATH2, ., 5, ., 1, ., 2, 10.82440.93230.7731yesno
Q32KR6FDFT_BOVIN2, ., 5, ., 1, ., 2, 10.51380.91470.7458yesno

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 Layer2.5.10.976
4th Layer2.5.1.210.991

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 ?
Query340
TIGR01559337 TIGR01559, squal_synth, farnesyl-diphosphate farne 1e-175
cd00683265 cd00683, Trans_IPPS_HH, Trans-Isoprenyl Diphosphat 4e-90
pfam00494262 pfam00494, SQS_PSY, Squalene/phytoene synthase 3e-52
COG1562288 COG1562, ERG9, Phytoene/squalene synthetase [Lipid 4e-46
cd00867236 cd00867, Trans_IPPS, Trans-Isoprenyl Diphosphate S 5e-26
cd00385243 cd00385, Isoprenoid_Biosyn_C1, Isoprenoid Biosynth 2e-24
TIGR03465266 TIGR03465, HpnD, squalene synthase HpnD 2e-08
PLN02632334 PLN02632, PLN02632, phytoene synthase 7e-07
>gnl|CDD|188157 TIGR01559, squal_synth, farnesyl-diphosphate farnesyltransferase Back     alignment and domain information 
 Score =  489 bits (1260), Expect = e-175
 Identities = 182/289 (62%), Positives = 218/289 (75%), Gaps = 10/289 (3%)

Query: 35  PHWAFCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPIL 94
           P   FCY +L+  SRSFA VIQ+L  +LRNAVCIFYLVLRALDTVEDD +I  D K+P+L
Sbjct: 1   PSLGFCYELLNLTSRSFAAVIQELPPELRNAVCIFYLVLRALDTVEDDMTISVDKKIPLL 60

Query: 95  IAFHRHVYDREWHFSCG-TKEYKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAK 153
             FH  +YD +W F+    ++ + ++D F  VS  FL+L   YQ+ I DIT+RMG GMA 
Sbjct: 61  RDFHEKIYDPDWRFTESDNEKDRQVLDDFPVVSLEFLKLKPKYQEVIADITRRMGNGMAD 120

Query: 154 FICKEV---ESIDDYDEYCYYVAGLVGLGLSKLFYASGTEDLAPDS---LSNSMGLFLQK 207
           FI KEV   +++ DYD+YC+YVAGLVG+GLS+LF ASG ED +      LSNSMGLFLQK
Sbjct: 121 FIDKEVTNEQTVGDYDKYCHYVAGLVGIGLSRLFVASGFEDPSLGESEALSNSMGLFLQK 180

Query: 208 TNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHV 267
           TNIIRDYLEDINE    RMFWPREIWSKY  KL D K  ENSDKA+QCLN++VTNAL H 
Sbjct: 181 TNIIRDYLEDINE---GRMFWPREIWSKYAKKLGDFKKPENSDKALQCLNELVTNALHHA 237

Query: 268 EDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRG 316
            DCL Y+S LRD +IF FCAIPQ+MAI TLALCYNN +VF+G VK+R+G
Sbjct: 238 TDCLTYLSRLRDQSIFNFCAIPQVMAIATLALCYNNPQVFQGNVKIRKG 286

This model describes farnesyl-diphosphate farnesyltransferase, also known as squalene synthase, as found in eukaryotes. This family is related to phytoene synthases. Tentatively identified archaeal homologs (excluded from this model) lack the C-terminal predicted transmembrane region universally conserved among members of this family. Length = 337
>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|173836 cd00867, Trans_IPPS, Trans-Isoprenyl Diphosphate Synthases Back     alignment and domain information
>gnl|CDD|173830 cd00385, Isoprenoid_Biosyn_C1, Isoprenoid Biosynthesis enzymes, Class 1 Back     alignment and domain information
>gnl|CDD|163278 TIGR03465, HpnD, squalene synthase HpnD Back     alignment and domain information
>gnl|CDD|215339 PLN02632, PLN02632, phytoene synthase Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 340
TIGR01559336 squal_synth farnesyl-diphosphate farnesyltransfera 100.0
PLN02632334 phytoene synthase 100.0
TIGR03464266 HpnC squalene synthase HpnC. This family of genes 100.0
cd00683265 Trans_IPPS_HH Trans-Isoprenyl Diphosphate Synthase 100.0
TIGR03465266 HpnD squalene synthase HpnD. The genes of this fam 100.0
COG1562288 ERG9 Phytoene/squalene synthetase [Lipid metabolis 100.0
PF00494267 SQS_PSY: Squalene/phytoene synthase; InterPro: IPR 100.0
KOG1459413 consensus Squalene synthetase [Lipid transport and 100.0
KOG4411292 consensus Phytoene/squalene synthetase [Lipid tran 100.0
cd00867236 Trans_IPPS Trans-Isoprenyl Diphosphate Synthases. 99.81
cd00385243 Isoprenoid_Biosyn_C1 Isoprenoid Biosynthesis enzym 99.73
KOG1459413 consensus Squalene synthetase [Lipid transport and 99.2
TIGR02749322 prenyl_cyano solanesyl diphosphate synthase. Membe 95.35
PLN02890422 geranyl diphosphate synthase 95.33
PRK10888323 octaprenyl diphosphate synthase; Provisional 95.14
cd00685259 Trans_IPPS_HT Trans-Isoprenyl Diphosphate Synthase 94.95
TIGR02748319 GerC3_HepT heptaprenyl diphosphate synthase compon 94.62
CHL00151323 preA prenyl transferase; Reviewed 93.78
PLN02857416 octaprenyl-diphosphate synthase 92.21
PF00348260 polyprenyl_synt: Polyprenyl synthetase; InterPro: 91.98
PRK10581299 geranyltranstransferase; Provisional 89.48
PF06330376 TRI5: Trichodiene synthase (TRI5); InterPro: IPR02 88.64
>TIGR01559 squal_synth farnesyl-diphosphate farnesyltransferase Back     alignment and domain information 
Probab=100.00  E-value=1.3e-60  Score=456.61  Aligned_cols=287  Identities=62%  Similarity=1.049  Sum_probs=262.3

