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I-TASSER results for job id Rv0442c

[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
10.06 3 3ar3A PTY Rep, Mult 226,229,233,237,337
20.04 2 1af0A CA Rep, Mult 401,402,405,406,409
30.04 2 1dz8A OXY Rep, Mult 221,225
40.04 2 4f4sN EFO Rep, Mult 93,94,97
50.04 2 2voyK III Rep, Mult 224,228,231,232,239
60.02 1 3huzP MG Rep, Mult 384,386
70.02 1 3nw3A MU2 Rep, Mult 463,464
80.02 1 4fe1B CLA Rep, Mult 72,76,78,79,342
90.02 1 2oa0A CZA Rep, Mult 42,45,46,231,232,233,237
100.02 1 2vn4A MAN Rep, Mult 438,439
110.02 1 4f8hA LMD Rep, Mult 83,86
120.02 1 2g38B MN Rep, Mult 152,155,156
130.02 1 4y32A 49F Rep, Mult 24,27,28,216,219
140.02 1 1z8qA OXY Rep, Mult 77,81
150.02 1 3ar7A PTY Rep, Mult 261,324,325
160.02 1 4xniA 78M Rep, Mult 89,96
170.02 1 3hbuP ZN Rep, Mult 204,258
180.02 1 2z8xA CA Rep, Mult 313,315,325,327,331
190.02 1 5tglA HEE Rep, Mult 289,347
200.02 1 1z9jB BCL Rep, Mult 71,72,75

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
10.0603g61A0.3767.100.0360.5773.6.3.44229,232
20.0602ckjA0.2877.410.0350.4721.17.1.4,1.17.3.2NA
30.0601m7xB0.3087.590.0560.5192.4.1.1887
40.0603b9jI0.1285.340.0690.1741.17.1.4,1.17.3.2298
50.0602vuaA0.2426.420.0490.3633.4.24.69422
60.0602pflA0.3137.890.0500.5462.3.1.54NA
70.0601ofdA0.2897.960.0420.5071.4.7.1NA
80.0601w27A0.3247.490.0580.5364.3.1.24NA
90.0603ffzA0.3406.980.0490.5283.4.24.69NA
100.0602jlzB0.2507.380.0630.4173.4.21.91378
110.0601fo4A0.3147.580.0510.5301.17.1.4NA
120.0603btaA0.3177.480.0280.5173.4.24.69466
130.0602pffA0.3077.660.0560.5132.3.1.41,2.3.1.86NA
140.0601eulA0.3057.750.0350.5193.6.3.8NA
150.0601od2A0.3366.620.0530.5056.3.4.14,6.4.1.2297
160.0601mc0A0.2106.920.0420.3373.1.4.17375
170.0601l9mB0.3127.440.0400.5112.3.2.13NA
180.0603k1dA0.3096.930.0660.4912.4.1.18NA
190.0602qf7B0.2857.840.0580.4976.4.1.1NA

