D-I-TASSER P14324

D-I-TASSER results for P14324

[Click result.zip to download all results on this page]

Summary of the Protein

Uniprot ID: P14324
Protein Name: Farnesyl pyrophosphate synthase
Gene Name: FDPS

Input Sequence in FASTA format

>P14324 (419 residues)
MPLSRWLRSVGVFLLPAPYWAPRERWLGSLRRPSLVHGYPVLAWHSARCWCQAWTEEPRA
LCSSLRMNGDQNSDVYAQEKQDFVQHFSQIVRVLTEDEMGHPEIGDAIARLKEVLEYNAI
GGKYNRGLTVVVAFRELVEPRKQDADSLQRAWTVGWCVELLQAFFLVADDIMDSSLTRRG
QICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPYYLNLIELFLQSSYQTEIGQTLD
LLTAPQGNVDLVRFTEKRYKSIVKYKTAFYSFYLPIAAAMYMAGIDGEKEHANAKKILLE
MGEFFQIQDDYLDLFGDPSVTGKIGTDIQDNKCSWLVVQCLQRATPEQYQILKENYGQKE
AEKVARVKALYEELDLPAVFLQYEEDSYSHIMALIEQYAAPLPPAVFLGLARKIYKRRK

Predicted Contact and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

D-I-TASSER simulation is guided by the consensus contact map (left figure) and distance map (right figure) derived based on confidence scores of AttentionPotential. In the contact, distance map and hydrogen bond networks, the axes mark the residue index along the sequence. For the contact map, each dot represents a residue pair with predicted contact, while for the distance map and hydrogen bond network, a color scale represents a distance of 1-20+ angstroms or a angle of 0-180 degree.

Information of Domain

No. of Domain	Domain	Domain Boundary	Length of Domain	Models of Domain	Sequence
1	P14324-D1	1-71	71		MPLSRWLRSVGVFLLPAPYWAPRERWLGSLRRPSLVHGYPVLAWHSARCWCQAWTEEPRALCSSLRMNGDQ
2	P14324-D2	72-216	145		NSDVYAQEKQDFVQHFSQIVRVLTEDEMGHPEIGDAIARLKEVLEYNAIGGKYNRGLTVVVAFRELVEPRKQDADSLQRAWTVGWCVELLQAFFLVADDIMDSSLTRRGQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQ
3	P14324-D3	217-302	86		PYYLNLIELFLQSSYQTEIGQTLDLLTAPQGNVDLVRFTEKRYKSIVKYKTAFYSFYLPIAAAMYMAGIDGEKEHANAKKILLEMG
4	P14324-D4	303-419	117		EFFQIQDDYLDLFGDPSVTGKIGTDIQDNKCSWLVVQCLQRATPEQYQILKENYGQKEAEKVARVKALYEELDLPAVFLQYEEDSYSHIMALIEQYAAPLPPAVFLGLARKIYKRRK

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.73

(a)

D-I-TASSER simulations generate a large ensemble of structural conformations, i.e. decoys. These decoys are clustered by SPICKER based on pairwise structure similarity to report up to five final models from the five largest clusters. Models are ranked in descending order of cluster size. If the simulations converge well, it is possible to have less than 5 models generated, which is usually an indication of good model quality.

(b)

The model confidence is quantitatified by estimated TM-score (eTM-score), calculated based on significance of threading template alignments, contact map satisfaction rate, mean absolute error between distance of model and distance of AttentionPotential, and convergence of D-I-TASSER simulations. eTM-score is typically in the range of [0, 1], with higher eTM-score signifies higher model confidence.

Proteins with similar structure

Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	2f8zF	0.81	1.21	0.997	0.826	model1_2f8zF.pdb.gz
2	1fpsA	0.79	1.99	0.693	0.831	model1_1fpsA.pdb.gz
3	4jzbA	0.78	1.72	0.360	0.816	model1_4jzbA.pdb.gz
4	2ewgA	0.78	1.74	0.377	0.816	model1_2ewgA.pdb.gz
5	3cc9B	0.77	1.64	0.325	0.797	model1_3cc9B.pdb.gz
6	6b02A	0.76	1.93	0.420	0.802	model1_6b02A.pdb.gz
7	4kk2A	0.76	2.10	0.444	0.807	model1_4kk2A.pdb.gz
8	2o1oA	0.73	2.29	0.255	0.778	model1_2o1oA.pdb.gz
9	7buuA	0.70	2.75	0.411	0.776	model1_7buuA.pdb.gz
10	3lk5A	0.69	2.64	0.191	0.764	model1_3lk5A.pdb.gz

