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I-TASSER results for job id Rv0911

[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 1 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
10.14 5 3oa4A ZN Rep, Mult 14,59,74,121
20.12 3 3oxhA PMB Rep, Mult 40,47,103,106,128
30.08 2 3oxhA XYL Rep, Mult 135,141,142,186
40.06 2 3vb0A FE2 Rep, Mult 143,205,207,241,251
50.06 2 2ei3A BPY Rep, Mult 24,28,32,244,245
60.03 1 2ei0A BP7 Rep, Mult 162,164,180,181,182
70.03 1 1lgtA BP3 Rep, Mult 50,51,52,58,138,139,140
80.03 1 3uomA CA Rep, Mult 212,214
90.03 1 1lkdA BP6 Rep, Mult 200,201,248,250

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
10.0841kmyA0.6594.030.1070.8991.13.11.3978,150
20.0771eilA0.6604.050.1020.9031.13.11.3978
30.0702ehzA0.6654.140.1040.9141.13.11.-78
40.0681f1uA0.6843.910.1110.9071.13.11.15NA
50.0671cjxA0.6704.210.1040.9101.13.11.2797,112
60.0673ecjA0.6853.950.1070.9101.13.11.15NA
70.0603mmtA0.4335.910.0770.6974.1.2.1318
80.0602z1sA0.3676.010.0670.6153.2.1.21162
90.0602e3zA0.4266.090.0610.7003.2.1.21211
100.0602zi8A0.6534.320.1140.9101.13.11.39150
110.0603mbfA0.4295.800.0660.6854.1.2.13NA
120.0603cmjA0.4215.720.0430.6733.2.1.21211
130.0601sqdA0.7073.870.0870.9381.13.11.27NA
140.0601gttD0.4255.560.0650.6934.1.1.68,5.3.3.10NA
150.0603aboA0.4275.650.0620.6774.3.1.775
160.0602zoxA0.4295.810.0640.6813.2.1.21153,162
170.0601fbaA0.4166.120.0730.6854.1.2.13NA
180.0601mpyA0.6844.120.1370.9261.13.11.2NA
190.0601t47A0.7023.910.1140.9261.13.11.27NA
200.0601yniB0.4236.050.0280.7043.5.3.23NA
210.0601wd9A0.4086.100.0530.7003.5.3.1527,222
220.0603lm4D0.6654.060.1130.8991.13.11.2115,122,145,162,164
230.0602e9lA0.4275.690.0540.6733.2.1.21NA
240.0601sqiA0.6764.120.1020.9071.13.11.2772
250.0602jf6B0.4236.060.0490.7003.2.1.105NA

(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
00.490.9240.870.330.943oxhA GO:0005886
10.120.7043.820.070.931sp9B GO:0003868 GO:0005737 GO:0006559 GO:0006572 GO:0009072 GO:0016491 GO:0016701 GO:0042802 GO:0046872 GO:0051213 GO:0055114
20.110.6964.140.100.933zgjB GO:0003868 GO:0009072 GO:0016701 GO:0046872 GO:0051213 GO:0055114
30.110.7003.970.100.925ec3A GO:0003868 GO:0005829 GO:0006559 GO:0006572 GO:0009072 GO:0016491 GO:0016701 GO:0046872 GO:0051213 GO:0055114 GO:0070062
40.110.6973.960.100.922r5vA GO:0003868 GO:0005506 GO:0009072 GO:0016491 GO:0016701 GO:0017000 GO:0033072 GO:0046872 GO:0050585 GO:0055114
50.100.3943.270.180.483kolA GO:0004462 GO:0046872 GO:0051213 GO:0055114
60.100.7084.110.080.951sp8D
70.100.7023.910.110.931t47A GO:0003868 GO:0006559 GO:0006572 GO:0009072 GO:0016491 GO:0016701 GO:0046872 GO:0051213 GO:0055114
80.100.6744.020.100.891sqiB GO:0000139 GO:0003868 GO:0005737 GO:0005783 GO:0005789 GO:0005794 GO:0006559 GO:0006572 GO:0009072 GO:0016020 GO:0016491 GO:0016701 GO:0046872 GO:0051213 GO:0055114
90.090.3832.890.150.463rmuA GO:0004493 GO:0005739 GO:0005759 GO:0016853 GO:0019626 GO:0046491 GO:0046872
100.090.6704.210.100.911cjxA GO:0003868 GO:0006559 GO:0006572 GO:0009072 GO:0016491 GO:0016701 GO:0046872 GO:0051213 GO:0055114
110.060.3913.080.130.463gm5A GO:0016829
120.060.3717.000.050.735e6uA GO:0002291 GO:0005886 GO:0006928 GO:0006954 GO:0007155 GO:0007157 GO:0007159 GO:0007160 GO:0007165 GO:0007229 GO:0008305 GO:0009986 GO:0016020 GO:0016021 GO:0016337 GO:0030198 GO:0030369 GO:0032403 GO:0034687 GO:0043113 GO:0046872 GO:0046982 GO:0050776 GO:0050839 GO:0050900 GO:0070062
130.060.3943.060.080.473oa4A GO:0046872
140.060.3872.930.190.471jc5B GO:0004493 GO:0016853
150.060.3286.200.050.561r3nA GO:0003837 GO:0008152 GO:0016787 GO:0016813 GO:0046872
160.060.3246.060.080.562cxiA GO:0000166 GO:0000287 GO:0003723 GO:0004812 GO:0004826 GO:0005524 GO:0005737 GO:0006412 GO:0006432 GO:0016874
170.060.3946.120.070.674ur9A GO:0004563 GO:0005975 GO:0006517 GO:0008152 GO:0016231 GO:0016787 GO:0016798
180.060.3316.530.030.614wxyC GO:0003824 GO:0008152 GO:0016829 GO:0036381 GO:0042819 GO:0042823


Consensus prediction of GO terms
 
Molecular Function GO:0003868 GO:0046872
GO-Score 0.38 0.38
Biological Processes GO:1901606 GO:0006558 GO:0009074 GO:0009063 GO:0006570 GO:0055114
GO-Score 0.43 0.43 0.43 0.43 0.43 0.38
Cellular Component GO:0005886
GO-Score 0.49

(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.