YRC Public Data Repository - Protein Structure Prediction

Protein:	SPS2_ARATH
Organism:	Arabidopsis thaliana
Length:	417 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

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Top Sequence Alignment Hits

Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for SPS2_ARATH.

Description	E-value	Query Range	Subject Range
SPS1_ARATH - Solanesyl diphosphate synthase 1 OS=Arabidopsis thaliana GN=SPS1 PE=1 SV=1	351.0	[0..1]	[417..1]
gi\|90200410 - gi\|90200410\|gb\|ABD92707.1\| solanesyl diphosphate synthase [Hevea brasiliensis]	350.0	[0..1]	[417..2]
gi\|114324644 - gi\|114324644\|gb\|ABI63627.1\| solanesyl diphosphate synthase [Lycopersicon esculentum]	332.0	[0..1]	[416..2]
gi\|62129446, gi\|... - gi\|62181813\|ref\|YP_218230.1\| octaprenyl diphosphate synthase [Salmonella enterica subsp. enterica se... lcl\|NC_016856.1_... - [gene=ispB] [protein=octaprenyl diphosphate synthase] [protein_id=YP_005239484.1] [location=3487069....	327.0	[0..93]	[415..59]
gi\|119775962, gi... - gi\|68545618\|ref\|ZP_00585168.1\| Trans-hexaprenyltranstransferase [Shewanella amazonensis SB2B], gi\|68...	325.0	[0..83]	[417..1]
gi\|19887236, gi\|... - gi\|20094211\|ref\|NP_614058.1\| geranylgeranyl pyrophosphate synthase [Methanopyrus kandleri AV19], gi\|...	325.0	[0..96]	[415..3]
gi\|187730997, gi... - gi\|75176121\|ref\|ZP_00696289.1\| COG0142: Geranylgeranyl pyrophosphate synthase [Shigella boydii BS512...	322.0	[0..93]	[415..1]
gi\|75228148 - gi\|75228148\|ref\|ZP_00714813.1\| COG0142: Geranylgeranyl pyrophosphate synthase [Escherichia coli B7A] gi\|75511910, gi\|... - gi\|75511910\|ref\|ZP_00734522.1\| COG0142: Geranylgeranyl pyrophosphate synthase [Escherichia coli 5363... gi\|194439175, gi... - gi\|83585435\|ref\|ZP_00924081.1\| COG0142: Geranylgeranyl pyrophosphate synthase [Escherichia coli 101-... gi\|157155105, gi... - gi\|75187993\|ref\|ZP_00701260.1\| COG0142: Geranylgeranyl pyrophosphate synthase [Escherichia coli E243... gi\|89109950, gi\|... - gi\|89109950\|ref\|AP_003730.1\| octaprenyl diphosphate synthase [Escherichia coli str. K-12 substr. W31... gi\|74313724, gi\|... - gi\|74313724\|ref\|YP_312143.1\| octaprenyl diphosphate synthase [Shigella sonnei Ss046], gi\|73857201\|gb... gi\|81246986, gi\|... - gi\|82545575\|ref\|YP_409522.1\| octaprenyl diphosphate synthase [Shigella boydii Sb227], gi\|81246986\|gb... gi\|110807053, gi... - gi\|110807053\|ref\|YP_690573.1\| octaprenyl diphosphate synthase [Shigella flexneri 5 str. 8401], gi\|11... gi\|238902289, gi... - gi\|238902289\|ref\|YP_002928085.1\| octaprenyl diphosphate synthase [Escherichia coli BW2952], gi\|23886... gi\|242378730, gi... - gi\|251786457\|ref\|YP_003000761.1\| hypothetical protein B21_03003 [Escherichia coli BL21], gi\|24237873... gi\|253323023, gi... - gi\|254289879\|ref\|YP_003055627.1\| octaprenyl diphosphate synthase [Escherichia coli BL21(DE3)], gi\|25... gi\|254163129, gi... - gi\|254163129\|ref\|YP_003046237.1\| octaprenyl diphosphate synthase [Escherichia coli B str. REL606], g... ISPB_ECOLI - Octaprenyl-diphosphate synthase (EC 2.5.1.-) (Octaprenyl pyrophosphate synthetase) (OPP synthetase) ... gi\|170765991, gi... - gi\|170765991\|ref\|ZP_02900802.1\| octaprenyl-diphosphate synthase [Escherichia albertii TW07627], gi\|1... ISPB_SHIFL - Octaprenyl-diphosphate synthase OS=Shigella flexneri GN=ispB PE=3 SV=1 gi\|169890557, gi... - gi\|170082722\|ref\|YP_001732042.1\| octaprenyl diphosphate synthase [Escherichia coli str. K-12 substr.... gi\|209920662, gi... - gi\|209920662\|ref\|YP_002294746.1\| octaprenyl diphosphate synthase [Escherichia coli SE11], gi\|2099139... gi\|194417271, gi... - gi\|194434492\|ref\|ZP_03066752.1\| octaprenyl-diphosphate synthase [Shigella dysenteriae 1012], gi\|1944... EG10017 - octaprenyl diphosphate synthase / Octaprenyl diphosphate synthase, isoprenoid biosynthesis gi\|218353624, gi... - gi\|218696892\|ref\|YP_002404559.1\| octaprenyl diphosphate synthase [Escherichia coli 55989], gi\|218353... gi\|218555757, gi... - gi\|218555757\|ref\|YP_002388670.1\| octaprenyl diphosphate synthase [Escherichia coli IAI1], gi\|2183625... gi\|24114476, gi\|... - gi\|24114476\|ref\|NP_708986.1\| octaprenyl diphosphate synthase [Shigella flexneri 2a str. 301], gi\|240... gi\|218706807, gi... - gi\|218706807\|ref\|YP_002414326.1\| octaprenyl diphosphate synthase [Escherichia coli UMN026], gi\|21843... gi\|30042784, gi\|... - gi\|30064525\|ref\|NP_838696.1\| octaprenyl diphosphate synthase [Shigella flexneri 2a str. 2457T], gi\|3... gi\|218701956, gi... - gi\|218701956\|ref\|YP_002409585.1\| octaprenyl diphosphate synthase [Escherichia coli IAI39], gi\|218371... gi\|169753491, gi... - gi\|170018563\|ref\|YP_001723517.1\| octaprenyl diphosphate synthase [Escherichia coli ATCC 8739], gi\|16... EG10017 - octaprenyl diphosphate synthase / Octaprenyl diphosphate synthase, isoprenoid biosynthesis	322.0	[0..93]	[415..1]

