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I-TASSER results for job id Rv3900c

[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
10.05 3 3k71G CA Rep, Mult 190,191,192,193,196,199
20.05 3 3erzD HG Rep, Mult 36,41,45
30.03 2 5ioaB ZN Rep, Mult 85,88
40.03 2 3cvsA NUC Rep, Mult 79,81
50.02 1 2vn4A MAN Rep, Mult 267,268
60.02 1 3jz0A APC Rep, Mult 139,144
70.02 1 4dfdA MG Rep, Mult 5,9,171
80.02 1 4o6nB MPG Rep, Mult 86,93
90.02 1 3r4iB CA Rep, Mult 43,65
100.02 1 4tt0B IOD Rep, Mult 176,177,180
110.02 1 3sl9A IMD Rep, Mult 62,103
120.02 1 2hcjB GDP Rep, Mult 141,142,143,144,145,146
130.02 1 2q8hA TF4 Rep, Mult 55,70,108,149,152
140.02 1 5ioeB ZN Rep, Mult 149,153
150.02 1 3pp5A CA Rep, Mult 82,85
160.02 1 1ncg0 III Rep, Mult 198,199,200,201,202,259,260,268,269,271
170.02 1 4eyaB NUC Rep, Mult 92,96
180.02 1 2qviA CA Rep, Mult 131,156,167,170
190.02 1 3bpxA SAL Rep, Mult 145,149
200.02 1 3rj1H SE Rep, Mult 115,120

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
10.0601hn0A0.3496.110.0380.5594.2.2.20NA
20.0602x0sA0.3466.620.0250.6112.7.9.1NA
30.0602gv9B0.3826.790.0380.6782.7.7.7176
40.0601g8mA0.3616.870.0540.6563.5.4.10,2.1.2.3NA
50.0602uv8G0.3417.330.0430.6532.3.1.86NA
60.0602zxqA0.3367.160.0390.6143.2.1.97NA
70.0602hg4C0.3417.160.0470.6432.3.1.94198,272
80.0601z0hB0.2905.840.0320.4533.4.24.69132
90.0601kv3A0.2776.910.0230.4982.3.2.13NA
100.0602pmzQ0.3456.770.0310.6052.7.7.6112
110.0601dceA0.3835.570.0500.5722.5.1.6076
120.0603dsxA0.2746.160.0380.4412.5.1.6075
130.0603h0gA0.3676.530.0500.6142.7.7.6102,105,107
140.0602epoB0.3055.590.0750.4733.2.1.52184
150.0602vz8B0.3376.990.0360.6142.3.1.85NA
160.0602vz9B0.3376.980.0290.6142.3.1.85NA
170.0601etuA0.1624.840.0280.2253.6.5.3NA
180.0602q3zA0.4215.560.0500.6302.3.2.13NA
190.0601js4A0.3586.440.0240.5923.2.1.4NA

(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
00.060.3086.720.040.552vr5A GO:0003824 GO:0004133 GO:0004177 GO:0004553 GO:0005975 GO:0005980 GO:0006508
10.060.2986.890.050.535e70C GO:0003824 GO:0003844 GO:0004553 GO:0005975 GO:0005977 GO:0005978 GO:0016740 GO:0016757 GO:0043169
20.060.2876.060.060.475e70B GO:0003824 GO:0003844 GO:0004553 GO:0005975 GO:0005977 GO:0005978 GO:0016740 GO:0016757 GO:0043169
30.060.3425.840.070.532ya1A GO:0003824 GO:0004553 GO:0005576 GO:0005618 GO:0005975 GO:0016020 GO:0016021 GO:0030246
40.060.3166.350.030.543amlA GO:0003824 GO:0003844 GO:0004553 GO:0005975 GO:0005978 GO:0005982 GO:0009501 GO:0009507 GO:0009536 GO:0016740 GO:0016757 GO:0019252 GO:0043169
50.060.2756.640.020.483uwxA GO:0000166 GO:0003677 GO:0003824 GO:0004518 GO:0005524 GO:0005737 GO:0006281 GO:0006289 GO:0006974 GO:0008270 GO:0009380 GO:0009381 GO:0009432 GO:0016887 GO:0046872 GO:0090305
60.060.4456.130.090.733k1dA GO:0003824 GO:0003844 GO:0004553 GO:0005886 GO:0005975 GO:0005977 GO:0005978 GO:0009250 GO:0016740 GO:0016757 GO:0040007 GO:0043169 GO:0045227
70.060.3306.010.040.534okdA GO:0003824 GO:0004553 GO:0005975
80.060.2806.900.040.501eh9A GO:0003824 GO:0004553 GO:0005737 GO:0005975 GO:0005992 GO:0008152 GO:0016787 GO:0016798 GO:0033942
90.060.3236.220.060.543fawA GO:0003824 GO:0004553 GO:0005576 GO:0005618 GO:0005975 GO:0016020 GO:0016021 GO:0030246
100.060.2986.220.020.492wskA GO:0003824 GO:0004133 GO:0004135 GO:0004553 GO:0005975 GO:0005977 GO:0005980 GO:0006974 GO:0008152 GO:0016787 GO:0016798
110.060.2696.260.010.443wdhA GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0046872 GO:0051060
120.060.3296.000.030.531bf2A GO:0003824 GO:0004553 GO:0005576 GO:0005975 GO:0005977 GO:0008152 GO:0016787 GO:0016798 GO:0019156 GO:0046872
130.060.3196.430.060.554aq1A GO:0046872
140.060.2915.270.030.421cdgA GO:0003824 GO:0005576 GO:0005975 GO:0016740 GO:0016757 GO:0030246 GO:0043169 GO:0043895 GO:0046872 GO:2001070
150.060.2177.010.040.403ucqA GO:0003824 GO:0005975
160.060.2746.940.060.493ttoA GO:0005975 GO:0009250 GO:0016740 GO:0016757 GO:0046527 GO:0046872 GO:0047849
170.060.3086.600.040.534aygA GO:0005975 GO:0009250 GO:0016740 GO:0016757 GO:0046527 GO:0046872 GO:0047849
180.060.3256.210.070.525cltA GO:0003824 GO:0003844 GO:0004553 GO:0005829 GO:0005975 GO:0005977 GO:0005978 GO:0006091 GO:0016740 GO:0016757 GO:0043169 GO:0070062


Consensus prediction of GO terms
 
Molecular Function GO:0016798 GO:0016758 GO:0043167
GO-Score 0.56 0.36 0.36
Biological Processes GO:0009250 GO:0005977
GO-Score 0.36 0.36
Cellular Component GO:0009507 GO:0005576 GO:0016021 GO:0009501 GO:0005618
GO-Score 0.06 0.06 0.06 0.06 0.06

(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.