D-I-TASSER results for Q9Y2Q9

Summary of the Protein

Uniprot ID: Q9Y2Q9


Protein Name: 28S ribosomal protein S28, mitochondrial


Gene Name: MRPS28

Input Sequence in FASTA format

>Q9Y2Q9 (187 residues)
MAALCRTRAVAAESHFLRVFLFFRPFRGVGTESGSESGSSNAKEPKTRAGGFASALERHS
ELLQKVEPLQKGSPKNVESFASMLRHSPLTQMGPAKDKLVIGRIFHIVENDLYIDFGGKF
HCVCRRPEVDGEKYQKGTRVRLRLLDLELTSRFLGATTDTTVLEANAVLLGIQESKDSRS
KEEHHEK

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	Q9Y2Q9-D1	1-187	187	MAALCRTRAVAAESHFLRVFLFFRPFRGVGTESGSESGSSNAKEPKTRAGGFASALERHSELLQKVEPLQKGSPKNVESFASMLRHSPLTQMGPAKDKLVIGRIFHIVENDLYIDFGGKFHCVCRRPEVDGEKYQKGTRVRLRLLDLELTSRFLGATTDTTVLEANAVLLGIQESKDSRSKEEHHEK

Top 1 final models from D-I-TASSER

Rank^a	Estimated TM-score^b
1	0.6325


(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	1miuA	0.47	4.89	0.018	0.733
2	5zn6A	0.45	5.18	0.041	0.754
3	5xguB	0.45	4.61	0.076	0.631
4	2id0A	0.45	4.21	0.051	0.620
5	7dcyA	0.44	4.30	0.089	0.626
6	6f3hA	0.43	4.63	0.039	0.610
7	1eh9A2	0.43	5.35	0.031	0.738
8	2v3eA	0.43	5.22	0.059	0.722
9	2jlnA	0.43	5.28	0.075	0.706
10	4pmwA	0.42	4.68	0.039	0.610



(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	0.81	heterocyclic compound binding
GO:0097159	0.81	organic cyclic compound binding
GO:0003723	0.78	RNA binding
GO:0044822	0.73	poly(A) 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:0009987	0.98	cellular process
GO:0008152	0.98	metabolic process
GO:0044260	0.97	cellular macromolecule metabolic process
GO:0034645	0.96	cellular macromolecule biosynthetic process
GO:0070125	0.68	mitochondrial translational elongation
GO:0044238	0.63	primary metabolic process
GO:0006807	0.59	nitrogen compound metabolic process
GO:0034641	0.58	cellular nitrogen compound metabolic process
GO:0044699	0.56	single-organism process
GO:1901564	0.51	organonitrogen compound metabolic process
GO:0019538	0.51	protein metabolic 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:0044444	1.00	cytoplasmic part
GO:0032991	1.00	macromolecular complex
GO:0005763	0.99	mitochondrial small ribosomal subunit






(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	2g3mF	0.397	5.92	0.064	0.749	3.2.1.20	NA
2	0.060	3dlaD	0.407	5.39	0.028	0.695	6.3.5.1	89,113
3	0.060	1clvA	0.409	5.34	0.073	0.695	3.2.1.1	NA
4	0.060	1cygA	0.409	5.62	0.087	0.717	2.4.1.19	NA
5	0.060	1uokA	0.400	5.20	0.079	0.674	3.2.1.10	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	3gxfC	0.381	5.13	0.047	0.636	0.51	PO4	140,168,169,171,172
2	0.01	2nt0D	0.425	5.34	0.054	0.733	0.49	GOL	101,102,103,115
3	0.01	2bxyA	0.411	5.65	0.063	0.749	0.56	TRE	155,158,159,160
4	0.01	1llwA	0.425	5.91	0.045	0.818	0.42	F3S	102,103,104,105,137
5	0.01	1lm1A	0.420	5.80	0.035	0.775	0.58	F3S	102,103,104,105,113,114,118
6	0.01	2nt1D	0.380	5.90	0.045	0.711	0.62	PO4	100,101,115,116,117
7	0.01	3gxiB	0.382	5.98	0.045	0.717	0.43	PO4	112,137,140



(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.