D-I-TASSER Q8NDH6

D-I-TASSER results for Q8NDH6

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

Summary of the Protein

Uniprot ID: Q8NDH6
Protein Name: Islet cell autoantigen 1-like protein
Gene Name: ICA1L

Input Sequence in FASTA format

>Q8NDH6 (482 residues)
MDSFGQPRPEDNQSVVRRMQKKYWKTKQVFIKATGKKEDEHLVASDAELDAKLEVFHSVQ
ETCTELLKIIEKYQLRLNVISEEENELGLFLKFQAERDATQAGKMMDATGKALCSSAKQR
LALCTPLSRLKQEVATFSQRAVSDTLMTINRMEQARTEYRGALLWMKDVSQELDPDTLKQ
MEKFRKVQMQVRNSKASFDKLKMDVCQKVDLLGASRCNMLSHSLTTYQRTLLGFWKKTAR
MMSQIHEACIGFHPYDFVALKQLQDTPSKISEDNKDEQIGGFLTEQLNKLVLSDEEASFE
SEQANKDHNEKHSQMREFGAPQFSNSENVAKDLPVDSLEGEDFEKEFSFLNNLLSSGSSS
TSEFTQECQTAFGSPSASLTSQEPSMGSEPLAHSSRFLPSQLFDLGFHVAGAFNNWVSQE
ESELCLSHTDNQPVPSQSPKKLTRSPNNGNQDMSAWFNLFADLDPLSNPDAIGHSDDELL
NA

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	Q8NDH6-D1	1-482	482		MDSFGQPRPEDNQSVVRRMQKKYWKTKQVFIKATGKKEDEHLVASDAELDAKLEVFHSVQETCTELLKIIEKYQLRLNVISEEENELGLFLKFQAERDATQAGKMMDATGKALCSSAKQRLALCTPLSRLKQEVATFSQRAVSDTLMTINRMEQARTEYRGALLWMKDVSQELDPDTLKQMEKFRKVQMQVRNSKASFDKLKMDVCQKVDLLGASRCNMLSHSLTTYQRTLLGFWKKTARMMSQIHEACIGFHPYDFVALKQLQDTPSKISEDNKDEQIGGFLTEQLNKLVLSDEEASFESEQANKDHNEKHSQMREFGAPQFSNSENVAKDLPVDSLEGEDFEKEFSFLNNLLSSGSSSTSEFTQECQTAFGSPSASLTSQEPSMGSEPLAHSSRFLPSQLFDLGFHVAGAFNNWVSQEESELCLSHTDNQPVPSQSPKKLTRSPNNGNQDMSAWFNLFADLDPLSNPDAIGHSDDELLNA

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5243

(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	2q13A	0.50	4.77	0.101	0.633	model1_2q13A.pdb.gz
2	4h8sA	0.50	4.24	0.088	0.612	model1_4h8sA.pdb.gz
3	4ckgA	0.46	5.06	0.071	0.606	model1_4ckgA.pdb.gz
4	4avmA	0.43	2.68	0.127	0.475	model1_4avmA.pdb.gz
5	1uruA	0.39	2.76	0.140	0.429	model1_1uruA.pdb.gz
6	4hpqC	0.37	5.00	0.034	0.485	model1_4hpqC.pdb.gz
7	4m0mA	0.23	7.14	0.047	0.367	model1_4m0mA.pdb.gz
8	3b70A	0.20	6.99	0.043	0.326	model1_3b70A.pdb.gz
9	2r09A	0.18	6.69	0.072	0.284	model1_2r09A.pdb.gz
10	4rs3A	0.18	6.99	0.054	0.282	model1_4rs3A.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	0.27	catalytic activity
GO:0008289	0.23	lipid binding
GO:0005543	0.22	phospholipid binding
GO:0035091	0.21	phosphatidylinositol binding
GO:1901981	0.20	phosphatidylinositol phosphate binding
GO:0019904	0.19	protein domain specific binding
GO:1901363	0.18	heterocyclic compound binding
GO:0097159	0.18	organic cyclic compound binding
GO:0070273	0.18	phosphatidylinositol-4-phosphate binding
GO:0019899	0.15	enzyme binding
GO:0043167	0.14	ion binding
GO:0016740	0.13	transferase activity
GO:0097367	0.12	carbohydrate derivative binding
GO:0046872	0.12	metal ion binding
GO:0035639	0.11	purine ribonucleoside triphosphate binding
GO:0032555	0.11	purine ribonucleotide binding
GO:0032550	0.11	purine ribonucleoside 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	1.00	biological regulation
GO:0050789	0.92	regulation of biological process
GO:0050794	0.90	regulation of cellular process
GO:0009987	0.86	cellular process
GO:0065008	0.83	regulation of biological quality
GO:0044699	0.81	single-organism process
GO:0016043	0.77	cellular component organization
GO:0044763	0.76	single-organism cellular process
GO:0051128	0.71	regulation of cellular component organization
GO:0034315	0.70	regulation of Arp2/3 complex-mediated actin nucleation

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	0.89	cytoplasmic part
GO:0005737	0.86	cytoplasm
GO:0016020	0.78	membrane
GO:0043226	0.72	organelle
GO:0044446	0.69	intracellular organelle part
GO:0043229	0.67	intracellular organelle
GO:0043227	0.67	membrane-bounded organelle
GO:0043231	0.64	intracellular membrane-bounded organelle
GO:0031090	0.55	organelle membrane
GO:0098588	0.54	bounding membrane of 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	1hn0A	0.300	7.14	0.051	0.490	4.2.2.20	NA
2	0.060	1jswB	0.278	4.96	0.038	0.344	4.3.1.1	NA
3	0.060	1i8qA	0.285	7.20	0.050	0.459	4.2.2.1	NA
4	0.060	2ebsB	0.280	7.38	0.026	0.463	3.2.1.150	NA
5	0.060	2vumA	0.280	7.11	0.018	0.444	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	2raj0	0.351	4.60	0.075	0.444	0.15	III	complex1.pdb.gz	116,131,209,224,225,228,235
2	0.01	1zww0	0.369	2.47	0.108	0.403	0.38	III	complex2.pdb.gz	111,112,113,116,117,124,224,228,229,231,232,235,239
3	0.01	1wdz0	0.309	3.18	0.055	0.348	0.37	III	complex3.pdb.gz	113,116,119,120,123,127,215,220,225,228,232,235
4	0.01	3sfzA	0.301	7.80	0.026	0.523	0.17	ADP	complex4.pdb.gz	32,33,34,163,164,167
5	0.01	3izaA	0.302	7.62	0.035	0.514	0.11	ATP	complex5.pdb.gz	32,33,34,35,36,37
6	0.01	2vkzG	0.343	7.53	0.043	0.577	0.10	FMN	complex6.pdb.gz	161,162,165

	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.