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I-TASSER results for job id Rv2558

[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
10.13 9 3nn4A HEM Rep, Mult 138,140,142,146,165,171,173,183,185,187,199,212,220
20.06 4 1n5sB ADL Rep, Mult 138,140,171,173,185,187,189,195,198,208,209,212,220
30.04 3 2zhcA MG Rep, Mult 73,77
40.03 2 1ecyA BGC Rep, Mult 34,118
50.03 2 3l76A LYS Rep, Mult 45,47,48,49,71,72
60.03 2 3g1bB MG Rep, Mult 136,138,224
70.01 1 3od4A ZN Rep, Mult 124,126
80.01 1 1s2vB MG Rep, Mult 45,73
90.01 1 3l76A THR Rep, Mult 41,42,43,44,45,73
100.01 1 3rj8A ZN Rep, Mult 126,127
110.01 1 3twaA MG Rep, Mult 176,212,234
120.01 1 2d2cA CLA Rep, Mult 55,72
130.01 1 3opkC MG Rep, Mult 131,132,133,227
140.01 1 2od6A OHA Rep, Mult 33,35,58,81,83,85,91,117
150.01 1 1n5qB TNC Rep, Mult 35,37,68,81,83,85,88,91,102,105,106,113,115
160.01 1 1frvB SF4 Rep, Mult 23,177
170.01 1 1iujB ZN Rep, Mult 89,92
180.01 1 3fgvB UNL Rep, Mult 138,185,220

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
10.0601m5sD0.4144.700.0590.6062.3.1.101NA
20.0601f1hL0.4215.490.0400.6916.3.1.2160,163
30.0601oj9A0.4095.380.0830.6611.4.3.4NA
40.0603bxvA0.6853.630.1150.8861.13.11.5558,82
50.0602gmjA0.4174.900.0430.6311.5.5.1NA
60.0602bmbA0.4165.570.0680.6992.5.1.15,2.7.6.3,4.1.2.25NA
70.0601e6yA0.4105.240.0330.6482.8.4.1161
80.0602v5aB0.4226.100.0400.7466.3.4.1489
90.0602gmhA0.4165.030.0290.6361.5.5.150,226
100.0602hjwA0.4166.220.0710.7336.3.4.14,6.4.1.2NA
110.0601v5vA0.4215.230.0350.6482.1.2.1088
120.0602vqdA0.4275.970.0700.7466.3.4.14,6.4.1.2NA
130.0602ys6A0.4175.900.0450.7126.3.4.13NA
140.0603nn1A0.5654.860.0920.8261.13.11.49141,173
150.0602qf7A0.4165.950.0490.6956.4.1.1NA
160.0602fknB0.4134.850.0470.6104.2.1.49NA
170.0601kfqB0.4504.860.0640.6785.4.2.2NA
180.0603lp8A0.4315.660.0300.7126.3.4.13NA
190.0601lgrA0.4065.510.0480.6656.3.1.2NA

(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
00.210.8051.720.100.873mcsB
10.180.7362.080.050.833f44A
20.100.7033.470.110.903gn6C GO:0046872
30.100.6853.590.130.882cb2A GO:0005737 GO:0016491 GO:0033755 GO:0046872 GO:0055114
40.100.6853.630.120.893bxvA GO:0046872
50.070.5934.330.040.844g2cB GO:0004601 GO:0005576 GO:0016491 GO:0016689 GO:0020037 GO:0030145 GO:0046872 GO:0052750 GO:0055114 GO:0098869
60.070.5794.560.050.843afvA GO:0004601 GO:0020037 GO:0046872 GO:0055114 GO:0098869
70.070.5694.770.060.854au9A GO:0004601 GO:0016491 GO:0020037 GO:0046872 GO:0055114 GO:0098869
80.070.5784.630.040.842y4eA GO:0004601 GO:0006974 GO:0015684 GO:0016491 GO:0016675 GO:0020037 GO:0033212 GO:0042597 GO:0046872 GO:0055114 GO:0098869
90.070.5804.620.060.855c2iA GO:0004601 GO:0020037 GO:0055114 GO:0098869
100.070.5754.600.060.834gs1B GO:0004601 GO:0020037 GO:0046872 GO:0055114 GO:0098869
110.070.5734.680.070.834gt2A GO:0004601 GO:0005623 GO:0015684 GO:0020037 GO:0033212 GO:0046872 GO:0055114 GO:0098869
120.060.3791.950.130.423bm7A
130.060.4015.160.060.614ngeD GO:0003824 GO:0004222 GO:0005739 GO:0005759 GO:0006508 GO:0008047 GO:0008233 GO:0008237 GO:0008270 GO:0016485 GO:0016787 GO:0043085 GO:0046872
140.060.4041.820.090.443kkfA GO:0046872
150.060.3802.110.130.423qmqC
160.060.3256.120.050.594oanA GO:0006810 GO:0030288
170.060.3642.020.120.402gffB GO:0005737 GO:0016853
180.060.3611.950.100.403kg0B GO:0016491 GO:0016703 GO:0017000 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0043169
GO-Score 0.53
Biological Processes GO:0055114
GO-Score 0.10
Cellular Component GO:0005737
GO-Score 0.10

(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.