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I-TASSER results for job id S692865

(Click on S692865_results.tar.bz2 to download the tarball file including all modeling results listed on this page. Click on Annotation of I-TASSER Output to read the instructions for how to interpret the results on this page. Model results are kept on the server for 60 days, there is no way to retrieve the modeling data older than 2 months)

  Submitted Sequence in FASTA format

  Predicted Secondary Structure

Sequence                  20                  40                  60                  80                 100                 120                 140                 160                 180                 200                 220                 240                 260                 280                 300                 320                 340                 360                 380                 400                 420                 440                 460                 480
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H:Helix; S:Strand; C:Coil

  Predicted Solvent Accessibility

Sequence                  20                  40                  60                  80                 100                 120                 140                 160                 180                 200                 220                 240                 260                 280                 300                 320                 340                 360                 380                 400                 420                 440                 460                 480
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Values range from 0 (buried residue) to 9 (highly exposed residue)

   Predicted normalized B-factor

(B-factor is a value to indicate the extent of the inherent thermal mobility of residues/atoms in proteins. In I-TASSER, this value is deduced from threading template proteins from the PDB in combination with the sequence profiles derived from sequence databases. The reported B-factor profile in the figure below corresponds to the normalized B-factor of the target protein, defined by B=(B'-u)/s, where B' is the raw B-factor value, u and s are respectively the mean and standard deviation of the raw B-factors along the sequence. Click here to read more about predicted normalized B-factor)

  Top 10 threading templates used by I-TASSER

(I-TASSER modeling starts from the structure templates identified by LOMETS from the PDB library. LOMETS is a meta-server threading approach containing multiple threading programs, where each threading program can generate tens of thousands of template alignments. I-TASSER only uses the templates of the highest significance in the threading alignments, the significance of which are measured by the Z-score, i.e. the difference between the raw and average scores in the unit of standard deviation. The templates in this section are the 10 best templates selected from the LOMETS threading programs. Usually, one template of the highest Z-score is selected from each threading program, where the threading programs are sorted by the average performance in the large-scale benchmark test experiments.)

Rank PDB
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(a)All the residues are colored in black; however, those residues in template which are identical to the residue in the query sequence are highlighted in color. Coloring scheme is based on the property of amino acids, where polar are brightly coloured while non-polar residues are colored in dark shade. (more about the colors used)
(b)Rank of templates represents the top ten threading templates used by I-TASSER.
(c)Ident1 is the percentage sequence identity of the templates in the threading aligned region with the query sequence.
(d)Ident2 is the percentage sequence identity of the whole template chains with query sequence.
(e)Cov represents the coverage of the threading alignment and is equal to the number of aligned residues divided by the length of query protein.
(f)Norm. Z-score is the normalized Z-score of the threading alignments. Alignment with a Normalized Z-score >1 mean a good alignment and vice versa.
(g)Download Align. provides the 3D structure of the aligned regions of the threading templates.
(h)The top 10 alignments reported above (in order of their ranking) are from the following threading programs:
       1: FFAS-3D   2: SPARKS-X   3: HHSEARCH2   4: HHSEARCH I   5: Neff-PPAS   6: HHSEARCH   7: pGenTHREADER   8: wdPPAS   9: PROSPECT2   10: SP3   

   Top 5 final models predicted by I-TASSER

(For each target, I-TASSER simulations generate a large ensemble of structural conformations, called decoys. To select the final models, I-TASSER uses the SPICKER program to cluster all the decoys based on the pair-wise structure similarity, and reports up to five models which corresponds to the five largest structure clusters. The confidence of each model is quantitatively measured by C-score that is calculated based on the significance of threading template alignments and the convergence parameters of the structure assembly simulations. C-score is typically in the range of [-5, 2], where a C-score of a higher value signifies a model with a higher confidence and vice-versa. TM-score and RMSD are estimated based on C-score and protein length following the correlation observed between these qualities. Since the top 5 models are ranked by the cluster size, it is possible that the lower-rank models have a higher C-score in rare cases. Although the first model has a better quality in most cases, it is also possible that the lower-rank models have a better quality than the higher-rank models as seen in our benchmark tests. If the I-TASSER simulations converge, it is possible to have less than 5 clusters generated; this is usually an indication that the models have a good quality because of the converged simulations.)
    (By right-click on the images, you can export image file or change the configurations, e.g. modifying the background color or stopping the spin of your models)
  • Download Model 1
  • C-score=1.61 (Read more about C-score)
  • Estimated TM-score = 0.94±0.05
  • Estimated RMSD = 3.9±2.6Å

