D-I-TASSER A0A1W2PR82

D-I-TASSER results for A0A1W2PR82

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

Summary of the Protein

Uniprot ID: A0A1W2PR82
Protein Name: Protein PERCC1
Gene Name: PERCC1

Input Sequence in FASTA format

>A0A1W2PR82 (267 residues)
MAAGVIRPLCDFQLPLLRHHPFLPSDPEPPETSEEEEEEEEEEEEEEGEGEGLGGCGRIL
PSSGRAEATEEAAPEGPGSPETPLQLLRFSELISDDIRRYFGRKDKGQDPDACDVYADSR
PPRSTARELYYADLVRLARGGSLEDEDTPEPRVPQGQVCRPGLSGDRAQPLGPLAELFDY
GLQQYWGSRAAAGWSLTLERKYGHITPMAQRKLPPSFWKEPTPSPLGLLHPGTPDFSDLL
ASWSTEACPELPGRGTPALEGARPAEA

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	A0A1W2PR82-D1	1-267	267		MAAGVIRPLCDFQLPLLRHHPFLPSDPEPPETSEEEEEEEEEEEEEEGEGEGLGGCGRILPSSGRAEATEEAAPEGPGSPETPLQLLRFSELISDDIRRYFGRKDKGQDPDACDVYADSRPPRSTARELYYADLVRLARGGSLEDEDTPEPRVPQGQVCRPGLSGDRAQPLGPLAELFDYGLQQYWGSRAAAGWSLTLERKYGHITPMAQRKLPPSFWKEPTPSPLGLLHPGTPDFSDLLASWSTEACPELPGRGTPALEGARPAEA

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.4581

(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	2y8nA	0.46	6.67	0.053	0.832	model1_2y8nA.pdb.gz
2	2cse1	0.44	6.18	0.041	0.745	model1_2cse1.pdb.gz
3	5zvs2	0.44	6.03	0.029	0.734	model1_5zvs2.pdb.gz
4	7kq3A	0.44	6.40	0.012	0.768	model1_7kq3A.pdb.gz
5	7lo5A	0.43	5.95	0.058	0.715	model1_7lo5A.pdb.gz
6	5w1hA	0.43	6.12	0.027	0.738	model1_5w1hA.pdb.gz
7	6druA	0.43	6.24	0.069	0.742	model1_6druA.pdb.gz
8	6rc9A1	0.43	5.84	0.042	0.697	model1_6rc9A1.pdb.gz
9	6iv9A	0.42	5.99	0.050	0.712	model1_6iv9A.pdb.gz
10	5a0uA	0.42	6.62	0.040	0.771	model1_5a0uA.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

./A0A1W2PR82-D1/GOsearchresult_final_MF.svg

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:0043722	0.07	4-hydroxyphenylacetate decarboxylase activity
GO:0003968	0.07	RNA-directed RNA polymerase activity
GO:0003723	0.07	RNA binding
GO:0000166	0.07	nucleotide binding

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]

./A0A1W2PR82-D1/GOsearchresult_final_BP.svg

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0060041	0.94	retina development in camera-type eye
GO:0042461	0.94	photoreceptor cell development
GO:0035082	0.94	axoneme assembly

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]

./A0A1W2PR82-D1/GOsearchresult_final_CC.svg

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0044424	0.99	intracellular part
GO:0005930	0.94	axoneme
GO:0044444	0.73	cytoplasmic part
GO:0005829	0.60	cytosol

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	2psnC	0.400	6.00	0.059	0.670	4.2.1.11	NA
2	0.060	3fvyA	0.389	6.09	0.040	0.652	3.4.14.4	115,117
3	0.060	1elsA	0.370	6.16	0.038	0.625	4.2.1.11	105
4	0.060	3ikmD	0.404	6.08	0.068	0.678	2.7.7.7	98,100
5	0.060	2x6fA	0.389	6.35	0.066	0.674	2.7.1.137 2.7.1.153 2.7.1.154	102

	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	0.01	1mwhA	0.439	6.18	0.037	0.749	0.14	GTG	complex1.pdb.gz	90,103,252
2	0.01	2yajA	0.456	6.64	0.049	0.824	0.12	4HP	complex2.pdb.gz	173,174,217
3	0.01	2vf7C	0.396	6.11	0.050	0.670	0.12	ADP	complex3.pdb.gz	90,91,95,96
4	0.01	2xh2A	0.375	6.31	0.051	0.637	0.18	2PG	complex4.pdb.gz	227,229,242,260
5	0.01	1oneA	0.381	5.98	0.052	0.625	0.17	UUU	complex5.pdb.gz	11,140,142
6	0.01	1n35A	0.440	6.17	0.037	0.749	0.12	QNA	complex6.pdb.gz	102,141,171
7	0.01	3hhmA	0.341	6.56	0.047	0.614	0.16	KWT	complex7.pdb.gz	100,177,178,214
8	0.01	1n1hA	0.439	6.19	0.046	0.745	0.16	CH1	complex8.pdb.gz	129,172,173,175,240
9	0.01	7enlA	0.378	6.01	0.047	0.625	0.16	2PG	complex9.pdb.gz	10,11,89,139,140,142
10	0.01	2xh4B	0.291	6.13	0.041	0.502	0.14	2PG	complex10.pdb.gz	93,94,179,209

	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.