Q ss_pred             hHHHHHHHHhhcCCCHHHHHHhcChhhhhHHHHHHHHHhhhhhccCCCCCChhhhHHHHHHHHHHHcccccccccC-Ccc
Q 019466           36 HWAFCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCG-TKE  114 (340)
Q Consensus        36 ~~~~c~~ilr~~s~sfyla~~lLP~~~R~av~alYAf~R~~DdI~D~~~~~~~~~~~~L~~w~~~l~~~~~~~~~g-~~~  114 (340)
                      ++++|.++++++|+|||+++.+||+++|++|+++|+|||.+|||+|+.+.+.+.|+..|++|.+.+....|.+..+ .+.
T Consensus         1 ~~~~C~~~l~~~SrSF~~ai~~Lp~~lR~aV~~~Yl~cR~~DdIeDd~~~~~~~kl~~l~~~~~~l~~~~~~~~~~~~~~   80 (336)
T TIGR01559         1 SLGFCYELLNLTSRSFAAVIQELPPELRNAVCIFYLVLRALDTVEDDMTISVDKKIPLLRDFHEKIYDPDWRFTESDNEK   80 (336)
T ss_pred             ChHHHHHHHhhcCccHHHHHHHcCHHHHHHHHHHHHHHHhccccccCCCCCHHHHHHHHHHHHHHHhccCcccCCCCChh
Confidence            3679999999999999999999999999999999999999999999988877788999999999998766655422 445


Q ss_pred             hhHHHhhHHHHHHHHHhcChhHHHHHHHHHHhhhhHHHhhhh-hhc--CCHHHHHHHHHhhhhHHHHHHHHHhcccCCCC
Q 019466          115 YKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFIC-KEV--ESIDDYDEYCYYVAGLVGLGLSKLFYASGTED  191 (340)
Q Consensus       115 ~~~l~~~l~~v~~~~~~~~~~~~~li~~~~~~~~~g~~~Dl~-~~~--~t~~eL~~Yc~~vAg~VG~l~~~il~~~~~~~  191 (340)
                      +..+...++.+...|..++++++++|.+++.+|++||++|+. ..|  +|++||+.|||+|||+||+|+++|++.+|..+
T Consensus        81 ~~~L~~~~~~v~~~~~~l~~~~~~~I~~~~~~M~~GMa~dl~~~~~~~~T~~dL~~YCy~VAG~VG~mlt~l~~~~~~~~  160 (336)
T TIGR01559        81 DRQVLDDFPVVSLEFLKLKPKYQEVIADITRRMGNGMADFIDKEVTNEQTVGDYDKYCHYVAGLVGIGLSRLFVASGFED  160 (336)
T ss_pred             hHHHHHhchHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHhcCcCCCCCHHHHHHHHhccccHHHHHHHHHHhhcCCCC
Confidence            567888999999999999999999999999999999999997 567  99999999999999999999999997643322


