Citrus Sinensis ID: 022601

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----
MGSLAAVLRHPDDLYPLLKLKMASRQAEKQIPPEPHWAFCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGTKEYKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFICKEVESIDDYDEYCYYVAGLVGLGLSKLFYASGTEDLAPDSLSNSMGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIFRFCAIPQVRCF
cHHHHHHHHccHHHHHHHHcHHHcccccccccccHHHHHHHHHHHHHcccHHHHHHHccHHHHHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHccccHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHcc
ccHHHHHHccHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHcccccccccccHHccHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHcHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccEEEEEcccEEcc
mgslaavlrhpddlypLLKLKMASrqaekqippephwAFCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRAldtveddtsiptdvkvPILIAFHRHvydrewhfscgtkEYKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFICKEvesiddydeyCYYVAGLVGLGLSKLFyasgtedlapdslsnsmglflqKTNIIRDYLEDineipkcrmfwprEIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIFRfcaipqvrcf
mgslaavlrhpddlyPLLKLKMASRQAEKQIPPEPHWAFCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDtveddtsiptdvkVPILIAFHRHVYDREWHFSCGTKEYKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFICKEVESIDDYDEYCYYVAGLVGLGLSKLFYASGTEDLAPDSLSNSMGLFLQKTNIIRDYLEDINEIpkcrmfwprEIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIFRFCAIPQVRCF
MGSLAAVLRHPDDLYPLLKLKMASRQAEKQIPPEPHWAFCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGTKEYKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFICKEVESIDDYDEYCYYVAGLVGLGLSKLFYASGTEDLAPDSLSNSMGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIFRFCAIPQVRCF
************DLYPLLKL**************PHWAFCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGTKEYKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFICKEVESIDDYDEYCYYVAGLVGLGLSKLFYASGTEDLAPDSLSNSMGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIFRFCAIPQVR**
*GSLAAVLRHPDDLYPLLKL******************FCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGTKEYKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFICKEVESIDDYDEYCYYVAGLVGLGLSKLFYASGTEDLAPDSLSNSMGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIFRFCAIPQVRCF
MGSLAAVLRHPDDLYPLLKLKMASRQAEKQIPPEPHWAFCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGTKEYKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFICKEVESIDDYDEYCYYVAGLVGLGLSKLFYASGTEDLAPDSLSNSMGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIFRFCAIPQVRCF
*GSLAAVLRHPDDLYPLLKLKMASRQAEKQIPPEPHWAFCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGTKEYKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFICKEVESIDDYDEYCYYVAGLVGLGLSKLFYASGTEDLAPDSLSNSMGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIFRFCAIPQVRCF
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MGSLAAVLRHPDDLYPLLKLKMASRQAEKQIPPEPHWAFCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGTKEYKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFICKEVESIDDYDEYCYYVAGLVGLGLSKLFYASGTEDLAPDSLSNSMGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIFRFCAIPQVRCF
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 ?
Query294 2.2.26 [Sep-21-2011]
P53800 411 Squalene synthase OS=Nico N/A no 0.989 0.708 0.872 1e-152
P53799 410 Squalene synthase OS=Arab yes no 0.989 0.709 0.819 1e-148
G0Y287 465 Botryococcus squalene syn N/A no 0.986 0.623 0.522 4e-84
Q9SDW9 461 Squalene synthase OS=Botr N/A no 0.972 0.620 0.537 2e-82
P53798 416 Squalene synthase OS=Mus yes no 0.955 0.675 0.512 9e-80
Q02769 416 Squalene synthase OS=Ratt yes no 0.948 0.670 0.508 1e-79
Q32KR6 417 Squalene synthase OS=Bos yes no 0.948 0.669 0.505 3e-76
Q5R6U3 417 Squalene synthase OS=Pong yes no 0.948 0.669 0.494 2e-75
P37268 417 Squalene synthase OS=Homo yes no 0.948 0.669 0.494 2e-75
Q54DR1 416 Squalene synthase OS=Dict yes no 0.955 0.675 0.481 5e-70
>sp|P53800|FDFT_NICBE Squalene synthase OS=Nicotiana benthamiana PE=2 SV=1 Back     alignment and function desciption
 Score =  538 bits (1386), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 254/291 (87%), Positives = 273/291 (93%)

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 EDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIFRFCAIPQV 291
           E+LKYE+NS KAVQCLNDMVTNAL HVEDCL YMSALRD +IFRFCAIPQV
Sbjct: 241 EELKYEDNSAKAVQCLNDMVTNALPHVEDCLTYMSALRDPSIFRFCAIPQV 291

