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# D-I-TASSER results for Q6PID6

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

Summary of the Protein

Uniprot ID: Q6PID6
Protein Name: Tetratricopeptide repeat protein 33
Gene Name: TTC33

Input Sequence in FASTA format

>Q6PID6 (262 residues) MASFGWKRKIGEKVSKVTSQQFEAEAADEKDVVDNDEGNWLHAIKRRKEILLEGCAEKSK QLKDEGASLAENKRYREAIQKWDEALQLTPNDATLYEMKSQVLMSLHEMFPAVHAAEMAV QQNPHSWESWQTLGRAQLGLGEIILAIRSFQVALHIYPMNPEIWKEDLSWARTLQEQQKV AQRIKKSEAPAEVTHFSPKSIPDYDFESDEIVAVCAAIAEKEKTVSANKTMVIVSASGAI ETVTEKEDGATPPDGSVFIKAR

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 | Q6PID6-D1 | 1-262 | 262 |  | MASFGWKRKIGEKVSKVTSQQFEAEAADEKDVVDNDEGNWLHAIKRRKEILLEGCAEKSKQLKDEGASLAENKRYREAIQKWDEALQLTPNDATLYEMKSQVLMSLHEMFPAVHAAEMAVQQNPHSWESWQTLGRAQLGLGEIILAIRSFQVALHIYPMNPEIWKEDLSWARTLQEQQKVAQRIKKSEAPAEVTHFSPKSIPDYDFESDEIVAVCAAIAEKEKTVSANKTMVIVSASGAIETVTEKEDGATPPDGSVFIKAR