  Proteins structurally close to the target in the PDB (as identified by TM-align)

(After the structure assembly simulation, I-TASSER uses the TM-align structural alignment program to match the first I-TASSER model to all structures in the PDB library. This section reports the top 10 proteins from the PDB that have the closest structural similarity, i.e. the highest TM-score, to the predicted I-TASSER model. Due to the structural similarity, these proteins often have similar function to the target. However, users are encouraged to use the data in the next section 'Predicted function using COACH' to infer the function of the target protein, since COACH has been extensively trained to derive biological functions from multi-source of sequence and structure features which has on average a higher accuracy than the function annotations derived only from the global structure comparison.)

Top 10 Identified stuctural analogs in PDB

to view
RankPDB HitTM-scoreRMSDaIDENaCovAlignment
15x5tA0.984 0.690.8000.992Download
25vbfA0.983 0.940.5130.996Download
31a4sA0.981 0.990.3450.996Download
43ek1A0.981 1.130.4160.996Download
53ifgA0.980 1.250.4200.998Download
61o01C0.980 1.110.3400.998Download
73jz4A0.979 1.370.4150.998Download
81o9jA0.979 1.150.3320.998Download
92o2rC0.978 1.250.3260.998Download
103k2wB0.978 1.220.3461.000Download

(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 function using COFACTOR and COACH

(This section reports biological annotations of the target protein by COFACTOR and COACH based on the I-TASSER structure prediction. While COFACTOR deduces protein functions (ligand-binding sites, EC and GO) using structure comparison and protein-protein networks, COACH is a meta-server approach that combines multiple function annotation results (on ligand-binding sites) from the COFACTOR, TM-SITE and S-SITE programs.)

  Ligand binding sites

to view
Ligand Binding Site Residues
10.63 250 4zxuB NAD Rep, Mult 150,151,152,153,154,159,177,179,180,210,214,215,228,229,230,231,234,237,238,252,253,254,286,383,385,411,449
20.59 212 4ou2A 6OA Rep, Mult 108,154,155,158,159,285,286,441,443,449
30.22 77 3n83C ADP Rep, Mult 150,151,153,177,179,180,210,214,215,228,229,230,231,234,238,333
40.04 17 3sz9B I3E Rep, Mult 155,280,285,286,287,441,443,449
50.04 16 3inlC BXB Rep, Mult 108,155,158,162,276,280,285,441,442,443

Download the residue-specific ligand binding probability, which is estimated by SVM.
Download the all possible binding ligands and detailed prediction summary.
Download the templates clustering results.
(a)C-score is the confidence score of the prediction. C-score ranges [0-1], where a higher score indicates a more reliable prediction.
(b)Cluster size is the total number of templates in a cluster.
(c)Lig Name is name of possible binding ligand. Click the name to view its information in the BioLiP database.
(d)Rep is a single complex structure with the most representative ligand in the cluster, i.e., the one listed in the Lig Name column.
Mult is the complex structures with all potential binding ligands in the cluster.

  Enzyme Commission (EC) numbers and active sites

to view
TM-scoreRMSDaIDENaCovEC NumberActive Site Residues
10.6432w8oA0.966 1.240.4120.985  198
20.5292w8nA0.961 1.780.4140.992  NA
30.4902ve5A0.977 1.100.3560.994  NA
40.4892ve5H0.975 1.140.3560.994  61,164,207
50.4881t90A0.961 1.490.2770.992  168

 Click on the radio buttons to visualize predicted active site residues.
(a)CscoreEC is the confidence score for the 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.