(a)	Query structure is shown in cartoon, while the structural analog is displayed using backbone trace.
(b)	Ranking of proteins is based on TM-score of the structural alignment between the query structure and known structures in the PDB library.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Gene Ontology (GO) Terms

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:0004659	1.00	prenyltransferase activity
GO:0004337	0.96	geranyltranstransferase activity
GO:0004161	0.94	dimethylallyltranstransferase activity

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Molecular Function. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0044763	1.00	single-organism cellular process
GO:0008152	1.00	metabolic process
GO:0006720	0.99	isoprenoid metabolic process
GO:0008299	0.98	isoprenoid biosynthetic process
GO:0016114	0.96	terpenoid biosynthetic process
GO:0008654	0.96	phospholipid biosynthetic process
GO:0045337	0.93	farnesyl diphosphate biosynthetic process

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Biological Process. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0044424	1.00	intracellular part
GO:0005737	0.94	cytoplasm
GO:0044444	0.63	cytoplasmic part

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Cellular Component. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Predicted Enzyme Commission (EC) Numbers

Top 5 enzyme homologs in PDB

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	EC Number	Predicted Active Site Residues
1	0.659	2f8zF	0.807	1.21	0.997	0.826	2.5.1.10 2.5.1.1	122,166,173,176,178,181,312,314,316,318,320,322,324,326,330,419
2	0.598	2ewgA	0.782	1.74	0.377	0.816	2.5.1.10	178,305
3	0.487	1rqiA	0.637	2.33	0.221	0.690	2.5.1.10	178,305
4	0.477	2ftzA	0.567	2.55	0.195	0.625	2.5.1.10	178,305
5	0.459	2j1pB	0.567	2.90	0.190	0.637	2.5.1.1 2.5.1.10 2.5.1.29	178,305

	Click on the radio buttons to visualize predicted active site residues.
(a)	Cscore^EC is the confidence score for the Enzyme Commission (EC) number prediction. Cscore^EC values range in between [0-1]; where a higher score indicates a more reliable EC number prediction.
(b)	TM-score is a measure of global structural similarity between query and template protein.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Ligand Binding Sites

Template proteins with similar binding site:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.85	2rahA	0.792	1.26	0.991	0.811	1.30	11P	complex1.pdb.gz	166,169,178,237,266,267,270,306,310
2	0.74	1zw5A	0.790	1.23	0.994	0.809	1.76	IPR	complex2.pdb.gz	122,123,126,162,179,267,270,305,306,309
3	0.66	2f92F	0.799	1.26	0.997	0.819	1.19	AHD	complex3.pdb.gz	169,173,178,266,267,270,309
4	0.56	3ph7C	0.716	1.37	0.333	0.738	1.62	GRG	complex4.pdb.gz	122,123,126,162,165,168,172,178,179,233,234,237,266,270,305
5	0.54	3n1vF	0.790	1.49	0.991	0.819	1.53	3N1	complex5.pdb.gz	123,125,126,129,271,272,305,410,413
6	0.48	2qis0	0.792	1.24	0.991	0.811	1.93	III	complex6.pdb.gz	103,104,106,107,110,164,168,171,172,192,193,195,196,199,200,202,203,206,207,210,214,219,220,223,224,227,231,234,235,237,238,239,241,242,258,261,265
7	0.45	1ubxA	0.785	1.92	0.684	0.828	1.22	FPP	complex7.pdb.gz	161,165,168,169,178,230,234,266
8	0.37	3n1wF	0.789	1.51	0.997	0.819	1.05	3N2	complex8.pdb.gz	125,126,129,271,272
9	0.32	2p1cA	0.777	1.88	0.374	0.816	1.16	GG3	complex9.pdb.gz	165,169,172,173,178,233,234,237,266,267,270,306,309
10	0.29	2i19B	0.781	1.76	0.374	0.816	1.15	MG	complex10.pdb.gz	169,173,237

	Click on the radio buttons to visualize predicted binding site and residues.
(a)	Cscore^LB is the confidence score of predicted binding site. Cscore^LB values range in between [0-1]; where a higher score indicates a more reliable ligand-binding site prediction.
(b)	BS-score is a measure of local similarity (sequence & structure) between template binding site and predicted binding site in the query structure. Based on large scale benchmarking analysis, we have observed that a BS-score >1 reflects a significant local match between the predicted and template binding site.
(c)	TM-score is a measure of global structural similarity between query and template protein.
(d)	RMSD^a the RMSD between residues that are structurally aligned by TM-align.
(e)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(f)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

[Click result.zip to download all results on this page]

References:
1.	Wei Zheng, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.