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I-TASSER results for job id Rv0164

[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
10.10 6 4n3eG 2AN Rep, Mult 21,23,32,36,93,108,110,121,144,148
20.09 5 2qimA ZEA Rep, Mult 36,37,42,81,91,93,108,148
30.07 4 3ojiA PYV Rep, Mult 48,49,68,74,76,79,81,104,139,143
40.07 4 2z9yA DDR Rep, Mult 36,42,45,70,77,81,93,104,121,125,143,147
50.05 3 4a81A 2AN Rep, Mult 20,22,35,93,108,121,123,137,140,141,144,145
60.05 3 3e85A NA Rep, Mult 43,46,47,49,50
70.03 2 3jrqB A8S Rep, Mult 49,75,76,93,95,105,121,139,143,144
80.02 1 1bv10 III Rep, Mult 33,37,38,40,41,43,44,52,53,54,55,86,88
90.02 1 3gkeC FES Rep, Mult 52,66,80,81,82
100.02 1 3tvqA DQH Rep, Mult 71,77,79,95,100,101,131,135,136,139

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
10.0662zfdB0.4623.770.0960.6402.7.11.18,23
20.0601qaxA0.4924.120.0870.7391.1.1.88NA
30.0601sczA0.5084.150.0600.7522.3.1.61NA
40.0602x4mA0.4874.510.0360.7213.4.23.4864
50.0602ewnA0.5233.930.0870.7276.3.4.15NA
60.0601xl7B0.5234.610.0630.8572.3.1.137NA
70.0601im0A0.5284.150.0780.7523.1.1.32,3.1.1.4NA
80.0601ciaA0.5034.790.0800.8012.3.1.28NA
90.0601q23B0.5064.680.0740.8012.3.1.28NA
100.0601bibA0.5053.720.0810.6966.3.4.15NA
110.0601t7nA0.5185.060.0530.8882.3.1.7NA
120.0602ii4A0.5284.540.0730.7952.3.1.16894,99
130.0602de6B0.6353.970.0760.9011.14.12.-NA
140.0601hdhA0.4894.820.1130.8013.1.6.1NA
150.0603b8kA0.4864.930.0790.8142.3.1.12NA
160.0601ndoA0.6204.120.0520.9441.14.12.12156
170.0602pmgB0.3585.270.0090.6655.4.2.2NA
180.0602vq5A0.6573.360.1120.8704.2.1.7868,96
190.0602ihwA0.5244.610.0730.7952.3.1.168NA
200.0603efsA0.4973.920.0590.7086.3.4.15NA

