D-I-TASSER results for Q9Y6Z2-D1

Input Sequence in FASTA format

>Q9Y6Z2 (57 residues)
MGTAVGPHHSPAPHDSALPARLLTSDFPYGRSCQIEQVKYSVPDTGLFQHWEGSIPT

Predicted Secondary Structure

                  20                  40
                   |                   |
Sequence
MGTAVGPHHSPAPHDSALPARLLTSDFPYGRSCQIEQVKYSVPDTGLFQHWEGSIPT
Prediction
CCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCSSSSSSSCCCCCCCCHHHCCCCCCC
Confidence
986667888999864433156650579997400442543048985211011367899

H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

                  20                  40
                   |                   |
Sequence
MGTAVGPHHSPAPHDSALPARLLTSDFPYGRSCQIEQVKYSVPDTGLFQHWEGSIPT
Prediction
854544444445446432324223561433451415525242444312432556358

Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Contact, Hydrogen and Distance Map Used in D-I-TASSER simulation

D-I-TASSER simulation is guided by the consensus contact map (left figure), distance map (middle figure) and Hydrogen bond network (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.

Top 10 threading templates used by D-I-TASSER

Rank	PDB hit	ID1	ID2	Cov	Norm. Zscore	Download alignment		20                  40                    |                   |
							SS	CCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCSSSSSSSCCCCCCCCHHHCCCCCCC
							Seq	MGTAVGPHHSPAPHDSALPARLLTSDFPYGRSCQIEQVKYSVPDTGLFQHWEGSIPT
1	7d8gA	0.02	0.02	1.47	0.52	CEthreader		ENIKIQSYKHDGKIHRVWSETTILKGTDHVVIGGNDHTLVTESITREPAIVYFHSEY
2	3t8sA1	0.04	0.04	1.93	0.55	EigenThreader		LVDDRRDCNLLGTVIQNKYLTVNALLEK-NAMRVTLDELHASDNPGCNEVNSVNCNT
3	3kcrE1	0.20	0.18	5.60	0.22	FFAS-3D		-GARQGTRARPQDHSQKVNKKMLSELVRQDRLIVVEKFSVEAPKTKLLAQ-------
4	1ntlA4	0.12	0.11	3.74	0.77	SPARKS-K		------RKQCKTPSDPENGLVHVHTGIEFGSRINYTCNQYRLIGSSSAVDWDTEAPI
5	2d7iA	0.12	0.07	2.46	0.68	CNFpred		--------------------SCMDCSE-SDHRIFMNTCNPSS----LTQQWLFEHTN
6	6e1jA1	0.02	0.02	1.30	0.83	DEthreader		-RVFDTDAPDTV-GHNVA-TANTIAGICGARQVEVTIPEEMLKGGVYT----KP---
7	2qlvB	0.06	0.05	2.32	0.61	MapAlign		----MVPVEIRWQQGGSKVYVTGSFLLPGTHRFRFIVDLPTATDQMGNFVNYIEV--
8	1ntjA1	0.16	0.16	5.23	0.71	MUSTER		--TLGQCPAPPLFPYAKPINPTDESTFPVGTSLKYECRPGYIKRQFSITVWTSPQDV
9	2pffB	0.18	0.18	5.74	0.44	HHsearch		PADATFAGHSLGVEVVFNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVN
10	3jctr	0.09	0.09	3.37	0.46	CEthreader		RQKKANVTHPELGVTVFLPILAVKKNLTKGTIIEVNVSELGMVTAGGGKYAQVTNEP


(a) ID1 is the number of template residues identical to query divided by number of aligned residues.
(b) ID2 is the number of template residues identical to query divided by query sequence length.
(c) Cov is equal the number of aligned template residues divided by query sequence length.
(d) Norm. Zscore is the normalized Z-score of the threading alignments. A Normalized Z-score >1 means a good alignment and is highlighted in bold.
(e) Download alignment lists the threading program used to identify the template, and provide the 3D structure of aligned regions of threading templates (threading[1-10].pdb.gz).
(f) Template residues identical to query sequence are highlighted in color.