Q ss_pred             C---ChhHHHHHHHHHHHHHHHHhchhhhhccCCCCcccccHHHHHhcCCChhhhhcccCCHHHHHHHHHHHHHHHHHHH
Q 019466          192 L---APDSLSNSMGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVE  268 (340)
Q Consensus       192 ~---~~~~~A~~lG~AlQltNiLRDi~eD~~~~~~GR~YLP~d~L~~~gv~~edl~~~~~~~~~~~~i~~~~~~a~~~l~  268 (340)
                      +   ...+.|.++|.|||+||||||++||++   +||||||.|+|.+||++.+++..+.+++++..++.+++.+|+.||.
T Consensus       161 ~~~~~~~~~A~~lG~aLQlTNIlRDv~ED~~---~GR~YlP~e~l~~~g~~~~dl~~~~~~~~~~~~l~~lv~~A~~~~~  237 (336)
T TIGR01559       161 PSLGESEALSNSMGLFLQKTNIIRDYLEDIN---EGRMFWPREIWSKYAKKLGDFKKPENSDKALQCLNELVTNALHHAT  237 (336)
T ss_pred             cchhhhHHHHHHHHHHHHHHHHHHHHHhHHh---CCCCCCCHHHHHHcCCCHHHhcCccccHHHHHHHHHHHHHHHHHHH
Confidence            2   235789999999999999999999998   9999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhccccccchhhhhhHHHHHHHHHHHhcCCCccccccccCHHHHHHHHHHH
Q 019466          269 DCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGMILILNMYF  325 (340)
Q Consensus       269 ~a~~~~~~lp~~~~~~~~~~p~~~a~~~l~~~~~~~dv~~~~v~~~r~~~~~~l~~~  325 (340)
                      .|..|+..++..+++.||+||..||++||+.+++|.++|++.||++|+....+.+++
T Consensus       238 ~al~yl~~l~~~~~~~fcaip~~mAi~TL~~~~~n~~~~~~~VKi~r~~~~~~~~~~  294 (336)
T TIGR01559       238 DCLTYLSRLRDQSIFNFCAIPQVMAIATLALCYNNPQVFQGNVKIRKGTTVKLILDS  294 (336)
T ss_pred             HHHHHHHhCCCcchhHHHHHHHHHHHHHHHHHhcChhhcCCCceecHHHHHHHHHHc
Confidence            999999999888888899999999999999999999999999999999988887655

This model describes farnesyl-diphosphate farnesyltransferase, also known as squalene synthase, as found in eukaryotes. This family is related to phytoene synthases. Tentatively identified archaeal homologs (excluded from this model) lack the C-terminal predicted transmembrane region universally conserved among members of this family.
>PLN02632 phytoene synthase Back     alignment and domain information
>TIGR03464 HpnC squalene synthase HpnC Back     alignment and domain information
>cd00683 Trans_IPPS_HH Trans-Isoprenyl Diphosphate Synthases, head-to-head Back     alignment and domain information
>TIGR03465 HpnD squalene synthase HpnD 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
>KOG1459 consensus Squalene synthetase [Lipid transport and metabolism] 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
>TIGR02749 prenyl_cyano solanesyl diphosphate synthase Back     alignment and domain information
>PLN02890 geranyl diphosphate synthase Back     alignment and domain information
>PRK10888 octaprenyl diphosphate synthase; Provisional Back     alignment and domain information
>cd00685 Trans_IPPS_HT Trans-Isoprenyl Diphosphate Synthases, head-to-tail Back     alignment and domain information
>TIGR02748 GerC3_HepT heptaprenyl diphosphate synthase component II Back     alignment and domain information
>CHL00151 preA prenyl transferase; Reviewed Back     alignment and domain information
>PLN02857 octaprenyl-diphosphate synthase Back     alignment and domain information
>PF00348 polyprenyl_synt: Polyprenyl synthetase; InterPro: IPR000092 A variety of isoprenoid compounds are synthesized by various organisms Back     alignment and domain information
>PRK10581 geranyltranstransferase; Provisional 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 ?
Query340
3lee_A340 Crystal Structure Of The Human Squalene Synthase Co 5e-87
3vj8_A343 Crystal Structure Of The Human Squalene Synthase Le 6e-87
1ezf_A340 Crystal Structure Of Human Squalene Synthase Length 7e-87
3vjd_A293 Crystal Structure Of The Y248a Mutant Of C(30) Caro 6e-05
2zco_A293 Crystal Structure Of The C(30) Carotenoid Dehydrosq 7e-05
4e9u_A287 Crystal Structure Of Dehydrosqualene Synthase (Crtm 7e-05
4f6v_A292 Crystal Structure Of Dehydrosqualene Synthase (Crtm 8e-05
3ae0_A293 Crystal Structure Of The C(30) Carotenoid Dehydrosq 9e-05
3adz_A293 Crystal Structure Of The C(30) Carotenoid Dehydrosq 7e-04
>pdb|3LEE|A Chain A, Crystal Structure Of The Human Squalene Synthase Complexed With Bph- 652 Length = 340 Back     alignment and structure 
Iteration: 1

