D-I-TASSER results for Q9Y5Z4-D1

Input Sequence in FASTA format

>Q9Y5Z4 (205 residues)
MAEPLQPDPGAAEDAAAQAVETPGWKAPEDAGPQPGSYEIRHYGPAKWVSTSVESMDWDS
AIQTGFTKLNSYIQGKNEKEMKIKMTAPVTSYVEPGSGPFSESTITISLYIPSEQQFDPP
RPLESDVFIEDRAEMTVFVRSFDGFSSAQKNQEQLLTLASILREDGKVFDEKVYYTAGYN
SPVKLLNRNNEVWLIQKNEPTKENE

Predicted Secondary Structure

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Sequence
MAEPLQPDPGAAEDAAAQAVETPGWKAPEDAGPQPGSYEIRHYGPAKWVSTSVESMDWDSAIQTGFTKLNSYIQGKNEKEMKIKMTAPVTSYVEPGSGPFSESTITISLYIPSEQQFDPPRPLESDVFIEDRAEMTVFVRSFDGFSSAQKNQEQLLTLASILREDGKVFDEKVYYTAGYNSPVKLLNRNNEVWLIQKNEPTKENE
Prediction
CCCCCCCCCCCCCCCCCCCCCCCCSSSSSSCCCCCCCSSSSSCCCCSSSSSSSCCCCHHHHHHHHHHHHHHHHCCCCCCCCSCCCCCCSSSSSSCCCCCCCCCSSSSSSSCCHHHCCCCCCCCCCCSSSSSSCCSSSSSSSSCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCSSSSSCCCCCCCCCCCSSSSSSSCCCCCCCCC
Confidence
9988756555567633588888875998632677898689981892899999638987899999999999985357888844047876799996488987776499999917454568999999955999959979999994885787899999999999999809965798579998189998889624799996587765579

H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

                  20                  40                  60                  80                 100                 120                 140                 160                 180                 200
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Sequence
MAEPLQPDPGAAEDAAAQAVETPGWKAPEDAGPQPGSYEIRHYGPAKWVSTSVESMDWDSAIQTGFTKLNSYIQGKNEKEMKIKMTAPVTSYVEPGSGPFSESTITISLYIPSEQQFDPPRPLESDVFIEDRAEMTVFVRSFDGFSSAQKNQEQLLTLASILREDGKVFDEKVYYTAGYNSPVKLLNRNNEVWLIQKNEPTKENE
Prediction
7454267444425453155352161412453466554011131561300003065452540234003201410335147635051212130203456465453301000001361474325155650404624532000011212243640452054036105746352575211000002224234220000021455646788

