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I-TASSER results for job id Rv2975c

[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
10.76 23 2btdA MG Rep, Mult 35,41,43
20.05 3 3q2qA IPE Rep, Mult 17,18,53,75
30.05 3 3pfdA IOD Rep, Mult 43,46,47
40.03 2 1gzmA C8E Rep, Mult 21,24
50.02 1 3rj1K SE Rep, Mult 51,52

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
10.0601c3cA0.5763.370.0630.8574.3.2.2NA
20.0601cc1L0.5813.230.1110.8571.12.99.6NA
30.0602bq1I0.5793.530.0370.8931.17.4.1NA
40.0602h5gB0.5883.460.1200.8931.2.1.41NA
50.0602wlaA0.5722.890.1080.8571.16.3.122,49,54,78
60.0601jq5A0.5713.430.0870.9051.1.1.635
70.0601y5nC0.5763.840.0830.9881.7.99.451
80.0602pulA0.5923.140.0540.8572.7.1.10060
90.0602o6yA0.6143.290.1730.8934.3.1.-NA
100.0601kizA0.5743.380.0850.8694.2.3.624,55,57
110.0601r03A0.5493.570.0390.8571.16.3.122,24,27
120.0602vroB0.5843.420.1070.8931.2.1.3NA
130.0603bhgA0.5983.270.0380.9174.3.2.2NA
140.0603e04D0.6183.240.1200.9414.2.1.2NA
150.0603d4sA0.5913.350.1120.8933.2.1.1758,70,73
160.0601y2mB0.6043.410.1190.9054.3.1.24NA
170.0601uzrB0.5823.250.0240.8691.17.4.1NA
180.0601smsA0.5783.470.0360.8691.17.4.1NA
190.0603lmdA0.6042.790.0950.8812.5.1.30NA

(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
00.450.8211.400.180.903cr3A GO:0000166 GO:0004371 GO:0005524 GO:0006071 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0019563
10.420.7222.670.160.931un8A GO:0000166 GO:0004371 GO:0005524 GO:0006071 GO:0008289 GO:0016301 GO:0016310 GO:0016740 GO:0019588 GO:0046872
20.160.8251.440.140.904lrzA GO:0000166 GO:0000287 GO:0004371 GO:0005524 GO:0005829 GO:0006071 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0019563 GO:0043531
30.100.5493.990.040.892hr5A GO:0005506 GO:0016491 GO:0046872 GO:0055114
40.100.5182.950.040.744di0B GO:0016491 GO:0046872 GO:0055114
50.090.6403.170.050.981yuxB GO:0005506 GO:0005737 GO:0016491 GO:0046872 GO:0055114
60.080.6083.220.040.923qhbA GO:0009536 GO:0009842 GO:0016491 GO:0046872 GO:0055114
70.070.5733.310.130.891b71A GO:0005506 GO:0005737 GO:0016491 GO:0046872 GO:0055114
80.070.5273.690.040.864k5rB GO:0000166 GO:0016491 GO:0055114 GO:0071949
90.070.5072.560.030.711j30A GO:0016491 GO:0046872 GO:0055114
100.070.4693.490.030.714lrxA GO:0004371 GO:0005829 GO:0006071 GO:0006974 GO:0016301 GO:0016310 GO:0016740 GO:0019563 GO:0042182 GO:0046365 GO:0047324
110.070.3964.060.130.744fc6B GO:0005102 GO:0005777 GO:0005778 GO:0006629 GO:0006631 GO:0006636 GO:0008670 GO:0016491 GO:0019166 GO:0044255 GO:0055114
120.070.6772.620.110.985f15A GO:0016020 GO:0016021 GO:0016740
130.070.4543.420.070.681wfzA GO:0005506 GO:0005737 GO:0005739 GO:0005759 GO:0005829 GO:0006879 GO:0008198 GO:0016226 GO:0032947 GO:0036455 GO:0044571 GO:0046872 GO:0051536 GO:0051537 GO:0051539 GO:0097428
140.060.3743.830.070.645ecjA GO:0000122 GO:0000902 GO:0001708 GO:0001827 GO:0003676 GO:0003677 GO:0003700 GO:0003714 GO:0003723 GO:0005634 GO:0006351 GO:0006355 GO:0007281 GO:0007566 GO:0008168 GO:0009566 GO:0010468 GO:0010976 GO:0010977 GO:0016740 GO:0019827 GO:0030718 GO:0030855 GO:0031490 GO:0032259 GO:0034972 GO:0040029 GO:0040037 GO:0044030 GO:0045892 GO:0045944 GO:0046872 GO:0048873 GO:0060817
150.060.4633.610.010.712iu4B GO:0004371 GO:0006071 GO:0006351 GO:0006355 GO:0016310
160.060.3954.070.040.704oytA GO:0003824 GO:0008168 GO:0016740 GO:0032259
170.060.3244.360.030.611j1iA GO:0016787
180.060.3782.490.040.521whuA GO:0000175 GO:0000957 GO:0000958 GO:0000962 GO:0000964 GO:0000965 GO:0003676 GO:0003723 GO:0004518 GO:0004527 GO:0004654 GO:0005737 GO:0005739 GO:0005758 GO:0006396 GO:0006397 GO:0006401 GO:0006402 GO:0006810 GO:0008266 GO:0016020 GO:0016740 GO:0016779 GO:0016787 GO:0034046 GO:0034599 GO:0035198 GO:0035458 GO:0035927 GO:0035928 GO:0043457 GO:0043631 GO:0044822 GO:0045025 GO:0045926 GO:0051260 GO:0061014 GO:0070207 GO:0070584 GO:0071042 GO:0071850 GO:0090503 GO:0097222 GO:2000627 GO:2000772


Consensus prediction of GO terms
 
Molecular Function GO:0005524 GO:0004371 GO:0046872 GO:0008289
GO-Score 0.73 0.73 0.53 0.42
Biological Processes GO:0016310 GO:0019588
GO-Score 0.73 0.42
Cellular Component GO:0044444
GO-Score 0.33

(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.