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I-TASSER results for job id Rv1491c

[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 1xvgA BRJ Rep, Mult 73,74,77,148,151,152
20.06 3 2fkwD BCL Rep, Mult 98,101
30.06 3 3zuyA PTY Rep, Mult 158,175,182,227,230,231,234
40.06 3 4v1fA BQ1 Rep, Mult 113,114,117
50.04 2 2xqtD CVM Rep, Mult 102,105,109
60.02 1 2y02A 2CV Rep, Mult 140,147
70.02 1 3u32K DCW Rep, Mult 75,113,120
80.02 1 3j47U III Rep, Mult 224,225,228
90.02 1 2q67A CA Rep, Mult 80,81
100.02 1 1vf5S III Rep, Mult 119,120
110.02 1 3zuxA TCH Rep, Mult 29,32,172,173,174,175
120.02 1 4amjB 2CV Rep, Mult 68,128
130.02 1 4bo3B U98 Rep, Mult 39,111,118,119
140.02 1 1xvfA 3CL Rep, Mult 73,192,195,196
150.02 1 1kfyB CE1 Rep, Mult 180,184
160.02 1 2wse4 CLA Rep, Mult 72,76
170.02 1 3a0bZ CLA Rep, Mult 75,78
180.02 1 2y02A 2CV Rep, Mult 213,216

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
10.0601pcaA0.4005.010.0630.5873.4.17.1NA
20.0602j2fA0.4445.610.0380.7101.14.19.2,1.14.99.6NA
30.0602bq1I0.4155.600.0650.6671.17.4.1NA
40.0603fg3A0.4006.670.0620.7544.2.1.92,1.13.11.40NA
50.0601fpsA0.4014.780.0380.5522.5.1.1,2.5.1.10NA
60.0601z1lA0.3795.360.0310.5873.1.4.17114
70.0602uw1B0.4295.550.0330.6861.14.99.6184
80.0601ayeA0.4045.010.1020.5913.4.17.15NA
90.0602fhbA0.3965.660.0340.6393.2.1.41NA
100.0601h8lA0.4095.390.0590.6513.4.17.2285,192
110.0601uwyA0.4125.460.0430.6593.4.17.12105
120.0602fknB0.4215.310.0560.6434.2.1.4934
130.0601g87B0.4015.730.0680.6673.2.1.4NA
140.0602fhcA0.3955.680.0340.6393.2.1.4112
150.0601fziA0.4495.530.0330.7221.14.13.25NA
160.0601mhyD0.4495.470.0330.7181.14.13.25NA
170.0603ffzA0.4175.360.0750.6633.4.24.69NA
180.0602vuaA0.2466.230.0130.4293.4.24.69146,150
190.0601pytA0.1854.770.0230.2663.4.17.1NA

(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
00.120.7083.260.120.854bwzA GO:0006810 GO:0006812 GO:0015299 GO:0016020 GO:0016021 GO:0046872 GO:0055085 GO:1902600
10.110.6703.690.090.854czbB GO:0005886 GO:0006810 GO:0006811 GO:0006812 GO:0006814 GO:0015297 GO:0015299 GO:0016020 GO:0016021 GO:0042802 GO:0055085 GO:1902600
20.070.6054.140.050.833zuxA GO:0016020 GO:0016021
30.070.4684.670.080.664a01A GO:0004427 GO:0005773 GO:0005774 GO:0006810 GO:0006811 GO:0009678 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0046872 GO:0055085
40.070.4526.070.060.784av3B GO:0000287 GO:0004427 GO:0005509 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006814 GO:0009678 GO:0015081 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0030955 GO:0035725 GO:0042803 GO:0046872
50.070.4635.970.080.814av6A GO:0000287 GO:0004427 GO:0005509 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006814 GO:0009678 GO:0015081 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0030955 GO:0035725 GO:0042803 GO:0046872
60.060.6553.560.100.824cz8A GO:0006810 GO:0006812 GO:0015299 GO:0016020 GO:0016021 GO:0055085 GO:1902600
70.060.6443.740.110.804atvA GO:0005886 GO:0006810 GO:0006811 GO:0006814 GO:0006885 GO:0015081 GO:0015297 GO:0015491 GO:0015992 GO:0016020 GO:0016021 GO:0035725 GO:0055085 GO:0098655
80.060.3295.460.050.513ug4C GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0046373 GO:0046556
90.060.3185.990.070.543k5pA GO:0004617 GO:0006564 GO:0008152 GO:0016491 GO:0016597 GO:0016616 GO:0051287 GO:0055114
100.060.6243.930.070.824n7wA GO:0016020 GO:0016021
110.060.2766.240.080.484rpfA GO:0000166 GO:0004413 GO:0005524 GO:0005737 GO:0006566 GO:0008652 GO:0009088 GO:0016301 GO:0016310 GO:0016740
120.060.2606.260.040.461pv9B GO:0005737 GO:0006508 GO:0008233 GO:0008237 GO:0016787 GO:0016805 GO:0046872 GO:0102009
130.060.2794.450.080.382fckA GO:0008080 GO:0016740 GO:0016746
140.060.2715.770.060.444gmvB GO:0005737 GO:0005856 GO:0005886 GO:0007165 GO:0016020 GO:0030027 GO:0030175 GO:0031252 GO:0042995 GO:0048675
150.060.2775.960.040.481u0uA GO:0003824 GO:0005737 GO:0008152 GO:0009058 GO:0016740 GO:0016746 GO:0016747 GO:0050198
160.060.2535.260.070.382wlkA GO:0005242 GO:0005244 GO:0006810 GO:0006811 GO:0006813 GO:0016020 GO:0016021 GO:0034765 GO:0071805
170.060.2475.150.040.372wzr1 GO:0000166 GO:0001172 GO:0003723 GO:0003724 GO:0003968 GO:0004197 GO:0004386 GO:0005198 GO:0005216 GO:0005524 GO:0006351 GO:0006508 GO:0006810 GO:0006811 GO:0008233 GO:0008234 GO:0016020 GO:0016032 GO:0016740 GO:0016779 GO:0016787 GO:0019012 GO:0019028 GO:0019030 GO:0019062 GO:0019082 GO:0030430 GO:0033644 GO:0034220 GO:0039694 GO:0039707 GO:0044161 GO:0044162 GO:0044385 GO:0046718 GO:0051259
180.060.2324.510.050.321flcB GO:0001681 GO:0016020 GO:0016021 GO:0016032 GO:0016787 GO:0016788 GO:0019012 GO:0019031 GO:0019062 GO:0019064 GO:0020002 GO:0033644 GO:0039654 GO:0039663 GO:0046718 GO:0046789 GO:0055036


Consensus prediction of GO terms
 
Molecular Function GO:0043169 GO:0015078 GO:0015298
GO-Score 0.47 0.43 0.43
Biological Processes GO:0015992 GO:0098662 GO:0030001
GO-Score 0.43 0.43 0.33
Cellular Component GO:0016021 GO:0071944
GO-Score 0.36 0.33

(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.