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                  60                  80                 100                 120                 140                 160                 180                 200                    |                   |                   |                   |                   |                   |                   |                   |                   |                   |
							SS	CCCCCCCCCCCCCCCCCCCCCCCCSSSSSSCCCCCCCSSSSSCCCCSSSSSSSCCCCHHHHHHHHHHHHHHHHCCCCCCCCSCCCCCCSSSSSSCCCCCCCCCSSSSSSSCCHHHCCCCCCCCCCCSSSSSSCCSSSSSSSSCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCSSSSSCCCCCCCCCCCSSSSSSSCCCCCCCCC
							Seq	MAEPLQPDPGAAEDAAAQAVETPGWKAPEDAGPQPGSYEIRHYGPAKWVSTSVESMDWDSAIQTGFTKLNSYIQGKNEKEMKIKMTAPVTSYVEPGSGPFSESTITISLYIPSEQQFDPPRPLESDVFIEDRAEMTVFVRSFDGFSSAQKNQEQLLTLASILREDGKVFDEKVYYTAGYNSPVKLLNRNNEVWLIQKNEPTKENE
1	3r8jA	0.97	0.84	23.52	1.33	DEthreader		------------------AVETPGWKAPAPQP---GSYEIRHYGPAKWVSTSVESMDWDSAIQTGFTKLNSYIQGKNEKEMKIKMTAPVTSYVEPGSGPFSESTITISLYIPSEQQFDPPRPLESDVFIEDRAEMTVFVRSFDGFSSAQKNQEQLLTLASILREDGKVFDEKVYYTAGYNSPVKLLNRNNEVWLIQK-N------
2	3r8jA	1.00	0.88	24.59	4.59	SPARKS-K		------------------AVETPGWKAPEDAGPQPGSYEIRHYGPAKWVSTSVESMDWDSAIQTGFTKLNSYIQGKNEKEMKIKMTAPVTSYVEPGSGPFSESTITISLYIPSEQQFDPPRPLESDVFIEDRAEMTVFVRSFDGFSSAQKNQEQLLTLASILREDGKVFDEKVYYTAGYNSPVKLLNRNNEVWLIQKN-------
3	3r8jA	1.00	0.87	24.45	1.68	MapAlign		-------------------VETPGWKAPEDAGPQPGSYEIRHYGPAKWVSTSVESMDWDSAIQTGFTKLNSYIQGKNEKEMKIKMTAPVTSYVEPGSGPFSESTITISLYIPSEQQFDPPRPLESDVFIEDRAEMTVFVRSFDGFSSAQKNQEQLLTLASILREDGKVFDEKVYYTAGYNSPVKLLNRNNEVWLIQKN-------
4	3r8jA	1.00	0.88	24.59	1.54	CEthreader		------------------AVETPGWKAPEDAGPQPGSYEIRHYGPAKWVSTSVESMDWDSAIQTGFTKLNSYIQGKNEKEMKIKMTAPVTSYVEPGSGPFSESTITISLYIPSEQQFDPPRPLESDVFIEDRAEMTVFVRSFDGFSSAQKNQEQLLTLASILREDGKVFDEKVYYTAGYNSPVKLLNRNNEVWLIQKN-------
5	3r8jA	1.00	0.88	24.59	3.08	MUSTER		------------------AVETPGWKAPEDAGPQPGSYEIRHYGPAKWVSTSVESMDWDSAIQTGFTKLNSYIQGKNEKEMKIKMTAPVTSYVEPGSGPFSESTITISLYIPSEQQFDPPRPLESDVFIEDRAEMTVFVRSFDGFSSAQKNQEQLLTLASILREDGKVFDEKVYYTAGYNSPVKLLNRNNEVWLIQKN-------
6	2hvaA	0.29	0.26	8.02	6.74	HHsearch		-------MLGMIRNSLFGSVETWPWQVLSTDV----SYEERACEGGKFATVEVTDKPVDEALREAMPKIMKYVGGTNDKGVGMGMTVPVSFAVFPNEDGSLQKKLKVWFRIPNQFQGSPPAPSDESVKIEEREGITVYSTQFGGYAKEADYVAHATQLRTTLEGTPATYQGDVYYCAGYDPPMKPYGRRNEVWLVKA--------
7	3r8jA	1.00	0.88	24.59	3.11	FFAS-3D		------------------AVETPGWKAPEDAGPQPGSYEIRHYGPAKWVSTSVESMDWDSAIQTGFTKLNSYIQGKNEKEMKIKMTAPVTSYVEPGSGPFSESTITISLYIPSEQQFDPPRPLESDVFIEDRAEMTVFVRSFDGFSSAQKNQEQLLTLASILREDGKVFDEKVYYTAGYNSPVKLLNRNNEVWLIQKN-------
8	2hvaA	0.27	0.25	7.64	1.57	EigenThreader		------MLGMIRNSLFGSVETWPWQVLSTG-GKEDVSYEERACEGGKFATVEVTDKPVDEALREAMPKIMKYVGGTNDKGVGMGMTVPVSFAVFPNEDGSLQKKLKVWFRIPNQFQGSPPAPSDESVKIEEREGITVYSTQFGGYAKEADYVAHATQLRTTLEGTPATYQGDVYYCAGYDPPMKPYGRRNEVWLVKA--------
9	3r8jA	1.00	0.88	24.59	3.12	CNFpred		------------------AVETPGWKAPEDAGPQPGSYEIRHYGPAKWVSTSVESMDWDSAIQTGFTKLNSYIQGKNEKEMKIKMTAPVTSYVEPGSGPFSESTITISLYIPSEQQFDPPRPLESDVFIEDRAEMTVFVRSFDGFSSAQKNQEQLLTLASILREDGKVFDEKVYYTAGYNSPVKLLNRNNEVWLIQKN-------
10	2hvaA	0.29	0.24	7.43	1.17	DEthreader		---------------------TWPWQVLSTGGKEDVSYEERACEGGKFATVEVTDKPVDEALREAMPKIMKYVGGTNDKGVGMGMTVPVSFAVFPNEDGSLQKKLKVWFRIPNQFQGSPPAPSDESVKIEEREGITVYSTQFGGYAKEADYVAHATQLRTTLEGTPATYQGDVYYCAG-YDP-MKPGRRNEVWLVKA--------


