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I-TASSER results for job id Rv0004

[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
10.06 3 2wieA CVM Rep, Mult 144,148
20.06 3 5jrcA CA Rep, Mult 80,147
30.06 3 1o6oA III Rep, Mult 73,76,77,81,144
40.04 2 1f59A III Rep, Mult 81,84,85,88,89,148,151
50.04 2 2wl3A CA Rep, Mult 73,129
60.04 2 4qjsU MG Rep, Mult 134,138
70.04 2 3luhB 5GP Rep, Mult 33,37
80.02 1 5jreB ADE Rep, Mult 72,133
90.02 1 5d92A 8K6 Rep, Mult 22,25,29
100.02 1 4u5tA 3CG Rep, Mult 26,33
110.02 1 2y6gA CA Rep, Mult 94,95,102
120.02 1 1bjyB CTC Rep, Mult 119,123,126
130.02 1 3pyoE MG Rep, Mult 55,70
140.02 1 1fbmD RTL Rep, Mult 137,144
150.02 1 3rj8A ZN Rep, Mult 112,113
160.02 1 3mi1B FE Rep, Mult 185,187

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
10.0601hbmA0.3105.120.0350.5032.8.4.1NA
20.0602ea4A0.3804.480.0420.5783.4.11.18112
30.0602hcsA0.4044.920.0900.6472.7.7.48,3.4.21.91130
40.0601t3qB0.3915.110.0580.6471.3.99.17NA
50.0602vdcA0.3945.800.0390.7061.4.1.13NA
60.0602vdcF0.4335.990.0550.7971.4.1.13NA
70.0601iq8A0.3784.540.0590.5612.4.2.29NA
80.0602vn7A0.3954.880.0450.6313.2.1.3NA
90.0601lcbA0.4045.100.0730.6522.1.1.45NA
100.0601bo7A0.4065.020.0780.6472.1.1.45NA
110.0601qhaA0.3925.170.0640.6742.7.1.1NA
120.0601z1wA0.3965.590.0630.6953.4.11.-NA
130.0602dqmA0.4155.570.0410.7493.4.11.2NA
140.0601b5dA0.3864.560.0490.5722.1.2.8NA
150.0601r58A0.3784.710.0330.5943.4.11.18NA
160.0601ut9A0.3805.180.0660.6313.2.1.4NA
170.0602gtqA0.4125.400.0540.7383.4.11.2NA
180.0601h16A0.3855.240.0550.6472.3.1.54NA
190.0602pulA0.3823.830.0450.5242.7.1.100NA