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|Q9SDW9|BSS_BOTBR Squalene synthase OS=Botryococcus braunii GN=BSS 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|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 ?
Query294
356538706 413 PREDICTED: squalene synthase-like [Glyci 0.989 0.704 0.903 1e-159
351726622 413 squalene synthase [Glycine max] gi|24635 0.989 0.704 0.903 1e-158
255641455 413 unknown [Glycine max] 0.989 0.704 0.903 1e-158
295822131 412 squalene synthase 2 [Glycyrrhiza uralens 0.989 0.706 0.900 1e-158
223972398 411 squalene synthetase [Euphorbia tirucalli 0.989 0.708 0.896 1e-158
133917969 412 squalene synthase 2 [Glycyrrhiza eurycar 0.989 0.706 0.896 1e-158
241062156 412 squalene synthase [Glycyrrhiza uralensis 0.989 0.706 0.896 1e-157
224924202 415 squalene synthase [Diospyros kaki] 0.989 0.701 0.893 1e-157
253993200 412 squalene synthase 2 [Glycyrrhiza uralens 0.989 0.706 0.896 1e-157
133917208 412 squalene synthase 2 [Glycyrrhiza uralens 0.989 0.706 0.893 1e-157
>gi|356538706|ref|XP_003537842.1| PREDICTED: squalene synthase-like [Glycine max] Back     alignment and taxonomy information
 Score =  566 bits (1458), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 263/291 (90%), Positives = 279/291 (95%)

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 EDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIFRFCAIPQV 291
           EDLKYEENS KAVQCLNDMVTNALMH EDCL YM+ALRD  IFRFCAIPQ+
Sbjct: 241 EDLKYEENSVKAVQCLNDMVTNALMHAEDCLTYMAALRDPPIFRFCAIPQI 291

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|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|223972398|dbj|BAH23428.1| squalene synthetase [Euphorbia tirucalli] gi|223972400|dbj|BAH23429.1| squalene synthetase [Euphorbia tirucalli] Back     alignment and taxonomy information
>gi|133917969|emb|CAJ77655.1| squalene synthase 2 [Glycyrrhiza eurycarpa] 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|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|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 ?
Query294
TAIR|locus:2139514 410 SQS1 "squalene synthase 1" [Ar 0.989 0.709 0.819 3.7e-135
TAIR|locus:2139534 413 SQS2 "squalene synthase 2" [Ar 0.989 0.704 0.784 6.8e-127
UNIPROTKB|F1NFJ9 418 FDFT1 "Uncharacterized protein 0.955 0.672 0.532 2.4e-76
MGI|MGI:102706 416 Fdft1 "farnesyl diphosphate fa 0.955 0.675 0.515 4e-74
RGD|61834 416 Fdft1 "farnesyl diphosphate fa 0.948 0.670 0.508 1.1e-73
UNIPROTKB|Q6IE76 417 fdft1 "FDFT1 protein" [Bos tau 0.948 0.669 0.505 1.3e-70
UNIPROTKB|I3LFX7 417 FDFT1 "Uncharacterized protein 0.948 0.669 0.501 1.3e-70
UNIPROTKB|Q32KR6 417 FDFT1 "Squalene synthase" [Bos 0.948 0.669 0.505 1.6e-70
UNIPROTKB|E9PNM1 410 FDFT1 "Squalene synthase" [Hom 0.945 0.678 0.498 2.6e-70
UNIPROTKB|P37268 417 FDFT1 "Squalene synthase" [Hom 0.948 0.669 0.494 8.9e-70
TAIR|locus:2139514 SQS1 "squalene synthase 1" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 1324 (471.1 bits), Expect = 3.7e-135, P = 3.7e-135
 Identities = 240/293 (81%), Positives = 272/293 (92%)

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 KLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIFRFCAIPQV 291
             KLEDLKYEEN++K+VQCLN+MVTNALMH+EDCLKYM +LRD +IFRFCAIPQ+
Sbjct:   241 KLEDLKYEENTNKSVQCLNEMVTNALMHIEDCLKYMVSLRDPSIFRFCAIPQI 293
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|P37268 FDFT1 "Squalene synthase" [Homo sapiens (taxid:9606)] 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, 10.87280.98970.7080N/Ano
Q02769FDFT_RAT2, ., 5, ., 1, ., 2, 10.50850.94890.6706yesno
P53798FDFT_MOUSE2, ., 5, ., 1, ., 2, 10.51200.95570.6754yesno
P53799FDFT_ARATH2, ., 5, ., 1, ., 2, 10.81910.98970.7097yesno
Q32KR6FDFT_BOVIN2, ., 5, ., 1, ., 2, 10.50510.94890.6690yesno

