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I-TASSER results for job id Rv2712c

[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 3 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
10.09 4 1izlD PHO Rep, Mult 98,99,102,103
20.05 2 3tmhE III Rep, Mult 25,30
30.05 2 4d3vA POL Rep, Mult 90,91
40.02 1 3mkvG CO3 Rep, Mult 37,38,74,76
50.02 1 2wsc2 CLA Rep, Mult 287,294
60.02 1 4ytrB TGK Rep, Mult 44,263,264
70.02 1 4c30I MG Rep, Mult 239,240
80.02 1 1e7fA DAO Rep, Mult 93,97
90.02 1 1bjyA CTC Rep, Mult 310,314
100.02 1 1s56B XE Rep, Mult 279,310,314
110.02 1 1xrmA III Rep, Mult 226,229
120.02 1 3fjuA ZN Rep, Mult 321,325
130.02 1 2jstB HLT Rep, Mult 258,261,296
140.02 1 1y10D CA Rep, Mult 177,196
150.02 1 1yrrB PO4 Rep, Mult 77,115,160,235
160.02 1 1q9xC CA Rep, Mult 49,286
170.02 1 1f8iB MG Rep, Mult 49,79

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
10.0601cygA0.4855.990.0500.7472.4.1.19159,162
20.0601g5aA0.4756.200.0730.7562.4.1.4148
30.0601ra0A0.5075.950.0860.7703.5.4.1NA
40.0601bf2A0.4866.350.0620.7873.2.1.68135,235
50.0601s46A0.4756.170.0700.7562.4.1.4261
60.0603a47A0.4736.000.0640.7393.2.1.10NA
70.0601izjA0.4805.690.0340.7243.2.1.135,3.2.1.1NA
80.0603ma8A0.4766.030.0470.7332.7.1.40286
90.0601d7fA0.4825.970.0360.7422.4.1.19NA
100.0603czkA0.4806.250.0910.7613.2.1.4898
110.0601a47A0.4845.870.0460.7392.4.1.19NA
120.0601ybqA0.4735.990.1170.7333.4.19.163,79,307
130.0602puzA0.4826.190.0850.7613.5.2.7NA
140.0603iv8D0.4885.880.0510.7423.5.1.25142
150.0602p50A0.4895.940.0900.7563.5.1.25NA
160.0602zicA0.4715.840.0330.7243.2.1.70NA
170.0602a3lA0.5075.790.0440.7813.5.4.6NA
180.0603m07A0.4775.940.0440.7393.2.1.141242,285
190.0602g3fA0.4896.010.0820.7613.5.2.7NA

(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
00.190.4816.150.070.762oofA GO:0005506 GO:0005737 GO:0006547 GO:0006548 GO:0008270 GO:0016787 GO:0016810 GO:0016812 GO:0019556 GO:0019557 GO:0046872 GO:0050480
10.070.5386.060.110.844ub9A GO:0016787 GO:0016810
20.070.5375.730.100.803mtwA GO:0016787 GO:0016810 GO:0046872
30.070.5316.140.080.834whbA GO:0016787 GO:0016810
40.070.5335.970.080.822qs8A GO:0016787 GO:0016810 GO:0046872
50.070.5235.810.100.784v1xE GO:0005737 GO:0016787 GO:0016810 GO:0018788 GO:0019381 GO:0046872
60.070.5215.810.070.793mkvA GO:0016787 GO:0016810 GO:0046872
70.070.5246.040.070.814c60A GO:0006508 GO:0016787 GO:0016805 GO:0016810 GO:0046872 GO:0102009 GO:1900817
80.070.5255.960.070.803be7A
90.070.4826.190.090.762gokA GO:0005506 GO:0005737 GO:0006547 GO:0006548 GO:0008270 GO:0016787 GO:0016810 GO:0016812 GO:0019556 GO:0019557 GO:0046872 GO:0050480
100.070.5205.880.090.793n2cA
110.070.4536.280.040.741m7jA GO:0016787 GO:0016810 GO:0016811 GO:0046872 GO:0047420
120.070.5145.850.080.784l9xB GO:0004040 GO:0016787 GO:0016810 GO:0046872
130.070.4905.740.080.734dykA GO:0004000 GO:0016787 GO:0016810 GO:0019700 GO:0046872 GO:0050270
140.070.4946.000.080.762p9bA GO:0016787 GO:0016810
150.070.4925.870.070.743hpaA
160.070.4666.330.060.761gkpA GO:0005737 GO:0016787 GO:0016810 GO:0046872
170.070.4676.100.050.733griB GO:0004151 GO:0006221 GO:0008270 GO:0016787 GO:0016810 GO:0016812 GO:0044205 GO:0046872
180.070.4735.990.120.731ybqA GO:0005737 GO:0005829 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008798 GO:0016787 GO:0016810 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0016810 GO:0046914
GO-Score 0.38 0.38
Biological Processes GO:0006548 GO:0043606 GO:0015942 GO:0006536
GO-Score 0.38 0.38 0.38 0.38
Cellular Component GO:0044424
GO-Score 0.38

(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.