D-I-TASSER results for P59780

Summary of the Protein

Uniprot ID: P59780


Protein Name: AP-3 complex subunit sigma-2


Gene Name: AP3S2

Input Sequence in FASTA format

>P59780 (193 residues)
MIQAILVFNNHGKPRLVRFYQRFPEEIQQQIVRETFHLVLKRDDNICNFLEGGSLIGGSD
YKLIYRHYATLYFVFCVDSSESELGILDLIQVFVETLDKCFENVCELDLIFHMDKVHYIL
QEVVMGGMVLETNMNEIVAQIEAQNRLEKSEGGLSAAPARAVSAVKNINLPEIPRNINIG
DLNIKVPNLSQFV

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	P59780-D1	1-193	193	MIQAILVFNNHGKPRLVRFYQRFPEEIQQQIVRETFHLVLKRDDNICNFLEGGSLIGGSDYKLIYRHYATLYFVFCVDSSESELGILDLIQVFVETLDKCFENVCELDLIFHMDKVHYILQEVVMGGMVLETNMNEIVAQIEAQNRLEKSEGGLSAAPARAVSAVKNINLPEIPRNINIGDLNIKVPNLSQFV

Top 1 final models from D-I-TASSER

Rank^a	Estimated TM-score^b
1	0.7507


(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	1w63Q	0.73	1.30	0.378	0.767
2	2jktI	0.71	1.04	0.387	0.736
3	2hf6A	0.64	1.63	0.200	0.700
4	2jkrM1	0.62	2.12	0.114	0.689
5	1w63M	0.61	2.37	0.104	0.700
6	5a1wH1	0.57	2.65	0.173	0.689
7	4g5eA1	0.37	5.58	0.076	0.648
8	3cuxA	0.36	6.22	0.051	0.700
9	1prxA	0.36	4.34	0.047	0.518
10	4pmwA	0.32	5.95	0.044	0.601



(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:0005215	0.64	transporter activity
GO:0022892	0.50	substrate-specific transporter 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:0051179	0.92	localization
GO:0006810	0.90	transport
GO:0051649	0.77	establishment of localization in cell
GO:0051641	0.75	cellular localization
GO:0016192	0.75	vesicle-mediated transport
GO:0046907	0.73	intracellular transport
GO:0009987	0.72	cellular process
GO:0044699	0.70	single-organism process
GO:0044763	0.64	single-organism cellular process
GO:0044765	0.56	single-organism transport
GO:0065007	0.51	biological regulation






(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:0044424	1.00	intracellular part
GO:0044444	0.89	cytoplasmic part
GO:0043229	0.75	intracellular organelle
GO:0043227	0.75	membrane-bounded organelle
GO:0043231	0.74	intracellular membrane-bounded organelle
GO:0044425	0.67	membrane part
GO:0032991	0.67	macromolecular complex
GO:0043234	0.66	protein complex
GO:0098796	0.65	membrane protein complex
GO:0044446	0.59	intracellular organelle part
GO:0030119	0.57	AP-type membrane coat adaptor complex






(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	3dt7A	0.436	6.16	0.067	0.829	4.1.1.32	NA
2	0.060	3ce6A	0.435	5.23	0.065	0.725	3.3.1.1	NA
3	0.060	2wybB	0.440	5.70	0.054	0.808	3.5.1.97	NA
4	0.060	2b0tA	0.436	5.77	0.076	0.782	1.1.1.42	126
5	0.060	2w00B	0.438	5.38	0.051	0.756	3.1.21.3	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	1bxgB	0.487	4.99	0.057	0.808	0.14	HCI	3,4,125
2	0.01	3kyqA	0.525	3.15	0.073	0.653	0.19	DPV	8,13,43
3	0.01	3ryiA	0.492	5.49	0.066	0.850	0.12	GTP	66,89,91,124
4	0.01	3e22A	0.494	5.29	0.056	0.829	0.11	GTP	5,124,126
5	0.01	1sa1A	0.480	5.61	0.059	0.865	0.12	GTP	20,21,125
6	0.01	3du7C	0.475	5.59	0.086	0.860	0.11	GTP	19,65,125,128
7	0.01	1bxg0	0.495	5.07	0.063	0.808	0.21	III	12,17,18,19



(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.