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

Your Input:
estExt_fgenesh4_pg.C_LG_IV1345
hypothetical protein (413 aa)
(Populus trichocarpa)
Predicted Functional Partners:
estExt_fgenesh4_pm.C_LG_VII0495
hypothetical protein (527 aa)
     •  0.914
gw1.II.3308.1
hypothetical protein (464 aa)
     •  0.914
gw1.XV.2734.1
hypothetical protein (466 aa)
     •  0.914
fgenesh4_pg.C_scaffold_418000002
hypothetical protein (473 aa)
     •  0.914
estExt_fgenesh4_pm.C_LG_V0246
hypothetical protein (526 aa)
     •  0.913
gw1.XIX.408.1
hypothetical protein (509 aa)
     •  0.911
fgenesh4_pg.C_LG_XIX000135
hypothetical protein (510 aa)
     •  0.909
eugene3.00060040
SubName- Full=Putative uncharacterized protein; (342 aa)
   • •• 0.907
eugene3.00190136
hypothetical protein (306 aa)
     •  0.900
gw1.V.3639.1
hypothetical protein (287 aa)
     •• 0.801

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 ?
Query294
TIGR01559337 TIGR01559, squal_synth, farnesyl-diphosphate farne 1e-157
cd00683265 cd00683, Trans_IPPS_HH, Trans-Isoprenyl Diphosphat 7e-84
pfam00494262 pfam00494, SQS_PSY, Squalene/phytoene synthase 1e-48
COG1562288 COG1562, ERG9, Phytoene/squalene synthetase [Lipid 2e-40
cd00867236 cd00867, Trans_IPPS, Trans-Isoprenyl Diphosphate S 3e-26
cd00385243 cd00385, Isoprenoid_Biosyn_C1, Isoprenoid Biosynth 5e-24
TIGR03465266 TIGR03465, HpnD, squalene synthase HpnD 2e-08
PLN02632334 PLN02632, PLN02632, phytoene synthase 6e-07
>gnl|CDD|188157 TIGR01559, squal_synth, farnesyl-diphosphate farnesyltransferase Back     alignment and domain information 
 Score =  442 bits (1138), Expect = e-157
 Identities = 165/264 (62%), Positives = 196/264 (74%), Gaps = 10/264 (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 EDCLKYMSALRDHAIFRFCAIPQV 291
            DCL Y+S LRD +IF FCAIPQV
Sbjct: 238 TDCLTYLSRLRDQSIFNFCAIPQV 261

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 294
TIGR01559336 squal_synth farnesyl-diphosphate farnesyltransfera 100.0
cd00683265 Trans_IPPS_HH Trans-Isoprenyl Diphosphate Synthase 100.0
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
COG1562288 ERG9 Phytoene/squalene synthetase [Lipid metabolis 100.0
PF00494267 SQS_PSY: Squalene/phytoene synthase; InterPro: IPR 100.0
KOG1459 413 consensus Squalene synthetase [Lipid transport and 100.0
KOG4411292 consensus Phytoene/squalene synthetase [Lipid tran 99.97
cd00867236 Trans_IPPS Trans-Isoprenyl Diphosphate Synthases. 99.82
cd00385243 Isoprenoid_Biosyn_C1 Isoprenoid Biosynthesis enzym 99.76
KOG1459413 consensus Squalene synthetase [Lipid transport and 99.11
PLN02890422 geranyl diphosphate synthase 96.26
TIGR02749322 prenyl_cyano solanesyl diphosphate synthase. Membe 96.16
cd00685259 Trans_IPPS_HT Trans-Isoprenyl Diphosphate Synthase 95.85
TIGR02748319 GerC3_HepT heptaprenyl diphosphate synthase compon 95.32
PRK10888323 octaprenyl diphosphate synthase; Provisional 95.1
CHL00151323 preA prenyl transferase; Reviewed 95.03
PLN02857416 octaprenyl-diphosphate synthase 94.92
PRK10581299 geranyltranstransferase; Provisional 94.17
PF00348260 polyprenyl_synt: Polyprenyl synthetase; InterPro: 92.78
COG0142322 IspA Geranylgeranyl pyrophosphate synthase [Coenzy 86.89
PF06330376 TRI5: Trichodiene synthase (TRI5); InterPro: IPR02 83.25
cd00868284 Terpene_cyclase_C1 Terpene cyclases, Class 1. Terp 81.46
>TIGR01559 squal_synth farnesyl-diphosphate farnesyltransferase Back     alignment and domain information 
Probab=100.00  E-value=3.2e-58  Score=429.59  Aligned_cols=255  Identities=63%  Similarity=1.067  Sum_probs=233.3