Top 1 final models from D-I-TASSER

Click to view | Ranka | Download | Estimated TM-scoreb
| 1 | model1.pdb.gz | 0.7402
(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 | 1w3bA | 0.78 | 3.15 | 0.143 | 0.935 | model1_1w3bA.pdb.gz
| 2 | 4a1sA | 0.78 | 3.77 | 0.098 | 0.977 | model1_4a1sA.pdb.gz
| 3 | 3sf4A | 0.77 | 3.84 | 0.098 | 0.977 | model1_3sf4A.pdb.gz
| 4 | 6tntJ | 0.77 | 2.94 | 0.106 | 0.924 | model1_6tntJ.pdb.gz
| 5 | 6mfvA | 0.77 | 3.31 | 0.102 | 0.935 | model1_6mfvA.pdb.gz
| 6 | 4bujB | 0.75 | 3.64 | 0.073 | 0.927 | model1_4bujB.pdb.gz
| 7 | 4ui9C | 0.75 | 3.21 | 0.096 | 0.908 | model1_4ui9C.pdb.gz
| 8 | 6af0A2 | 0.74 | 3.59 | 0.133 | 0.931 | model1_6af0A2.pdb.gz
| 9 | 5udiA | 0.73 | 3.65 | 0.113 | 0.912 | model1_5udiA.pdb.gz
| 10 | 5dseA | 0.72 | 3.81 | 0.111 | 0.916 | model1_5dseA.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:0003824 | 0.71 | catalytic activity
GO:0016740 | 0.61 | transferase activity
GO:0036094 | 0.59 | small molecule binding
GO:0016757 | 0.59 | transferase activity, transferring glycosyl groups
GO:0016262 | 0.56 | protein N-acetylglucosaminyltransferase activity
GO:0097363 | 0.55 | protein O-GlcNAc transferase activity
GO:0046972 | 0.55 | histone acetyltransferase activity (H4-K16 specific)
GO:0043996 | 0.55 | histone acetyltransferase activity (H4-K8 specific)
GO:0043995 | 0.55 | histone acetyltransferase activity (H4-K5 specific)
GO:0005547 | 0.55 | phosphatidylinositol-3,4,5-trisphosphate binding
GO:0030234 | 0.51 | enzyme regulator activity
GO:0048029 | 0.50 | monosaccharide binding
GO:0042277 | 0.50 | peptide binding
GO:0019904 | 0.50 | protein domain specific binding
GO:0008134 | 0.50 | transcription factor binding
GO:0008047 | 0.50 | enzyme activator activity
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:0009987 | 0.97 | cellular process
GO:0044699 | 0.81 | single-organism process
GO:0008152 | 0.79 | metabolic process
GO:0071704 | 0.78 | organic substance metabolic process
GO:0044237 | 0.76 | cellular metabolic process
GO:0065007 | 0.73 | biological regulation
GO:0044238 | 0.73 | primary metabolic process
GO:0050794 | 0.72 | regulation of cellular process
GO:0044763 | 0.72 | single-organism cellular process
GO:0044260 | 0.70 | cellular macromolecule metabolic process
GO:0016043 | 0.68 | cellular component organization
GO:0048518 | 0.64 | positive regulation of biological process
GO:0044767 | 0.63 | single-organism developmental process
GO:0080090 | 0.62 | regulation of primary metabolic process
GO:0031323 | 0.62 | regulation of cellular metabolic process
GO:0060255 | 0.61 | regulation of macromolecule metabolic process
GO:0044710 | 0.61 | single-organism metabolic process
GO:0022607 | 0.61 | cellular component assembly
GO:0009889 | 0.61 | regulation of biosynthetic process
GO:2000112 | 0.60 | regulation of cellular macromolecule biosynthetic process
GO:0051179 | 0.60 | localization
GO:0051171 | 0.60 | regulation of nitrogen compound metabolic process
GO:0019538 | 0.60 | protein metabolic process
GO:0010468 | 0.60 | regulation of gene expression
GO:0007165 | 0.60 | signal transduction
GO:0048856 | 0.59 | anatomical structure development
GO:0043933 | 0.59 | macromolecular complex subunit organization
GO:0032268 | 0.59 | regulation of cellular protein metabolic process
GO:0065003 | 0.58 | macromolecular complex assembly
GO:0050896 | 0.58 | response to stimulus
GO:0048583 | 0.58 | regulation of response to stimulus
GO:0044267 | 0.58 | cellular protein metabolic process
GO:0043412 | 0.58 | macromolecule modification
GO:0032501 | 0.58 | multicellular organismal process
GO:0048522 | 0.57 | positive regulation of cellular process
GO:0044707 | 0.57 | single-multicellular organism process
GO:0006464 | 0.57 | cellular protein modification process
GO:0080134 | 0.56 | regulation of response to stress
GO:0051173 | 0.56 | positive regulation of nitrogen compound metabolic process
GO:0031328 | 0.56 | positive regulation of cellular biosynthetic process
GO:0010628 | 0.56 | positive regulation of gene expression
GO:0010557 | 0.56 | positive regulation of macromolecule biosynthetic process
GO:0051641 | 0.55 | cellular localization
GO:0051252 | 0.55 | regulation of RNA metabolic process
GO:0051128 | 0.55 | regulation of cellular component organization
GO:0006996 | 0.55 | organelle organization
GO:0002684 | 0.55 | positive regulation of immune system process
GO:0048519 | 0.54 | negative regulation of biological process
GO:0044723 | 0.54 | single-organism carbohydrate metabolic process
GO:0032270 | 0.54 | positive regulation of cellular protein metabolic process
GO:0018193 | 0.54 | peptidyl-amino acid modification
GO:0006355 | 0.54 | regulation of transcription, DNA-templated
GO:0051716 | 0.53 | cellular response to stimulus
GO:0048523 | 0.53 | negative regulation of cellular process
GO:0033043 | 0.53 | regulation of organelle organization
GO:0031399 | 0.53 | regulation of protein modification process
GO:0006473 | 0.53 | protein acetylation
GO:0006461 | 0.53 | protein complex assembly
GO:0065008 | 0.52 | regulation of biological quality
GO:0045893 | 0.52 | positive regulation of transcription, DNA-templated
GO:0042221 | 0.52 | response to chemical
GO:0035556 | 0.52 | intracellular signal transduction
GO:0031324 | 0.52 | negative regulation of cellular metabolic process
GO:0031060 | 0.52 | regulation of histone methylation
GO:0010605 | 0.52 | negative regulation of macromolecule metabolic process
GO:0009605 | 0.52 | response to external stimulus
GO:0008219 | 0.52 | cell death
GO:0006325 | 0.52 | chromatin organization
GO:0051569 | 0.51 | regulation of histone H3-K4 methylation
GO:0051239 | 0.51 | regulation of multicellular organismal process
GO:0051049 | 0.51 | regulation of transport
GO:0043414 | 0.51 | macromolecule methylation
GO:0043207 | 0.51 | response to external biotic stimulus
GO:0042325 | 0.51 | regulation of phosphorylation
GO:0006493 | 0.51 | protein O-linked glycosylation
GO:0006357 | 0.51 | regulation of transcription from RNA polymerase II promoter
GO:1901700 | 0.50 | response to oxygen-containing compound
GO:1901135 | 0.50 | carbohydrate derivative metabolic process
GO:0090526 | 0.50 | regulation of gluconeogenesis involved in cellular glucose homeostasis
GO:0080182 | 0.50 | histone H3-K4 trimethylation
GO:0070887 | 0.50 | cellular response to chemical stimulus
GO:0061087 | 0.50 | positive regulation of histone H3-K27 methylation
GO:0060341 | 0.50 | regulation of cellular localization
GO:0048585 | 0.50 | negative regulation of response to stimulus
GO:0048015 | 0.50 | phosphatidylinositol-mediated signaling
GO:0045944 | 0.50 | positive regulation of transcription from RNA polymerase II promoter
GO:0045936 | 0.50 | negative regulation of phosphate metabolic process
GO:0045862 | 0.50 | positive regulation of proteolysis
GO:0043984 | 0.50 | histone H4-K16 acetylation
GO:0043982 | 0.50 | histone H4-K8 acetylation
GO:0043981 | 0.50 | histone H4-K5 acetylation
GO:0032922 | 0.50 | circadian regulation of gene expression
GO:0031397 | 0.50 | negative regulation of protein ubiquitination
GO:0010941 | 0.50 | regulation of cell death
GO:0010033 | 0.50 | response to organic substance
GO:0009966 | 0.50 | regulation of signal transduction
GO:0006915 | 0.50 | apoptotic process
GO:0006110 | 0.50 | regulation of glycolytic process