(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	0.8548


(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	3r8jA	0.86	0.77	0.972	0.873
2	2hvaA	0.70	3.01	0.265	0.829
3	6xl5G2	0.63	3.34	0.073	0.776
4	3b49A	0.61	3.74	0.114	0.780
5	1jyhA	0.59	3.18	0.099	0.737
6	3d6yA	0.59	4.29	0.073	0.795
7	2kcuA	0.58	3.35	0.087	0.722
8	1d6sA	0.35	4.76	0.074	0.537
9	3bjuA	0.33	5.18	0.060	0.527
10	4x0vA	0.31	5.67	0.024	0.541



(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:1901363	0.77	heterocyclic compound binding
GO:0097159	0.77	organic cyclic compound binding
GO:0020037	0.73	heme binding






(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:0009987	0.94	cellular process
GO:0050794	0.87	regulation of cellular process
GO:0044699	0.85	single-organism process
GO:0044763	0.83	single-organism cellular process
GO:0016043	0.74	cellular component organization
GO:0048518	0.72	positive regulation of biological process
GO:0048522	0.71	positive regulation of cellular process
GO:0006996	0.71	organelle organization
GO:0035794	0.70	positive regulation of mitochondrial membrane permeability
GO:0010940	0.70	positive regulation of necrotic cell death
GO:0010917	0.70	negative regulation of mitochondrial membrane potential






(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:0043227	1.00	membrane-bounded organelle
GO:0044464	0.98	cell part
GO:0044424	0.96	intracellular part
GO:0044444	0.94	cytoplasmic part
GO:0043229	0.94	intracellular organelle
GO:0043231	0.93	intracellular membrane-bounded organelle
GO:0031988	0.80	membrane-bounded vesicle
GO:0070062	0.79	extracellular exosome
GO:0005739	0.71	mitochondrion
GO:0005737	0.70	cytoplasm






(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	3h9mA	0.432	5.11	0.045	0.683	4.1.3.-	NA
2	0.060	3ikmD	0.411	4.81	0.076	0.634	2.7.7.7	69
3	0.060	1ahuA	0.420	4.77	0.079	0.644	1.1.3.38 1.1.3.13	NA
4	0.060	3aawA	0.444	5.19	0.047	0.727	2.7.2.4	67
5	0.060	1ebgA	0.428	4.85	0.079	0.663	4.2.1.11	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	1d5yA	0.549	3.45	0.065	0.717	0.51	QNA	65,66,69,73
2	0.01	1d5yC	0.548	3.47	0.059	0.722	0.46	QNA	66,67,70,71,83,85
3	0.01	2j0xB	0.456	5.10	0.048	0.732	0.73	PO4	65,67,108
4	0.01	3ab4E	0.436	5.26	0.060	0.712	0.67	THR	73,85,109
5	0.01	3ab4C	0.439	5.04	0.042	0.707	0.50	THR	68,69,70,71,72,125
6	0.01	2cdqA	0.455	5.04	0.054	0.727	0.46	SAM	83,84,115,120



(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.