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I-TASSER results for job id Rv2956

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

 Input Sequence in FASTA format
 Predicted Secondary Structure
 Predicted Solvent Accessibility
 Predicted Normalized B-facotr
 Top 10 threading templates used by I-TASSER
 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 higher value signifies a model with a high 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.)
 Proteins structureally close to the target in 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.)


 Predicted function using COACH

(This section reports biological annotations of the target protein by COACH based on the I-TASSER structure prediction. COACH is a meta-server approach that combines multiple function annotation results from the COFACTOR, TM-SITE and S-SITE programs.)


  Ligand binding sites

Rank C-score Cluster
size
PDB
Hit
Lig
Name
Download
Complex
Ligand Binding Site Residues
10.22 12 3nvkI SAM Rep, Mult 47,49,53,69,70,71,110,111,112,164,165,166
20.11 6 5lqnA 72O Rep, Mult 47,49,69,70,71,110,111,112,113,165,166,167
30.06 3 1kczA MG Rep, Mult 163,189,242
40.04 2 1gsaA MG Rep, Mult 163,189
50.02 1 3jwgA MG Rep, Mult 47,160
60.02 1 3bb1H MG Rep, Mult 115,163
70.02 1 1hdxB CXL Rep, Mult 9,220
80.02 1 1qgxA MG Rep, Mult 161,189

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

RankCscoreECPDB
Hit
TM-scoreRMSDaIDENaCovEC NumberActive Site Residues
10.0671suiA0.5663.640.1010.7282.1.1.104NA
20.0673e05D0.5542.620.0910.6422.1.1.13248
30.0671f38A0.5313.060.1080.6342.1.1.-NA
40.0672avdA0.5563.840.1030.7202.1.1.-NA
50.0671nt2A0.5533.070.1030.6672.1.1.-NA
60.0673grzB0.5113.070.1100.6172.1.1.-NA
70.0673bwmA0.5603.450.0950.6872.1.1.6NA
80.0673hnrA0.5243.090.1130.6302.1.1.-NA
90.0673c3yA0.5733.590.1120.7332.1.1.104121
100.0661pjzA0.5223.960.0510.6872.1.1.6752,67,72,144
110.0661g8aA0.5453.190.0870.6672.1.1.-NA
120.0662iftA0.5063.270.0710.6172.1.1.5248,50,163
130.0662ex4A0.5403.110.0650.6632.1.1.-166
140.0601fbnA0.5503.440.0820.6792.1.1.-NA
150.0601susD0.5643.630.0950.7242.1.1.104163
160.0602ytzA0.5603.460.0730.7002.1.1.32163
170.0602o2sA0.5494.370.0730.7491.3.1.9NA
180.0602a14A0.5603.990.0910.7282.1.1.4947,196
190.0602bh2A0.5753.430.0930.7082.1.1.-NA
200.0601kpiA0.5633.580.0680.7082.1.1.79NA
210.0602opbB0.5713.910.0570.7492.1.1.2847,72,196
220.0603cbgA0.5783.520.0840.7282.1.1.-204
230.0601ri1A0.5573.270.1050.6792.1.1.5647
240.0601xxlA0.5583.230.1080.6792.1.1.-NA
250.0602h11B0.5613.470.0750.7042.1.1.6754,80
260.0602e5wA0.5543.770.0520.7082.5.1.16NA
270.0602cl5A0.5593.490.1060.6872.1.1.6NA
280.0602pffD0.5394.650.0780.7532.3.1.8647,51,54
290.0603eppB0.5733.710.0820.7242.1.1.5647,107
300.0602i62C0.5624.070.0770.7412.1.1.147,79
310.0601mjfA0.5523.730.0580.7042.5.1.16NA
320.0603duwA0.5753.580.0910.7242.1.1.-173

