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I-TASSER results for job id Rv1351

[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
10.14 8 2kikA ZN Rep, Mult 52,72,75
20.05 3 4f8hB LMD Rep, Mult 66,67,70
30.03 2 3u39C CA Rep, Mult 8,10
40.03 2 1usyF HIS Rep, Mult 68,72
50.03 2 4j8vH RU7 Rep, Mult 64,65
60.02 1 4a18L ZN Rep, Mult 43,48,91,95
70.02 1 3v2dF MG Rep, Mult 60,61
80.02 1 1h7gB MG Rep, Mult 12,13
90.02 1 1ibk0 III Rep, Mult 24,25,26
100.02 1 1l0l2 III Rep, Mult 2,3,6,36,104,105
110.02 1 1n1gA BCP Rep, Mult 95,98,99
120.02 1 3gz8A APR Rep, Mult 9,18
130.02 1 1jwyB MG Rep, Mult 16,17
140.02 1 3r33A CA Rep, Mult 100,101
150.02 1 2f7fA NIO Rep, Mult 41,42,43,56,58
160.02 1 1oxnA ZN Rep, Mult 43,48,73,91
170.02 1 1dkdD III Rep, Mult 4,18,31,71,74,77,78

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
10.0602plaA0.4253.850.0570.6971.1.1.837
20.0602he9A0.4264.870.0850.8445.2.1.8NA
30.0601n1eA0.4614.130.0520.7431.1.1.8NA
40.0602z04B0.4294.170.0410.7254.1.1.21NA
50.0602w22A0.3304.360.0560.5873.1.1.3NA
60.0601yrlC0.4253.900.0580.6971.1.1.8678
70.0603g17G0.4294.460.0660.7611.1.1.169NA
80.0601x0xA0.4254.180.0570.7251.1.1.837
90.0602gw2A0.4434.430.0560.8075.2.1.88
100.0603h2zA0.4484.260.0500.7611.1.1.1745,82
110.0603k2cC0.4314.800.0850.8445.2.1.8NA
120.0601yrlA0.4283.840.0480.6881.1.1.8665
130.0602nqtA0.4194.530.0440.7611.2.1.38NA
140.0601txgA0.4483.740.0310.6971.1.1.94NA
150.0601n4tA0.3494.750.0460.6513.1.4.3770
160.0602k7nA0.4424.590.0650.8265.2.1.88
170.0602e7zA0.4374.220.0380.7434.2.1.7182
180.0601clhA0.4264.780.0530.8265.2.1.818
190.0602wghB0.4294.510.0470.7801.17.4.195

(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
00.200.4833.420.110.721s62A GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0017038 GO:0032153 GO:0043213 GO:0046718 GO:0051301 GO:0071237
10.070.5073.750.150.802k9kA GO:0005886 GO:0006810 GO:0015031 GO:0015343 GO:0015891 GO:0016021 GO:0030288 GO:0031992 GO:0044718
20.070.5213.660.090.781tolA GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0009405 GO:0015031 GO:0016020 GO:0016021 GO:0016032 GO:0017038 GO:0019012 GO:0019028 GO:0019062 GO:0019076 GO:0032153 GO:0033644 GO:0039666 GO:0043213 GO:0046718 GO:0051301 GO:0071237
30.070.4853.590.040.734g7xB GO:0005215 GO:0006810 GO:0016020 GO:0016021
40.070.4534.160.100.712m2kA GO:0006810
50.060.4203.830.160.671u07A GO:0005886 GO:0006810 GO:0015031 GO:0015343 GO:0015889 GO:0015891 GO:0016020 GO:0016021 GO:0030288 GO:0031233 GO:0031992 GO:0042914 GO:0043213 GO:0044718
60.060.3373.640.050.513qvjA GO:0006807 GO:0036361
70.060.3005.180.050.612w1tA GO:0003677 GO:0006351 GO:0006355 GO:0030435
80.060.3904.240.070.702d0jA GO:0000139 GO:0005794 GO:0005975 GO:0006486 GO:0015018 GO:0016020 GO:0016021 GO:0016740 GO:0030203 GO:0030204 GO:0046872 GO:0050650
90.060.3974.550.090.723i6sA GO:0004252 GO:0005618 GO:0006508 GO:0008233 GO:0008236 GO:0016787
100.060.4774.590.090.882v50D GO:0005215 GO:0005886 GO:0006810 GO:0006855 GO:0015238 GO:0016020 GO:0016021 GO:0046677
110.060.5004.340.060.844dnrA GO:0005215 GO:0005375 GO:0005507 GO:0005886 GO:0006810 GO:0006811 GO:0006812 GO:0006825 GO:0006878 GO:0008324 GO:0010272 GO:0010273 GO:0015080 GO:0015673 GO:0015679 GO:0016020 GO:0016021 GO:0046688 GO:0060003 GO:1902601
120.060.3704.940.080.725en5C GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015307 GO:0016020 GO:0016021 GO:0042493 GO:0042802 GO:0046618
130.060.3454.960.020.653ge6A GO:0000166 GO:0016491 GO:0055114
140.060.3134.830.040.583qivA
150.060.4064.020.070.684mt1A GO:0005215 GO:0006810 GO:0016020 GO:0016021
160.060.4565.180.070.893nogA GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015307 GO:0016020 GO:0016021 GO:0042493 GO:0042802 GO:0046618
170.060.3055.030.070.594i0wD GO:0004252 GO:0006508 GO:0008233 GO:0008236 GO:0016787
180.060.3245.100.070.643jb9Y GO:0000166 GO:0000387 GO:0000974 GO:0003676 GO:0003723 GO:0005634 GO:0005681 GO:0006397 GO:0007049 GO:0008380 GO:0017070 GO:0036002 GO:0045292 GO:0046872 GO:0071006 GO:0071007


Consensus prediction of GO terms
 
Molecular Function GO:0015343 GO:0031992
GO-Score 0.07 0.07
Biological Processes GO:0045184 GO:1901653 GO:0044763 GO:0044765 GO:0071236 GO:0015833 GO:0030260 GO:0019058 GO:0046678
GO-Score 0.60 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50
Cellular Component GO:0031226 GO:0016021
GO-Score 0.50 0.34

(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.