Top 1 final models from D-I-TASSER

Rank^a	Estimated TM-score^b
1	0.5777


(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.
1	5d9bA	0.46	3.67	0.073	0.947
2	3sc7X	0.45	3.66	0.036	0.947
3	2h47H	0.45	3.79	0.036	0.983
4	2aq5A	0.45	3.48	0.056	0.895
5	3s8vA	0.45	3.90	0.091	0.965
6	3s94A1	0.45	3.57	0.019	0.912
7	3a0fA1	0.45	3.76	0.094	0.930
8	2ce8A	0.41	3.79	0.113	0.877
9	5fkqA2	0.41	3.66	0.057	0.877
10	3g4hB	0.40	3.96	0.057	0.877



(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:0030234	0.54	enzyme regulator activity
GO:0016491	0.53	oxidoreductase activity
GO:0004867	0.51	serine-type endopeptidase inhibitor activity






(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:

Biological Process (BP)


GO term	Cscore^GO	Name
GO:2000279	0.07	negative regulation of DNA biosynthetic process
GO:1903634	0.07	negative regulation of leucine-tRNA ligase activity
GO:1903629	0.07	positive regulation of dUTP diphosphatase activity
GO:1903625	0.07	negative regulation of DNA catabolic process
GO:1903611	0.07	negative regulation of calcium-dependent ATPase activity
GO:1903052	0.07	positive regulation of proteolysis involved in cellular protein catabolic process
GO:1903011	0.07	negative regulation of bone development
GO:1902679	0.07	negative regulation of RNA biosynthetic process
GO:1901896	0.07	positive regulation of calcium-transporting ATPase activity
GO:1901671	0.07	positive regulation of superoxide dismutase activity
GO:1901318	0.07	negative regulation of sperm motility
GO:0097421	0.07	liver regeneration
GO:0055114	0.07	oxidation-reduction process
GO:0051344	0.07	negative regulation of cyclic-nucleotide phosphodiesterase activity
GO:0050848	0.07	regulation of calcium-mediated signaling
GO:0050680	0.07	negative regulation of epithelial cell proliferation
GO:0045723	0.07	positive regulation of fatty acid biosynthetic process
GO:0045717	0.07	negative regulation of fatty acid biosynthetic process
GO:0045019	0.07	negative regulation of nitric oxide biosynthetic process
GO:0043547	0.07	positive regulation of GTPase activity
GO:0043066	0.07	negative regulation of apoptotic process
GO:0034260	0.07	negative regulation of GTPase activity
GO:0032515	0.07	negative regulation of phosphoprotein phosphatase activity
GO:0032091	0.07	negative regulation of protein binding
GO:0019853	0.07	L-ascorbic acid biosynthetic process
GO:0016036	0.07	cellular response to phosphate starvation
GO:0010922	0.07	positive regulation of phosphatase activity
GO:0010907	0.07	positive regulation of glucose metabolic process
GO:0010867	0.07	positive regulation of triglyceride biosynthetic process
GO:0009405	0.07	pathogenesis
GO:0007568	0.07	aging
GO:0007283	0.07	spermatogenesis
GO:0006874	0.07	cellular calcium ion homeostasis
GO:0006469	0.07	negative regulation of protein kinase activity
GO:0001822	0.07	kidney development






(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:

Cellular Component (CC)


GO term	Cscore^GO	Name
GO:0005576	1.00	extracellular region
GO:0044464	0.80	cell part
GO:0044424	0.50	intracellular part






(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:

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	2rl2A	0.367	3.94	0.019	0.825	2.5.1.7	NA
2	0.060	2ayaA	0.410	4.03	0.000	0.877	2.7.7.7	NA
3	0.060	1a0jA	0.374	4.06	0.036	0.877	3.4.21.4	NA
4	0.060	1uv4A	0.440	3.78	0.091	0.947	3.2.1.99	NA
5	0.060	1sgfG	0.415	3.96	0.036	0.965	3.4.21.35	NA



(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	Predicted binding site residues
1	0.01	2hjbB	0.451	3.82	0.036	0.983	0.45	PZM	2,5,26,49,50,51
2	0.01	2q7qA	0.392	4.19	0.109	0.965	0.49	C2B	4,6,25,49,50
3	0.01	2hj4A	0.395	4.16	0.073	0.965	0.46	PNZ	2,53,54
4	0.01	1n7dA	0.430	3.88	0.036	0.983	0.51	UUU	27,28,29,30,49



(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.

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.