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I-TASSER results for job id Rv2033c

[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
10.12 6 3qy6A FE Rep, Mult 102,138,166,195
20.04 2 3dg3A MG Rep, Mult 102,138,166
30.04 2 4jyeA 1N7 Rep, Mult 34,35,36,37,249
40.02 1 4i6kA CIT Rep, Mult 3,16,17,46,102,104,140,167
50.02 1 3ij6D NA Rep, Mult 125,133,135
60.02 1 1qhyA MG Rep, Mult 95,166
70.02 1 1mwoA ZN Rep, Mult 32,35,240,245
80.02 1 3id7A ZN Rep, Mult 133,167,195
90.02 1 2b0qA MG Rep, Mult 257,271
100.02 1 2dvuC GRE Rep, Mult 139,142,232
110.02 1 1nuiA MG Rep, Mult 114,166
120.02 1 1pokB ASN Rep, Mult 139,167,169
130.02 1 1r2rD DMS Rep, Mult 24,25,234
140.02 1 3ibsA MG Rep, Mult 93,95
150.02 1 3v1pB BMP Rep, Mult 3,42,75,77,140,141,233,234
160.02 1 1eywA PEL Rep, Mult 249,259,262
170.02 1 2v0nA MG Rep, Mult 118,166,168
180.02 1 3csvA ZN Rep, Mult 114,117

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
10.1841tqxA0.5064.330.0730.6895.1.3.1NA
20.0671dvjA0.5264.080.0990.7004.1.1.23NA
30.0671m5wF0.5394.400.0600.7502.6.99.2141,232
40.0662h6rB0.4994.310.0950.6795.3.1.1NA
50.0661v5xA0.4784.240.0920.6505.3.1.24166
60.0661hg3A0.5074.310.1080.6935.3.1.1NA
70.0663exrA0.5084.350.0960.7044.1.1.85170
80.0661tqjC0.4924.250.0680.6685.1.3.1139
90.0662v81A0.4844.220.0700.6614.1.2.21NA
100.0661nsjA0.4864.250.0700.6645.3.1.24166
110.0663f4wA0.5103.990.1270.6754.1.2.-NA
120.0661w0mA0.5104.350.1020.7005.3.1.1NA
130.0662yw3E0.4734.200.1050.6394.1.2.14NA
140.0661jfxA0.4924.270.0900.6713.2.1.17NA
150.0661mxsA0.4874.110.0820.6504.1.2.14NA
160.0661xi3A0.4664.370.1240.6432.5.1.3NA
170.0602qt3B0.6204.580.0890.8543.5.99.4268
180.0601a4lA0.6224.680.0940.8643.5.4.4167
190.0601wcgA0.6014.630.0630.8463.2.1.147NA
200.0601k6wA0.6184.600.0850.8573.5.4.1NA
210.0601qw7A0.6294.120.0830.8213.1.8.1NA
220.0601gnxA0.5964.760.1170.8503.2.1.21NA
230.0603ihnA0.6244.040.0960.8043.5.2.3NA
240.0601gkpA0.6533.540.0740.8143.5.2.2NA
250.0602icsA0.6044.270.0790.8073.5.4.2NA
260.0601onxA0.6434.300.1010.8643.4.19.-NA
270.0602ftyA0.6504.080.0820.8393.5.2.2166,167
280.0602z26A0.6163.980.0920.7893.5.2.3NA
290.0601ynyB0.6523.730.0820.8213.5.2.2166
300.0602qt3A0.6204.650.0840.8613.5.99.4130,132
310.0601itqA0.6403.990.0890.8293.4.13.19NA
320.0601zzmA0.6043.670.0920.7683.1.21.-NA
330.0602ftwA0.6503.780.0730.8293.5.2.2NA
340.0601ybqA0.6424.290.1010.8643.4.19.1NA
350.0603cmjA0.5994.720.0870.8503.2.1.21NA

(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
00.270.7452.620.130.844i6kA GO:0016787
10.270.6364.220.090.853ij6A GO:0016787 GO:0046872
20.160.7093.260.080.854dlfA GO:0016787
30.110.7193.000.130.842ffiA GO:0016787 GO:0047554
40.100.6693.860.100.862f6kA GO:0016787 GO:0046872
50.100.6583.860.110.854qrnA GO:0016787 GO:0046872
60.100.6553.980.100.854icmA GO:0016787 GO:0046872
70.100.6613.920.080.864ofcA GO:0001760 GO:0005829 GO:0006568 GO:0006569 GO:0008270 GO:0016787 GO:0016829 GO:0016831 GO:0046872 GO:0046874 GO:0051259 GO:0070062 GO:1904984 GO:1905004 GO:1905012
80.100.6713.580.120.844mupB GO:0016787 GO:0016853
90.090.6803.540.110.844d8lA GO:0016787 GO:0019619 GO:0047554
100.090.5025.310.070.764dziC GO:0016787
110.090.6533.990.100.852gwgA GO:0016787 GO:0046872
120.090.6653.890.090.852dvtA GO:0016787 GO:0046872
130.090.6724.140.100.884qroA GO:0016787 GO:0046872
140.070.6274.030.080.833nurA GO:0016787
150.070.6043.670.090.771zzmA GO:0004536 GO:0006308 GO:0016787 GO:0016788 GO:0016888 GO:0046872
160.070.4954.030.060.663guwA GO:0016788 GO:0046872
170.070.6774.150.090.884hjwC GO:0001760 GO:0006568 GO:0016787 GO:0046872 GO:1904984
180.070.6524.130.070.864eraA GO:0001760 GO:0006568 GO:0016787 GO:0046872 GO:1904984
190.070.5334.850.050.771hizA GO:0000272 GO:0004553 GO:0005576 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0031176 GO:0045493
200.070.5255.030.060.762j6xH GO:0000166 GO:0003824 GO:0010181 GO:0016491 GO:0046872 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0016787 GO:0046872
GO-Score 0.64 0.34
Biological Processes
GO-Score
Cellular Component
GO-Score

(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.