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I-TASSER results for job id Rv1429

[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 5 2yx4A GLN Rep, Mult 369,376,377
20.08 4 3rbmD B73 Rep, Mult 403,407
30.04 2 3b2xA NA Rep, Mult 369,370,372,373,375
40.04 2 1bjeA AZI Rep, Mult 359,407
50.04 2 1a9x1 III Rep, Mult 160,161,163,164,186,187,188
60.04 2 5awvB GHP Rep, Mult 382,385
70.04 2 1lm1A F3S Rep, Mult 297,298,299,302,317,318,322,326
80.02 1 2einL ZN Rep, Mult 375,388
90.02 1 1v51A ZN Rep, Mult 353,357
100.02 1 3ak1C EDO Rep, Mult 396,399
110.02 1 2e85B CA Rep, Mult 385,388
120.02 1 2e75G OPC Rep, Mult 351,355
130.02 1 5i50A NUC Rep, Mult 408,411

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
10.0603b9jJ0.2156.910.0250.3531.17.1.4,1.17.3.2321,342
20.0601z1wA0.3956.880.0670.6373.4.11.-NA
30.0602vdcA0.3677.330.0500.6231.4.1.13NA
40.0601t3tA0.4037.260.0580.6906.3.5.3NA
50.0602c4mC0.3697.190.0490.6262.4.1.1332
60.0601yiqA0.3667.320.0310.6261.1.99.-NA
70.0603b9jC0.2977.210.0360.5001.17.3.2,1.17.1.4328
80.0603b9jI0.1535.240.0810.2161.17.1.4,1.17.3.2170,286
90.0601r9mB0.3637.820.0260.6663.4.14.5NA
100.0601fa9A0.3676.980.0470.6042.4.1.1NA
110.0602vdcF0.3797.500.0370.6521.4.1.13NA
120.0601h54B0.3687.210.0390.6282.4.1.8NA
130.0602ckjA0.3697.220.0380.6281.17.1.4,1.17.3.2163
140.0603bq5A0.3497.600.0470.6112.1.1.14NA
150.0601bxrA0.3897.050.0450.6446.3.5.5NA
160.0603gpbA0.3667.070.0520.6072.4.1.1183
170.0601itwB0.3657.310.0640.6301.1.1.42293
180.0602gtqA0.4176.760.0650.6783.4.11.2NA
190.0601z68A0.3687.440.0240.6373.4.21.-398

