D-I-TASSER results for Q8IYB8-D2

Input Sequence in FASTA format

>Q8IYB8 (114 residues)
NTSLFVPLTVKPQGPSADGDVGAELTRPLDKNEVKKVLDKFYKRKEIQKLGADYGLDARL
FHQAFISFRNYIMQSHSLDVDIHIVLNDICFGAAHADDLFPFFLRHAKQIFPVL

Predicted Secondary Structure

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Sequence
NTSLFVPLTVKPQGPSADGDVGAELTRPLDKNEVKKVLDKFYKRKEIQKLGADYGLDARLFHQAFISFRNYIMQSHSLDVDIHIVLNDICFGAAHADDLFPFFLRHAKQIFPVL
Prediction
CCCCSSSSSCCCCCCCCCCCCHHHHHCCCCHHHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCC
Confidence
984124321478899533551266504578899999999998169999999992931999999999999985267889920454699887177863567799999999863799

H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

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Sequence
NTSLFVPLTVKPQGPSADGDVGAELTRPLDKNEVKKVLDKFYKRKEIQKLGADYGLDARLFHQAFISFRNYIMQSHSLDVDIHIVLNDICFGAAHADDLFPFFLRHAKQIFPVL
Prediction
854214325153546474341034024415464024103512636304510673413431134014303420265760423010001201542440430121014204532447

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                    |                   |                   |                   |                   |
							SS	CCCCSSSSSCCCCCCCCCCCCHHHHHCCCCHHHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCC
							Seq	NTSLFVPLTVKPQGPSADGDVGAELTRPLDKNEVKKVLDKFYKRKEIQKLGADYGLDARLFHQAFISFRNYIMQSHSLDVDIHIVLNDICFGAAHADDLFPFFLRHAKQIFPVL
1	3rc3A1	0.88	0.75	20.98	1.17	DEthreader		TSFVPLTVKPQ-----------P-----LDKNEVKKVLDKFYKRKEIQKLGADYGLDARLFHQAFISFRNYI-QSHSLDVDIHIVLNDICFGAAHADDLFPFFLRHAKQIFPVL
2	3rc3A1	0.99	0.86	24.08	2.15	SPARKS-K		NTSLFVPLTVKPQP--------------LDKNEVKKVLDKFYKRKEIQKLGADYGLDARLFHQAFISFRNYI-QSHSLDVDIHIVLNDICFGAAHADDLFPFFLRHAKQIFPVL
3	3rc3A	0.98	0.84	23.60	1.76	MapAlign		-TSLFVPLTVKP--------------QPLDKNEVKKVLDKFYKRKEIQKLGADYGLDARLFHQAFISFRNYIQ-SHSLDVDIHIVLNDICFGAAHADDLFPFFLRHAKQIFPVL
4	3rc3A1	1.00	0.87	24.32	1.57	CEthreader		NTSLFVPLTVKPQ--------------PLDKNEVKKVLDKFYKRKEIQKLGADYGLDARLFHQAFISFRNYI-QSHSLDVDIHIVLNDICFGAAHADDLFPFFLRHAKQIFPVL
5	3rc3A1	1.00	0.86	24.07	1.98	MUSTER		NTSLFVPLTVKPQ--------------PLDKNEVKKVLDKFYKRKEIQKLGADYGLDARLFHQAFISFRNYI--SHSLDVDIHIVLNDICFGAAHADDLFPFFLRHAKQIFPVL
6	3rc3A1	1.00	0.87	24.32	4.28	HHsearch		NTSLFVPLTVKPQ--------------PLDKNEVKKVLDKFYKRKEIQKLGADYGLDARLFHQAFISFRNYI-QSHSLDVDIHIVLNDICFGAAHADDLFPFFLRHAKQIFPVL
7	3rc3A1	0.98	0.85	23.84	1.87	FFAS-3D		NTSLFVPLTVKP--------------QPLDKNEVKKVLDKFYKRKEIQKLGADYGLDARLFHQAFISFRNYIQ-SHSLDVDIHIVLNDICFGAAHADDLFPFFLRHAKQIFPVL
8	3rc3A1	0.97	0.84	23.61	1.25	EigenThreader		NTSLFVPLTVKP--------------QPLDKNEVKKVLDKFYKRKEIQKLGADYGLDARLFHQAFISFRNYIQS-HSLDVDIHIVLNDICFGAAHADDLFPFFLRHAKQIFPVL
9	3rc3A	1.00	0.88	24.56	1.03	CNFpred		NTSLFVPLTVKPQ--------------PLDKNEVKKVLDKFYKRKEIQKLGADYGLDARLFHQAFISFRNYIMQSHSLDVDIHIVLNDICFGAAHADDLFPFFLRHAKQIFPVL
10	3rc3A	0.88	0.75	20.98	1.17	DEthreader		TSFVPLTVKPQ-----------P-----LDKNEVKKVLDKFYKRKEIQKLGADYGLDARLFHQAFISFRNYI-QSHSLDVDIHIVLNDICFGAAHADDLFPFFLRHAKQIFPVL


