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I-TASSER results for job id Rv3466

[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
10.15 14 3b6aE ZCT Rep, Mult 61,65,66,67,85,100,101,103,105,109,110,113,114,136,139
20.08 8 2ns8C III Rep, Mult 61,64,104,105,106,114,117,118,132,135,136,140
30.05 5 3zqlB QNA Rep, Mult 38,40,41,44,45
40.03 3 3b6cB SDN Rep, Mult 61,65,67,81,109,110,113,117,139
50.02 2 3lsjA COA Rep, Mult 78,124,209,210,213
60.02 2 2ns70 III Rep, Mult 103,115,128,129,130,132,133,137,140,141,143,144,145,147,148,168,169,170,195,199,200,203,207,208,210,211,212,214
70.02 2 3angD DCC Rep, Mult 164,168,172,185,187,188
80.02 2 3lspA QNA Rep, Mult 27,28,29,33,40,43
90.01 1 3b6cA SDN Rep, Mult 113,116,117,120
100.01 1 1b48A GSH Rep, Mult 14,48
110.01 1 2wse1 CLA Rep, Mult 104,107
120.01 1 3zqlA QNA Rep, Mult 27,28,29,39,40,43,47,48
130.01 1 3mi1B FE Rep, Mult 117,127
140.01 1 3l26B MG Rep, Mult 172,174,176
150.01 1 1bjyB CTC Rep, Mult 54,58,61
160.01 1 1vf2A GTX Rep, Mult 21,48
170.01 1 3c9iB XE Rep, Mult 78,82
180.01 1 3aqtA RCO Rep, Mult 74,77,78,81,119,120,124
190.01 1 3aqtB RCO Rep, Mult 66,78,81,82,85,116,117,120,139
200.01 1 3anpD DCC Rep, Mult 140,143,144,147,148

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
10.0602yyjA0.4315.270.0810.6711.14.13.3NA
20.0601kwgA0.4296.090.0700.7933.2.1.23NA
30.0601e5dA0.4115.420.0450.6761.-.-.-67,82
40.0601fa9A0.4225.180.0630.6582.4.1.1NA
50.0602weiA0.3066.350.0420.5632.7.1.1786,99
60.0603ffzA0.4265.670.0300.7253.4.24.6925
70.0601n6bA0.4205.560.0770.6891.14.14.111
80.0602i2xA0.4424.970.0790.6712.1.1.90100
90.0603m07A0.4225.610.0740.7213.2.1.14187
100.0603c6gB0.4225.230.0360.6711.14.13.1578,85,137,142
110.0603i3kA0.4215.130.0360.6441.14.13.70NA
120.0603juvA0.4185.220.0450.6581.14.13.7078,85
130.0603cf4A0.4275.090.0600.6711.2.99.284
140.0602w0aA0.3716.070.0640.6761.14.13.70NA
150.0603ikmD0.4246.100.0530.7612.7.7.7NA
160.0601xc6A0.4405.790.0390.7663.2.1.2354
170.0601z11A0.4235.480.0540.7031.14.14.1NA
180.0602z1qB0.4185.210.0820.6761.3.99.3NA
190.0601og5B0.4235.560.0590.6941.14.13.48,1.14.13.49,1.14.13.8078,134,142

(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
00.360.8831.780.120.953b6aA GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677
10.320.5533.930.100.774ichA GO:0003677 GO:0006351 GO:0006355
20.280.8002.860.090.972y31A GO:0003677 GO:0006351 GO:0006355 GO:0045892
30.280.7472.490.110.882hxiB GO:0003677 GO:0006351 GO:0006355 GO:0045892
40.270.7003.600.080.913zqgA GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677 GO:0046872
50.250.7702.500.110.903bqyA GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677
60.240.6642.910.090.813zqfA GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677 GO:0046872
70.230.7373.080.080.904auxA GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677 GO:0046872
80.220.7343.060.140.902hxoA GO:0003677 GO:0006351 GO:0006355 GO:0045892
90.220.7323.210.060.931z0xA GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677
100.210.7073.030.120.872g7lA GO:0003677 GO:0006351 GO:0006355 GO:0045892
110.200.7432.550.060.872vprA GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677 GO:0046872
120.180.5963.600.120.783on2B GO:0003677 GO:0006351 GO:0006355
130.180.5622.770.110.683fiwA GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677
140.180.5813.400.070.743bniA GO:0003677 GO:0006351 GO:0006355
150.170.6143.220.110.753bjbB GO:0003677 GO:0006351 GO:0006355
160.170.5893.490.140.772np5A GO:0003677 GO:0006351 GO:0006355
170.160.5284.060.070.732zcnD GO:0003677 GO:0006351 GO:0006355
180.160.6013.270.130.772f07A GO:0003677 GO:0006351 GO:0006355
190.160.5473.840.100.734za6A GO:0003677
200.160.5663.510.100.753he0C GO:0003677 GO:0006351 GO:0006355
210.140.5463.750.100.743g7rB GO:0003677 GO:0003700 GO:0006351 GO:0006355
220.120.5283.960.080.733vprA GO:0003677 GO:0006351 GO:0006355 GO:0042802
230.110.5453.910.070.734me9A GO:0003677 GO:0006351 GO:0006355
240.110.5543.380.100.714hkuA GO:0003677 GO:0006351 GO:0006355
250.100.5284.290.060.772wuiA GO:0003677 GO:0006351 GO:0006355
260.090.5274.100.070.733geuA GO:0003677 GO:0006351 GO:0006355
270.080.6312.900.120.771zk8A GO:0003677 GO:0006351 GO:0006355
280.070.5573.770.070.753qkxA GO:0003677 GO:0006351 GO:0006355
290.070.5533.280.080.712dg8B GO:0003677 GO:0006351 GO:0006355
300.070.5414.050.140.752genA GO:0003677 GO:0003700 GO:0006351 GO:0006355
310.070.5864.000.060.801t33A GO:0003677 GO:0003700 GO:0006351 GO:0006355
320.070.5383.900.130.742nx4A GO:0003677 GO:0006351 GO:0006355
330.070.6083.570.080.803c07A GO:0003677 GO:0006351 GO:0006355
340.070.5484.270.090.783vibC GO:0003677 GO:0006351 GO:0006355
350.070.5583.800.040.752hyjA GO:0003677 GO:0003700 GO:0006351 GO:0006355


Consensus prediction of GO terms
 
Molecular Function GO:0003677 GO:0043169
GO-Score 0.83 0.55
Biological Processes GO:0045892 GO:0046677
GO-Score 0.76 0.53
Cellular Component
GO-Score

(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.