Q ss_pred             hHHHHHHHHhhcCccHHHHHHhcChhhhHHHHHHHHHHhhhccccCCCCCChhhhHHHHHHHHHHHccccccccc-CCCc
Q 022601           36 HWAFCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSC-GTKE  114 (294)
Q Consensus        36 ~~~~c~~~~r~~~~sfy~a~~llP~~~R~a~~alYAf~R~~DdI~D~~~~~~~~k~~~L~~w~~~l~~~~~~~~~-g~~~  114 (294)
                      ++++|.++++++|+|||+++++||+++|++++++|+|||++|||+|+.+.+.+.|...|++|.+.+.+..|.+.. +.+.
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            368999999999999999999999999999999999999999999998888888999999999999875554542 2455


Q ss_pred             cHHHHhhHHHHHHHHHhcChhHHHHHHHHHHHhhhHHHhhhh-hhc--CCHHHHHHHHHhhhhHHHHHHHHhhcccCCCC
Q 022601          115 YKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFIC-KEV--ESIDDYDEYCYYVAGLVGLGLSKLFYASGTED  191 (294)
Q Consensus       115 ~~~l~~al~~~~~~~~~~~~~~~~li~~~~~~m~~g~~~Dl~-~~~--~t~~dL~~Y~~~vAg~Vg~l~~~ll~~~~~~~  191 (294)
                      +..+++.++.+...|..++++++++|.+++.+|++||++|+. ..|  +|++||+.|||+|||+||+|+++|++..|..+
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            567888899999999999999999999999999999999995 567  99999999999999999999999997643322


Q ss_pred             C---ChhHHHHHHHHHHHHHHHHhchhhhhhcCCCCCccccHHHHHhcCCChhhhhcccCCHHHHHHHHHHHHHHHHHHH
Q 022601          192 L---APDSLSNSMGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVE  268 (294)
Q Consensus       192 ~---~~~~~A~~lG~AlQltniLRDi~~D~~~~~~gR~YLP~d~l~~~gv~~edl~~~~~~~~~~~~i~~~~~~A~~~l~  268 (294)
                      +   ...+.|.++|.|||+||||||++||+.   +||||||.|+|.+||++.+++..+++++++.+++.+++.+|+.||+
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   246899999999999999999999999   9999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhCCCchhhhhhhhhhhhc
Q 022601          269 DCLKYMSALRDHAIFRFCAIPQVRC  293 (294)
Q Consensus       269 ~A~~~~~~lp~~~~~~~c~~p~~~~  293 (294)
                      +|.+|+..|+.+++|.||+||++||
T Consensus       238 ~al~yl~~l~~~~~~~fcaip~~mA  262 (336)
T TIGR01559       238 DCLTYLSRLRDQSIFNFCAIPQVMA  262 (336)
T ss_pred             HHHHHHHhCCCcchhHHHHHHHHHH
Confidence            9999999999999999999999987

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.
>cd00683 Trans_IPPS_HH Trans-Isoprenyl Diphosphate Synthases, head-to-head Back     alignment and domain information
>PLN02632 phytoene synthase Back     alignment and domain information
>TIGR03464 HpnC squalene synthase HpnC 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
>PLN02890 geranyl diphosphate synthase Back     alignment and domain information
>TIGR02749 prenyl_cyano solanesyl diphosphate synthase 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
>PRK10888 octaprenyl diphosphate synthase; Provisional Back     alignment and domain information
>CHL00151 preA prenyl transferase; Reviewed Back     alignment and domain information
>PLN02857 octaprenyl-diphosphate synthase Back     alignment and domain information
>PRK10581 geranyltranstransferase; Provisional 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
>COG0142 IspA Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism] 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
>cd00868 Terpene_cyclase_C1 Terpene cyclases, Class 1 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 ?
Query294
1ezf_A340 Crystal Structure Of Human Squalene Synthase Length 7e-75
3vj8_A343 Crystal Structure Of The Human Squalene Synthase Le 8e-75
3lee_A340 Crystal Structure Of The Human Squalene Synthase Co 8e-75
3vjd_A293 Crystal Structure Of The Y248a Mutant Of C(30) Caro 6e-05
4f6v_A292 Crystal Structure Of Dehydrosqualene Synthase (Crtm 7e-05
2zco_A293 Crystal Structure Of The C(30) Carotenoid Dehydrosq 7e-05
4e9u_A287 Crystal Structure Of Dehydrosqualene Synthase (Crtm 7e-05
3ae0_A293 Crystal Structure Of The C(30) Carotenoid Dehydrosq 9e-05
3adz_A293 Crystal Structure Of The C(30) Carotenoid Dehydrosq 6e-04
>pdb|1EZF|A Chain A, Crystal Structure Of Human Squalene Synthase Length = 340 Back     alignment and structure 
Iteration: 1