(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
00.220.7112.650.060.872rrlA GO:0009424 GO:0044780 GO:0044781
10.060.4455.160.050.741qgkA GO:0000059 GO:0000060 GO:0005634 GO:0005635 GO:0005643 GO:0005654 GO:0005737 GO:0005829 GO:0006309 GO:0006606 GO:0006607 GO:0006610 GO:0006810 GO:0006886 GO:0007079 GO:0007080 GO:0008139 GO:0008270 GO:0008536 GO:0008565 GO:0015031 GO:0016020 GO:0016032 GO:0019054 GO:0019899 GO:0019904 GO:0030953 GO:0031291 GO:0031965 GO:0034399 GO:0040001 GO:0043234 GO:0044822 GO:0045184 GO:0051879 GO:0070062 GO:0071782 GO:0075733 GO:0090307
20.060.3465.980.060.652q5dB GO:0000059 GO:0000060 GO:0005634 GO:0005635 GO:0005643 GO:0005654 GO:0005737 GO:0005829 GO:0006309 GO:0006606 GO:0006607 GO:0006610 GO:0006810 GO:0006886 GO:0007079 GO:0007080 GO:0008139 GO:0008270 GO:0008536 GO:0008565 GO:0015031 GO:0016020 GO:0016032 GO:0019054 GO:0019899 GO:0019904 GO:0030953 GO:0031291 GO:0031965 GO:0034399 GO:0040001 GO:0043234 GO:0044822 GO:0045184 GO:0051879 GO:0070062 GO:0071782 GO:0075733 GO:0090307
30.060.3275.860.020.611b3uA GO:0000086 GO:0000159 GO:0000184 GO:0000188 GO:0000775 GO:0003823 GO:0004722 GO:0005634 GO:0005694 GO:0005737 GO:0005739 GO:0005829 GO:0006275 GO:0006355 GO:0006461 GO:0006470 GO:0006672 GO:0006915 GO:0007059 GO:0007084 GO:0007143 GO:0008380 GO:0008601 GO:0010033 GO:0015630 GO:0016020 GO:0019932 GO:0030111 GO:0030155 GO:0030308 GO:0034047 GO:0040008 GO:0042518 GO:0045595 GO:0046982 GO:0051232 GO:0051306 GO:0051754 GO:0070062 GO:0070262 GO:1903538 GO:2001241
40.060.4184.970.040.695hdtA GO:0000775 GO:0000785 GO:0003677 GO:0005524 GO:0005634 GO:0005654 GO:0005694 GO:0005829 GO:0007049 GO:0007062 GO:0007064 GO:0007067 GO:0008283 GO:0008285 GO:0042127 GO:0051301
50.060.2715.740.040.505gapA GO:0000244 GO:0000350 GO:0000386 GO:0000389 GO:0000398 GO:0003676 GO:0003723 GO:0005634 GO:0005681 GO:0005682 GO:0006397 GO:0008380 GO:0017070 GO:0030529 GO:0030619 GO:0030620 GO:0030623 GO:0046540 GO:0071013 GO:0097157
60.060.4235.320.100.734xriA GO:0005622 GO:0006886 GO:0008536
70.060.3545.270.050.571oyzA GO:0006974 GO:0046677
80.060.4155.360.070.723nd2A GO:0000059 GO:0000060 GO:0000176 GO:0005087 GO:0005634 GO:0005643 GO:0005737 GO:0006606 GO:0006607 GO:0006610 GO:0006612 GO:0006656 GO:0006810 GO:0006886 GO:0008139 GO:0008536 GO:0008565 GO:0015031 GO:0031965 GO:0034399 GO:0043547 GO:0051028 GO:0051292 GO:0060188
90.060.3166.030.030.591wa5B GO:0000176 GO:0005634 GO:0005643 GO:0005654 GO:0005737 GO:0005829 GO:0006606 GO:0006607 GO:0006612 GO:0006810 GO:0008139 GO:0008565 GO:0015031 GO:0031144 GO:0048471
100.060.3145.500.010.553eqmA GO:0002677 GO:0004497 GO:0005506 GO:0005783 GO:0005789 GO:0006694 GO:0006703 GO:0008209 GO:0008395 GO:0009055 GO:0010760 GO:0016020 GO:0016125 GO:0016491 GO:0016705 GO:0016712 GO:0019825 GO:0020037 GO:0046872 GO:0055114 GO:0060736 GO:0070330
110.060.3835.390.030.655frpA GO:0000794 GO:0000798 GO:0005198 GO:0005634 GO:0005829 GO:0006302 GO:0007049 GO:0007064 GO:0007067 GO:0007076 GO:0007126 GO:0007129 GO:0034990 GO:0051301
120.060.3294.730.030.483zefE GO:0000244 GO:0000350 GO:0000386 GO:0000389 GO:0000398 GO:0003676 GO:0003723 GO:0005634 GO:0005681 GO:0005682 GO:0006397 GO:0008380 GO:0017070 GO:0030529 GO:0030619 GO:0030620 GO:0030623 GO:0046540 GO:0071013 GO:0097157
130.060.3464.210.040.503bdzA GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0016709 GO:0020037 GO:0046232 GO:0046872 GO:0055114
140.060.4295.810.060.765f0nA GO:0000070 GO:0000794 GO:0005634 GO:0005829 GO:0006302 GO:0006974 GO:0007064 GO:0007076 GO:0007126 GO:0007129 GO:0034501 GO:0051455 GO:0071168 GO:0071459 GO:2000817
150.060.3074.730.020.504uadA GO:0005634 GO:0005643 GO:0005654 GO:0005737 GO:0005829 GO:0006606 GO:0006607 GO:0006810 GO:0008139 GO:0008565 GO:0015031 GO:0016020 GO:0045944 GO:0060135
160.060.3535.710.040.652w91A GO:0005576 GO:0005618 GO:0005737 GO:0016020 GO:0033925
170.060.2596.050.050.492ihvA GO:0000287 GO:0003824 GO:0016740 GO:0030976 GO:0033848 GO:0046872
180.060.3145.740.010.595gamA GO:0000244 GO:0000350 GO:0000386 GO:0000389 GO:0000398 GO:0003676 GO:0003723 GO:0005634 GO:0005681 GO:0005682 GO:0006397 GO:0008380 GO:0017070 GO:0030529 GO:0030619 GO:0030620 GO:0030623 GO:0046540 GO:0071013 GO:0097157


Consensus prediction of GO terms
 
Molecular Function GO:0008270 GO:0008139 GO:0008536 GO:0051879 GO:0008565 GO:0044822 GO:0019904 GO:0003823 GO:0005524 GO:0003677 GO:0004722 GO:0008601 GO:0046982
GO-Score 0.12 0.12 0.12 0.12 0.12 0.12 0.12 0.06 0.06 0.06 0.06 0.06 0.06
Biological Processes GO:1902589 GO:0070925 GO:0030031
GO-Score 0.43 0.43 0.43
Cellular Component GO:0044444 GO:0044461 GO:1903561 GO:0031988 GO:0031981
GO-Score 0.47 0.43 0.36 0.36 0.36

(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.