(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	0.7455


(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	3rc3A1	0.83	0.95	0.908	0.860
2	5w1hA3	0.52	3.71	0.162	0.807
3	4txdA	0.52	3.92	0.037	0.842
4	1gpeA	0.52	4.35	0.054	0.860
5	4yntA	0.52	4.49	0.036	0.860
6	3dwbA	0.51	4.54	0.046	0.842
7	1cf3A	0.50	4.20	0.045	0.825
8	4iuwA2	0.47	4.57	0.045	0.833
9	3gdnA	0.46	4.63	0.117	0.816
10	3fimB	0.45	4.61	0.086	0.825



(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:0003678	1.00	DNA helicase activity
GO:0003677	1.00	DNA binding
GO:0003723	0.81	RNA binding
GO:0034458	0.74	3'-5' RNA helicase activity
GO:0004004	0.74	ATP-dependent RNA helicase activity
GO:0003725	0.74	double-stranded RNA 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:0032508	1.00	DNA duplex unwinding
GO:0008152	0.93	metabolic process
GO:0071704	0.91	organic substance metabolic process
GO:0044238	0.91	primary metabolic process
GO:0044237	0.91	cellular metabolic process
GO:0090304	0.90	nucleic acid metabolic process
GO:0044260	0.90	cellular macromolecule metabolic process
GO:0016070	0.89	RNA metabolic process
GO:0044699	0.86	single-organism process
GO:0065007	0.85	biological regulation
GO:0016071	0.85	mRNA metabolic process
GO:0050794	0.84	regulation of cellular process
GO:0044763	0.84	single-organism cellular process
GO:0006396	0.84	RNA processing
GO:0080090	0.83	regulation of primary metabolic process
GO:0060255	0.83	regulation of macromolecule metabolic process
GO:0051171	0.83	regulation of nitrogen compound metabolic process
GO:0048522	0.83	positive regulation of cellular process
GO:0031323	0.83	regulation of cellular metabolic process
GO:0051173	0.82	positive regulation of nitrogen compound metabolic process
GO:0051128	0.82	regulation of cellular component organization
GO:0031325	0.82	positive regulation of cellular metabolic process
GO:0010604	0.82	positive regulation of macromolecule metabolic process
GO:0000965	0.82	mitochondrial RNA 3'-end processing
GO:0006401	0.79	RNA catabolic process
GO:0006402	0.78	mRNA catabolic process
GO:0051252	0.75	regulation of RNA metabolic process
GO:0048523	0.75	negative regulation of cellular process
GO:0043933	0.75	macromolecular complex subunit organization
GO:0070827	0.74	chromatin maintenance
GO:0070584	0.74	mitochondrion morphogenesis
GO:0043066	0.74	negative regulation of apoptotic process
GO:0035946	0.74	mitochondrial mRNA surveillance
GO:0035945	0.74	mitochondrial ncRNA surveillance
GO:0030307	0.74	positive regulation of cell growth
GO:0006310	0.74	DNA recombination
GO:0000962	0.74	positive regulation of mitochondrial RNA catabolic process
GO:0000958	0.74	mitochondrial mRNA catabolic process






(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:0005759	1.00	mitochondrial matrix
GO:0043226	0.88	organelle
GO:0043229	0.87	intracellular organelle
GO:0043231	0.86	intracellular membrane-bounded organelle
GO:0005739	0.83	mitochondrion
GO:0032991	0.82	macromolecular complex
GO:0043234	0.79	protein complex
GO:0005634	0.77	nucleus
GO:0098798	0.76	mitochondrial protein complex
GO:0000178	0.76	exosome (RNase complex)
GO:0000177	0.75	cytoplasmic exosome (RNase complex)
GO:0045025	0.74	mitochondrial degradosome






(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	3dwbA	0.511	4.54	0.046	0.842	3.4.24.71	NA
2	0.060	3dnyT	0.436	4.42	0.117	0.754	3.6.5.3	81
3	0.060	1hwxA	0.458	3.60	0.055	0.702	1.4.1.3	NA
4	0.060	2e1rA	0.475	4.11	0.126	0.816	3.6.5.3	83
5	0.060	1p1jA	0.476	4.57	0.063	0.833	5.5.1.4	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	3mvoA	0.487	3.83	0.022	0.719	0.11	NDP	21,37,38
2	0.01	1nqtD	0.389	4.88	0.011	0.702	0.18	ADP	21,22,105



(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.