(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

Homologous GO templates in PDB 
RankCscoreGOTM-scoreRMSDaIDENaCovPDB HitAssociated GO Terms
00.220.7471.900.150.812py6A GO:0008168 GO:0016740 GO:0032259
10.180.5663.640.100.731suiA GO:0008168 GO:0008171 GO:0009699 GO:0009809 GO:0016740 GO:0032259 GO:0042409 GO:0046872
20.160.5353.320.140.651o54A GO:0016429 GO:0030488 GO:0031515
30.140.5903.500.080.742hnkB GO:0008168 GO:0008171 GO:0016740 GO:0032259
40.130.5493.020.100.653mb5A GO:0008033 GO:0008168 GO:0016429 GO:0016740 GO:0030488 GO:0031515 GO:0032259
50.070.5232.570.100.612esrA GO:0003676 GO:0008168 GO:0016740 GO:0031167 GO:0032259
60.070.5292.830.080.623p9nA GO:0003676 GO:0008168 GO:0031167 GO:0032259
70.070.4882.980.100.591ws6A GO:0008168 GO:0016740 GO:0031167 GO:0032259
80.070.5262.830.090.632fhpA GO:0003676 GO:0008168 GO:0031167 GO:0032259
90.070.5813.580.090.733duwA GO:0008168 GO:0008171 GO:0016740 GO:0032259
100.070.5183.190.070.622fpoC GO:0003676 GO:0006364 GO:0008168 GO:0016740 GO:0031167 GO:0032259 GO:0052913 GO:0070475
110.070.5903.230.100.724ymgB GO:0008171 GO:0032259 GO:0046872 GO:0051536 GO:0051539
120.070.5692.980.090.693ntvA GO:0008171 GO:0032259
130.070.5883.730.080.744ckcD GO:0000166 GO:0003723 GO:0003824 GO:0004482 GO:0004484 GO:0004651 GO:0005525 GO:0006351 GO:0006353 GO:0006355 GO:0006370 GO:0006397 GO:0008152 GO:0008168 GO:0016740 GO:0016779 GO:0016787 GO:0019012 GO:0032259 GO:0036265 GO:0046872 GO:0050355 GO:0098507
140.070.5193.210.070.634qtuB GO:0000056 GO:0000447 GO:0005634 GO:0005730 GO:0005737 GO:0006364 GO:0008152 GO:0008168 GO:0008757 GO:0016435 GO:0016740 GO:0032259 GO:0070476
150.070.5723.710.080.733tr6A GO:0008168 GO:0008171 GO:0016740 GO:0032259
160.070.4773.050.070.575bxyA GO:0008168 GO:0032259
170.070.5063.270.070.622iftA GO:0003676 GO:0006364 GO:0008168 GO:0016740 GO:0031167 GO:0032259 GO:0052913
180.070.5773.930.080.743bgvB GO:0003723 GO:0004482 GO:0005634 GO:0005654 GO:0005730 GO:0005845 GO:0006366 GO:0006370 GO:0006397 GO:0008168 GO:0016740 GO:0032259 GO:0036265 GO:0043235
190.070.5563.840.100.722avdA GO:0005739 GO:0008168 GO:0008171 GO:0016020 GO:0016021 GO:0016740 GO:0032259
200.070.5733.590.110.733c3yA GO:0008168 GO:0008171 GO:0016740 GO:0032259 GO:0042409 GO:0046872
210.070.5683.720.110.724pcaA GO:0008168 GO:0008171 GO:0016740 GO:0032259 GO:0046872 GO:0051536 GO:0051539
220.070.5783.520.080.733cbgA GO:0008168 GO:0008171 GO:0016740 GO:0032259 GO:0046872
230.070.5643.360.100.694p7kA GO:0000287 GO:0005737 GO:0005739 GO:0005829 GO:0005886 GO:0006584 GO:0007565 GO:0007612 GO:0007614 GO:0008168 GO:0008171 GO:0008210 GO:0009712 GO:0014070 GO:0016020 GO:0016021 GO:0016036 GO:0016206 GO:0016740 GO:0030424 GO:0030425 GO:0032259 GO:0032496 GO:0032502 GO:0035814 GO:0042135 GO:0042417 GO:0042420 GO:0042493 GO:0043197 GO:0044297 GO:0045211 GO:0045963 GO:0046498 GO:0046500 GO:0046872 GO:0048265 GO:0048609 GO:0048662 GO:0050668 GO:0051930 GO:0070062
240.070.5733.700.070.733tfwA GO:0008168 GO:0008171 GO:0016740 GO:0032259
250.070.5513.320.070.683ccfB GO:0008152 GO:0008168 GO:0016740 GO:0030798 GO:0032259
260.070.5563.420.070.693e7pA GO:0046872 GO:0051536 GO:0051539
270.070.5473.420.100.693c3pA GO:0008168 GO:0008171 GO:0016740 GO:0032259
280.070.5583.420.090.693kkzA GO:0046872 GO:0051536 GO:0051539
290.070.5463.380.090.683mggB GO:0008168 GO:0016740 GO:0032259


Consensus prediction of GO terms
 
Molecular Function GO:0016426 GO:0043169
GO-Score 0.54 0.36
Biological Processes GO:0001510 GO:0006400 GO:0009808 GO:1901362 GO:0044550 GO:0019438
GO-Score 0.54 0.54 0.36 0.36 0.36 0.36
Cellular Component GO:0043527
GO-Score 0.54

(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 result.tar.bz2 to download the tarball file including all modelling results listed on this page]



Please cite the following articles when you use the I-TASSER server:
1. J Yang, R Yan, A Roy, D Xu, J Poisson, Y Zhang. The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12: 7-8, 2015.
2. J Yang, Y Zhang. I-TASSER server: new development for protein structure and function predictions, Nucleic Acids Research, 43: W174-W181, 2015.
3.A Roy, A Kucukural, Y Zhang. I-TASSER: a unified platform for automated protein structure and function prediction. Nature Protocols, 5: 725-738, 2010.
4.Y Zhang. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9: 40, 2008.