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I-TASSER results for job id Rv2161c

[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
10.34 10 3fgcA FMN Rep, Mult 34,35,81,82,84,113,114,115,116,178,179,180,182,185,199
20.10 4 1luc0 III Rep, Mult 13,14,37,38,39,60,62,64,65,67,68,70,71,72,87,89,91,92,95,96,99,102,103,122,123,124,163,164,166,167,168
30.04 1 1ezwA MG Rep, Mult 70,73,74
40.03 1 3b4yA FLC Rep, Mult 40,116,199,233,253,260,261,287
50.03 1 1uh3A UUU Rep, Mult 189,208,211,212,215
60.03 1 2v3eA NND Rep, Mult 142,144,158
70.03 1 3gxfB PO4 Rep, Mult 21,25,73,74,76

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
10.2441xkjA0.7992.520.1300.9101.14.14.328,100
20.1691tqxA0.5883.300.0530.7155.1.3.1NA
30.1591xbzB0.5753.290.0850.6944.1.1.8593
40.1561rpxA0.5833.470.0860.7155.1.3.1NA
50.1473exrA0.5863.230.0740.7054.1.1.85NA
60.1411rhcA0.8152.400.1750.9131.1.99.5116
70.1283ct7A0.5743.740.1050.7225.1.3.-NA
80.1172v81A0.5393.590.1180.6774.1.2.21NA
90.0821h1yB0.5793.330.0840.7055.1.3.131
100.0822fliC0.5893.350.0780.7155.1.3.1NA
110.0811h1yA0.5783.420.0830.7085.1.3.1NA
120.0803inpA0.5843.530.0630.7195.1.3.1NA
130.0793f4wA0.5693.470.1240.7014.1.2.-NA
140.0731nsjA0.5283.510.0740.6565.3.1.24NA
150.0731tqjC0.5843.310.1100.7085.1.3.1NA
160.0732czfA0.5623.160.1140.6674.1.1.23NA
170.0713cu2B0.5893.400.0520.7195.1.3.1NA
180.0701v5xA0.5233.490.1430.6465.3.1.24NA
190.0672cz5A0.5513.460.1140.6704.1.1.23NA
200.0671vqtA0.5073.140.0960.6084.1.1.2389
210.0601wcgA0.6274.060.0550.8263.2.1.147NA
220.0603a47A0.6274.200.0510.8303.2.1.10NA
230.0602e3zA0.6273.970.0630.8193.2.1.21NA
240.0603m07A0.6214.200.0780.8193.2.1.141NA
250.0601lucA0.8302.330.1700.9201.14.14.3NA
260.0601ezwA0.7742.730.1840.8851.5.99.11178
270.0601nqkA0.7922.200.2090.8751.14.14.5115,131,178,187
280.0602ekcB0.6203.790.0750.7854.2.1.20NA
290.0602bfgA0.6174.090.0540.8123.2.1.3786
300.0601wzaA0.6194.270.0490.8263.2.1.1NA
310.0601izjA0.6264.300.0650.8333.2.1.135,3.2.1.1NA
320.0601fhlA0.6254.120.0710.8193.2.1.89NA
330.0601m53A0.6154.310.0310.8235.4.99.12NA
340.0602jf6B0.6253.960.0520.8093.2.1.105NA
350.0602djxA0.6144.450.0810.8261.3.3.1NA
360.0601hjqA0.6283.870.0810.8063.2.1.89NA
370.0603f4vA0.6224.050.0520.8123.2.1.21NA
380.0602d0gA0.6254.320.0690.8333.2.1.135NA
390.0603c8nA0.7822.690.1780.8991.-.-.-NA

(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
00.430.9071.280.220.942b81C GO:0004497 GO:0005886 GO:0016491 GO:0016705 GO:0055114
10.400.8272.500.180.932i7gB GO:0004497 GO:0016705 GO:0055114
20.390.8292.530.230.923raoB GO:0016705 GO:0055114
30.360.8302.330.170.921lucA GO:0004497 GO:0008218 GO:0016491 GO:0016705 GO:0047646 GO:0055114
40.340.7992.890.180.925aecA GO:0004497 GO:0016491 GO:0016705 GO:0055114
50.320.7582.440.200.851f07A GO:0005737 GO:0006730 GO:0015948 GO:0016491 GO:0016705 GO:0018537 GO:0019386 GO:0055114
60.300.8262.460.160.931yw1A GO:0004497 GO:0016491 GO:0016705 GO:0055114
70.290.8032.490.130.913fgcD GO:0004497 GO:0008218 GO:0016491 GO:0016705 GO:0047646 GO:0055114
80.290.8292.330.170.923fgcA GO:0004497 GO:0008218 GO:0016491 GO:0016705 GO:0047646 GO:0055114
90.280.7922.200.210.881nqkA GO:0004497 GO:0008726 GO:0009408 GO:0016491 GO:0016705 GO:0042802 GO:0046306 GO:0055114
100.270.7612.900.180.884us5C GO:0004497 GO:0016705 GO:0055114
110.250.8152.400.170.911rhcA GO:0016705 GO:0055114
120.250.8172.910.170.945dqpA GO:0004497 GO:0016705 GO:0055114
130.220.8222.700.180.943sdoA GO:0004497 GO:0016491 GO:0016705 GO:0055114
140.210.7992.640.170.913c8nA GO:0004497 GO:0005618 GO:0005829 GO:0005886 GO:0005975 GO:0016491 GO:0016614 GO:0016705 GO:0045454 GO:0052749 GO:0055114 GO:0070967
150.180.8193.030.130.953b9nB GO:0000166 GO:0004497 GO:0016705 GO:0055114
160.170.8232.710.180.943sdoB GO:0004497 GO:0016491 GO:0016705 GO:0055114
170.160.7742.730.180.891ezwA GO:0005737 GO:0006730 GO:0015948 GO:0016491 GO:0016705 GO:0018537 GO:0019386 GO:0055114
180.160.7722.520.210.871z69A GO:0005737 GO:0006730 GO:0015948 GO:0016491 GO:0016705 GO:0018537 GO:0019386 GO:0055114
190.070.4994.270.100.672yswA GO:0003824 GO:0003855 GO:0008652 GO:0009073 GO:0009423 GO:0016829


Consensus prediction of GO terms
 
Molecular Function GO:0047646
GO-Score 0.36
Biological Processes GO:0055114 GO:0008218
GO-Score 0.91 0.36
Cellular Component GO:0005886
GO-Score 0.43

(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.