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I-TASSER results for job id Rv1929c

[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
10.40 4 2nsfA ZN Rep, Mult 40,106,110
20.14 2 1jqkB SF4 Rep, Mult 158,182,186
30.07 1 2z8yD SF4 Rep, Mult 15,17,18,23

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
10.0603cmmC0.4405.330.0500.7016.3.2.1971
20.0603e7xA0.4155.240.0440.6786.1.1.13120
30.0601e3aB0.4285.320.0440.7063.5.1.11NA
40.0603cskA0.4155.750.0520.6963.4.14.4NA
50.0602d1rA0.4215.910.0580.7431.13.12.7NA
60.0603l8cB0.4165.300.0430.6826.1.1.13NA
70.0602xaaA0.4225.620.0480.7201.1.1.1NA
80.0603d64A0.3875.670.0450.6453.3.1.1NA
90.0601kywC0.3875.390.0430.6352.1.1.68NA
100.0602nyaA0.4785.650.0650.8131.7.99.4NA
110.0601rjwA0.4155.580.0430.7061.1.1.1NA
120.0603e7wA0.4105.310.0550.6786.1.1.13163
130.0603ecqB0.4135.850.0730.7293.2.1.97NA
140.0602z8yP0.4375.380.0690.7152.3.1.169NA
150.0603b7wA0.4185.280.0640.6926.2.1.231,118,120
160.0601kqfA0.4915.890.0590.8411.2.1.2NA
170.0601pj6A0.4216.510.0460.8181.5.3.10NA
180.0602ow6A0.3996.150.0490.7483.2.1.114NA
190.0602jkpB0.4355.840.0480.7623.2.1.20NA

(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
00.480.8821.580.140.942nsfA GO:0046872
10.070.5414.950.080.804x8bA GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0046872 GO:0052699 GO:0055114
20.070.4915.890.060.841kqfA GO:0008430 GO:0008863 GO:0009055 GO:0009061 GO:0009326 GO:0015944 GO:0016020 GO:0016491 GO:0030151 GO:0030288 GO:0036397 GO:0042597 GO:0043546 GO:0045333 GO:0046872 GO:0047111 GO:0051536 GO:0051539 GO:0055114
30.060.3665.790.050.632ivfA GO:0016491 GO:0030151 GO:0046872 GO:0051536 GO:0051539 GO:0055114
40.060.4485.710.040.763egwA GO:0005886 GO:0008940 GO:0009055 GO:0009061 GO:0009325 GO:0016020 GO:0016491 GO:0030151 GO:0031224 GO:0031235 GO:0042126 GO:0042128 GO:0043546 GO:0044799 GO:0046872 GO:0051536 GO:0051539 GO:0055114
50.060.3075.750.020.533gcfA GO:0016491 GO:0046872 GO:0051213 GO:0051536 GO:0051537 GO:0055114
60.060.3505.990.040.632x7gA GO:0000166 GO:0000245 GO:0000287 GO:0001525 GO:0004672 GO:0004674 GO:0005524 GO:0005634 GO:0005654 GO:0005730 GO:0005737 GO:0006397 GO:0006468 GO:0008284 GO:0008380 GO:0010628 GO:0016301 GO:0016310 GO:0016740 GO:0030154 GO:0035063 GO:0035556 GO:0043525 GO:0044822 GO:0045070 GO:0045071 GO:0045087 GO:0045787 GO:0048024 GO:0071889
70.060.3055.610.050.523b8gA GO:0004042 GO:0005737 GO:0006526 GO:0008080 GO:0008652 GO:0016740 GO:0016746
80.060.3606.680.020.734v4cA GO:0016491 GO:0018706 GO:0030151 GO:0046872 GO:0055114
90.060.3255.690.060.565evoA GO:0016491 GO:0045174 GO:0055114 GO:0098869
100.060.3565.350.010.591uwyA GO:0004180 GO:0004181 GO:0004185 GO:0005615 GO:0005886 GO:0006508 GO:0006518 GO:0008233 GO:0008237 GO:0008270 GO:0009653 GO:0009986 GO:0016020 GO:0016485 GO:0016787 GO:0031225 GO:0046872 GO:0070062
110.060.2946.130.050.544hea3 GO:0005886 GO:0008137 GO:0009055 GO:0016020 GO:0016491 GO:0016651 GO:0030151 GO:0042773 GO:0046872 GO:0048038 GO:0051536 GO:0051537 GO:0051539 GO:0055114
120.060.3496.030.020.641dmrA GO:0009055 GO:0016491 GO:0030151 GO:0042597 GO:0046872 GO:0050626 GO:0055114
130.060.4785.650.070.812nyaA GO:0005506 GO:0006777 GO:0008940 GO:0009055 GO:0009061 GO:0016491 GO:0030151 GO:0030288 GO:0042128 GO:0042597 GO:0046872 GO:0051536 GO:0051539 GO:0055114
140.060.3365.710.050.573fwnA GO:0004616 GO:0005829 GO:0006098 GO:0016491 GO:0019521 GO:0042802 GO:0042803 GO:0055114
150.060.3106.210.060.592vpwA GO:0016491 GO:0030151 GO:0046872 GO:0051536 GO:0051539 GO:0055114
160.060.4875.460.040.813ml1A GO:0005506 GO:0006777 GO:0008940 GO:0009055 GO:0016491 GO:0030151 GO:0042128 GO:0042597 GO:0046872 GO:0051536 GO:0051539 GO:0055114
170.060.3146.070.030.573amgB GO:0004553 GO:0005576 GO:0005975 GO:0006073 GO:0008152 GO:0008422 GO:0009251 GO:0009986 GO:0016787 GO:0016798
180.060.3865.990.040.701fdiA GO:0005829 GO:0008863 GO:0009055 GO:0015942 GO:0015944 GO:0016491 GO:0030151 GO:0046872 GO:0051536 GO:0051539 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0051536 GO:0046914 GO:0003824
GO-Score 0.36 0.36 0.33
Biological Processes GO:0044710
GO-Score 0.47
Cellular Component GO:0009326 GO:0030288 GO:0044799 GO:0031235
GO-Score 0.07 0.07 0.06 0.06

(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.