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I-TASSER results for job id Rv2499c

[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
10.21 13 2q78H MLC Rep, Mult 68,89,90,91,92,122,123,124,125
20.14 7 1yliA COA Rep, Mult 91,94,121,122,124,125,167
30.03 2 3azaA KM0 Rep, Mult 71,72,85
40.03 2 2b3m0 III Rep, Mult 46,50,54,55,56,59,60,62,63,64,65,66,67,68,72,76,82,83,87,92,93,95,96,98,110,112,113,114,115,116,117,118,120,121,122
50.03 2 2o011 CLA Rep, Mult 129,130
60.01 1 2pyhB CA Rep, Mult 50,53
70.01 1 2f3xA MLC Rep, Mult 99,103,114,153
80.01 1 3kvzF ENV Rep, Mult 61,66,88,90,91,92
90.01 1 4dz4A UNK Rep, Mult 130,151
100.01 1 3kv8A FAH Rep, Mult 115,116
110.01 1 3az8C S21 Rep, Mult 71,82,85,122,124
120.01 1 1vpmC COA Rep, Mult 116,117,118,119,140,142,153,154,171,173
130.01 1 2f410 III Rep, Mult 90,92,95,96,114,115,116,117,118,120,121,122

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
10.1411lo8A0.4952.760.1360.5843.1.2.23122,135,169
20.1003ir3A0.5602.630.1540.6594.2.1.-71
30.0661u1zB0.4923.270.1100.6164.2.1.-NA
40.0661z6bA0.4893.180.1470.6164.2.1.-NA
50.0601iq6B0.6292.250.2780.7194.2.1.1771
60.0603d6xB0.4822.780.1510.5844.2.1.-NA
70.0601y7uA0.4742.910.1070.5783.1.2.2095,102
80.0601d0cA0.3755.530.0430.6861.14.13.39NA
90.0602ortA0.3854.960.0350.6221.14.13.39NA
100.0603el6A0.4363.440.0550.5624.2.1.6195
110.0601pn4C0.5772.760.1100.6814.2.1.-NA
120.0603khpA0.5773.340.1310.7411.-.-.-71
130.0601nosA0.3635.320.0450.6491.14.13.39NA
140.0601t3qB0.4055.850.0570.7461.3.99.17NA
150.0603e7gC0.4125.310.0410.7031.14.13.39NA
160.0601s9cD0.5812.880.1350.6974.2.1.10771
170.0601mkaA0.4913.870.0840.6654.2.1.6089
180.0602vkzG0.6403.120.0920.7782.3.1.38,3.1.2.14NA
190.0602pffB0.5853.540.0710.7512.3.1.8649,100
200.0603b7kC0.5012.810.0780.6003.1.2.1122
210.0601pn4D0.5892.720.1090.6924.2.1.-NA
220.0602hx5A0.4582.850.1480.5573.1.2.-50
230.0601pn0C0.3985.320.0380.6761.14.13.787

(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
00.410.6971.990.300.783exzB
10.390.7501.340.310.791q6wC
20.390.7332.220.280.824ffuI GO:0016491 GO:0055114
30.340.6612.700.160.794rltA GO:0005886 GO:0019171 GO:0040007
40.310.6422.570.210.765cpgA GO:0004312 GO:0005835 GO:0006633 GO:0016829 GO:0055114
50.310.7462.790.200.884e3eA GO:0009436 GO:0015977 GO:0016829 GO:0016833 GO:0043427
60.250.6552.640.200.782c2iA GO:0004300 GO:0006629 GO:0006631 GO:0006633 GO:0016829 GO:0018812
70.250.6292.250.280.721iq6B GO:0004312 GO:0005835 GO:0006629 GO:0006631 GO:0006633 GO:0016829 GO:0055114
80.240.5602.630.150.663ir3A GO:0005730 GO:0005737 GO:0005739 GO:0006629 GO:0006631 GO:0016829
90.200.6262.300.200.713k67A GO:0004312 GO:0005835 GO:0006633 GO:0055114
100.170.5812.880.140.701s9cD GO:0000038 GO:0001649 GO:0003857 GO:0005102 GO:0005739 GO:0005777 GO:0005778 GO:0005782 GO:0006629 GO:0006631 GO:0006635 GO:0006699 GO:0008209 GO:0008210 GO:0016020 GO:0016491 GO:0016508 GO:0016616 GO:0016829 GO:0016853 GO:0033540 GO:0033989 GO:0036109 GO:0036111 GO:0036112 GO:0042803 GO:0043231 GO:0044594 GO:0055114 GO:0060009
110.170.5022.900.160.614mtuA GO:0016829 GO:0046872
120.170.4912.790.120.582fs2B GO:0010124 GO:0016289 GO:0016787 GO:0016790
130.140.5772.760.110.681pn4C GO:0003824 GO:0005777 GO:0006629 GO:0006631 GO:0006635 GO:0008152 GO:0016491 GO:0016616 GO:0016829 GO:0016853 GO:0055114
140.130.4633.060.180.572okhA GO:0005737 GO:0006633 GO:0016836
150.130.4683.200.080.583f5oA GO:0005634 GO:0005737 GO:0005739 GO:0005819 GO:0005829 GO:0005856 GO:0016787 GO:0035338 GO:0047617 GO:0051289 GO:0070062
160.100.6962.780.200.832bi0A GO:0005886
170.090.4993.160.160.623az9G GO:0005737 GO:0006633 GO:0016836
180.080.4973.060.150.615buwA GO:0005737 GO:0006629 GO:0006633 GO:0009245 GO:0016829 GO:0016836 GO:0019171 GO:0047451
190.070.5873.090.140.723khpC
200.070.6063.040.100.733kh8A
210.070.5892.720.110.691pn4D GO:0003824 GO:0005777 GO:0006629 GO:0006631 GO:0006635 GO:0008152 GO:0016491 GO:0016616 GO:0016829 GO:0016853 GO:0055114
220.070.5862.820.130.701s9cG GO:0000038 GO:0001649 GO:0003857 GO:0005102 GO:0005739 GO:0005777 GO:0005778 GO:0005782 GO:0006629 GO:0006631 GO:0006635 GO:0006699 GO:0008209 GO:0008210 GO:0016020 GO:0016491 GO:0016508 GO:0016616 GO:0016829 GO:0016853 GO:0033540 GO:0033989 GO:0036109 GO:0036111 GO:0036112 GO:0042803 GO:0043231 GO:0044594 GO:0055114 GO:0060009


Consensus prediction of GO terms
 
Molecular Function GO:0016491 GO:0019171 GO:0004312
GO-Score 0.39 0.34 0.31
Biological Processes GO:0055114 GO:0040007 GO:0006633
GO-Score 0.58 0.34 0.31
Cellular Component GO:0005886 GO:0005835
GO-Score 0.34 0.31

(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.