 Score =  317 bits (813), Expect = 5e-87,   Method: Compositional matrix adjust.
 Identities = 156/287 (54%), Positives = 204/287 (71%), Gaps = 6/287 (2%)
Query: 40  CYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHR 99
           CY  L++ SRSFA VIQ L  ++RNAVCIFYLVLRALDT+EDD +I  + KVP+L  FH 
Sbjct: 13  CYKYLNQTSRSFAAVIQALDGEMRNAVCIFYLVLRALDTLEDDMTISVEKKVPLLHNFHS 72
Query: 100 HVYDREWHFSCGTKEYKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFICKEV 159
            +Y  +W F    ++ + +++ F  +S  F  L + YQ  I DI +RMG GMA+F+ K V
Sbjct: 73  FLYQPDWRFMESKEKDRQVLEDFPTISLEFRNLAEKYQTVIADICRRMGIGMAEFLDKHV 132
Query: 160 ESIDDYDEYCYYVAGLVGLGLSKLFYASGTED--LAPDS-LSNSMGLFLQKTNIIRDYLE 216
            S  ++D+YC+YVAGLVG+GLS+LF AS  ED  +  D+  +NSMGLFLQKTNIIRDYLE
Sbjct: 133 TSEQEWDKYCHYVAGLVGIGLSRLFSASEFEDPLVGEDTERANSMGLFLQKTNIIRDYLE 192
Query: 217 DINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSA 276
           D       R FWP+E+WS+YV KL D    EN D AVQCLN+++TNAL H+ D + Y+S 
Sbjct: 193 DQQ---GGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELITNALHHIPDVITYLSR 249
Query: 277 LRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGMILILNM 323
           LR+ ++F FCAIPQ+MAI TLA CYNN +VF+G VK+R+G  + L M
Sbjct: 250 LRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGAVKIRKGQAVTLMM 296
>pdb|3VJ8|A Chain A, Crystal Structure Of The Human Squalene Synthase Length = 343 Back     alignment and structure
>pdb|1EZF|A Chain A, Crystal Structure Of Human Squalene Synthase Length = 340 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|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|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|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|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 ?
Query340
3vj8_A343 Squalene synthase; farnesyl-diphosphate farnesyltr 1e-116
3acx_A293 Dehydrosqualene synthase; CRTM, carotenoid biosynt 7e-12
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 1e-06
>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
 Score =  340 bits (873), Expect = e-116
 Identities = 154/291 (52%), Positives = 200/291 (68%), Gaps = 6/291 (2%)

Query: 34  EPHWAFCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPI 93
                 CY  L++ SRSFA VIQ L  ++RNAVCIFYLVLRALDT+EDD +I  + KVP+
Sbjct: 10  SSSLKTCYKYLNQTSRSFAAVIQALDGEMRNAVCIFYLVLRALDTLEDDMTISVEKKVPL 69

Query: 94  LIAFHRHVYDREWHFSCGTKEYKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAK 153
           L  FH  +Y  +W F    ++ + +++ F  +S  F  L + YQ  I DI +RMG GMA+
Sbjct: 70  LHNFHSFLYQPDWRFMESKEKDRQVLEDFPTISLEFRNLAEKYQTVIADICRRMGIGMAE 129

Query: 154 FICKEVESIDDYDEYCYYVAGLVGLGLSKLFYASGTEDLAPDS---LSNSMGLFLQKTNI 210
           F+ K V S  ++D+YC+YVAGLVG+GLS+LF AS  ED         +NSMGLFLQKTNI
Sbjct: 130 FLDKHVTSEQEWDKYCHYVAGLVGIGLSRLFSASEFEDPLVGEDTERANSMGLFLQKTNI 189

Query: 211 IRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDC 270
           IRDYLED       R FWP+E+WS+YV KL D    EN D AVQCLN+++TNAL H+ D 
Sbjct: 190 IRDYLEDQQG---GREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELITNALHHIPDV 246

