D-I-TASSER Q5T9L3

D-I-TASSER results for Q5T9L3

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

Summary of the Protein

Uniprot ID: Q5T9L3
Protein Name: Protein wntless homolog
Gene Name: WLS

Input Sequence in FASTA format

>Q5T9L3 (541 residues)
MAGAIIENMSTKKLCIVGGILLVFQIIAFLVGGLIAPGPTTAVSYMSVKCVDARKNHHKT
KWFVPWGPNHCDKIRDIEEAIPREIEANDIVFSVHIPLPHMEMSPWFQFMLFILQLDIAF
KLNNQIRENAEVSMDVSLAYRDDAFAEWTEMAHERVPRKLKCTFTSPKTPEHEGRYYECD
VLPFMEIGSVAHKFYLLNIRLPVNEKKKINVGIGEIKDIRLVGIHQNGGFTKVWFAMKTF
LTPSIFIIMVWYWRRITMMSRPPVLLEKVIFALGISMTFINIPVEWFSIGFDWTWMLLFG
DIRQGIFYAMLLSFWIIFCGEHMMDQHERNHIAGYWKQVGPIAVGSFCLFIFDMCERGVQ
LTNPFYSIWTTDIGTELAMAFIIVAGICLCLYFLFLCFMVFQVFRNISGKQSSLPAMSKV
RRLHYEGLIFRFKFLMLITLACAAMTVIFFIVSQVTEGHWKWGGVTVQVNSAFFTGIYGM
WNLYVFALMFLYAPSHKNYGEDQSNGDLGVHSGEELQLTTTITHVDGPTEIYKLTRKEAQ
E

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	Q5T9L3-D1	1-41,225-293,469-541	183		MAGAIIENMSTKKLCIVGGILLVFQIIAFLVGGLIAPGPTTHQNGGFTKVWFAMKTFLTPSIFIIMVWYWRRITMMSRPPVLLEKVIFALGISMTFINIPVEWFSIGFDWVNSAFFTGIYGMWNLYVFALMFLYAPSHKNYGEDQSNGDLGVHSGEELQLTTTITHVDGPTEIYKLTRKEAQE
2	Q5T9L3-D2	42-224	183		AVSYMSVKCVDARKNHHKTKWFVPWGPNHCDKIRDIEEAIPREIEANDIVFSVHIPLPHMEMSPWFQFMLFILQLDIAFKLNNQIRENAEVSMDVSLAYRDDAFAEWTEMAHERVPRKLKCTFTSPKTPEHEGRYYECDVLPFMEIGSVAHKFYLLNIRLPVNEKKKINVGIGEIKDIRLVGI
3	Q5T9L3-D3	294-468	175		TWMLLFGDIRQGIFYAMLLSFWIIFCGEHMMDQHERNHIAGYWKQVGPIAVGSFCLFIFDMCERGVQLTNPFYSIWTTDIGTELAMAFIIVAGICLCLYFLFLCFMVFQVFRNISGKQSSLPAMSKVRRLHYEGLIFRFKFLMLITLACAAMTVIFFIVSQVTEGHWKWGGVTVQ