 Score =  276 bits (707), Expect = 7e-75,   Method: Compositional matrix adjust.
 Identities = 138/255 (54%), Positives = 180/255 (70%), Gaps = 6/255 (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 LRDHAIFRFCAIPQV 291
           LR+ ++F FCAIPQV
Sbjct: 250 LRNQSVFNFCAIPQV 264
>pdb|3VJ8|A Chain A, Crystal Structure Of The Human Squalene Synthase Length = 343 Back     alignment and structure
>pdb|3LEE|A Chain A, Crystal Structure Of The Human Squalene Synthase Complexed With Bph- 652 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|4F6V|A Chain A, Crystal Structure Of Dehydrosqualene Synthase (Crtm) From S. Aureus Complexed With Bph-1034, Mg2+ And Fmp. Length = 292 Back     alignment and structure
>pdb|2ZCO|A Chain A, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Length = 293 Back     alignment and structure
>pdb|4E9U|A Chain A, Crystal Structure Of Dehydrosqualene Synthase (Crtm) From S. Aureus Complexed With A Thiocyanate Inhibitor Length = 287 Back     alignment and structure
>pdb|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 ?
Query294
3vj8_A343 Squalene synthase; farnesyl-diphosphate farnesyltr 1e-100
3acx_A293 Dehydrosqualene synthase; CRTM, carotenoid biosynt 6e-12
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-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 =  297 bits (763), Expect = e-100
 Identities = 137/261 (52%), Positives = 177/261 (67%), Gaps = 6/261 (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 LKYMSALRDHAIFRFCAIPQV 291
           + Y+S LR+ ++F FCAIPQV
Sbjct: 247 ITYLSRLRNQSVFNFCAIPQV 267
>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 ?
Query294
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 96.84
2q80_A301 Geranylgeranyl pyrophosphate synthetase; isoprenoi 96.25
1v4e_A299 Octoprenyl-diphosphate synthase; trans-type prenyl 96.19
3tc1_A315 Octaprenyl pyrophosphate synthase; all alpha-helic 96.08
3lmd_A360 Geranylgeranyl pyrophosphate synthase; isoprenyl d 95.95
3apz_A348 Geranyl diphosphate synthase; prenyltransferase, a 95.76
1rtr_A301 Geranyltranstransferase; 2.50A {Staphylococcus aur 95.71
4dhd_A358 Polyprenyl synthetase; isoprenoid synthesis, isopr 95.68
3uca_A324 Geranyltranstransferase; isoprenoid synthesis, iso 95.66
3mzv_A341 Decaprenyl diphosphate synthase; transferase, stru 95.63
2ftz_A284 Geranyltranstransferase; TM0161, structural GE joi 95.56
3nf2_A352 Putative polyprenyl synthetase; isoprenyl diphosph 95.51
3ipi_A295 Geranyltranstransferase; isoprene biosynthesis, he 95.48
3aqb_B325 Component B of hexaprenyl diphosphate synthase; pr 95.4
3pko_A334 Geranylgeranyl pyrophosphate synthase; isoprenyl d 95.35
4f62_A317 Geranyltranstransferase; enzyme function initiativ 95.23
3oyr_A345 Trans-isoprenyl diphosphate synthase; isoprenyl sy 95.22
1wmw_A330 Geranylgeranyl diphosphate synthetase; GGPP, preny 95.21
3m0g_A297 Farnesyl diphosphate synthase; structural genomics 95.11
3p8r_A302 Geranyltranstransferase; isoprenyl synthase, struc 94.84
2qis_A374 Farnesyl pyrophosphate synthetase; trans-prenyltra 94.83
3lom_A313 Geranyltranstransferase; geranyltransferase, struc 94.63
2ihi_A395 Pyrophosphate synthase; PV092040, structural genom 94.57
1yhl_A362 Farnesyl pyrophosphate synthase; farnesyl diphosph 94.54
3lsn_A304 Geranyltranstransferase; structural genomics, prot 94.51
2h8o_A335 Geranyltranstransferase; geranyltransferase,agroba 94.51
2azj_A289 Geranylgeranyl pyrophosphate synthetase; hexpps, t 94.51
1uby_A367 FPS, farnesyl diphosphate synthase; transferase, i 94.48
2e8v_A340 Geranylgeranyl pyrophosphate synthetase; prenyltra 94.46
3ts7_A324 Geranyltranstransferase; isoprenoid synthesis, far 94.37
1wy0_A342 Geranylgeranyl pyrophosphate synthetase; pyrococcu 94.19
3pde_A309 Farnesyl-diphosphate synthase; isoprenyl diphospha 94.05
3p8l_A302 Geranyltranstransferase; isoprenyl synthase, struc 94.02
2her_A368 Fragment, farnesyl pyrophosphate synthase; farnesy 93.98
3lk5_A380 Geranylgeranyl pyrophosphate synthase; structural 93.28
1rqj_A299 Geranyltranstransferase; bisphosphonate, isoprenyl 93.16
3dyh_A390 Farnesyl pyrophosphate synthase; protein-bisphosph 93.04
3llw_A311 Geranyltranstransferase (ISPA); structural genomic 89.24
3kra_B274 Geranyl diphosphate synthase small subunit; prenyl 89.2
3npk_A291 Geranyltranstransferase; isoprene biosynthesis, SG 89.15
3mav_A395 Farnesyl pyrophosphate synthase; PV092040, structu 86.03
2q58_A368 Fragment, farnesyl pyrophosphate synthase; farnesy 85.48
2j1p_A293 Geranylgeranyl pyrophosphate synthetase; transfera 84.49
3kb9_A382 EPI-isozizaene synthase; terpenoid cyclase, alpha- 80.1
>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=1.8e-57  Score=426.35  Aligned_cols=259  Identities=53%  Similarity=0.916  Sum_probs=238.6