  Gene Ontology (GO) terms
Top 10 homologous GO templates in PDB 
RankCscoreGOTM-scoreRMSDaIDENaCovPDB HitAssociated GO Terms
1 0.620.9766 1.10 0.36 0.992wmeA GO:0016491 GO:0055114 GO:0008152 GO:0008802 GO:0006578
2 0.490.9693 1.16 0.33 0.993iwkH GO:0016491 GO:0019145 GO:0000166 GO:0008152 GO:0055114
3 0.490.9612 1.49 0.28 0.991t90A GO:0055114 GO:0016491 GO:0018478 GO:0004491 GO:0008152
4 0.490.9736 1.36 0.41 1.002w8pA GO:0005625 GO:0007417 GO:0042803 GO:0007269 GO:0009450 GO:0042135 GO:0046459 GO:0006541 GO:0004777 GO:0016491 GO:0051289 GO:0006083 GO:0006536 GO:0006681 GO:0007268 GO:0006749 GO:0006650 GO:0006006 GO:0005739 GO:0005759 GO:0022904 GO:0055114 GO:0006105 GO:0008152 GO:0016620
5 0.480.9191 1.34 0.31 0.943pqaB GO:0008911 GO:0016491 GO:0055114 GO:0008152
6 0.480.9797 1.25 0.42 1.003ifgA GO:0055114 GO:0016491 GO:0009013 GO:0008152 GO:0016620
7 0.480.9791 1.15 0.33 1.001o9jA GO:0016491 GO:0055114 GO:0004029 GO:0005737 GO:0008152
8 0.480.9797 1.11 0.34 1.001o01C GO:0016491 GO:0005759 GO:0005739 GO:0055114 GO:0004029 GO:0008152 GO:0004030 GO:0035094 GO:0055093 GO:0071398 GO:0007268 GO:0033574 GO:0042802 GO:0001889 GO:0009055 GO:0032496 GO:0006066 GO:0032870 GO:0006805 GO:0032570 GO:0006069 GO:0005975 GO:0042136
9 0.480.9791 1.37 0.41 1.003jz4A GO:0055114 GO:0016491 GO:0008152 GO:0016620
10 0.480.9775 1.22 0.35 1.003k2wB GO:0008802 GO:0055114 GO:0016491 GO:0008152

Consensus prediction of GO terms
Molecular Function GO:0008802 GO:0000166 GO:0019145 GO:0004491 GO:0018478 GO:0042803 GO:0004777 GO:0008911
GO-Score 0.62 0.49 0.49 0.49 0.49 0.49 0.49 0.48
Biological Process GO:0006578 GO:0006541 GO:0006536 GO:0007269 GO:0006083 GO:0006105 GO:0051289 GO:0046459 GO:0006681 GO:0006650
GO-Score 0.62 0.49 0.49 0.49 0.49 0.49 0.49 0.49 0.49 0.49
Cellular Component GO:0005759 GO:0005625
GO-Score 0.49 0.49

(a)CscoreGO is a combined measure for evaluating global and local similarity between query and template protein. It's range is [0-1] and higher values indicate more confident predictions.
(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.
(f)The second table shows a consensus GO terms amongst the top scoring templates. The GO-Score associated with each prediction is defined as the average weight of the GO term, where the weights are assigned based on CscoreGO of the template.

[Click on S692865_results.tar.bz2 to download the tarball file including all modeling results listed on this page]

Please cite the following articles when you use the I-TASSER server:
  • 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. Cell Reports Methods, 1: 100014 (2021).
  • Chengxin Zhang, Peter L. Freddolino, and Yang Zhang. COFACTOR: improved protein function prediction by combining structure, sequence and protein-protein interaction information. Nucleic Acids Research, 45: W291-299 (2017).
  • Jianyi Yang, Yang Zhang. I-TASSER server: new development for protein structure and function predictions, Nucleic Acids Research, 43: W174-W181, 2015.