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:0044444 | 0.95 | cytoplasmic part
GO:0043226 | 0.89 | organelle
GO:0043229 | 0.87 | intracellular organelle
GO:0044422 | 0.84 | organelle part
GO:0044446 | 0.83 | intracellular organelle part
GO:0043227 | 0.82 | membrane-bounded organelle
GO:0043231 | 0.81 | intracellular membrane-bounded organelle
GO:0005737 | 0.76 | cytoplasm
GO:0032991 | 0.69 | macromolecular complex
GO:0016020 | 0.65 | membrane
GO:0043234 | 0.60 | protein complex
GO:0005829 | 0.57 | cytosol
GO:0044428 | 0.56 | nuclear part
GO:0005634 | 0.54 | nucleus

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 | 0.232 | 1w3bB | 0.780 | 3.06 | 0.146 | 0.935 | 2.4.1.- | 130,147,158,174
| 2 | 0.228 | 1w3bA | 0.781 | 3.15 | 0.143 | 0.935 | 2.4.1.- | 142,145
| 3 | 0.067 | 1ouvA | 0.600 | 4.42 | 0.073 | 0.844 | 3.5.2.6 | 113
| 4 | 0.066 | 2c0lA | 0.598 | 3.93 | 0.095 | 0.737 | 2.3.1.176 | 113,133,146
| 5 | 0.060 | 1hn0A | 0.505 | 5.30 | 0.042 | 0.782 | 4.2.2.20 | 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
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
| 1 | 0.08 | 3hymL | 0.688 | 3.84 | 0.119 | 0.893 | 0.62 | III | complex1.pdb.gz | 39,47,55,60,64,67,92,94,97,98,101,104,131,132,135,138,139,143,165,166,168,172,175,176,206,209,210
| 2 | 0.03 | 1fchA | 0.545 | 3.62 | 0.160 | 0.672 | 0.63 | III | complex2.pdb.gz | 64,67,68,70,71,82,98,101,105,135
| 3 | 0.02 | 2j9q1 | 0.612 | 4.14 | 0.095 | 0.763 | 0.64 | III | complex3.pdb.gz | 5,71,73,104,105,131,132,135,138,139,141
| 4 | 0.02 | 2gl7D | 0.583 | 5.34 | 0.066 | 0.916 | 0.92 | III | complex4.pdb.gz | 134,137,142,144,148,152
| 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.