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I-TASSER results for job id Rv1540

[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
10.57 12 1kskA URA Rep, Mult 139,142,171,235,236,237,271
20.23 8 2i82D NUC Rep, Mult 100,102,103,104,105,108,133,136,137,138,139,140,152,155,156,159,162,163,165,169,197,200,207,232,233,234,235,252,253
30.09 5 3hjwA RQA Rep, Mult 102,134,135,136,137,139,140,169,171,231,232,236,237,238,249,271,273
40.03 1 2istA BCT Rep, Mult 79,81
50.03 1 2istA BCT Rep, Mult 302,305
60.02 1 1n38A CH1 Rep, Mult 171,172,173,174
70.02 1 3lwrA RQA Rep, Mult 102,137,139

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
10.1221ze2B0.2095.420.0170.3214.2.1.70139,171
20.1211s71B0.4053.380.1780.4804.2.1.70139,171
30.1131k8wA0.4333.420.1300.5194.2.1.70139,171
40.0603k1dA0.3987.150.0390.7312.4.1.18NA
50.0601dj0A0.4484.050.0920.5755.4.99.12139
60.0601pj6A0.3686.350.0570.6141.5.3.10NA
70.0601m7xB0.3926.950.0340.7242.4.1.1838
80.0601r3fA0.3953.170.1360.4684.2.1.70171
90.0602fhbA0.3907.080.0560.7373.2.1.41NA
100.0601s0kA0.3836.050.0440.6273.2.1.18NA
110.0602fhcA0.3966.580.0600.6883.2.1.41137
120.0601hwxA0.3626.360.0270.6101.4.1.3NA
130.0601vs3A0.4224.190.1050.5455.4.99.12139
140.0601l5jA0.3776.480.0500.6464.2.1.382,97,141
150.0603ctzA0.3706.390.0730.6333.4.11.9NA
160.0601rp5A0.3956.300.0380.6563.4.-.-NA
170.0601yq2A0.3696.610.0660.6463.2.1.23NA
180.0603fwmA0.3726.330.0530.6172.4.1.129,NA
190.0602vr5A0.3706.610.0380.6593.2.1.-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
00.560.9351.340.340.972istA GO:0000027 GO:0000455 GO:0001522 GO:0003723 GO:0005829 GO:0006364 GO:0009451 GO:0009982 GO:0016853 GO:0019239
10.460.6082.500.330.672i82A GO:0000455 GO:0001522 GO:0003723 GO:0006364 GO:0008033 GO:0009451 GO:0009982 GO:0016853 GO:0019239 GO:0031118 GO:0031119
20.370.6532.480.330.721xpiA GO:0000455 GO:0001522 GO:0003723 GO:0005829 GO:0006364 GO:0009451 GO:0009982 GO:0016853 GO:0019239
30.360.4143.470.100.501kskA GO:0000455 GO:0001522 GO:0003723 GO:0005829 GO:0006364 GO:0009451 GO:0009982 GO:0016853 GO:0016866
40.070.4734.380.100.624iqmA GO:0001522 GO:0003723 GO:0004730 GO:0005634 GO:0005739 GO:0005759 GO:0008033 GO:0009451 GO:0009982 GO:0016853 GO:0044822 GO:0070902
50.070.4484.050.090.571dj0A GO:0000049 GO:0001522 GO:0003723 GO:0008033 GO:0009451 GO:0009982 GO:0016853 GO:0031119
60.060.4224.190.100.551vs3A GO:0001522 GO:0003723 GO:0008033 GO:0009451 GO:0009982 GO:0016853 GO:0031119
70.060.4013.610.170.492omlA GO:0000455 GO:0001522 GO:0003723 GO:0005829 GO:0006364 GO:0009451 GO:0009982 GO:0016853 GO:0016866
80.060.2917.090.050.553a2fA GO:0000166 GO:0003676 GO:0003677 GO:0003887 GO:0004518 GO:0004519 GO:0006260 GO:0008408 GO:0016740 GO:0016779 GO:0016787 GO:0071897 GO:0090305
90.060.3196.700.040.561tgoA GO:0000166 GO:0003676 GO:0003677 GO:0003824 GO:0003887 GO:0004518 GO:0004527 GO:0006260 GO:0008152 GO:0008408 GO:0016740 GO:0016779 GO:0016787 GO:0071897 GO:0090305
100.060.3106.920.050.561d5aA GO:0000166 GO:0003676 GO:0003677 GO:0003824 GO:0003887 GO:0004518 GO:0004527 GO:0006260 GO:0008152 GO:0008408 GO:0016740 GO:0016779 GO:0016787 GO:0046872 GO:0071897 GO:0090305
110.060.3005.830.040.471wn7A GO:0000166 GO:0003676 GO:0003677 GO:0003887 GO:0006260 GO:0008408 GO:0016740 GO:0016779 GO:0071897 GO:0090305
120.060.2936.250.060.483cuzA GO:0003824 GO:0004474 GO:0005737 GO:0006097 GO:0006099 GO:0016740
130.060.2556.820.050.462rh4B GO:0016491 GO:0017000 GO:0055114
140.060.2836.790.040.503n5mA GO:0003824 GO:0008483 GO:0016740 GO:0030170
150.060.2587.130.050.482qpxA GO:0016787 GO:0046872
160.060.2345.710.070.361q7rA GO:0004359 GO:0006541 GO:0006543 GO:0016787 GO:0016829 GO:0036381 GO:0042819 GO:0042823
170.060.2516.630.030.444cukB GO:0000166 GO:0008152 GO:0008720 GO:0016491 GO:0016616 GO:0051287 GO:0055114
180.060.2245.610.060.344aqyD GO:0003723 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0015935 GO:0019843 GO:0030529 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0009982 GO:0003723 GO:0019239
GO-Score 0.91 0.91 0.85
Biological Processes GO:0000455 GO:0000027 GO:0031119
GO-Score 0.90 0.56 0.46
Cellular Component GO:0005829
GO-Score 0.82

(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.