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# D-I-TASSER results for Q9Y2X3

#### [Click result.zip to download all results on this page]

Summary of the Protein

Uniprot ID: Q9Y2X3
Protein Name: Nucleolar protein 58
Gene Name: NOP58

Input Sequence in FASTA format

>Q9Y2X3 (529 residues) MLVLFETSVGYAIFKVLNEKKLQEVDSLWKEFETPEKANKIVKLKHFEKFQDTAEALAAF TALMEGKINKQLKKVLKKIVKEAHEPLAVADAKLGGVIKEKLNLSCIHSPVVNELMRGIR SQMDGLIPGVEPREMAAMCLGLAHSLSRYRLKFSADKVDTMIVQAISLLDDLDKELNNYI MRCREWYGWHFPELGKIISDNLTYCKCLQKVGDRKNYASAKLSELLPEEVEAEVKAAAEI SMGTEVSEEDICNILHLCTQVIEISEYRTQLYEYLQNRMMAIAPNVTVMVGELVGARLIA HAGSLLNLAKHAASTVQILGAEKALFRALKSRRDTPKYGLIYHASLVGQTSPKHKGKISR MLAAKTVLAIRYDAFGEDSSSAMGVENRAKLEARLRTLEDRGIRKISGTGKALAKTEKYE HKSEVKTYDPSGDSTLPTCSKKRKIEQVDKEDEITEKKAKKAKIKVKVEEEEEEKVAEEE ETSVKKKKKRGKKKHIKEEPLSEEEPCTSTAIASPEKKKKKKKKRENED

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

Contact Map | Distance Map

D-I-TASSER simulation is guided by the consensus contact map (left figure) and distance map (right figure) derived based on confidence scores of DeepPotential. 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 | Models of Domain | Sequence
1 | Q9Y2X3-D1 | 1-156 | 156 |  | MLVLFETSVGYAIFKVLNEKKLQEVDSLWKEFETPEKANKIVKLKHFEKFQDTAEALAAFTALMEGKINKQLKKVLKKIVKEAHEPLAVADAKLGGVIKEKLNLSCIHSPVVNELMRGIRSQMDGLIPGVEPREMAAMCLGLAHSLSRYRLKFSAD
2 | Q9Y2X3-D2 | 157-529 | 373 |  | KVDTMIVQAISLLDDLDKELNNYIMRCREWYGWHFPELGKIISDNLTYCKCLQKVGDRKNYASAKLSELLPEEVEAEVKAAAEISMGTEVSEEDICNILHLCTQVIEISEYRTQLYEYLQNRMMAIAPNVTVMVGELVGARLIAHAGSLLNLAKHAASTVQILGAEKALFRALKSRRDTPKYGLIYHASLVGQTSPKHKGKISRMLAAKTVLAIRYDAFGEDSSSAMGVENRAKLEARLRTLEDRGIRKISGTGKALAKTEKYEHKSEVKTYDPSGDSTLPTCSKKRKIEQVDKEDEITEKKAKKAKIKVKVEEEEEEKVAEEEETSVKKKKKRGKKKHIKEEPLSEEEPCTSTAIASPEKKKKKKKKRENED

Top 1 final models from D-I-TASSER

Click to view | Ranka | Download | Estimated TM-scoreb
| 1 | model1.pdb.gz | 0.71
(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 DeepPotential, 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)
Click to view | Rank | PDB Hit | TM-score | RMSDa | IDENa | Cov. | Download Alignment
--- | --- | --- | --- | --- | --- | --- | ---
| 1 | 5wlcSB | 0.48 | 2.96 | 0.522 | 0.520 | model1_5wlcSB.pdb.gz
| 2 | 5oqlU | 0.48 | 2.86 | 0.460 | 0.516 | model1_5oqlU.pdb.gz
| 3 | 5wyj3E | 0.46 | 2.96 | 0.506 | 0.508 | model1_5wyj3E.pdb.gz
| 4 | 3id5A | 0.43 | 2.42 | 0.230 | 0.461 | model1_3id5A.pdb.gz
| 5 | 2ozbE | 0.42 | 2.32 | 0.290 | 0.450 | model1_2ozbE.pdb.gz
| 6 | 2nnwA | 0.42 | 2.38 | 0.241 | 0.444 | model1_2nnwA.pdb.gz
| 7 | 5oqlT | 0.40 | 3.76 | 0.288 | 0.454 | model1_5oqlT.pdb.gz
| 8 | 5ganF | 0.40 | 5.84 | 0.104 | 0.539 | model1_5ganF.pdb.gz
| 9 | 1nt2B2 | 0.30 | 1.85 | 0.255 | 0.312 | model1_1nt2B2.pdb.gz
| 10 | 2bnxB | 0.22 | 6.69 | 0.059 | 0.338 | model1_2bnxB.pdb.gz
(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) | RMSDa is the RMSD between residues that are structurally aligned by TM-align.
(d) | IDENa 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 | CscoreGO | Name
GO:0003723 | 1.00 | RNA binding
GO:0030515 | 0.99 | snoRNA binding
Download full result of the above consensus prediction.

