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I-TASSER results for job id Rv1203c

[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
10.10 4 3e6yB III Rep, Mult 9,40,47,48,76,79,80,83,87,113,116
20.08 3 2qfcB III Rep, Mult 1,5,6,8,9,37,40,41,44,73,76,79,113
30.08 3 1qpiA IMD Rep, Mult 119,120,122,123
40.03 1 2vq2A SO3 Rep, Mult 110,112,113
50.03 1 1fchA III Rep, Mult 53,54,56,57,89,93
60.03 1 2amxB CO Rep, Mult 141,148,151
70.03 1 3u24A ZN Rep, Mult 181,184
80.03 1 1iw7F MG Rep, Mult 151,159
90.03 1 2np5C NDS Rep, Mult 87,88,90,102
100.03 1 1dpmA ZN Rep, Mult 119,151
110.03 1 4a1sB III Rep, Mult 1,2,5,33,37,40,41,44,47,48,62,78,81,82,85,88,116,119,120,126,129,130,136,161,165,168,171,172,174,186
120.03 1 1o9fA FSC Rep, Mult 5,9,41,44,45,76,111,112,115

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
10.0601ia7A0.5914.380.0920.8873.2.1.4NA
20.0601j0mA0.5715.200.0900.9494.2.2.12NA
30.0602cqsA0.5574.980.0850.9072.4.1.2054
40.0601g87B0.5624.390.0740.8513.2.1.4NA
50.0603ebgA0.5854.410.0440.9123.4.11.-NA
60.0601fp3A0.6014.650.0900.9545.1.3.8113
70.0601f1sA0.5684.850.0220.9234.2.2.1NA
80.0602vn4A0.5814.990.0790.9493.2.1.3106,139
90.0601fo2A0.5714.520.0560.8973.2.1.11345,150
100.0601w3bA0.6453.420.1290.8352.4.1.-12,21
110.0601n4pB0.5474.760.0340.8922.5.1.59,2.5.1.-NA
120.0601hcuB0.5695.060.0860.9493.2.1.113NA
130.0601nxcA0.5685.160.0810.9433.2.1.113NA
140.0601l2aE0.5954.730.0980.9283.2.1.494
150.0601tnzL0.5474.760.0340.8922.5.1.595
160.0601ksdA0.6114.470.1460.9073.2.1.4114,117
170.0601w3bB0.6343.600.1200.8512.4.1.-NA
180.0602ri9B0.5575.000.0610.9233.2.1.113113
190.0601z1wA0.5814.560.0690.8873.4.11.-NA