Query: 271 LKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGMILIL 321
           + Y+S LR+ ++F FCAIPQ+MAI TLA CYNN +VF+G VK+R+G  + L
Sbjct: 247 ITYLSRLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGAVKIRKGQAVTL 297
>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
>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 ?
Query340
3vj8_A343 Squalene synthase; farnesyl-diphosphate farnesyltr 100.0
4hd1_A294 Squalene synthase HPNC; MCSG, structural genomics, 100.0
3acx_A293 Dehydrosqualene synthase; CRTM, carotenoid biosynt 100.0
3rmg_A334 Octaprenyl-diphosphate synthase; structural genomi 95.98
3tc1_A315 Octaprenyl pyrophosphate synthase; all alpha-helic 95.82
1v4e_A299 Octoprenyl-diphosphate synthase; trans-type prenyl 95.75
2q80_A301 Geranylgeranyl pyrophosphate synthetase; isoprenoi 95.67
3lmd_A360 Geranylgeranyl pyrophosphate synthase; isoprenyl d 95.64
3mzv_A341 Decaprenyl diphosphate synthase; transferase, stru 95.44
3nf2_A352 Putative polyprenyl synthetase; isoprenyl diphosph 95.15
3aqb_B325 Component B of hexaprenyl diphosphate synthase; pr 94.87
3apz_A348 Geranyl diphosphate synthase; prenyltransferase, a 94.72
3pko_A334 Geranylgeranyl pyrophosphate synthase; isoprenyl d 94.6
2ihi_A395 Pyrophosphate synthase; PV092040, structural genom 94.4
2e8v_A340 Geranylgeranyl pyrophosphate synthetase; prenyltra 94.3
3oyr_A345 Trans-isoprenyl diphosphate synthase; isoprenyl sy 94.21
1rtr_A301 Geranyltranstransferase; 2.50A {Staphylococcus aur 94.19
2ftz_A284 Geranyltranstransferase; TM0161, structural GE joi 94.04
1wmw_A330 Geranylgeranyl diphosphate synthetase; GGPP, preny 94.04
3uca_A324 Geranyltranstransferase; isoprenoid synthesis, iso 93.92
1wy0_A342 Geranylgeranyl pyrophosphate synthetase; pyrococcu 93.88
4f62_A317 Geranyltranstransferase; enzyme function initiativ 93.63
2h8o_A335 Geranyltranstransferase; geranyltransferase,agroba 93.54
3lom_A313 Geranyltranstransferase; geranyltransferase, struc 93.25
2her_A368 Fragment, farnesyl pyrophosphate synthase; farnesy 93.11
3p8l_A302 Geranyltranstransferase; isoprenyl synthase, struc 92.86
1rqj_A299 Geranyltranstransferase; bisphosphonate, isoprenyl 92.34
4dhd_A358 Polyprenyl synthetase; isoprenoid synthesis, isopr 92.29
3ipi_A295 Geranyltranstransferase; isoprene biosynthesis, he 92.06
3p8r_A302 Geranyltranstransferase; isoprenyl synthase, struc 91.89
3ts7_A324 Geranyltranstransferase; isoprenoid synthesis, far 91.77
3m0g_A297 Farnesyl diphosphate synthase; structural genomics 91.64
3pde_A309 Farnesyl-diphosphate synthase; isoprenyl diphospha 91.56
3lsn_A304 Geranyltranstransferase; structural genomics, prot 91.54
1yhl_A362 Farnesyl pyrophosphate synthase; farnesyl diphosph 90.69
2azj_A289 Geranylgeranyl pyrophosphate synthetase; hexpps, t 90.35
2qis_A374 Farnesyl pyrophosphate synthetase; trans-prenyltra 90.16
1uby_A367 FPS, farnesyl diphosphate synthase; transferase, i 88.93
3dyh_A390 Farnesyl pyrophosphate synthase; protein-bisphosph 87.83
3lk5_A380 Geranylgeranyl pyrophosphate synthase; structural 87.74
2q58_A368 Fragment, farnesyl pyrophosphate synthase; farnesy 84.72
>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
Probab=100.00  E-value=2.3e-61  Score=464.23  Aligned_cols=293  Identities=53%  Similarity=0.905  Sum_probs=269.7

Q ss_pred             CCCchhHHHHHHHHhhcCCCHHHHHHhcChhhhhHHHHHHHHHhhhhhccCCCCCChhhhHHHHHHHHHHHccccccccc
Q 019466           31 IPPEPHWAFCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSC  110 (340)
Q Consensus        31 ~~l~~~~~~c~~ilr~~s~sfyla~~lLP~~~R~av~alYAf~R~~DdI~D~~~~~~~~~~~~L~~w~~~l~~~~~~~~~  110 (340)
                      -++++++++|.++++++|+|||+++++||++.|++++++|+|||.+|||+|+.+.++++|..+|++|++.+....|.+..
T Consensus         7 ~~l~~~~~~C~~~l~~~srsF~la~~lLp~~~R~av~alYaf~R~aDdI~D~~~~~~~~k~~~L~~~~~~l~~~~~~~~~   86 (343)
T 3vj8_A            7 DSLSSSLKTCYKYLNQTSRSFAAVIQALDGEMRNAVCIFYLVLRALDTLEDDMTISVEKKVPLLHNFHSFLYQPDWRFME   86 (343)
T ss_dssp             -CCCHHHHHHHHHHHHHHGGGHHHHHTCCTTHHHHHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHHTTCTTCCCCC
T ss_pred             ccchHHHHHHHHHHHhcCCcHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhccccCCHHHHHHHHHHHHHHHhcchhhhcC
Confidence            36889999999999999999999999999999999999999999999999998878888999999999999876555653