(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
00.060.3776.790.040.602yd0A GO:0001525 GO:0002250 GO:0002376 GO:0002474 GO:0004175 GO:0004177 GO:0005138 GO:0005151 GO:0005164 GO:0005576 GO:0005615 GO:0005737 GO:0005783 GO:0005788 GO:0005789 GO:0005829 GO:0005886 GO:0006508 GO:0006509 GO:0008217 GO:0008233 GO:0008235 GO:0008237 GO:0008270 GO:0009617 GO:0016020 GO:0016021 GO:0016787 GO:0019885 GO:0042277 GO:0043171 GO:0043231 GO:0045088 GO:0045444 GO:0045766 GO:0046872 GO:0070006 GO:0070062
10.060.4276.880.050.695ab0A GO:0002250 GO:0002376 GO:0002474 GO:0004175 GO:0004177 GO:0005783 GO:0005788 GO:0005789 GO:0005886 GO:0006508 GO:0008217 GO:0008233 GO:0008237 GO:0008270 GO:0016020 GO:0016021 GO:0016787 GO:0019885 GO:0042277 GO:0043171 GO:0046872 GO:0070006
20.060.3927.030.060.654xo4A GO:0004177 GO:0005737 GO:0005886 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0016020 GO:0016787 GO:0042277 GO:0042802 GO:0043171 GO:0046872 GO:0070006
30.060.3627.040.060.594qpeA GO:0004177 GO:0006508 GO:0008237 GO:0008270 GO:0016787 GO:0046872
40.060.3567.150.040.593ebgA GO:0004177 GO:0005737 GO:0005829 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0016787 GO:0046872
50.060.4276.330.050.664kx7A GO:0001525 GO:0002003 GO:0002005 GO:0003081 GO:0004177 GO:0005765 GO:0005886 GO:0005887 GO:0005903 GO:0006508 GO:0007267 GO:0008233 GO:0008237 GO:0008270 GO:0008283 GO:0009897 GO:0016020 GO:0016021 GO:0016324 GO:0016477 GO:0016787 GO:0031410 GO:0032835 GO:0042277 GO:0043171 GO:0045177 GO:0046872 GO:0070006 GO:0070062
60.060.4196.480.050.655ab0C GO:0002250 GO:0002376 GO:0002474 GO:0004175 GO:0004177 GO:0005783 GO:0005788 GO:0005789 GO:0005886 GO:0006508 GO:0008217 GO:0008233 GO:0008237 GO:0008270 GO:0016020 GO:0016021 GO:0016787 GO:0019885 GO:0042277 GO:0043171 GO:0046872 GO:0070006
70.060.3717.240.040.625dllA GO:0004177 GO:0006508 GO:0008237 GO:0008270 GO:0016787
80.060.4226.850.060.685c97A GO:0000209 GO:0002480 GO:0004177 GO:0005576 GO:0005622 GO:0005765 GO:0005829 GO:0005886 GO:0005887 GO:0006508 GO:0007165 GO:0007267 GO:0007565 GO:0008217 GO:0008233 GO:0008237 GO:0008270 GO:0016020 GO:0016021 GO:0016787 GO:0030163 GO:0030659 GO:0031905 GO:0042277 GO:0043171 GO:0046872 GO:0048471 GO:0060395 GO:0061024 GO:0070006
90.060.3796.620.040.594fyrA GO:0001525 GO:0001618 GO:0004177 GO:0004872 GO:0005615 GO:0005737 GO:0005765 GO:0005793 GO:0005829 GO:0005886 GO:0005887 GO:0006508 GO:0006725 GO:0007275 GO:0008233 GO:0008237 GO:0008270 GO:0009897 GO:0012506 GO:0016020 GO:0016021 GO:0016032 GO:0016787 GO:0030154 GO:0031983 GO:0035814 GO:0042277 GO:0043171 GO:0046718 GO:0046872 GO:0070006 GO:0070062
100.060.4086.520.060.644wz9B GO:0005737 GO:0005886 GO:0006508 GO:0008237 GO:0008270 GO:0042277 GO:0043171 GO:0070006
110.060.4097.160.050.684fkeA GO:0001525 GO:0001618 GO:0004177 GO:0005737 GO:0005886 GO:0006508 GO:0007275 GO:0008233 GO:0008237 GO:0008270 GO:0016020 GO:0016021 GO:0016032 GO:0016787 GO:0030154 GO:0042277 GO:0043171 GO:0046718 GO:0046872 GO:0070006
120.060.3607.010.040.595furI GO:0000086 GO:0001075 GO:0001129 GO:0003682 GO:0005634 GO:0005654 GO:0005669 GO:0006351 GO:0006355 GO:0006366 GO:0006367 GO:0006368 GO:0006508 GO:0008237 GO:0008270 GO:0014070 GO:0033276 GO:0043565 GO:0044212 GO:0045944 GO:0051123 GO:1901796
130.060.3897.300.060.663q7jA GO:0004177 GO:0005737 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0016787 GO:0046872
140.060.3217.040.050.533b7rL GO:0004177 GO:0004301 GO:0004463 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0005886 GO:0006508 GO:0006691 GO:0008233 GO:0008237 GO:0008270 GO:0010043 GO:0016787 GO:0019370 GO:0042277 GO:0043171 GO:0043434 GO:0044822 GO:0046872 GO:0060509 GO:0070006 GO:0070062
150.060.3246.910.040.534gaaA GO:0004463 GO:0005737 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0016787 GO:0019370 GO:0046872
160.060.3197.220.070.553ciaA GO:0004177 GO:0006508 GO:0008237 GO:0008270 GO:0016787 GO:0046872
170.060.3066.830.070.502xpyA GO:0004177 GO:0004301 GO:0004463 GO:0005634 GO:0005737 GO:0005886 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0016787 GO:0030163 GO:0042277 GO:0043171 GO:0044255 GO:0046872 GO:0070006
180.060.2827.260.020.484fgmA GO:0004177 GO:0006508 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0046914 GO:0008235 GO:0033218
GO-Score 0.57 0.36 0.36
Biological Processes GO:0019538 GO:0044248 GO:1901565 GO:0006518
GO-Score 0.57 0.36 0.36 0.36
Cellular Component GO:0044424 GO:0071944
GO-Score 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.