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I-TASSER results for job id Rv0177

[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 6 5stdB UNN Rep, Mult 74,106,107,111,145,147,149,161,180,182,184
20.07 4 1a2k0 III Rep, Mult 99,100,125,126,128,129,131,132,133,134,140,142,144,145,146,163,165,167,169,178,179,180,181
30.07 4 4fcmA III Rep, Mult 61,62,65,66,69,94,95,174,175,176
40.03 2 3biwE CA Rep, Mult 109,110
50.03 2 3hx8D IMD Rep, Mult 70,141,166,177
60.03 2 1gybB III Rep, Mult 130,131,132,135
70.03 2 2vt5H ROK Rep, Mult 97,98
80.02 1 2bngB CA Rep, Mult 59,170
90.02 1 4jolA III Rep, Mult 35,38
100.02 1 2z77C HE7 Rep, Mult 66,73,77
110.02 1 1nr5B CO Rep, Mult 91,98
120.02 1 1wraA FE Rep, Mult 53,56,162,179
130.02 1 3i8hT MG Rep, Mult 177,178
140.02 1 1ia5A MAN Rep, Mult 122,124

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
10.0961hkxA0.4873.280.1160.6302.7.11.17138
20.0662ux0A0.4963.290.0920.6412.7.11.1798,105
30.0668choA0.4502.770.0980.5545.3.3.1176
40.0601hcuB0.4234.870.0460.6793.2.1.11371
50.0602d0vA0.4345.040.0430.7011.1.99.8NA
60.0602v7oA0.3015.500.0550.5222.7.11.17NA
70.0603gzxB0.5133.550.0680.6791.14.12.18NA
80.0601kb0A0.4364.750.0570.6741.1.99.-NA
90.0603cxhN0.3385.470.0500.6201.10.2.2NA
100.0601oygA0.4215.770.0500.7662.4.1.10NA
110.0601lrwC0.4355.030.0380.6901.1.99.8167
120.0601nu3B0.4483.840.0760.6093.3.2.8142
130.0601kitA0.4205.660.0530.7883.2.1.18NA
140.0601kv9A0.4424.720.0690.6791.1.99.-NA
150.0601g72A0.4325.020.0310.6851.1.99.873
160.0604stdA0.5102.760.0940.6254.2.1.94NA
170.0602epoB0.4314.290.0630.6363.2.1.5263
180.0601sa3A0.4414.000.0220.6363.1.21.4127
190.0603hmjA0.4165.480.0520.7342.3.1.8688
200.0601e3vB0.4383.350.0470.5765.3.3.1104
210.0601w6sC0.4335.060.0380.6901.1.99.8NA
220.0601o7hB0.5204.060.0710.7171.14.12.1285,93,95,121