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Predicted Domain #1

Region A:
Residues: [1-92]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MMMSCRNIDL GTSVLDHSCS SSSTSRRFLF GNSSKTVCMI GGRSCVGNLV FLRRDLATCR  60
   61 AVPAKSKENS LVNGIGQDQT VMLNLRQESR KP

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below are all of our de novo (Rosetta) predictions for this domain.
Click here to view only most confident match.

		MCM Score	SCOP Match	SCOP Description
View	Download	0.498	d.93.1	SH2 domain
View	Download	0.498	d.93.1	SH2 domain
View	Download	0.455	d.93.1	SH2 domain
View	Download	0.432	d.93.1	SH2 domain
View	Download	0.416	d.93.1	SH2 domain
View	Download	0.393	d.93.1	SH2 domain
View	Download	0.376	d.106.1	Sterol carrier protein, SCP
View	Download	0.357	b.101.1	Ribonuclease domain of colicin E3
View	Download	0.357	b.101.1	Ribonuclease domain of colicin E3
View	Download	0.331	d.93.1	SH2 domain

Predicted Domain #2

Region A:
Residues: [93-417]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ISLETLFEVV ADDLQRLNDN LLSIVGAENP VLISAAEQIF SAGGKRMRPG LVFLVSRATA  60
   61 ELAGLKELTV EHRRLGEIIE MIHTASLIHD DVLDESDMRR GRETVHELFG TRVAVLAGDF 120
  121 MFAQASWYLA NLENLEVIKL ISQVIKDFAS GEIKQASSLF DCDVKLDDYM LKSYYKTASL 180
  181 VAASTKGAAI FSKVESKVAE QMYQFGKNLG LSFQVVDDIL DFTQSTEQLG KPAANDLAKG 240
  241 NITAPVIFAL ENEPRLREII ESEFCEPGSL EEAIEIVRNR GGIKKAQELA KEKAELALKN 300
  301 LNCLPRSGFR SALEDMVMFN LERID

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	82.0
Match:	1wy0A
Description:	Crystal structure of geranylgeranyl pyrophosphate synthetase from Pyrococcus horikoshii Ot3
Matching Structure (courtesy of the PDB):

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2

View Structure Prediction Details

Top Sequence Alignment Hits