D-I-TASSER results for Q9ULI3-D9

Input Sequence in FASTA format

>Q9ULI3 (39 residues)
SSASVNSCAVNPCLHNGECVADNTSRGYHCRCPPSWQGD

Predicted Secondary Structure

                  20
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Sequence
SSASVNSCAVNPCLHNGECVADNTSRGYHCRCPPSWQGD
Prediction
CCCCCCCCCCCCCCCCCSSSSCCCCCCSSSSCCCCCCCC
Confidence
986667678887524973886068983488748777789

H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

                  20
                   |
Sequence
SSASVNSCAVNPCLHNGECVADNTSRGYHCRCPPSWQGD
Prediction
875636615443134514132445453240303563768

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 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.

Top 10 threading templates used by D-I-TASSER

Rank	PDB hit	ID1	ID2	Cov	Norm. Zscore	Download alignment		20                    |
							SS	CCCCCCCCCCCCCCCCCSSSSCCCCCCSSSSCCCCCCCC
							Seq	SSASVNSCAVNPCLHNGECVADNTSRGYHCRCPPSWQGD
1	5fmaA1	0.28	0.26	7.85	1.00	DEthreader		RQD-VNECGKPLCRHGGTCHNEV-G-SYRCVCRATHTER
2	1edmB	0.37	0.33	9.90	2.71	SPARKS-K		--VDGDQCESNPCLNGGSCKDDI--NSYECWCPFGFEGK
3	1epgA	0.19	0.18	5.79	0.61	MapAlign		--SYPGCPSSYYCLNGGVCMHIESLDSYTCNCVIGYRCQ
4	3ca7A	0.21	0.21	6.54	0.39	CEthreader		FPTYKCPFDAWYCLNDAHCFAVADLPVYSCECAIGFMGQ
5	1edmB	0.34	0.31	9.21	2.59	MUSTER		--VDGDQCESNPCLNGGSCKD--DINSYECWCPFGFEGK
6	3poyA2	0.24	0.23	7.18	1.06	HHsearch		CEGPSTTCQEDSCSNQGVCLQQW--DGFSCDCSMSFSGP
7	1edmB	0.37	0.33	9.90	0.58	FFAS-3D		--VDGDQCESNPCLNGGSCKDD--INSYECWCPFGFEGK
8	1vlaA	0.00	0.00	1.00	0.52	EigenThreader		GGKDAGLGCTGDVVIDQKIEIEPRIFHLKYIFDGEKVEK
9	1z1yA	0.19	0.18	5.79	1.42	CNFpred		--CVLDVCQYMNCGESGECIVEYLIQSAGCSCAIGMVPN
10	5fmaA	0.28	0.26	7.85	1.00	DEthreader		RQD-VNECGKPLCRHGGTCHNEV-G-SYRCVCRATHTER


(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	0.5826


(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.
1	2vj3A	0.74	1.61	0.297	0.949
2	5mwbA	0.74	1.78	0.270	0.949
3	1w0yL1	0.73	1.56	0.297	0.949
4	1edmB	0.73	1.35	0.371	0.897
5	4xbmB	0.72	1.93	0.263	0.949
6	4d90A	0.71	1.60	0.324	0.923
7	5uk5A	0.70	1.88	0.231	0.974
8	2vj2B	0.69	1.68	0.324	0.897
9	4cbzA	0.68	1.79	0.333	0.872
10	5fmaA1	0.68	1.55	0.297	0.923



(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:0043167	0.70	ion binding
GO:0005102	0.70	receptor binding
GO:0046872	0.69	metal ion binding
GO:0005509	0.67	calcium ion binding
GO:0005112	0.59	Notch binding
GO:1901363	0.57	heterocyclic compound binding
GO:0097159	0.57	organic cyclic compound binding
GO:0019899	0.55	enzyme binding
GO:0098772	0.54	molecular function regulator
GO:0004872	0.54	receptor activity
GO:0030234	0.53	enzyme regulator activity
GO:0003676	0.52	nucleic acid binding
GO:0046983	0.51	protein dimerization activity
GO:0044877	0.51	macromolecular complex binding
GO:0004857	0.51	enzyme inhibitor activity
GO:0003677	0.50	DNA 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:0065007	0.90	biological regulation
GO:0044699	0.90	single-organism process
GO:0050789	0.88	regulation of biological process
GO:0009987	0.87	cellular process
GO:0050794	0.83	regulation of cellular process
GO:0044763	0.83	single-organism cellular process
GO:0032502	0.81	developmental process
GO:0044767	0.72	single-organism developmental process
GO:0051239	0.69	regulation of multicellular organismal process
GO:0048518	0.68	positive regulation of biological process
GO:0048856	0.67	anatomical structure development
GO:2000026	0.65	regulation of multicellular organismal development
GO:0048522	0.63	positive regulation of cellular process
GO:0048519	0.63	negative regulation of biological process
GO:0045595	0.63	regulation of cell differentiation
GO:0060284	0.61	regulation of cell development
GO:0048583	0.61	regulation of response to stimulus
GO:0048523	0.60	negative regulation of cellular process
GO:0023051	0.60	regulation of signaling
GO:0022603	0.60	regulation of anatomical structure morphogenesis
GO:0010646	0.60	regulation of cell communication
GO:0007165	0.60	signal transduction
GO:0032501	0.59	multicellular organismal process
GO:0009653	0.59	anatomical structure morphogenesis
GO:0009966	0.58	regulation of signal transduction
GO:0051960	0.57	regulation of nervous system development
GO:0048584	0.57	positive regulation of response to stimulus
GO:0044707	0.57	single-multicellular organism process
GO:0050767	0.56	regulation of neurogenesis
GO:0019222	0.56	regulation of metabolic process
GO:0080090	0.55	regulation of primary metabolic process
GO:0060255	0.55	regulation of macromolecule metabolic process
GO:0048869	0.55	cellular developmental process
GO:0031323	0.55	regulation of cellular metabolic process
GO:0009967	0.55	positive regulation of signal transduction
GO:0051241	0.54	negative regulation of multicellular organismal process
GO:0007166	0.54	cell surface receptor signaling pathway
GO:0051093	0.53	negative regulation of developmental process
GO:0051128	0.52	regulation of cellular component organization
GO:0045664	0.52	regulation of neuron differentiation
GO:0016043	0.52	cellular component organization
GO:0007389	0.51	pattern specification process
GO:0051961	0.50	negative regulation of nervous system development
GO:0051240	0.50	positive regulation of multicellular organismal process
GO:0010468	0.50	regulation of gene expression
GO:0006928	0.50	movement of cell or subcellular component
GO:0003002	0.50	regionalization






(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:0044464	0.93	cell part
GO:0044424	0.79	intracellular part
GO:0016020	0.74	membrane
GO:0043226	0.65	organelle
GO:0044444	0.64	cytoplasmic part
GO:0044425	0.63	membrane part
GO:0044421	0.61	extracellular region part
GO:0043227	0.60	membrane-bounded organelle
GO:0005886	0.55	plasma membrane
GO:0044459	0.52	plasma membrane part
GO:0005576	0.52	extracellular region
GO:0043229	0.51	intracellular organelle






(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	0.303	1ccfA	0.601	1.88	0.294	0.872	3.4.21.6	8,13,17,19,28,30,32,38
2	0.060	1t3tA	0.483	2.37	0.051	0.923	6.3.5.3	22
3	0.060	3ilwA	0.487	2.85	0.026	0.923	5.99.1.3	NA
4	0.060	2lgsA	0.479	2.52	0.026	1.000	6.3.1.2	NA
5	0.060	3ensA	0.483	1.77	0.171	0.769	3.4.21.6	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	0.12	1w0yL	0.735	1.56	0.297	0.949	1.00	FUC	16,18,31,32,33
2	0.06	1dvaL	0.708	1.35	0.306	0.923	1.20	UUU	7,10,26,27,28,39
3	0.05	2vj3A	0.740	1.61	0.297	0.949	0.44	CA	13,14,36,37



(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.