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I-TASSER results for job id Rv0970

[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 43 3a7kA RET Rep, Mult 61,76,80,96,99,100,103,162,165,166,169,196,200
20.09 12 1qhjA PH1 Rep, Mult 14,21,157,194,197,198,201,202,205,209
30.03 5 1mgyA BR Rep, Mult 45,49,60,61,196,200
40.02 4 1p8hA LI1 Rep, Mult 16,17,20,38,39,42,43,49
50.02 5 2i20A LI1 Rep, Mult 111,152,155,156,159,160,163,167
60.01 2 3mbvA BXC Rep, Mult 20,23,35,38,39,42,49
70.01 3 1brrA ARC Rep, Mult 70,71,74,75,78,82
80.01 1 2i1xA LI1 Rep, Mult 9,12,13,17,53
90.01 2 1brrA ARC Rep, Mult 149,150,153,157,202
100.01 3 1kmeA SQU Rep, Mult 40,43,44,47,51,60
110.01 2 1c8sA LI1 Rep, Mult 96,100,103,104,166
120.01 2 2wscI CLA Rep, Mult 196,199,200
130.01 1 1jv6A LI1 Rep, Mult 160,163,164,167,168
140.01 1 1c8sA SQU Rep, Mult 11,15,18,194,201
150.01 2 3am6A CLR Rep, Mult 17,18,21,22,205
160.01 1 1cwqA TRD Rep, Mult 13,42,43,49
170.01 2 1p8hA LI1 Rep, Mult 111,156,159,160,163,164,167
180.00 1 1gzmB C8E Rep, Mult 10,190,191,194
190.00 1 3pdjB 3PJ Rep, Mult 107,110
200.00 1 1jv6A LI1 Rep, Mult 153,156,160,195,198

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
10.0601jswB0.4844.880.0480.7624.3.1.1NA
20.0603e04D0.5154.050.0750.7194.2.1.248
30.0601y5nC0.4834.580.0470.7291.7.99.476
40.0601f1oA0.5003.940.0880.6864.3.2.2NA
50.0601t3cA0.4115.370.0660.6813.4.24.69NA
60.0601occA0.5245.070.0490.8571.9.3.1NA
70.0603ig5A0.4895.700.0680.8486.3.2.2NA
80.0601i0aA0.5104.350.0370.7294.3.2.1NA
90.0601xmeA0.5614.740.0780.8521.9.3.1NA
100.0601k7wD0.5204.180.0370.7294.3.2.1NA
110.0601dofA0.4824.310.0720.7004.3.2.2NA
120.0602e9fB0.5134.320.0370.7244.3.2.1NA
130.0603iam40.4695.170.0600.7291.6.99.5NA
140.0603gzhA0.4985.100.0710.7904.3.2.2NA
150.0601cc1L0.4955.060.0310.7671.12.99.6NA
160.0601qleA0.4864.980.0690.7811.9.3.1NA
170.0601vdkA0.4715.040.0740.7524.2.1.2NA
180.0602fenD0.4904.400.0390.7005.5.1.2NA
190.0601m56A0.5524.810.0710.8711.9.3.142

(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
00.410.7892.060.080.871cwqA GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0015992 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
10.320.8081.660.080.872z55A GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0015992 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
20.320.7762.200.130.875awzA GO:0005216 GO:0006811 GO:0016020 GO:0016021 GO:0034220
30.290.8071.950.110.884fbzA GO:0005216 GO:0006811 GO:0016020 GO:0016021 GO:0034220
40.280.8011.700.130.874l35A GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0015992 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
50.280.7951.680.080.863qbgA GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
60.270.7182.400.050.844yziA GO:0005216 GO:0006811 GO:0016020 GO:0016021 GO:0034220 GO:0046872
70.270.7981.760.100.865ahzA GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
80.260.8061.640.100.874qi1A GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0015992 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
90.260.7971.780.090.884hyjA GO:0005216 GO:0006811 GO:0007602 GO:0010461 GO:0016020 GO:0016021 GO:0018298 GO:0034220
100.260.6931.640.090.741c8sA GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0015992 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
110.250.7822.100.090.895azdA GO:0005216 GO:0006811 GO:0016020 GO:0016021 GO:0034220
120.250.7752.090.120.863am6A GO:0005216 GO:0006811 GO:0016020 GO:0016021 GO:0034220
130.240.7452.350.120.864klyB GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0010461 GO:0015992 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
140.230.7812.420.050.894xtnA GO:0005216 GO:0006811 GO:0016020 GO:0016021 GO:0034220
150.220.8041.690.080.871uazA GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0015992 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
160.210.7881.850.130.862ksyA GO:0005216 GO:0006811 GO:0016020 GO:0016021 GO:0034220
170.210.6982.580.040.844knfC GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0010461 GO:0015992 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
180.210.7252.100.120.814jq6B GO:0005216 GO:0006811 GO:0007602 GO:0010461 GO:0016020 GO:0016021 GO:0018298 GO:0034220


Consensus prediction of GO terms
 
Molecular Function GO:0005216 GO:0009881
GO-Score 0.86 0.71
Biological Processes GO:0034220 GO:0015992 GO:0018298 GO:0007602
GO-Score 0.86 0.71 0.71 0.71
Cellular Component GO:0016021 GO:0005886
GO-Score 0.86 0.71

(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.