(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
00.290.7802.070.140.902rerA GO:0003824 GO:0008152 GO:0008168 GO:0008171 GO:0016740 GO:0017000 GO:0032259
10.260.7932.600.140.943p0lA GO:0005739 GO:0005758 GO:0005829 GO:0006082 GO:0006694 GO:0006699 GO:0006700 GO:0006701 GO:0006703 GO:0006810 GO:0006869 GO:0007420 GO:0007584 GO:0007623 GO:0008203 GO:0008211 GO:0008289 GO:0008584 GO:0009635 GO:0009636 GO:0010033 GO:0010212 GO:0010288 GO:0010628 GO:0014070 GO:0014823 GO:0015485 GO:0016101 GO:0017085 GO:0017127 GO:0017143 GO:0018879 GO:0018894 GO:0018958 GO:0018963 GO:0030061 GO:0031667 GO:0032367 GO:0032869 GO:0034698 GO:0035094 GO:0035457 GO:0042493 GO:0042542 GO:0042747 GO:0043005 GO:0043025 GO:0043434 GO:0043524 GO:0043627 GO:0044255 GO:0044321 GO:0044344 GO:0045471 GO:0046677 GO:0048168 GO:0048545 GO:0050769 GO:0050810 GO:0051412 GO:0060992 GO:0061370 GO:0071222 GO:0071236 GO:0071248 GO:0071276 GO:0071312 GO:0071320 GO:0071333 GO:0071346 GO:0071371 GO:0071372 GO:0071373 GO:0071378 GO:0071407 GO:0071549 GO:0071560 GO:0071872
20.250.8272.420.130.971em2A GO:0005737 GO:0005739 GO:0005765 GO:0005768 GO:0006629 GO:0006694 GO:0006701 GO:0006810 GO:0006839 GO:0006869 GO:0008202 GO:0008203 GO:0008289 GO:0015485 GO:0016020 GO:0016021 GO:0031902
30.250.7922.830.130.983ojiB GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042803 GO:0043086 GO:0080163
40.240.7302.950.110.933qszB GO:0008289
50.240.7752.920.130.984oicA GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0009738 GO:0010427 GO:0043086 GO:0080163
60.230.7813.020.110.993nefA GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042803 GO:0043086 GO:0080163
70.230.7832.930.110.983k3kA GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042802 GO:0042803 GO:0043086 GO:0080163
80.230.6872.680.100.853cnwA GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0009738 GO:0010427 GO:0043086 GO:0080163
90.220.7902.610.100.962r55A GO:0005829 GO:0006700 GO:0006810 GO:0006869 GO:0008289 GO:0032052
100.220.7753.030.120.983kdhA GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042803 GO:0043086 GO:0080163
110.220.6823.150.110.882bk0A GO:0006952 GO:0009607
120.210.7792.840.120.982mouA GO:0006810 GO:0006869 GO:0008289
130.210.7862.720.100.983w9rA GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042803 GO:0043086 GO:0080163
140.210.7192.560.110.884n0gC GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042803 GO:0043086 GO:0080163
150.200.7352.750.090.913rt0C GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042803 GO:0043086 GO:0080163
160.190.7702.720.130.945brlA GO:0005739 GO:0005783 GO:0005829 GO:0006810 GO:0006869 GO:0008289 GO:0015485 GO:0016023 GO:0034435
170.190.7182.810.090.894jdlB GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0043086 GO:0080163
180.160.6782.860.050.841z94B GO:0006950
190.120.7342.990.090.932psoB GO:0005096 GO:0005737 GO:0005739 GO:0005811 GO:0005829 GO:0007165 GO:0008289 GO:0016020 GO:0031966 GO:0043542 GO:0043547 GO:0051056 GO:0090051 GO:0097498
200.120.7342.990.100.933fo5A GO:0005737 GO:0005829 GO:0006631 GO:0008289 GO:0009266 GO:0009409 GO:0016787 GO:0035338 GO:0035556 GO:0047617 GO:0052689 GO:0070062


Consensus prediction of GO terms
 
Molecular Function GO:0008168 GO:0015248 GO:0033293 GO:0019212 GO:0042802 GO:0060089 GO:0019888 GO:0042562 GO:0046983 GO:0015485
GO-Score 0.57 0.53 0.49 0.49 0.49 0.49 0.49 0.49 0.49 0.45
Biological Processes GO:0016999 GO:0071548 GO:0043279 GO:0006721 GO:1901655 GO:0050802 GO:0009404 GO:0046686 GO:0043523 GO:0046677 GO:0071345 GO:0046546 GO:0031667 GO:0009636 GO:0035455 GO:0007417 GO:0051591 GO:0006805 GO:0001678 GO:0071363 GO:0030301 GO:0008406 GO:0050767 GO:0071375 GO:0060416 GO:0071385 GO:0071219 GO:0046483 GO:0034699 GO:0071774 GO:0008210 GO:0042537 GO:0051385 GO:0060322 GO:0010720 GO:0009314 GO:0043066 GO:0071871 GO:0071559 GO:0032354 GO:0071870 GO:0000302 GO:0034341 GO:0048167 GO:0051962 GO:0032366 GO:0071248 GO:0008206 GO:0043648 GO:0010604 GO:0010468 GO:0071331 GO:1901215 GO:0032868 GO:0009749 GO:1901617 GO:0019218 GO:0046890 GO:0072330 GO:0032496 GO:0071215 GO:0009755 GO:0043666 GO:0044092 GO:0006701 GO:0008203
GO-Score 0.57 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.49 0.49 0.49 0.49 0.45 0.45
Cellular Component GO:0036477 GO:0005743 GO:0042995 GO:0031970 GO:0044297 GO:0044455 GO:0010008 GO:0005770 GO:0005764 GO:0098852 GO:0071944 GO:0031224
GO-Score 0.53 0.53 0.53 0.53 0.53 0.53 0.50 0.50 0.50 0.50 0.49 0.40

(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.