D-I-TASSER results for Q07020

Summary of the Protein

Uniprot ID: Q07020


Protein Name: 60S ribosomal protein L18


Gene Name: RPL18

Input Sequence in FASTA format

>Q07020 (188 residues)
MGVDIRHNKDRKVRRKEPKSQDIYLRLLVKLYRFLARRTNSTFNQVVLKRLFMSRTNRPP
LSLSRMIRKMKLPGRENKTAVVVGTITDDVRVQEVPKLKVCALRVTSRARSRILRAGGKI
LTFDQLALDSPKGCGTVLLSGPRKGREVYRHFGKAPGTPHSHTKPYVRSKGRKFERARGR
RASRGYKN

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	Q07020-D1	1-188	188	MGVDIRHNKDRKVRRKEPKSQDIYLRLLVKLYRFLARRTNSTFNQVVLKRLFMSRTNRPPLSLSRMIRKMKLPGRENKTAVVVGTITDDVRVQEVPKLKVCALRVTSRARSRILRAGGKILTFDQLALDSPKGCGTVLLSGPRKGREVYRHFGKAPGTPHSHTKPYVRSKGRKFERARGRRASRGYKN

Top 1 final models from D-I-TASSER

Rank^a	Estimated TM-score^b
1	0.8416


(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	3j3bQ	0.94	1.55	0.989	0.989
2	3u5eQ	0.93	1.47	0.543	0.973
3	3j39Q	0.93	1.84	0.684	0.989
4	5xxbP	0.91	1.93	0.581	0.984
5	1vx7S	0.91	1.65	0.573	0.979
6	5t2aI	0.91	1.75	0.495	0.973
7	5xy3Q	0.89	2.04	0.492	0.979
8	3zf7I	0.87	2.32	0.465	0.984
9	4a17N	0.86	1.90	0.522	0.942
10	2zkro	0.58	2.01	0.916	0.633



(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:0003723	1.00	RNA binding
GO:0003735	0.99	structural constituent of ribosome






(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:0006412	1.00	translation






(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:0044446	1.00	intracellular organelle part
GO:0044444	0.98	cytoplasmic part
GO:0022625	0.97	cytosolic large 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	1r9jB	0.418	5.67	0.061	0.750	2.2.1.1	NA
2	0.060	2epoB	0.374	5.76	0.052	0.697	3.2.1.52	NA
3	0.060	1ry2A	0.429	6.31	0.071	0.867	6.2.1.1	NA
4	0.060	1jqkF	0.436	5.54	0.058	0.761	1.2.99.2	126
5	0.060	1b0pA	0.421	5.47	0.049	0.750	1.2.7.1	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	0.01	2g25B	0.479	5.57	0.060	0.835	0.17	TDK	52,126,132
2	0.01	3lq2A	0.478	5.47	0.049	0.830	0.22	TDP	66,83,100,101,102
3	0.01	3lq4B	0.476	5.52	0.049	0.830	0.22	TDP	35,48,128
4	0.01	2o1xD	0.454	5.50	0.061	0.808	0.13	TDP	57,58,59,84,85
5	0.01	1qgdA	0.440	5.69	0.044	0.793	0.14	TPP	97,135,137
6	0.01	2qtcA	0.479	5.46	0.049	0.830	0.30	TDK	84,141,147
7	0.01	2r8pB	0.444	5.72	0.033	0.803	0.18	T6F	30,31,35,102
8	0.01	2gk6A	0.464	5.19	0.060	0.777	0.12	UUU	43,44,45,46
9	0.01	3lplA	0.451	5.82	0.081	0.835	0.18	TDP	75,98,99,100
10	0.01	2g25A	0.480	5.60	0.065	0.840	0.16	TDK	101,102,128



(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.