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.657

(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	7drtB	0.83	2.70	0.974	0.895	model1_7drtB.pdb.gz
2	4zwjA	0.51	5.19	0.048	0.647	model1_4zwjA.pdb.gz
3	5nddA	0.48	5.77	0.052	0.634	model1_5nddA.pdb.gz
4	7zi0A	0.47	5.47	0.033	0.614	model1_7zi0A.pdb.gz
5	7f1qR	0.46	4.77	0.084	0.579	model1_7f1qR.pdb.gz
6	6lw5A	0.46	4.80	0.066	0.577	model1_6lw5A.pdb.gz
7	7figR	0.46	5.01	0.058	0.579	model1_7figR.pdb.gz
8	8i2gR	0.46	5.15	0.050	0.580	model1_8i2gR.pdb.gz
9	4jkvA	0.45	5.36	0.042	0.586	model1_4jkvA.pdb.gz
10	7jniA	0.45	5.33	0.052	0.580	model1_7jniA.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:0017147	0.78	Wnt-protein 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]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0065007	0.91	biological regulation
GO:0050789	0.91	regulation of biological process
GO:0050794	0.90	regulation of cellular process
GO:0044699	0.85	single-organism process
GO:0050708	0.83	regulation of protein secretion
GO:0023051	0.83	regulation of signaling
GO:0010646	0.83	regulation of cell communication
GO:0050714	0.82	positive regulation of protein secretion
GO:0030177	0.82	positive regulation of Wnt signaling pathway
GO:0032502	0.67	developmental process
GO:0044767	0.65	single-organism developmental process
GO:0032501	0.64	multicellular organismal process
GO:0007389	0.63	pattern specification process
GO:0061356	0.54	regulation of Wnt protein secretion
GO:0061357	0.53	positive regulation of Wnt protein secretion
GO:0009653	0.52	anatomical structure morphogenesis

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:0044444	1.00	cytoplasmic part
GO:0016020	0.93	membrane
GO:0044422	0.87	organelle part
GO:0044446	0.86	intracellular organelle part
GO:0044425	0.80	membrane part
GO:0044431	0.77	Golgi apparatus part
GO:0044440	0.72	endosomal part
GO:0044432	0.71	endoplasmic reticulum part
GO:0098590	0.69	plasma membrane region
GO:0044433	0.67	cytoplasmic vesicle part
GO:0097458	0.66	neuron part
GO:0043231	0.58	intracellular membrane-bounded organelle
GO:0045211	0.56	postsynaptic membrane
GO:0042734	0.56	presynaptic membrane
GO:0031594	0.56	neuromuscular junction
GO:0031302	0.56	intrinsic component of endosome membrane
GO:0031228	0.56	intrinsic component of Golgi membrane
GO:0031227	0.56	intrinsic component of endoplasmic reticulum membrane
GO:0030285	0.56	integral component of synaptic vesicle membrane
GO:0005887	0.56	integral component of plasma membrane

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	3no9A	0.321	6.98	0.062	0.490	4.2.1.2	NA
2	0.060	3gtdA	0.321	7.02	0.044	0.490	4.2.1.2	NA
3	0.060	1m56A	0.345	6.35	0.048	0.490	1.9.3.1	NA
4	0.060	1tj7A	0.322	6.57	0.035	0.475	4.3.2.1	NA
5	0.060	3d4sA	0.381	4.51	0.083	0.471	3.2.1.17	233,240

	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	0.06	3pqrA	0.435	3.93	0.066	0.512	0.15	RET	complex1.pdb.gz	230,231,234
2	0.04	3oe9A	0.392	4.43	0.077	0.479	0.20	ITD	complex2.pdb.gz	296,297,300
3	0.01	2rbsA	0.128	5.81	0.043	0.177	0.23	269	complex3.pdb.gz	228,231,232,235
4	0.01	2z73A	0.431	4.74	0.068	0.540	0.10	RET	complex4.pdb.gz	183,184,185,189,225
5	0.01	3oduA	0.393	4.78	0.080	0.490	0.28	OLC	complex5.pdb.gz	232,240,244
6	0.01	3hukA	0.130	5.64	0.032	0.177	0.21	J0Z	complex6.pdb.gz	103,189,228
7	0.01	3gupB	0.126	6.15	0.023	0.179	0.33	0PY	complex7.pdb.gz	106,109,111,228
8	0.01	2razX	0.127	5.82	0.043	0.176	0.15	259	complex8.pdb.gz	106,107,285
9	0.01	3dqbA	0.434	3.88	0.066	0.510	0.32	UUU	complex9.pdb.gz	185,220,222,223
10	0.01	3ht6A	0.130	5.68	0.041	0.179	0.23	JZ0	complex10.pdb.gz	103,106,230

	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.