Q ss_pred             CCchhHHHHHHHHhhcCccHHHHHHhcChhhhHHHHHHHHHHhhhccccCCCCCChhhhHHHHHHHHHHHcccccccccC
Q 022601           32 PPEPHWAFCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCG  111 (294)
Q Consensus        32 ~~~~~~~~c~~~~r~~~~sfy~a~~llP~~~R~a~~alYAf~R~~DdI~D~~~~~~~~k~~~L~~w~~~l~~~~~~~~~g  111 (294)
                      ++++++++|.++++++|+|||+++++||+++|++++++|+|||++|||+|+++.+++.|..+|+||++.+.+..|.+..+
T Consensus         8 ~l~~~~~~C~~~l~~~srsF~la~~lLp~~~R~av~alYaf~R~aDdI~D~~~~~~~~k~~~L~~~~~~l~~~~~~~~~~   87 (343)
T 3vj8_A            8 SLSSSLKTCYKYLNQTSRSFAAVIQALDGEMRNAVCIFYLVLRALDTLEDDMTISVEKKVPLLHNFHSFLYQPDWRFMES   87 (343)
T ss_dssp             CCCHHHHHHHHHHHHHHGGGHHHHHTCCTTHHHHHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHHTTCTTCCCCCC
T ss_pred             cchHHHHHHHHHHHhcCCcHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhccccCCHHHHHHHHHHHHHHHhcchhhhcCC
Confidence            58899999999999999999999999999999999999999999999999998888899999999999998754445534


Q ss_pred             CCccHHHHhhHHHHHHHHHhcChhHHHHHHHHHHHhhhHHHhhhhhhcCCHHHHHHHHHhhhhHHHHHHHHhhcccCCCC
Q 022601          112 TKEYKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFICKEVESIDDYDEYCYYVAGLVGLGLSKLFYASGTED  191 (294)
Q Consensus       112 ~~~~~~l~~al~~~~~~~~~~~~~~~~li~~~~~~m~~g~~~Dl~~~~~t~~dL~~Y~~~vAg~Vg~l~~~ll~~~~~~~  191 (294)
                      ++...+++..++.++..|..++..++++|.+++..|.+||++|+.++|+|++||+.|||+|||+||+|+++|++..+..+
T Consensus        88 ~~~~~~ll~~~p~v~~~f~~l~~~~~~~i~~~~~~m~~gm~~dl~~~~~t~~~L~~Yc~~vAg~VG~l~~~l~~~~~~~~  167 (343)
T 3vj8_A           88 KEKDRQVLEDFPTISLEFRNLAEKYQTVIADICRRMGIGMAEFLDKHVTSEQEWDKYCHYVAGLVGIGLSRLFSASEFED  167 (343)
T ss_dssp             CSTTTHHHHTHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHGGGCCCCSHHHHHHHHHHHTHHHHHHHHHHHHHHTSSC
T ss_pred             ChhhHHHHhcCcHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHhccCCCCCHHHHHHHHHhCcHHHHHHHHHHhCCCCCcc
Confidence            55666788888888889988998899999999999999999999989999999999999999999999999998643212