| Click the graph to show a high resolution version.
(a) | CscoreGO is the confidence score of predicted GO terms. CscoreGO 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 CscoreGO:
[0.4,0.5) | [0.5,0.6) | [0.6,0.7) | [0.7,0.8) | [0.8,0.9) | [0.9,1.0]

Biological Process (BP)

GO term | CscoreGO | Name
GO:0071704 | 0.99 | organic substance metabolic process
GO:0044237 | 0.99 | cellular metabolic process
GO:0006396 | 0.98 | RNA processing
GO:0006364 | 0.88 | rRNA processing
GO:0043412 | 0.87 | macromolecule modification
GO:0000154 | 0.86 | rRNA modification

Download full result of the above consensus prediction.

| Click the graph to show a high resolution version.
(a) | CscoreGO is the confidence score of predicted GO terms. CscoreGO 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 CscoreGO:
[0.4,0.5) | [0.5,0.6) | [0.6,0.7) | [0.7,0.8) | [0.8,0.9) | [0.9,1.0]

Cellular Component (CC)

GO term | CscoreGO | Name
GO:0044424 | 1.00 | intracellular part
GO:0044428 | 0.99 | nuclear part
GO:0030529 | 0.99 | intracellular ribonucleoprotein complex
GO:0032040 | 0.87 | small-subunit processome
GO:0031428 | 0.87 | box C/D snoRNP complex
GO:0043226 | 0.50 | organelle

Download full result of the above consensus prediction.

| Click the graph to show a high resolution version.
(a) | CscoreGO is the confidence score of predicted GO terms. CscoreGO 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 CscoreGO:
[0.4,0.5) | [0.5,0.6) | [0.6,0.7) | [0.7,0.8) | [0.8,0.9) | [0.9,1.0]

Predicted Enzyme Commission (EC) Numbers

| Top 5 enzyme homologs in PDB
Click to view | Rank | CscoreEC | PDB Hit | TM-score | RMSDa | IDENa | Cov. | EC Number | Predicted Active Site Residues
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
| 1 | 0.060 | 1wz2A | 0.305 | 7.60 | 0.052 | 0.510 | 6.1.1.4 | NA
| 2 | 0.060 | 2e28A | 0.308 | 7.45 | 0.065 | 0.497 | 2.7.1.40 | NA
| 3 | 0.060 | 1s5jA | 0.309 | 7.33 | 0.050 | 0.490 | 2.7.7.7 | NA
| 4 | 0.060 | 1ofdA | 0.303 | 7.43 | 0.047 | 0.490 | 1.4.7.1 | NA
| 5 | 0.060 | 2r7oA | 0.344 | 7.69 | 0.034 | 0.571 | 2.7.7.48 | NA
| Click on the radio buttons to visualize predicted active site residues.
(a) | CscoreEC is the confidence score for the Enzyme Commission (EC) number prediction. CscoreEC 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) | RMSDa is the RMSD between residues that are structurally aligned by TM-align.
(d) | IDENa 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:
Click to view | Rank | CscoreLB | PDB Hit | TM-score | RMSDa | IDENa | Cov. | BS-score | Lig. Name | Download Complex | Predicted binding site residues
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
No Binding sites was predicted
| Click on the radio buttons to visualize predicted binding site and residues.
(a) | CscoreLB is the confidence score of predicted binding site. CscoreLB 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) | RMSDa the RMSD between residues that are structurally aligned by TM-align.
(e) | IDENa 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.

#### [Click result.zip to download all results on this page]

References:
1. | Wei Zheng, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.