Q ss_pred             CCcchhHHHhhHHHHHHHHHhcChhHHHHHHHHHHhhhhHHHhhhhhhcCCHHHHHHHHHhhhhHHHHHHHHHhcccCCC
Q 019466          111 GTKEYKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFICKEVESIDDYDEYCYYVAGLVGLGLSKLFYASGTE  190 (340)
Q Consensus       111 g~~~~~~l~~~l~~v~~~~~~~~~~~~~li~~~~~~~~~g~~~Dl~~~~~t~~eL~~Yc~~vAg~VG~l~~~il~~~~~~  190 (340)
                      +++.+.+++..++.++..|..++..++++|.+++.+|.+||++|+.++|+|++||+.|||+|||+||+|+++|+|..+.+
T Consensus        87 ~~~~~~~ll~~~p~v~~~f~~l~~~~~~~i~~~~~~m~~gm~~dl~~~~~t~~~L~~Yc~~vAg~VG~l~~~l~~~~~~~  166 (343)
T 3vj8_A           87 SKEKDRQVLEDFPTISLEFRNLAEKYQTVIADICRRMGIGMAEFLDKHVTSEQEWDKYCHYVAGLVGIGLSRLFSASEFE  166 (343)
T ss_dssp             CCSTTTHHHHTHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHGGGCCCCSHHHHHHHHHHHTHHHHHHHHHHHHHHTSS
T ss_pred             CChhhHHHHhcCcHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHhccCCCCCHHHHHHHHHhCcHHHHHHHHHHhCCCCCc
Confidence            45566678888888999999999999999999999999999999998999999999999999999999999999974321


Q ss_pred             CC---ChhHHHHHHHHHHHHHHHHhchhhhhccCCCCcccccHHHHHhcCCChhhhhcccCCHHHHHHHHHHHHHHHHHH
Q 019466          191 DL---APDSLSNSMGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHV  267 (340)
Q Consensus       191 ~~---~~~~~A~~lG~AlQltNiLRDi~eD~~~~~~GR~YLP~d~L~~~gv~~edl~~~~~~~~~~~~i~~~~~~a~~~l  267 (340)
                      ++   ...+.|.++|.|+|+||||||++||+.   +||||||.|+|.+||+++++|..++.+++++.++++++.+|+.||
T Consensus       167 ~~~~~~~~~~A~~lG~AlQltNilRDv~eD~~---~gR~YlP~e~l~~~g~~~~dl~~~~~~~~~~~~l~~l~~~A~~~~  243 (343)
T 3vj8_A          167 DPLVGEDTERANSMGLFLQKTNIIRDYLEDQQ---GGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELITNALHHI  243 (343)
T ss_dssp             CHHHHHCHHHHHHHHHHHHHHHHHHTHHHHHH---TTCCCSCHHHHTTTCSSGGGGGSGGGHHHHHHHHHHHHHHHHTTH
T ss_pred             cchhhhHHHHHHHHHHHHHHHHHHHHhHHHHh---CCCeeCCHHHHHHcCCCHHHHhcccCCHHHHHHHHHHHHHHHHHH
Confidence            11   246899999999999999999999999   999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhccccccchhhhhhHHHHHHHHHHHhcCCCccccccccCHHHHHHHHHHHh
Q 019466          268 EDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGMILILNMYFF  326 (340)
Q Consensus       268 ~~a~~~~~~lp~~~~~~~~~~p~~~a~~~l~~~~~~~dv~~~~v~~~r~~~~~~l~~~~  326 (340)
                      .+|..++..+|..+.+.+|++|..++++++..++++++||++++++++++++|++|++.
T Consensus       244 ~~a~~~~~~L~~~~~~~~~~ip~~lA~~tL~~i~~~~~v~~~rvkisr~~~~~l~~ra~  302 (343)
T 3vj8_A          244 PDVITYLSRLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGAVKIRKGQAVTLMMDAT  302 (343)
T ss_dssp             HHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHHTTCGGGGTSCCCCCHHHHHHHHHHCS
T ss_pred             HHHHHHHHhCCccchhhHHHHHHHHHHHHHHHHHhCCccccCCCcccHHHHHHHHHHhC
Confidence            99999999999886677999999999999999999999999999999999999999985
>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
>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
>3rmg_A Octaprenyl-diphosphate synthase; structural genomics, protein structure initiative, isoprene biosynthesis, transferase; 2.30A {Bacteroides thetaiotaomicron} Back     alignment and structure
>3tc1_A Octaprenyl pyrophosphate synthase; all alpha-helices fold, transferase; 2.00A {Helicobacter pylori} 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
>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
>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
>3nf2_A Putative polyprenyl synthetase; isoprenyl diphosphate synthase, structural genomics, PSI, PR structure initiative, nysgrc; 2.20A {Streptomyces coelicolor} 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
>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
>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
>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
>3oyr_A Trans-isoprenyl diphosphate synthase; isoprenyl synthase, PSI, protein structure initiative; HET: IPE; 2.00A {Caulobacter crescentus} Back     alignment and structure
>1rtr_A Geranyltranstransferase; 2.50A {Staphylococcus aureus} SCOP: a.128.1.1 Back     alignment and structure
>2ftz_A Geranyltranstransferase; TM0161, structural GE joint center for structural genomics, JCSG, protein structu initiative, PSI; HET: MLY; 1.90A {Thermotoga maritima} Back     alignment and structure
>1wmw_A Geranylgeranyl diphosphate synthetase; GGPP, prenyl diphosphate synthase, structural genom riken structural genomics/proteomics initiative; 1.55A {Thermus thermophilus} Back     alignment and structure
>3uca_A Geranyltranstransferase; isoprenoid synthesis, isoprenoid diphosphate synthase; 2.00A {Clostridium perfringens} 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
>4f62_A Geranyltranstransferase; enzyme function initiative, structural genomics; 2.10A {Marinomonas SP} 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
>3lom_A Geranyltranstransferase; geranyltransferase, structural genomics, PSI, protein structure initiative, nysgrc; 2.30A {Legionella pneumophila subsp} Back     alignment and structure
>3p8l_A Geranyltranstransferase; isoprenyl synthase, structural genomics, PSI, protein struct initiative, nysgrc; 2.00A {Enterococcus faecalis} 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
>4dhd_A Polyprenyl synthetase; isoprenoid synthesis, isoprenoid diphosphate synthase, trans; 1.65A {Pyrobaculum calidifontis} PDB: 4gp1_A* 4gp2_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
>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
>3ts7_A Geranyltranstransferase; isoprenoid synthesis, farnesyl diphosphate synthase; 1.94A {Methylococcus capsulatus} Back     alignment and structure
>3m0g_A Farnesyl diphosphate synthase; structural genomics, protein structure initiative, NYSGXRC, biosynthesis, transferase, PSI-2; 1.90A {Rhodobacter capsulatus} PDB: 3lvs_A Back     alignment and structure
>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
>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
>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
>2azj_A Geranylgeranyl pyrophosphate synthetase; hexpps, trans-prenyltransferase; 2.40A {Sulfolobus solfataricus} PDB: 2azk_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
>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
>3lk5_A Geranylgeranyl pyrophosphate synthase; structural genomics, protein structure initiative, geranylge pyrophosphate synthase; 1.90A {Corynebacterium glutamicum} PDB: 3qqv_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

