D-I-TASSER P0C7P2

D-I-TASSER results for P0C7P2

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

Summary of the Protein

Uniprot ID: P0C7P2
Protein Name: Putative protein RFPL3S
Gene Name: RFPL3S

Input Sequence in FASTA format

>P0C7P2 (107 residues)
MQTDTSNLSARSCRFCVMSPLRTLLRSSEMRRKLLAVSASKVISTVKRKTSCSASGQKPT
PCLSSTSKAQISPDFSFFNSVSSSKIKTFHEETSLFQIFIGMLCGNT

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	P0C7P2-D1	1-107	107		MQTDTSNLSARSCRFCVMSPLRTLLRSSEMRRKLLAVSASKVISTVKRKTSCSASGQKPTPCLSSTSKAQISPDFSFFNSVSSSKIKTFHEETSLFQIFIGMLCGNT

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.6077

(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	6vejA	0.68	3.45	0.038	0.981	model1_6vejA.pdb.gz
2	4wd7A	0.66	2.63	0.058	0.869	model1_4wd7A.pdb.gz
3	6xe6A	0.64	3.52	0.087	0.963	model1_6xe6A.pdb.gz
4	2lkgA	0.64	2.98	0.048	0.906	model1_2lkgA.pdb.gz
5	1sj8A2	0.63	3.17	0.028	0.906	model1_1sj8A2.pdb.gz
6	3d2rB1	0.63	3.49	0.037	0.953	model1_3d2rB1.pdb.gz
7	1y8pA	0.62	3.71	0.047	0.953	model1_1y8pA.pdb.gz
8	3crlB1	0.61	3.53	0.028	0.944	model1_3crlB1.pdb.gz
9	2q8gA1	0.61	3.75	0.037	0.953	model1_2q8gA1.pdb.gz
10	1gkzA1	0.58	3.79	0.009	0.953	model1_1gkzA1.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:0005524	0.43	ATP binding
GO:0004740	0.43	pyruvate dehydrogenase (acetyl-transferring) kinase activity
GO:0004674	0.32	protein serine/threonine kinase 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:0071398	0.43	cellular response to fatty acid
GO:0010906	0.43	regulation of glucose metabolic process
GO:0010510	0.43	regulation of acetyl-CoA biosynthetic process from pyruvate
GO:2000377	0.32	regulation of reactive oxygen species metabolic process
GO:2000209	0.32	regulation of anoikis
GO:0097411	0.32	hypoxia-inducible factor-1alpha signaling pathway
GO:0071333	0.32	cellular response to glucose stimulus
GO:0055067	0.32	monovalent inorganic cation homeostasis
GO:0050691	0.32	regulation of defense response to virus by host
GO:0046890	0.32	regulation of lipid biosynthetic process
GO:0046850	0.32	regulation of bone remodeling
GO:0045453	0.32	bone resorption
GO:0043066	0.32	negative regulation of apoptotic process
GO:0042594	0.32	response to starvation
GO:0035357	0.32	peroxisome proliferator activated receptor signaling pathway
GO:0032869	0.32	cellular response to insulin stimulus
GO:0032844	0.32	regulation of homeostatic process
GO:0031669	0.32	cellular response to nutrient levels
GO:0019395	0.32	fatty acid oxidation
GO:0018105	0.32	peptidyl-serine phosphorylation
GO:0016236	0.32	macroautophagy
GO:0007169	0.32	transmembrane receptor protein tyrosine kinase signaling pathway
GO:0006633	0.32	fatty acid 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:0044464	0.88	cell part
GO:0044424	0.59	intracellular part
GO:0016020	0.59	membrane
GO:0044446	0.53	intracellular organelle part
GO:0043229	0.53	intracellular organelle
GO:0043227	0.53	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	0.060	3e04D	0.532	4.13	0.067	0.888	4.2.1.2	NA
2	0.060	2frvD	0.529	4.22	0.051	0.906	1.12.2.1	NA
3	0.060	2oa6D	0.557	4.16	0.048	0.944	4.2.3.9	NA
4	0.060	1qleA	0.528	4.44	0.065	0.953	1.9.3.1	NA
5	0.060	1vdkA	0.529	4.16	0.038	0.897	4.2.1.2	NA

	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:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.01	3s8gA	0.577	3.79	0.049	0.925	0.78	OLC	complex1.pdb.gz	13,102,103,105

	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.