(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
00.170.5622.760.130.675d9rA GO:0009507 GO:0009528 GO:0009536 GO:0009658 GO:0009706 GO:0009941 GO:0010020 GO:0016020 GO:0016021 GO:0031357 GO:0043621
10.150.5203.070.120.663a76B GO:0009636 GO:0016829 GO:0042597
20.110.5483.590.040.712cw9A GO:0000166 GO:0005524 GO:0005739 GO:0005743 GO:0005759 GO:0006626 GO:0006810 GO:0015031 GO:0016020 GO:0030150 GO:0051087
30.090.4852.990.100.615ig4E GO:0000166 GO:0004672 GO:0004674 GO:0004683 GO:0005516 GO:0005524 GO:0006468 GO:0016301 GO:0016310 GO:0016740
40.090.4893.430.060.653j7yd GO:0005739 GO:0005743 GO:0005840 GO:0030529 GO:0044822 GO:0070125 GO:0070126
50.080.4892.670.060.605ig0A GO:0000166 GO:0004672 GO:0004674 GO:0004683 GO:0005516 GO:0005524 GO:0006468 GO:0016301 GO:0016310 GO:0016740
60.070.5443.700.060.732fxtA GO:0000166 GO:0001405 GO:0005524 GO:0005739 GO:0005743 GO:0006626 GO:0006810 GO:0015031 GO:0016020 GO:0030150 GO:0030674 GO:0051087
70.070.5373.660.070.714xzzA GO:0016740
80.070.5182.970.030.654lehA GO:0016829 GO:0033988
90.070.5222.940.030.654l8oA GO:0016829 GO:0033988
100.070.5172.980.060.654l8pA GO:0016829 GO:0033988
110.070.4963.290.090.642ux0A GO:0000082 GO:0000165 GO:0000166 GO:0004672 GO:0004674 GO:0004683 GO:0004723 GO:0005088 GO:0005516 GO:0005524 GO:0005654 GO:0005829 GO:0005886 GO:0006468 GO:0006470 GO:0006816 GO:0007275 GO:0007399 GO:0014733 GO:0016020 GO:0016301 GO:0016310 GO:0016529 GO:0016740 GO:0030073 GO:0030154 GO:0030666 GO:0033017 GO:0042803 GO:0043547 GO:0046777 GO:0051259 GO:0051924 GO:0060333 GO:0097481 GO:1900034 GO:1901897
120.070.4773.330.090.612w2cH GO:0000082 GO:0000165 GO:0000166 GO:0001558 GO:0001666 GO:0002026 GO:0002028 GO:0003254 GO:0004672 GO:0004674 GO:0004683 GO:0005088 GO:0005516 GO:0005524 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0005886 GO:0006357 GO:0006468 GO:0006816 GO:0008016 GO:0010389 GO:0010613 GO:0010649 GO:0010666 GO:0010880 GO:0010881 GO:0014704 GO:0014911 GO:0016020 GO:0016301 GO:0016310 GO:0016529 GO:0016740 GO:0018105 GO:0018107 GO:0019871 GO:0030007 GO:0030315 GO:0030666 GO:0031432 GO:0031594 GO:0032469 GO:0033017 GO:0034704 GO:0035022 GO:0042383 GO:0042803 GO:0043025 GO:0043194 GO:0043234 GO:0043547 GO:0044325 GO:0046777 GO:0048471 GO:0048661 GO:0050998 GO:0051259 GO:0055119 GO:0060048 GO:0060314 GO:0060333 GO:0060341 GO:0061049 GO:0070374 GO:0071277 GO:0086003 GO:0086091 GO:0098901 GO:0098909 GO:1900034 GO:1901725 GO:1901844 GO:1901897 GO:1902306 GO:1902514 GO:2000650
130.070.4793.180.060.612f86B GO:0000165 GO:0000166 GO:0004672 GO:0004674 GO:0004683 GO:0005516 GO:0005524 GO:0005737 GO:0006468 GO:0010628 GO:0016301 GO:0016310 GO:0016740 GO:0018105 GO:0018107 GO:0030424 GO:0042995 GO:0043005 GO:0043204 GO:0044325 GO:0046872 GO:0072375 GO:1904115
140.070.4582.900.050.583b7cA GO:0004067 GO:0016787
150.060.3266.000.060.642nn6E GO:0000175 GO:0000176 GO:0000177 GO:0000178 GO:0000467 GO:0003723 GO:0004532 GO:0005634 GO:0005654 GO:0005730 GO:0005737 GO:0005829 GO:0006364 GO:0006401 GO:0017091 GO:0034427 GO:0034473 GO:0034475 GO:0034476 GO:0043488 GO:0043928 GO:0071028 GO:0071035 GO:0071038 GO:0071042
160.060.3085.250.050.514pc9A GO:0006810 GO:0008643 GO:0030288 GO:0042597
170.060.3325.540.030.614l5cC GO:0003824 GO:0005634 GO:0005737 GO:0006166 GO:0009116 GO:0016740 GO:0016757 GO:0016763 GO:0017061 GO:0019509
180.060.3115.470.050.533rscA GO:0008152 GO:0016758 GO:0016999


Consensus prediction of GO terms
 
Molecular Function GO:0032559 GO:0032550 GO:0035639 GO:0005515
GO-Score 0.39 0.39 0.39 0.34
Biological Processes GO:0043572 GO:0009657
GO-Score 0.34 0.34
Cellular Component GO:0031966 GO:0031356 GO:0031353
GO-Score 0.38 0.34 0.34

(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.