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 340
d1ezfa_333 a.128.1.2 (A:) Squalene synthase {Human (Homo sapi 3e-77
>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 =  238 bits (608), Expect = 3e-77
 Identities = 155/289 (53%), Positives = 201/289 (69%), Gaps = 6/289 (2%)

Query: 38  AFCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAF 97
             CY  L++ SRSFA VIQ L  ++RNAVCIFYLVLRALDT+EDD +I  + KVP+L  F
Sbjct: 4   KTCYKYLNQTSRSFAAVIQALDGEMRNAVCIFYLVLRALDTLEDDMTISVEKKVPLLHNF 63

Query: 98  HRHVYDREWHFSCGTKEYKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFICK 157
           H  +Y  +W F    ++ + +++ F  +S  F  L + YQ  I DI +RMG GMA+F+ K
Sbjct: 64  HSFLYQPDWRFMESKEKDRQVLEDFPTISLEFRNLAEKYQTVIADICRRMGIGMAEFLDK 123

Query: 158 EVESIDDYDEYCYYVAGLVGLGLSKLFYASGTEDLAPDSL---SNSMGLFLQKTNIIRDY 214
            V S  ++D+YC+YVAGLVG+GLS+LF AS  ED         +NSMGLFLQKTNIIRDY
Sbjct: 124 HVTSEQEWDKYCHYVAGLVGIGLSRLFSASEFEDPLVGEDTERANSMGLFLQKTNIIRDY 183

Query: 215 LEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYM 274
           LED       R FWP+E+WS+YV KL D    EN D AVQCLN+++TNAL H+ D + Y+
Sbjct: 184 LEDQQ---GGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELITNALHHIPDVITYL 240

Query: 275 SALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGMILILNM 323
           S LR+ ++F FCAIPQ+MAI TLA CYNN +VF+G VK+R+G  + L M
Sbjct: 241 SRLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGAVKIRKGQAVTLMM 289

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query340
d1ezfa_333 Squalene synthase {Human (Homo sapiens) [TaxId: 96 100.0
d2q80a1291 Geranylgeranyl pyrophosphate synthetase {Human (Ho 95.82
d1v4ea_280 Octoprenyl-diphosphate synthase {Thermotoga mariti 94.44
d1kiya_354 Trichodiene synthase {Fusarium sporotrichioides [T 93.12
d1fpsa_348 Farnesyl diphosphate synthase (geranyltranstransfe 87.66
d1rqja_299 Farnesyl diphosphate synthase (geranyltranstransfe 81.75
>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=8.6e-60  Score=449.90  Aligned_cols=288  Identities=54%  Similarity=0.926  Sum_probs=254.7