Q ss_pred             C---ChhHHHHHHHHHHHHHHHHhchhhhhhcCCCCCccccHHHHHhcCCChhhhhcccCCHHHHHHHHHHHHHHHHHHH
Q 022601          192 L---APDSLSNSMGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVE  268 (294)
Q Consensus       192 ~---~~~~~A~~lG~AlQltniLRDi~~D~~~~~~gR~YLP~d~l~~~gv~~edl~~~~~~~~~~~~i~~~~~~A~~~l~  268 (294)
                      +   ...+.|.++|.|+|+||||||+++|+.   +||+|||.|+|.+||++.+||.++++++++++++++++++|+.||.
T Consensus       168 ~~~~~~~~~A~~lG~AlQltNilRDv~eD~~---~gR~YlP~e~l~~~g~~~~dl~~~~~~~~~~~~l~~l~~~A~~~~~  244 (343)
T 3vj8_A          168 PLVGEDTERANSMGLFLQKTNIIRDYLEDQQ---GGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELITNALHHIP  244 (343)
T ss_dssp             HHHHHCHHHHHHHHHHHHHHHHHHTHHHHHH---TTCCCSCHHHHTTTCSSGGGGGSGGGHHHHHHHHHHHHHHHHTTHH
T ss_pred             chhhhHHHHHHHHHHHHHHHHHHHHhHHHHh---CCCeeCCHHHHHHcCCCHHHHhcccCCHHHHHHHHHHHHHHHHHHH
Confidence            2   356899999999999999999999999   9999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhCCCchhhhhhhhhhhhc
Q 022601          269 DCLKYMSALRDHAIFRFCAIPQVRC  293 (294)
Q Consensus       269 ~A~~~~~~lp~~~~~~~c~~p~~~~  293 (294)
                      +|++++..||+++.+.||+||+.+|
T Consensus       245 ~a~~~~~~L~~~~~~~~~~ip~~lA  269 (343)
T 3vj8_A          245 DVITYLSRLRNQSVFNFCAIPQVMA  269 (343)
T ss_dssp             HHHHHHHTCCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCccchhhHHHHHHHHH
Confidence            9999999999999999999999886
>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
>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
>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
>3tc1_A Octaprenyl pyrophosphate synthase; all alpha-helices fold, transferase; 2.00A {Helicobacter pylori} 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
>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
>1rtr_A Geranyltranstransferase; 2.50A {Staphylococcus aureus} SCOP: a.128.1.1 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
>3uca_A Geranyltranstransferase; isoprenoid synthesis, isoprenoid diphosphate synthase; 2.00A {Clostridium perfringens} 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
>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
>3nf2_A Putative polyprenyl synthetase; isoprenyl diphosphate synthase, structural genomics, PSI, PR structure initiative, nysgrc; 2.20A {Streptomyces coelicolor} 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
>3aqb_B Component B of hexaprenyl diphosphate synthase; prenyltransferase, transferase; 2.40A {Micrococcus luteus} PDB: 3aqc_B* Back     alignment and structure
>3pko_A Geranylgeranyl pyrophosphate synthase; isoprenyl diphosphate synthase, structural genomics, PSI, PR structure initiative, nysgrc; HET: CIT; 1.98A {Lactobacillus brevis} PDB: 3n3d_A Back     alignment and structure
>4f62_A Geranyltranstransferase; enzyme function initiative, structural genomics; 2.10A {Marinomonas SP} 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
>1wmw_A Geranylgeranyl diphosphate synthetase; GGPP, prenyl diphosphate synthase, structural genom riken structural genomics/proteomics initiative; 1.55A {Thermus thermophilus} 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
>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
>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
>3lom_A Geranyltranstransferase; geranyltransferase, structural genomics, PSI, protein structure initiative, nysgrc; 2.30A {Legionella pneumophila subsp} 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
>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
>2h8o_A Geranyltranstransferase; geranyltransferase,agrobacterium tumefaciens, structural GEN PSI-2, protein structure initiative; 1.60A {Agrobacterium tumefaciens} Back     alignment and structure
>2azj_A Geranylgeranyl pyrophosphate synthetase; hexpps, trans-prenyltransferase; 2.40A {Sulfolobus solfataricus} PDB: 2azk_A 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
>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
>3ts7_A Geranyltranstransferase; isoprenoid synthesis, farnesyl diphosphate synthase; 1.94A {Methylococcus capsulatus} 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
>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
>3p8l_A Geranyltranstransferase; isoprenyl synthase, structural genomics, PSI, protein struct initiative, nysgrc; 2.00A {Enterococcus faecalis} 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
>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
>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
>3llw_A Geranyltranstransferase (ISPA); structural genomics, PSI, protein structure initiative, nysgrc; 2.30A {Helicobacter pylori} PDB: 3q1o_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
>3npk_A Geranyltranstransferase; isoprene biosynthesis, SGX, structural genomics protein structure initiative; 1.50A {Campylobacter jejuni} Back     alignment and structure
>3mav_A Farnesyl pyrophosphate synthase; PV092040, structural genomics, structural genomics consortium, SGC, transferase, isoprene biosynthesis; 2.10A {Plasmodium vivax} PDB: 3cc9_A* 3ez3_A* 3ldw_A* 3mys_A* 3ph7_A* 3rbm_A* 3ryw_A* Back     alignment and structure
>2q58_A Fragment, farnesyl pyrophosphate synthase; farnesyl diphosphate synthase, structural genomics, structur genomics consortium, SGC; HET: ZOL; 2.37A {Cryptosporidium parvum} PDB: 2o1o_A* Back     alignment and structure
>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
>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

