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I-TASSER results for job id Rv2817c

[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
10.44 7 3godB MN Rep, Mult 111,155,220,235
20.09 2 1lm1A F3S Rep, Mult 255,256,258,259,260,271,272,274,278,279
30.05 1 2c3oA SF4 Rep, Mult 163,175,188,189,191,192,243,246,247
40.05 1 3c46A 2HP Rep, Mult 200,234,235

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
10.0601lehA0.3696.010.0460.5711.4.1.962
20.0601s76D0.3427.060.0580.6102.7.7.6NA
30.0601ps9A0.3756.390.0370.6041.3.1.34196
40.0603c46B0.4207.050.0510.7492.7.7.6235,244
50.0602e1qA0.3896.780.0290.6601.17.3.2,1.17.1.4NA
60.0601a17A0.1764.760.0620.2403.1.3.16139,156
70.0602aw5B0.3746.870.0650.6481.1.1.40NA
80.0602ohyB0.3755.980.0670.5865.4.3.6NA
90.0603ikmD0.3926.970.0600.6862.7.7.7113
100.0602ckjA0.3627.140.0590.6331.17.1.4,1.17.3.2115
110.0601o0sA0.3756.860.0510.6451.1.1.38NA
120.0603b9jC0.3126.180.0470.4971.17.3.2,1.17.1.4NA
130.0601vlbA0.3996.340.0480.6421.2.99.7145
140.0601b0pA0.4266.800.0270.7491.2.7.1NA
150.0602zxqA0.3866.670.0330.6483.2.1.97165
160.0601gq2A0.3696.720.0590.6301.1.1.40NA
170.0602rnpC0.3086.940.0450.5442.7.7.6NA
180.0601aroP0.3576.610.0640.5952.7.7.6NA
190.0602pdaA0.4266.850.0330.7511.2.7.1147

(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
00.490.9020.880.200.924xtkE GO:0003677 GO:0004518 GO:0004519 GO:0016787 GO:0043571 GO:0046872 GO:0051607 GO:0090305
10.370.8452.050.220.912yzsB GO:0003677 GO:0004518 GO:0004519 GO:0016787 GO:0043571 GO:0046872 GO:0051607 GO:0090305
20.280.7183.390.210.834n06B GO:0003677 GO:0003723 GO:0004518 GO:0004519 GO:0016787 GO:0043571 GO:0046872 GO:0051607 GO:0090305
30.260.5723.940.100.703godA GO:0003677 GO:0004518 GO:0004519 GO:0016787 GO:0043571 GO:0046872 GO:0051607 GO:0090305
40.260.6842.820.170.764wj0A GO:0003677 GO:0004518 GO:0004519 GO:0016787 GO:0043571 GO:0046872 GO:0051607 GO:0090305
50.240.6483.990.090.815fclA GO:0003677 GO:0004518 GO:0004519 GO:0016787 GO:0043571 GO:0046872 GO:0051607 GO:0090305
60.160.5034.440.120.674qdlC GO:0003677 GO:0004518 GO:0004519 GO:0005737 GO:0006281 GO:0006974 GO:0008821 GO:0016787 GO:0017108 GO:0043571 GO:0046872 GO:0051607 GO:0090305
70.150.5283.940.120.635dqzB GO:0003677 GO:0004518 GO:0004519 GO:0005737 GO:0006281 GO:0006974 GO:0008821 GO:0016787 GO:0017108 GO:0043571 GO:0046872 GO:0051607 GO:0090305
80.060.4256.590.050.711b25A GO:0009055 GO:0016491 GO:0016625 GO:0046872 GO:0051536 GO:0051539 GO:0055114
90.060.4366.690.040.731aorA GO:0009055 GO:0016491 GO:0016625 GO:0033726 GO:0046872 GO:0051536 GO:0051539 GO:0055114
100.060.4146.660.050.704z3wC GO:0009055 GO:0016491 GO:0016625 GO:0051536 GO:0055114
110.060.3526.230.040.572yl2B GO:0000166 GO:0001894 GO:0003824 GO:0003989 GO:0004075 GO:0005524 GO:0005730 GO:0005737 GO:0005739 GO:0005829 GO:0006084 GO:0006629 GO:0006631 GO:0006633 GO:0006768 GO:0006853 GO:0008152 GO:0015629 GO:0016874 GO:0031325 GO:0035338 GO:0044268 GO:0046872 GO:0051289 GO:0055088 GO:0070062 GO:0071380 GO:2001295
120.060.3266.810.050.562y2lB GO:0008658 GO:0008955 GO:0016020 GO:0016021 GO:0016740 GO:0016746 GO:0016757
130.060.2966.550.030.483egwB GO:0005737 GO:0005886 GO:0008940 GO:0009055 GO:0009061 GO:0009325 GO:0016020 GO:0016491 GO:0031224 GO:0031235 GO:0042126 GO:0042128 GO:0044799 GO:0046872 GO:0051536 GO:0051538 GO:0051539 GO:0055114
140.060.3096.920.040.544iibA GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0030245 GO:0102483
150.060.2776.110.030.434lk3B GO:0005739 GO:0005794 GO:0016020 GO:0016021 GO:0016829 GO:0016831 GO:0032580 GO:0033320 GO:0042803 GO:0048040 GO:0051262 GO:0070062 GO:0070403
160.060.2496.720.050.424ee9A GO:0004553 GO:0005975 GO:0008152 GO:0008810 GO:0016787 GO:0016798
170.060.2466.270.040.393hv9A GO:0000160 GO:0000166 GO:0005622 GO:0006355
180.060.2265.140.040.324j4mB GO:0004222 GO:0006508 GO:0008237 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0046872 GO:0003677 GO:0004519
GO-Score 0.87 0.87 0.87
Biological Processes GO:0051607 GO:0043571 GO:0090305
GO-Score 0.87 0.87 0.87
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.