(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
00.240.9252.130.110.984ut1A GO:0005198 GO:0009424 GO:0044780
10.090.6652.770.110.732d4yA GO:0005198 GO:0005576 GO:0009288 GO:0009424 GO:0044780 GO:0071973
20.060.3296.720.060.484ry2A GO:0005524 GO:0006508 GO:0006810 GO:0008233 GO:0008234 GO:0016020 GO:0016021 GO:0016887 GO:0022885 GO:0042626 GO:0043213 GO:0055085
30.060.2337.260.020.375c73A GO:0000166 GO:0005524 GO:0006810 GO:0016021 GO:0016887 GO:0042626 GO:0055085
40.060.3667.050.050.564m1mA GO:0000086 GO:0000166 GO:0002481 GO:0002485 GO:0002489 GO:0002591 GO:0005524 GO:0005886 GO:0006810 GO:0006855 GO:0008559 GO:0009986 GO:0015893 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0042623 GO:0042626 GO:0042908 GO:0046581 GO:0055085 GO:0070062 GO:0072089
50.060.3736.810.050.574f4cA GO:0000166 GO:0005524 GO:0006810 GO:0006855 GO:0008559 GO:0010038 GO:0015562 GO:0016020 GO:0016021 GO:0016324 GO:0016787 GO:0016887 GO:0042626 GO:0042908 GO:0045087 GO:0050829 GO:0055085 GO:0093002
60.060.2917.770.050.502r6fB 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
70.060.2947.520.050.493uwxA 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
80.060.2957.240.040.492r6fA 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
90.060.2806.210.030.403b5xA GO:0000166 GO:0005319 GO:0005524 GO:0005886 GO:0006810 GO:0006869 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0034040 GO:0042626 GO:0043190 GO:0055085
100.060.3196.440.050.463wmgA GO:0000166 GO:0005524 GO:0006810 GO:0016020 GO:0016021 GO:0016887 GO:0042626 GO:0055085
110.060.3097.170.060.503zqjD GO:0000166 GO:0003677 GO:0003824 GO:0004518 GO:0005524 GO:0005618 GO:0005737 GO:0005829 GO:0005886 GO:0006281 GO:0006289 GO:0006974 GO:0008270 GO:0009380 GO:0009381 GO:0009432 GO:0016887 GO:0046872 GO:0060543 GO:0090305
120.060.2807.130.040.443b5wA GO:0000166 GO:0005319 GO:0005524 GO:0005886 GO:0006810 GO:0006869 GO:0008144 GO:0008289 GO:0015437 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0034040 GO:0042626 GO:0043190 GO:0055085 GO:1901264
130.060.2857.980.050.503pihA 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
140.060.3036.770.080.454q4aA GO:0000166 GO:0005524 GO:0006810 GO:0006869 GO:0016020 GO:0016021 GO:0016887 GO:0034040 GO:0042626 GO:0046872 GO:0055085
150.060.2866.630.070.434ayxA GO:0000166 GO:0005215 GO:0005524 GO:0005739 GO:0005743 GO:0006810 GO:0016020 GO:0016021 GO:0016887 GO:0032592 GO:0042626 GO:0042803 GO:0055085
160.060.2926.630.040.434pl0B GO:0000166 GO:0005524 GO:0005886 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0016887 GO:0030153 GO:0042626 GO:0043213 GO:0055085
170.060.2896.260.050.413qf4B GO:0000166 GO:0005524 GO:0005886 GO:0006810 GO:0016020 GO:0016021 GO:0016887 GO:0042626 GO:0055085
180.060.2437.310.040.403gd7A GO:0000166 GO:0005215 GO:0005224 GO:0005254 GO:0005260 GO:0005524 GO:0005737 GO:0005765 GO:0005768 GO:0005769 GO:0005829 GO:0005886 GO:0006695 GO:0006810 GO:0006811 GO:0006821 GO:0006904 GO:0007585 GO:0008643 GO:0009986 GO:0015106 GO:0015108 GO:0015423 GO:0015609 GO:0015701 GO:0015768 GO:0016020 GO:0016021 GO:0016323 GO:0016324 GO:0016787 GO:0016820 GO:0016887 GO:0017081 GO:0019869 GO:0019899 GO:0030165 GO:0030301 GO:0030660 GO:0031205 GO:0031234 GO:0031901 GO:0033613 GO:0034707 GO:0035774 GO:0042626 GO:0042956 GO:0043190 GO:0043225 GO:0043234 GO:0045921 GO:0048240 GO:0051454 GO:0055037 GO:0055085 GO:0060081 GO:0070062 GO:0071320 GO:1902161 GO:1902476 GO:1902943 GO:1990060


Consensus prediction of GO terms
 
Molecular Function GO:0032550 GO:0016820 GO:0015405 GO:0035639 GO:0032559 GO:0043492 GO:0005198
GO-Score 0.36 0.36 0.36 0.36 0.36 0.36 0.30
Biological Processes GO:0044765 GO:0044780
GO-Score 0.36 0.30
Cellular Component GO:0009424
GO-Score 0.30

(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.