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 294
d1ezfa_333 a.128.1.2 (A:) Squalene synthase {Human (Homo sapi 6e-64
>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 =  202 bits (514), Expect = 6e-64
 Identities = 137/257 (53%), Positives = 177/257 (68%), Gaps = 6/257 (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 SALRDHAIFRFCAIPQV 291
           S LR+ ++F FCAIPQV
Sbjct: 241 SRLRNQSVFNFCAIPQV 257

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query294
d1ezfa_333 Squalene synthase {Human (Homo sapiens) [TaxId: 96 100.0
d2q80a1291 Geranylgeranyl pyrophosphate synthetase {Human (Ho 96.35
d1v4ea_280 Octoprenyl-diphosphate synthase {Thermotoga mariti 95.09
d1kiya_354 Trichodiene synthase {Fusarium sporotrichioides [T 94.24
d1fpsa_348 Farnesyl diphosphate synthase (geranyltranstransfe 91.7
d1rqja_299 Farnesyl diphosphate synthase (geranyltranstransfe 90.63
d1rtra_290 Farnesyl diphosphate synthase (geranyltranstransfe 88.73
>d1ezfa_ a.128.1.2 (A:) Squalene synthase {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
class: All alpha proteins
fold: Terpenoid synthases
superfamily: Terpenoid synthases
family: Squalene synthase
domain: Squalene synthase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.8e-56  Score=416.12  Aligned_cols=256  Identities=54%  Similarity=0.924  Sum_probs=234.7

Q ss_pred             hhHHHHHHHHhhcCccHHHHHHhcChhhhHHHHHHHHHHhhhccccCCCCCChhhhHHHHHHHHHHHcccccccccCCCc
Q 022601           35 PHWAFCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGTKE  114 (294)
Q Consensus        35 ~~~~~c~~~~r~~~~sfy~a~~llP~~~R~a~~alYAf~R~~DdI~D~~~~~~~~k~~~L~~w~~~l~~~~~~~~~g~~~  114 (294)
                      +++++|.++++++|+|||+++++||+++|++++++|+|||.+|||+|+...+.+.|...|++|++.+.+..+....+.+.
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            47899999999999999999999999999999999999999999999988888899999999999998743222224556


Q ss_pred             cHHHHhhHHHHHHHHHhcChhHHHHHHHHHHHhhhHHHhhhhhhcCCHHHHHHHHHhhhhHHHHHHHHhhcccCCCC---
Q 022601          115 YKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFICKEVESIDDYDEYCYYVAGLVGLGLSKLFYASGTED---  191 (294)
Q Consensus       115 ~~~l~~al~~~~~~~~~~~~~~~~li~~~~~~m~~g~~~Dl~~~~~t~~dL~~Y~~~vAg~Vg~l~~~ll~~~~~~~---  191 (294)
                      +++++.++++++..|..+++.++..+.++++.|..||..++.++|+|++||+.|||+|||+||+|+++|++..+...   
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            77899999999999999998888899999999999999988889999999999999999999999999998643222   


Q ss_pred             CChhHHHHHHHHHHHHHHHHhchhhhhhcCCCCCccccHHHHHhcCCChhhhhcccCCHHHHHHHHHHHHHHHHHHHHHH
Q 022601          192 LAPDSLSNSMGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCL  271 (294)
Q Consensus       192 ~~~~~~A~~lG~AlQltniLRDi~~D~~~~~~gR~YLP~d~l~~~gv~~edl~~~~~~~~~~~~i~~~~~~A~~~l~~A~  271 (294)
                      .+..+.|.++|.|+|+||||||+++|++   +||||||.|+|++||++.+++.+++.+++++.++.+++++|+.||++|.
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            2346789999999999999999999999   9999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhCCCchhhhhhhhhhhhc
Q 022601          272 KYMSALRDHAIFRFCAIPQVRC  293 (294)
Q Consensus       272 ~~~~~lp~~~~~~~c~~p~~~~  293 (294)
                      +|+..||.++.+.||.||++++
T Consensus       238 ~y~~~lp~~~~~~~~~~~~~~a  259 (333)
T d1ezfa_         238 TYLSRLRNQSVFNFCAIPQVMA  259 (333)
T ss_dssp             HHHHTCCCHHHHHHHHHHHHHH
T ss_pred             HHHHHCCchhHHHHHHHHHHHH
Confidence            9999999999999999999876
>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
>d1rtra_ a.128.1.1 (A:) Farnesyl diphosphate synthase (geranyltranstransferase) {Staphylococcus aureus [TaxId: 1280]} Back     information, alignment and structure