Q ss_pred             hhHHHHHHHHhhcCCCHHHHHHhcChhhhhHHHHHHHHHhhhhhccCCCCCChhhhHHHHHHHHHHHcccccccccCCcc
Q 019466           35 PHWAFCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGTKE  114 (340)
Q Consensus        35 ~~~~~c~~ilr~~s~sfyla~~lLP~~~R~av~alYAf~R~~DdI~D~~~~~~~~~~~~L~~w~~~l~~~~~~~~~g~~~  114 (340)
                      +++++|.++++++|+|||+++++||+++|++++++|+|||.+|||+|+...+.+.|...|++|++.+....+....+.+.
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            36899999999999999999999999999999999999999999999988888889999999999998743322224556


Q ss_pred             hhHHHhhHHHHHHHHHhcChhHHHHHHHHHHhhhhHHHhhhhhhcCCHHHHHHHHHhhhhHHHHHHHHHhcccCCCC---
Q 019466          115 YKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFICKEVESIDDYDEYCYYVAGLVGLGLSKLFYASGTED---  191 (340)
Q Consensus       115 ~~~l~~~l~~v~~~~~~~~~~~~~li~~~~~~~~~g~~~Dl~~~~~t~~eL~~Yc~~vAg~VG~l~~~il~~~~~~~---  191 (340)
                      +++++.++++++..|..+++.++..+.+++..|..||..++..+|+|++||+.|||+|||+||+|+++|+|.++...   
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            77899999999999999998888889899999999999888889999999999999999999999999999743222   


Q ss_pred             CChhHHHHHHHHHHHHHHHHhchhhhhccCCCCcccccHHHHHhcCCChhhhhcccCCHHHHHHHHHHHHHHHHHHHHHH
Q 019466          192 LAPDSLSNSMGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCL  271 (340)
Q Consensus       192 ~~~~~~A~~lG~AlQltNiLRDi~eD~~~~~~GR~YLP~d~L~~~gv~~edl~~~~~~~~~~~~i~~~~~~a~~~l~~a~  271 (340)
                      ....+.|.++|+|||+|||||||+||++   +||||||.|+|.+||++++++.+++.++++..++.+++++|+.||+.|.
T Consensus       161 ~~~~~~A~~lG~AlQltNIlRDi~eD~~---~gR~YlP~e~l~~~g~~~~dl~~~~~~~~~~~~~~~l~~~A~~~~~~a~  237 (333)
T d1ezfa_         161 GEDTERANSMGLFLQKTNIIRDYLEDQQ---GGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELITNALHHIPDVI  237 (333)
T ss_dssp             HHCHHHHHHHHHHHHHHHHHHTHHHHHH---HTCCCSCHHHHTTTCSSGGGGGSGGGHHHHHHHHHHHHHHHHTTHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhHHHHh---CCcEECCHHHHHHcCCCHHHHHhccchHHHHHHHHHHHHHHHHHHHHHH
Confidence            1235789999999999999999999999   9999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhccccccchhhhhhHHHHHHHHHHHhcCCCccccccccCHHHHHHHHHHH
Q 019466          272 KYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGMILILNMYF  325 (340)
Q Consensus       272 ~~~~~lp~~~~~~~~~~p~~~a~~~l~~~~~~~dv~~~~v~~~r~~~~~~l~~~  325 (340)
                      .|+..||..+++.+|++|..++..++.++++|+++|.++|+++|+++..+++++
T Consensus       238 ~y~~~lp~~~~~~~~~~~~~~a~~tl~~~~~~~~~~~~~vkisr~~~~~l~~~~  291 (333)
T d1ezfa_         238 TYLSRLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGAVKIRKGQAVTLMMDA  291 (333)
T ss_dssp             HHHHTCCCHHHHHHHHHHHHHHHHHHHHHTTCGGGGTSCCCC----------CT
T ss_pred             HHHHHCCchhHHHHHHHHHHHHHHHHHHHHcCchhcCCCeEeeHHHHHHHHHHh
Confidence            999999998877899999999999999999999999999999999998887655
>d2q80a1 a.128.1.1 (A:6-296) Geranylgeranyl pyrophosphate synthetase {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1v4ea_ a.128.1.1 (A:) Octoprenyl-diphosphate synthase {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1kiya_ a.128.1.5 (A:) Trichodiene synthase {Fusarium sporotrichioides [TaxId: 5514]} 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
>d1rqja_ a.128.1.1 (A:) Farnesyl diphosphate synthase (geranyltranstransferase) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure