D-I-TASSER results for O15347

Summary of the Protein

Uniprot ID: O15347


Protein Name: High mobility group protein B3


Gene Name: HMGB3

Input Sequence in FASTA format

>O15347 (200 residues)
MAKGDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKF
DEMAKADKVRYDREMKDYGPAKGGKKKKDPNAPKRPPSGFFLFCSEFRPKIKSTNPGISI
GDVAKKLGEMWNNLNDSEKQPYITKAAKLKEKYEKDVADYKSKGKFDGAKGPAKVARKKV
EEEDEEEEEEEEEEEEEEDE

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

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	Sequence
1	O15347-D1	1-200	200	MAKGDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYDREMKDYGPAKGGKKKKDPNAPKRPPSGFFLFCSEFRPKIKSTNPGISIGDVAKKLGEMWNNLNDSEKQPYITKAAKLKEKYEKDVADYKSKGKFDGAKGPAKVARKKVEEEDEEEEEEEEEEEEEEDE

Top 1 final models from D-I-TASSER

Rank^a	Estimated TM-score^b
1	0.5943


(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	2gzkA	0.68	2.49	0.484	0.785
2	7cttA	0.52	5.11	0.039	0.815
3	2yrqA	0.46	4.22	0.438	0.655
4	6co7A	0.46	4.96	0.055	0.720
5	3d19A	0.46	4.61	0.041	0.700
6	3dbyT	0.46	4.88	0.068	0.725
7	2cs1A	0.35	1.99	0.239	0.395
8	1v64A	0.35	3.14	0.170	0.430
9	2crjA	0.34	2.29	0.264	0.390
10	1lwmA	0.34	2.15	0.372	0.375



(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	0.99	heterocyclic compound binding
GO:0097159	0.99	organic cyclic compound binding
GO:0003677	0.98	DNA binding
GO:0008301	0.86	DNA binding, bending
GO:0043566	0.83	structure-specific DNA binding
GO:0000217	0.80	DNA secondary structure binding
GO:0000400	0.79	four-way junction 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:0009987	0.97	cellular process
GO:0016043	0.88	cellular component organization
GO:0006996	0.82	organelle organization
GO:0051276	0.81	chromosome organization
GO:0071103	0.80	DNA conformation change
GO:0032392	0.78	DNA geometric change
GO:0008152	0.63	metabolic process
GO:0044237	0.62	cellular metabolic process
GO:0071704	0.61	organic substance metabolic process
GO:0044238	0.61	primary metabolic process
GO:0044260	0.60	cellular macromolecule metabolic process
GO:0034641	0.56	cellular nitrogen compound metabolic process
GO:0090304	0.55	nucleic acid metabolic process
GO:0065007	0.54	biological regulation
GO:0050789	0.53	regulation of biological process
GO:0050794	0.51	regulation of cellular 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:0005634	1.00	nucleus
GO:0044446	0.74	intracellular organelle part
GO:0044428	0.67	nuclear part
GO:0032991	0.65	macromolecular complex
GO:0005737	0.50	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	3b9jI	0.183	5.99	0.057	0.330	1.17.1.4 1.17.3.2	NA
2	0.060	2iveA	0.414	4.97	0.035	0.675	1.3.3.4	NA
3	0.060	2ajqA	0.437	5.71	0.047	0.780	2.7.7.7	124
4	0.060	2f6dA	0.410	6.14	0.054	0.770	3.2.1.3	NA
5	0.060	1xmeA	0.413	5.26	0.056	0.670	1.9.3.1	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	0.33	1cktA	0.317	1.97	0.803	0.355	1.37	QNA	11,13,17,20,21,24,38
2	0.11	2gzkA	0.682	2.49	0.484	0.785	1.26	QNA	10,11,13,14,17,21,24,25,35,37,95,100,101,104,120,124,125,128,131,150,153,157
3	0.11	2gzkA	0.682	2.49	0.484	0.785	1.24	QNA	11,14,15,16,38,42,43,46,49,50,61,64,68,93,94,95,97,101,105,108,120
4	0.10	1cktA	0.317	1.97	0.803	0.355	1.19	UUU	96,98,100,120,121,124,125,128,131
5	0.04	1j47A	0.336	1.94	0.224	0.370	1.19	QNA	95,98,100,120,121,124,125,128,131,132,139,143,150
6	0.03	1j46A	0.335	1.97	0.224	0.370	1.24	QNA	95,98,100,101,120,121,124,125,128,131,132,139,143,150



(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.