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I-TASSER results for job id Rv1049

[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 2 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
10.46 38 4llnB NUC Rep, Mult 20,24,58,59,60,70,71,74,78,88,95,96,97
20.10 10 3q5fA NUC Rep, Mult 20,58,59,60,70,71,74,88,95,96,97
30.04 4 4fx4A NUC Rep, Mult 36,38,39,68,69,72,75,76,82
40.03 4 4rgsA V55 Rep, Mult 26,37,40,41,44,116
50.03 3 3hsrC BT6 Rep, Mult 22,26,124
60.03 5 4em0B KAN Rep, Mult 19,22,23,26,37,40,41,44,66,116,120
70.03 4 2gxg0 III Rep, Mult 6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,24,37,41,66,67,116,117,120,121,122,123,124,127,130,131,133,134,136,137,140,141,143,144,147
80.02 2 3bpxA NA Rep, Mult 36,39,76,79
90.02 2 3hsrD BT6 Rep, Mult 11,12,140
100.01 1 3kp2A PNN Rep, Mult 23,26,30,34,37,38,40,41,112
110.01 1 3fm5C MG Rep, Mult 135,138
120.01 1 2frhA CA Rep, Mult 5,6,14
130.01 1 3gezA CA Rep, Mult 146
140.01 1 3bpxA NA Rep, Mult 46,47,50,100,101
150.01 1 3bpxB SAL Rep, Mult 9,12,13,16,20
160.01 1 3bpxA SAL Rep, Mult 16,20
170.01 1 2yr2B ZN Rep, Mult 90,92
180.01 2 3bpxA SAL Rep, Mult 41,44,48,65,66
190.01 1 2fbhA ZN Rep, Mult 29,30,31,32
200.01 1 3hsrB BT6 Rep, Mult 9,12,13

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
10.0602rnpC0.3435.720.0340.6892.7.7.6NA
20.0603ilwA0.4764.210.1170.6695.99.1.3NA
30.0601x54A0.4694.750.0970.7706.1.1.22NA
40.0601zaoA0.4892.150.0510.5612.7.11.127
50.0603fofA0.4664.520.0930.7575.99.1.-NA
60.0601bgwA0.4474.400.1140.6825.99.1.3NA
70.0601fokA0.5654.020.1150.7773.1.21.4NA
80.0602gaiA0.4914.410.1170.7905.99.1.2NA
90.0601aroP0.5424.310.1530.8312.7.7.6NA
100.0601k3pA0.4704.850.1040.8042.3.3.1NA
110.0601mj9A0.5493.890.0670.7372.3.1.48NA
120.0602h12E0.4954.850.0590.8312.3.3.165
130.0603kalA0.4674.970.0910.8116.3.2.3NA
140.0603k9fA0.4934.370.1110.7105.99.1.-NA
150.0601gl9B0.4884.530.1560.7975.99.1.3NA
160.0601fy7A0.5493.630.0760.7232.3.1.48NA
170.0603gh4A0.4524.810.0810.7633.2.1.5269
180.0601cy7A0.4804.510.1260.7905.99.1.2NA
190.0603lomA0.4634.510.1030.7702.5.1.1031

(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
00.610.7532.430.970.914fx0B GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355
10.500.7462.420.180.911lj9A GO:0003677 GO:0003700 GO:0006351 GO:0006355
20.440.7972.100.230.933f3xA GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0044212
30.410.7922.130.220.914b8xA GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0044212
40.400.7742.260.170.933bpxA GO:0003677 GO:0003700 GO:0006351 GO:0006355
50.390.7692.320.210.912pexB GO:0003677 GO:0003700 GO:0006351 GO:0006355
60.380.7972.180.200.921z9cC GO:0003677 GO:0003700 GO:0005737 GO:0006351 GO:0006355 GO:0044212
70.380.8371.640.190.934gxoA GO:0003677 GO:0003700 GO:0006351 GO:0006355
80.360.6872.800.190.861jgsA GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0009408 GO:0044212 GO:0045892 GO:0046677 GO:0071236
90.360.8032.540.170.954hblD GO:0003677 GO:0003700 GO:0006351 GO:0006355
100.360.7562.440.260.933q5fA GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0009405
110.350.7422.840.170.935aipA GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0010124 GO:0045892
120.350.7593.140.210.973zmdC GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0044212
130.340.7451.460.200.823hseB GO:0003677 GO:0003700 GO:0006351 GO:0006355
140.340.6493.250.140.851s3jA GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0006367 GO:0044212
150.330.7082.860.230.934aijB GO:0003677 GO:0003700 GO:0006351 GO:0006355
160.320.7911.820.180.902fbiA GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0010124 GO:0044212 GO:0045892
170.310.7562.500.180.913bjaA GO:0003677 GO:0003700 GO:0006351 GO:0006355
180.310.7352.410.200.892nnnA GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0044212
190.310.7003.090.150.924rguB GO:0003677 GO:0003700 GO:0006351 GO:0006355
200.310.7372.910.140.933broB GO:0003677 GO:0003700 GO:0006351 GO:0006355
210.300.6693.070.170.902nyxB GO:0003677 GO:0003700 GO:0005886 GO:0006351 GO:0006355 GO:0044212
220.300.5544.260.120.862ethA GO:0003677 GO:0003700 GO:0006351 GO:0006355
230.290.7982.330.140.943s2wA GO:0003677 GO:0003700 GO:0006351 GO:0006355
240.290.7392.540.150.934em0B GO:0003677 GO:0003700 GO:0006351 GO:0006355
250.280.6563.090.150.853bddA
260.280.7433.030.140.933nrvC GO:0003677 GO:0003700 GO:0006351 GO:0006355
270.280.7023.240.180.912bv6A GO:0003677 GO:0003700 GO:0005737 GO:0006351 GO:0006355 GO:0009405
280.280.7152.790.140.914fhtB GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0044212
290.270.5743.930.120.862a61A GO:0003677 GO:0003700 GO:0006351 GO:0006355
300.260.7622.700.180.925cyvB GO:0003677 GO:0003700 GO:0006351 GO:0006355
310.230.7302.810.250.912fbhA GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0044212 GO:0046872
320.220.7032.940.120.903g3zA GO:0003677 GO:0003700 GO:0006351 GO:0006355
330.180.6853.090.210.922rdpA GO:0003677 GO:0003700 GO:0006351 GO:0006355
340.170.6103.250.090.794rbrA GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0009405 GO:0016020 GO:0016021
350.160.5783.060.090.762frhA GO:0003677 GO:0005737 GO:0006351 GO:0006355 GO:0009405 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0003700 GO:0044212
GO-Score 0.96 0.67
Biological Processes GO:0006355
GO-Score 0.96
Cellular Component GO:0005829
GO-Score 0.61

(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.