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I-TASSER results for job id Rv3033

[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 7 1aq4A RQA Rep, Mult 145,147,148,149,161,163,165,170,172
20.04 3 2ckjA FES Rep, Mult 120,121,124,132,133,134,148
30.03 2 3lw5L CLA Rep, Mult 13,18,50
40.03 2 4il6R HEM Rep, Mult 17,21
50.03 2 2bs0B QNA Rep, Mult 62,65,76,78,88
60.03 2 2g4lA SO4 Rep, Mult 93,96,97
70.03 2 3jcuX CLA Rep, Mult 9,13
80.03 2 4bntD 36E Rep, Mult 6,10
90.03 2 2qkdA ZN Rep, Mult 63,77,134,148
100.03 2 3eubS FES Rep, Mult 67,68,69,71,72,73,74
110.01 1 3mouB XE Rep, Mult 18,46,91
120.01 1 3d5aC MG Rep, Mult 10,53
130.01 1 1zseB QNA Rep, Mult 138,139,143,145,162
140.01 1 2izmB QNA Rep, Mult 63,65,67,68,73,75,80,91
150.01 1 3aydA UUU Rep, Mult 111,147
160.01 1 3a44B ZN Rep, Mult 134,148,154
170.01 1 2byoA LNL Rep, Mult 117,124
180.01 1 2b2dB RQA Rep, Mult 91,93,94,99,101,120

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
10.0602ea4A0.4884.950.0660.8023.4.11.1818,100
20.0602a8jB0.4525.540.0250.7863.4.25.-160
30.0601hn0A0.4445.330.0960.7914.2.2.20NA
40.0602ckjA0.4534.400.0730.6591.17.1.4,1.17.3.2NA
50.0601l7kB0.4475.130.0400.7645.1.3.3NA
60.0601tlbA0.4505.310.0400.7971.3.3.3NA
70.0603b9jJ0.4554.450.0580.6701.17.1.4,1.17.3.215,17
80.0602a8iA0.4605.090.0690.7643.4.25.-121
90.0603b9jC0.4095.130.0340.6811.17.3.2,1.17.1.4NA
100.0602htaA0.4465.260.0470.7755.1.3.-NA
110.0601lf6A0.4465.400.0430.8133.2.1.3NA
120.0603mwxA0.4554.880.0560.7475.1.3.375
130.0601ygaA0.4625.800.0850.8745.1.3.3NA
140.0603fmrB0.4835.410.0600.8353.4.11.18NA
150.0601ojnA0.4665.240.0430.8134.2.2.1122
160.0601b65A0.4475.090.0330.7423.4.11.998,126
170.0602e1qA0.4634.210.0730.6651.17.3.2,1.17.1.4NA
180.0601seoD0.3524.800.0770.5603.4.19.5159
190.0604matA0.4464.840.0710.7143.4.11.18NA

(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
00.180.5114.610.040.792vtuJ GO:0003723 GO:0005198 GO:0019012 GO:0019028 GO:0039617
10.070.4755.060.070.804xhfB GO:0005886 GO:0006120 GO:0006810 GO:0006811 GO:0006814 GO:0008137 GO:0009276 GO:0010181 GO:0016020 GO:0016021 GO:0016491 GO:0016655 GO:0055114
20.070.4874.470.080.764p6vC GO:0005886 GO:0006810 GO:0006811 GO:0006814 GO:0009276 GO:0010181 GO:0016020 GO:0016021 GO:0016491 GO:0016655 GO:0055114
30.070.4284.960.060.712dfiA GO:0004177 GO:0006508 GO:0008233 GO:0008235 GO:0016787 GO:0046872 GO:0070006 GO:0070084
40.070.4885.060.050.805d6eA GO:0004177 GO:0005737 GO:0005829 GO:0005886 GO:0006508 GO:0008233 GO:0008235 GO:0016485 GO:0016787 GO:0018206 GO:0022400 GO:0031365 GO:0044822 GO:0046872 GO:0070006 GO:0070084
50.070.4805.430.070.833fm3A GO:0004177 GO:0005737 GO:0005829 GO:0006508 GO:0008233 GO:0008235 GO:0016787 GO:0046872 GO:0070006 GO:0070084
60.070.4694.990.060.773j2iA GO:0003677 GO:0003700 GO:0003723 GO:0005634 GO:0005654 GO:0005730 GO:0005737 GO:0006351 GO:0006355 GO:0006364 GO:0006417 GO:0007050 GO:0008283 GO:0016020 GO:0030529 GO:0031625 GO:0043066 GO:0044822 GO:0045597 GO:0045892 GO:0070062
70.070.4704.600.060.754xa7A GO:0000166 GO:0005886 GO:0006810 GO:0006811 GO:0006814 GO:0009276 GO:0010181 GO:0016020 GO:0016021 GO:0016491 GO:0016655 GO:0055114
80.070.4464.920.040.731o0xA GO:0004177 GO:0006508 GO:0008233 GO:0008235 GO:0016787 GO:0046872 GO:0070006 GO:0070084
90.070.4894.130.040.713dczA GO:0005886 GO:0009055 GO:0010181 GO:0016020 GO:0016021 GO:0022900 GO:0055114
100.070.4355.100.040.744fukA GO:0004177 GO:0005737 GO:0006508 GO:0008233 GO:0008235 GO:0016787 GO:0022626 GO:0046872 GO:0070006 GO:0070084
110.070.4384.710.030.703s6bA GO:0004177 GO:0005737 GO:0006464 GO:0006508 GO:0008233 GO:0008235 GO:0016787 GO:0022626 GO:0046872 GO:0070006 GO:0070084
120.070.4644.720.070.753lwxA GO:0005506 GO:0005886 GO:0006810 GO:0006811 GO:0006814 GO:0009276 GO:0010181 GO:0016020 GO:0016021 GO:0016491 GO:0016655 GO:0055114
130.070.3385.910.060.644ipaC GO:0003677 GO:0016787
140.060.4444.670.040.703mx6B GO:0004177 GO:0006508 GO:0008233 GO:0008235 GO:0016787 GO:0046872 GO:0070006 GO:0070084
150.060.4385.080.060.731qxwA GO:0004177 GO:0006508 GO:0008233 GO:0008235 GO:0016787 GO:0046872 GO:0070006 GO:0070084
160.060.4424.610.040.704fo8C GO:0004177 GO:0006508 GO:0008233 GO:0008235 GO:0016787 GO:0046872 GO:0070006 GO:0070084
170.060.4114.520.060.652i0oA GO:0003824 GO:0004721 GO:0004722 GO:0006470 GO:0016787 GO:0043169 GO:0046872
180.060.4795.250.070.833s1sA GO:0003676 GO:0003677 GO:0006306 GO:0008168 GO:0008170 GO:0032259 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0003676
GO-Score 0.37
Biological Processes GO:0070084 GO:0006814 GO:0006120 GO:0022400 GO:0031365 GO:0016485 GO:0018206
GO-Score 0.13 0.13 0.07 0.07 0.07 0.07 0.07
Cellular Component GO:0071944 GO:0019030
GO-Score 0.37 0.37

(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.