D-I-TASSER O95749

D-I-TASSER results for O95749

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

Summary of the Protein

Uniprot ID: O95749
Protein Name: Geranylgeranyl pyrophosphate synthase
Gene Name: GGPS1

Input Sequence in FASTA format

>O95749 (300 residues)
MEKTQETVQRILLEPYKYLLQLPGKQVRTKLSQAFNHWLKVPEDKLQIIIEVTEMLHNAS
LLIDDIEDNSKLRRGFPVAHSIYGIPSVINSANYVYFLGLEKVLTLDHPDAVKLFTRQLL
ELHQGQGLDIYWRDNYTCPTEEEYKAMVLQKTGGLFGLAVGLMQLFSDYKEDLKPLLNTL
GLFFQIRDDYANLHSKEYSENKSFCEDLTEGKFSFPTIHAIWSRPESTQVQNILRQRTEN
IDIKKYCVHYLEDVGSFEYTRNTLKELEAKAYKQIDARGGNPELVALVKHLSKMFKEENE

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 DeepPotential. 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	O95749-D1	1-300	300		MEKTQETVQRILLEPYKYLLQLPGKQVRTKLSQAFNHWLKVPEDKLQIIIEVTEMLHNASLLIDDIEDNSKLRRGFPVAHSIYGIPSVINSANYVYFLGLEKVLTLDHPDAVKLFTRQLLELHQGQGLDIYWRDNYTCPTEEEYKAMVLQKTGGLFGLAVGLMQLFSDYKEDLKPLLNTLGLFFQIRDDYANLHSKEYSENKSFCEDLTEGKFSFPTIHAIWSRPESTQVQNILRQRTENIDIKKYCVHYLEDVGSFEYTRNTLKELEAKAYKQIDARGGNPELVALVKHLSKMFKEENE

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.9504

(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 DeepPotential, 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	6v0kA	0.95	1.29	0.495	0.977	model1_6v0kA.pdb.gz
2	2q80A	0.93	0.85	0.996	0.950	model1_2q80A.pdb.gz
3	2dh4A	0.90	2.22	0.413	0.967	model1_2dh4A.pdb.gz
4	2ewgA	0.85	2.62	0.168	0.970	model1_2ewgA.pdb.gz
5	4jyxA	0.85	2.19	0.206	0.940	model1_4jyxA.pdb.gz
6	6kd7A	0.85	2.51	0.231	0.963	model1_6kd7A.pdb.gz
7	2f8zF	0.85	2.63	0.199	0.970	model1_2f8zF.pdb.gz
8	5h9dA	0.85	2.47	0.195	0.953	model1_5h9dA.pdb.gz
9	6w7iA	0.85	2.73	0.171	0.970	model1_6w7iA.pdb.gz
10	3aqbB	0.85	2.63	0.199	0.960	model1_3aqbB.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:0016765	1.00	transferase activity, transferring alkyl or aryl (other than methyl) groups
GO:0004659	0.88	prenyltransferase activity
GO:0004311	0.51	farnesyltranstransferase 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:0044699	1.00	single-organism process
GO:0044763	0.98	single-organism cellular process
GO:0008152	0.95	metabolic process
GO:0044710	0.93	single-organism metabolic process
GO:0071704	0.91	organic substance metabolic process
GO:0044237	0.91	cellular metabolic process
GO:0044238	0.84	primary metabolic process
GO:0006629	0.79	lipid metabolic process
GO:0044255	0.78	cellular lipid metabolic process
GO:0006720	0.77	isoprenoid metabolic process
GO:0009058	0.73	biosynthetic process
GO:1901576	0.72	organic substance biosynthetic process
GO:0044711	0.71	single-organism biosynthetic process
GO:0044249	0.68	cellular biosynthetic process
GO:0008610	0.61	lipid biosynthetic process
GO:0008299	0.56	isoprenoid 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:0044444	0.85	cytoplasmic part
GO:0043226	0.53	organelle
GO:0043229	0.52	intracellular organelle
GO:0043231	0.50	intracellular membrane-bounded organelle

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	0.523	2ftzA	0.733	2.38	0.234	0.813	2.5.1.10	73,184
2	0.522	1wmwA	0.845	2.69	0.209	0.960	2.5.1.-	73,184
3	0.505	2z4yB	0.820	1.60	0.427	0.850	2.5.1.29	73
4	0.496	2f89F	0.849	2.63	0.202	0.970	2.5.1.1 2.5.1.10	73,184
5	0.451	2h8oA	0.696	2.52	0.241	0.787	2.5.1.10	73,184

	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	0.94	2q80F	0.933	0.79	0.996	0.947	1.84	GRG	complex1.pdb.gz	64,68,73,126,151,152,155,156,185,188,202
2	0.87	2q80A	0.935	0.85	0.996	0.950	1.69	MG	complex2.pdb.gz	64,68,126
3	0.85	2q80A	0.935	0.85	0.996	0.950	1.40	MG	complex3.pdb.gz	64,68,202
4	0.74	2zeuB	0.880	2.08	0.409	0.930	1.46	B71	complex4.pdb.gz	28,31,53,64,73,151,155,159,184,185,188,212
5	0.73	2z78A	0.901	2.33	0.412	0.963	1.43	H86	complex5.pdb.gz	28,32,53,57,60,61,63,64,68,73,122,126,152,156,184,185,188,212
6	0.73	2e93A	0.872	1.65	0.426	0.907	1.59	B29	complex6.pdb.gz	24,25,28,53,54,57,60,61,64,73,74,96,119,122,123,126,151,155,156,184,185,188,202
7	0.72	2e8uB	0.891	1.76	0.423	0.930	1.70	IPE	complex7.pdb.gz	61,64,68,73,122,151,185,188,212
8	0.68	2z52B	0.852	2.03	0.413	0.897	1.64	H23	complex8.pdb.gz	60,64,68,73,96,119,122,123,126,151,188,212
9	0.67	2z7iA	0.891	1.99	0.416	0.943	1.41	742	complex9.pdb.gz	35,57,61,64,68,73,151,152,156,159,177,185,188,212
10	0.64	2e8uA	0.834	1.77	0.425	0.867	0.93	IPE	complex10.pdb.gz	57,61,74,184,185

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.