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I-TASSER results for job id Rv3657c

[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
10.06 3 3rdhA 3RD Rep, Mult 7,46,47,113,116
20.06 3 3prqZ CLA Rep, Mult 172,175,176
30.06 3 4xk8L CLA Rep, Mult 46,142
40.04 2 3dtuC DMU Rep, Mult 78,81,82,85
50.04 2 3qqvA MG Rep, Mult 47,52,181
60.04 2 2e75G OPC Rep, Mult 127,131
70.02 1 2i5wA CA Rep, Mult 164,166,172
80.02 1 3omiC TRD Rep, Mult 72,75,79
90.02 1 4evbA ZN Rep, Mult 133,137
100.02 1 2np5C NDS Rep, Mult 121,122,124,128
110.02 1 5d6kA 97M Rep, Mult 47,48,54,128,132
120.02 1 3fyeC TRD Rep, Mult 46,110,118
130.02 1 1c6mA KR Rep, Mult 62,63,85,121
140.02 1 4eiyA CLR Rep, Mult 163,166,167,174,181,182,188
150.02 1 2hk6A FE Rep, Mult 140,144
160.02 1 3dtuC DXC Rep, Mult 63,66,67,70,75,78
170.02 1 4uk1E MG Rep, Mult 136,139

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
10.0603g0sA0.4795.300.0350.8224.2.1.52NA
20.0601f7bA0.4815.240.0980.8064.1.3.381
30.0602weiA0.3795.690.0690.6812.7.1.1784
40.0602pcqA0.4854.980.0830.7804.2.1.52NA
50.0601i09A0.4835.060.0780.7852.7.11.26,2.7.1.3747
60.0602x6fA0.4865.090.0480.7912.7.1.137,2.7.1.153,2.7.1.15488
70.0601occA0.4955.350.0470.8381.9.3.1NA
80.0601xkyA0.4825.260.0720.8014.2.1.52NA
90.0601xl9A0.4875.130.0670.7964.2.1.52NA
100.0601qleA0.3855.850.0910.7071.9.3.1NA
110.0601u59A0.4424.860.0750.6962.7.10.2,2.7.1.11247
120.0602vc6A0.4805.060.0800.7914.2.1.52139
130.0603eb2B0.4894.810.0530.7914.2.1.52NA
140.0601iduA0.4824.610.0810.7021.11.1.10NA
150.0603hngA0.4284.740.0600.6442.7.10.147,50
160.0601y6bA0.4394.780.0720.6652.7.10.1,2.7.1.11254
170.0603bi8A0.4885.140.0490.8064.2.1.52NA
180.0602fp0B0.4844.910.0870.7443.2.1.14350,186
190.0603ihyC0.5045.070.0760.8172.7.1.13735,69,140

(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
00.070.5743.530.110.723jc8Ca GO:0016020 GO:0016021
10.070.5372.020.130.602vmbA GO:0005886 GO:0006810 GO:0008565 GO:0009306 GO:0015031 GO:0015627 GO:0015628 GO:0016020 GO:0016021
20.070.5382.150.130.602vmaA GO:0005886 GO:0006810 GO:0008565 GO:0009306 GO:0015031 GO:0015627 GO:0015628 GO:0016020 GO:0016021
30.070.5314.500.060.835doqB GO:0016020 GO:0016021 GO:0055114
40.070.5374.590.070.813j9tQ GO:0000220 GO:0000329 GO:0005773 GO:0005774 GO:0006810 GO:0006811 GO:0007034 GO:0007035 GO:0015078 GO:0015991 GO:0015992 GO:0016020 GO:0033179 GO:0046961
50.070.5354.690.070.845doqA GO:0016020 GO:0016021
60.070.4795.110.120.804he8I GO:0005886 GO:0006810 GO:0008137 GO:0016020 GO:0016021 GO:0016491 GO:0042773 GO:0048038 GO:0050136 GO:0055114
70.070.4771.850.160.532whnA GO:0005886 GO:0006810 GO:0009306 GO:0016020 GO:0016021
80.060.5104.970.070.834he8G GO:0005886 GO:0008137 GO:0016020 GO:0016021 GO:0016491 GO:0042773 GO:0048038 GO:0055114
90.060.3835.960.060.723k6sC GO:0004872 GO:0005886 GO:0007155 GO:0007229 GO:0008305 GO:0009887 GO:0009986 GO:0016020 GO:0016021 GO:0030198 GO:0034113 GO:0046872 GO:0050900 GO:1903955
100.060.3466.190.040.684nenA GO:0004872 GO:0005886 GO:0007155 GO:0007229 GO:0008305 GO:0009887 GO:0009986 GO:0016020 GO:0016021 GO:0030198 GO:0034113 GO:0046872 GO:0050900 GO:1903955
110.060.3815.280.060.664jcmA GO:0003824 GO:0005975 GO:0016740 GO:0030246 GO:0043169 GO:0046872 GO:2001070
120.060.3755.080.030.613mcaA GO:0000166 GO:0002181 GO:0002182 GO:0003746 GO:0003924 GO:0005525 GO:0005622 GO:0005737 GO:0005829 GO:0006412 GO:0006414 GO:0006417 GO:0032790
130.060.4245.350.060.731nfgA GO:0005737 GO:0016787 GO:0016810 GO:0046872
140.060.3595.410.090.592q5lA GO:0000287 GO:0003824 GO:0009851 GO:0016829 GO:0016831 GO:0030976 GO:0046872 GO:0047434
150.060.3396.060.060.644nehA GO:0004872 GO:0005886 GO:0007155 GO:0007229 GO:0008305 GO:0009887 GO:0009986 GO:0016020 GO:0016021 GO:0030198 GO:0034113 GO:0046872 GO:0050900 GO:1903955
160.060.4985.200.070.824he8F GO:0005886 GO:0008137 GO:0016020 GO:0016021 GO:0016491 GO:0042773 GO:0048038 GO:0055114
170.060.3225.210.080.542ex5A GO:0003677 GO:0004518 GO:0004519 GO:0006314 GO:0009507 GO:0009536 GO:0016787 GO:0046872 GO:0090305
180.060.3435.370.040.603ed5A GO:0008152 GO:0016787


Consensus prediction of GO terms
 
Molecular Function GO:0008565 GO:0046961
GO-Score 0.13 0.07
Biological Processes GO:0051234
GO-Score 0.37
Cellular Component GO:0031224
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.