(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
00.240.4782.680.090.574gcoA GO:0000003 GO:0005737 GO:0007275 GO:0008340 GO:0009408 GO:0030544 GO:0032780 GO:0042030 GO:0051879
10.230.7353.420.090.955a6cB GO:0000132 GO:0000166 GO:0000922 GO:0001965 GO:0005092 GO:0005654 GO:0005737 GO:0005829 GO:0005856 GO:0005886 GO:0005911 GO:0005912 GO:0005913 GO:0005938 GO:0007052 GO:0007155 GO:0007165 GO:0007186 GO:0007267 GO:0008022 GO:0017016 GO:0030054 GO:0030695 GO:0034332 GO:0042802 GO:0043547 GO:0045177 GO:0050790 GO:0051661 GO:0060487 GO:0090557 GO:0097431 GO:0098609 GO:0098641
20.230.7123.870.100.953txmA GO:0000502 GO:0005838 GO:0005875 GO:0008541 GO:0043161
30.220.7223.650.110.943q15A GO:0004721 GO:0006470 GO:0016787
40.210.7773.440.110.985g05O GO:0005634 GO:0005654 GO:0005680 GO:0005829 GO:0007049 GO:0007067 GO:0016567 GO:0019903 GO:0031145 GO:0042787 GO:0043161 GO:0051301 GO:0051436 GO:0051437 GO:0051439 GO:0070979
50.200.7453.510.120.954gyoB GO:0004721 GO:0006470 GO:0016787
60.200.6534.220.060.954jhrA GO:0000132 GO:0000166 GO:0000922 GO:0001965 GO:0005092 GO:0005737 GO:0005856 GO:0005938 GO:0007052 GO:0030695 GO:0042802 GO:0045177 GO:0050790 GO:0051661 GO:0060487 GO:0097431
70.190.5052.250.120.572vyiA GO:0005737 GO:0005829 GO:0016020 GO:0016032 GO:1903071 GO:1904288
80.190.7393.460.100.941hz4A GO:0000166 GO:0003677 GO:0003700 GO:0005524 GO:0005975 GO:0006351 GO:0006355 GO:0042802 GO:0045893 GO:0045913 GO:0048031
90.180.7083.640.060.944i1aB GO:0004721 GO:0006470 GO:0016787
100.180.7173.760.080.955a5bQ GO:0000502 GO:0005198 GO:0006511 GO:0008541 GO:0034515 GO:0043248
110.160.7253.620.070.944i9eA GO:0004721 GO:0006470 GO:0016787
120.150.4982.380.130.582lniA GO:0005634 GO:0005737 GO:0005794 GO:0006950 GO:0008022 GO:0030544 GO:0043209 GO:0043234 GO:0044822 GO:0051087
130.140.6573.780.070.884d10B GO:0000122 GO:0000715 GO:0003714 GO:0004871 GO:0005634 GO:0005654 GO:0005737 GO:0006283 GO:0006366 GO:0007165 GO:0008180 GO:0008283 GO:0010388 GO:0030182 GO:0035914 GO:0045892 GO:1903507
140.130.4912.440.120.583gz1A GO:0005737 GO:0006950 GO:0009405
150.110.5353.230.160.682fo7A
160.110.4993.070.070.603uq3A GO:0003729 GO:0005737 GO:0006457 GO:0008104 GO:0030544 GO:0042030 GO:0043086 GO:0051879
170.110.6393.560.120.865a31F GO:0005634 GO:0005654 GO:0005680 GO:0005737 GO:0005813 GO:0005819 GO:0005829 GO:0005876 GO:0007091 GO:0008283 GO:0016567 GO:0019903 GO:0031145 GO:0042787 GO:0043161 GO:0051436 GO:0051437 GO:0051439 GO:0070979
180.110.5053.470.100.642dbaA GO:0005634 GO:0005737 GO:0005913 GO:0007275 GO:0007517 GO:0030154 GO:0048471 GO:0051879 GO:0061077 GO:0098609 GO:0098641
190.110.4632.810.080.561elwA GO:0005634 GO:0005737 GO:0005794 GO:0006950 GO:0008022 GO:0030544 GO:0043209 GO:0043234 GO:0044822 GO:0051087
200.100.4531.700.140.494cgwA GO:0097255
210.070.4882.570.140.574cgvB GO:0097255
220.060.3945.950.080.733vylA GO:0046872
230.060.4082.070.090.453k9iA
240.060.3945.730.080.702jc4A GO:0003677 GO:0004518 GO:0004519 GO:0005622 GO:0006281 GO:0008853 GO:0016787 GO:0090305


Consensus prediction of GO terms
 
Molecular Function GO:0031072 GO:0004857 GO:0060590 GO:0031267 GO:0045296 GO:1901265 GO:0036094 GO:0098632 GO:0016791 GO:0019902
GO-Score 0.47 0.47 0.47 0.46 0.46 0.46 0.46 0.46 0.43 0.42
Biological Processes GO:0043462 GO:0010259 GO:0009266 GO:0006950 GO:0051346 GO:0044700 GO:0051642 GO:0043087 GO:0045216 GO:0051657 GO:0040001 GO:0060479 GO:0051294 GO:0007154 GO:0051345 GO:0051716 GO:0061028 GO:0022610 GO:0060428 GO:0016311 GO:1904667 GO:0000209 GO:1904668 GO:1901990 GO:0051439 GO:2000060 GO:0000280 GO:0043161
GO-Score 0.47 0.47 0.47 0.47 0.47 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.43 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.39
Cellular Component GO:0071944 GO:0099568 GO:0072686 GO:0070161 GO:0000922 GO:0022624 GO:0031461 GO:0000152 GO:0005654 GO:0005829 GO:0016020
GO-Score 0.46 0.46 0.46 0.46 0.46 0.46 0.42 0.42 0.39 0.39 0.35

(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.