D-I-TASSER Q6ZSJ9

D-I-TASSER results for Q6ZSJ9

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

Summary of the Protein

Uniprot ID: Q6ZSJ9
Protein Name: Protein shisa-6
Gene Name: SHISA6

Input Sequence in FASTA format

>Q6ZSJ9 (500 residues)
MALRRLLLLLLLSLESLDLLPSVHGARGRAANRTLSAGGAAVGGRRAGGALARGGRELNG
TARAPGIPEAGSRRGQPAAAVAAAASAAVTYETCWGYYDVSGQYDKEFECNNSESGYLYC
CGTCYYRFCCKKRHEKLDQRQCTNYQSPVWVQTPSTKVVSPGPENKYDPEKDKTNFTVYI
TCGVIAFVIVAGVFAKVSYDKAHRPPREMNIHRALADILRQQGPIPIAHCERETISAIDT
SPKENTPVRSSSKNHYTPVRTAKQTPEKPRMNNILTSATEPYDLSFSRSFQNLAHLPPSY
ESAVKTNPSKYSSLKRLTDKEADEYYMRRRHLPDLAARGTLPLNVIQMSQQKPLPRERPR
RPIRAMSQDRVLSPDRGLPDEFSMPYDRILSDEQLLSTERLHSQDPLLSPERTAFPEQSL
SRAISHTDVFVSTPVLDRYRMSKMHSHPSASNNSYATLGQSQTAAKRHAFASRRHNTVEQ
LHYIPGHHTCYTASKTEVTV

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	Q6ZSJ9-D1	1-174	174		MALRRLLLLLLLSLESLDLLPSVHGARGRAANRTLSAGGAAVGGRRAGGALARGGRELNGTARAPGIPEAGSRRGQPAAAVAAAASAAVTYETCWGYYDVSGQYDKEFECNNSESGYLYCCGTCYYRFCCKKRHEKLDQRQCTNYQSPVWVQTPSTKVVSPGPENKYDPEKDKT
2	Q6ZSJ9-D2	175-298	124		NFTVYITCGVIAFVIVAGVFAKVSYDKAHRPPREMNIHRALADILRQQGPIPIAHCERETISAIDTSPKENTPVRSSSKNHYTPVRTAKQTPEKPRMNNILTSATEPYDLSFSRSFQNLAHLPP
3	Q6ZSJ9-D3	299-500	202		SYESAVKTNPSKYSSLKRLTDKEADEYYMRRRHLPDLAARGTLPLNVIQMSQQKPLPRERPRRPIRAMSQDRVLSPDRGLPDEFSMPYDRILSDEQLLSTERLHSQDPLLSPERTAFPEQSLSRAISHTDVFVSTPVLDRYRMSKMHSHPSASNNSYATLGQSQTAAKRHAFASRRHNTVEQLHYIPGHHTCYTASKTEVTV

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.4

(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	5n0bA	0.40	7.33	0.031	0.650	model1_5n0bA.pdb.gz
2	7k66A	0.40	7.71	0.052	0.674	model1_7k66A.pdb.gz
3	4bxsV	0.39	7.35	0.045	0.642	model1_4bxsV.pdb.gz
4	4kf7A	0.39	7.79	0.049	0.666	model1_4kf7A.pdb.gz
5	6zngA	0.39	7.43	0.055	0.636	model1_6zngA.pdb.gz
6	4i2wA	0.39	7.04	0.036	0.622	model1_4i2wA.pdb.gz
7	7kiyA	0.39	7.99	0.040	0.678	model1_7kiyA.pdb.gz
8	4kxfK	0.39	7.60	0.047	0.644	model1_4kxfK.pdb.gz
9	7ml7A	0.39	7.71	0.057	0.660	model1_7ml7A.pdb.gz
10	5mqrA	0.38	7.64	0.037	0.646	model1_5mqrA.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:0003824	0.50	catalytic activity
GO:0046872	0.49	metal ion binding
GO:0046914	0.48	transition metal ion binding
GO:0005215	0.46	transporter activity
GO:0022857	0.45	transmembrane transporter activity
GO:0015267	0.44	channel activity
GO:0015075	0.44	ion transmembrane transporter activity
GO:0005216	0.43	ion channel activity
GO:0004872	0.42	receptor activity
GO:0099600	0.40	transmembrane receptor activity
GO:0022836	0.40	gated channel 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:0050794	0.99	regulation of cellular process
GO:0065008	0.98	regulation of biological quality
GO:0023051	0.98	regulation of signaling
GO:0010646	0.98	regulation of cell communication
GO:0048172	0.97	regulation of short-term neuronal synaptic plasticity

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	1.00	cell part
GO:0044425	0.99	membrane part
GO:0044459	0.98	plasma membrane part
GO:0043234	0.98	protein complex
GO:0045202	0.97	synapse
GO:0032281	0.97	AMPA glutamate receptor complex

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	1t3tA	0.362	6.98	0.040	0.564	6.3.5.3	NA
2	0.060	1q16A	0.323	7.93	0.038	0.556	1.7.99.4	NA
3	0.060	2vdcA	0.343	7.70	0.037	0.576	1.4.1.13	NA
4	0.060	3b8eC	0.341	7.91	0.051	0.602	3.6.3.9	225
5	0.060	1aroP	0.322	7.32	0.041	0.526	2.7.7.6	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:

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	1llwA	0.355	7.88	0.029	0.616	0.31	F3S	complex1.pdb.gz	97,98,99,127
2	0.01	1f31A	0.357	8.08	0.037	0.630	0.33	UUU	complex2.pdb.gz	101,102,122,145
3	0.01	1ofdA	0.346	7.44	0.054	0.568	0.33	F3S	complex3.pdb.gz	105,122,123,124,125,126
4	0.01	1g9aA	0.307	8.25	0.043	0.556	0.15	BAB	complex4.pdb.gz	94,97,98
5	0.01	1llzA	0.353	8.00	0.033	0.624	0.33	F3S	complex5.pdb.gz	94,95,96,97,128,129
6	0.01	1llzA	0.353	8.00	0.033	0.624	0.16	FMN	complex6.pdb.gz	121,122,123,145
7	0.01	3q43A	0.378	7.79	0.057	0.656	0.13	D66	complex7.pdb.gz	132,135,136,143
8	0.01	3mdjC	0.347	7.71	0.042	0.580	0.22	BES	complex8.pdb.gz	108,109,110,123,135,142
9	0.01	5acnA	0.356	7.88	0.043	0.616	0.14	F3S	complex9.pdb.gz	96,124,150,151
10	0.01	2zxgA	0.373	8.05	0.057	0.662	0.13	S23	complex10.pdb.gz	119,120,121,134,138

	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.