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I-TASSER results for job id Rv1003

[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
10.61 30 5hw4A SAM Rep, Mult 13,87,88,89,92,93,117,118,138,163,189,191,192,218,219,220

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
10.1931vhvB0.6143.210.1370.7402.1.1.9813,18,20,88,91,115,117,163
20.1801wdeA0.6533.580.1910.8072.1.1.988,87,91,115
30.1571vceA0.6213.310.1130.7542.1.1.98NA
40.0752e0kB0.5723.770.1400.7402.1.1.130115
50.0721ve2A0.5673.380.1850.7052.1.1.10737
60.0671s4dE0.5933.810.1580.7752.1.1.107NA
70.0603bfjA0.4445.110.0710.6421.1.1.202NA
80.0602hrbA0.4385.400.0860.6771.1.1.18497
90.0601v9aB0.5573.800.1430.7192.1.1.107NA
100.0603igyB0.4475.430.0910.6845.4.2.1190
110.0601o0sA0.4545.520.0720.7021.1.1.38NA
120.0601gz3A0.4535.430.0640.6981.1.1.38NA
130.0602esdA0.4475.510.0750.6951.2.1.920
140.0602a9fA0.4415.690.0520.6811.1.1.39NA
150.0601gq2A0.4575.390.0570.6951.1.1.40NA
160.0603bfjT0.4405.190.0710.6461.1.1.202NA
170.0601q16A0.3566.580.0380.6281.7.99.4NA
180.0603c39A0.4445.940.0720.7162.7.2.3NA
190.0602cunA0.4625.850.0600.7262.7.2.3NA
200.0602z6rB0.6173.300.1180.7512.1.1.9813,18,88
210.0602p9tA0.4435.780.0730.7092.7.2.3NA
220.0602dvmA0.4645.260.0470.6981.1.1.38NA
230.0601wmaA0.4435.310.1060.6741.1.1.184NA
240.06013pkA0.4625.900.0800.7402.7.2.3NA
250.0601n5dA0.4425.480.1150.6811.1.1.184,1.1.1.189,1.1.1.197NA

(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
00.510.7651.350.430.803kwpA GO:0000453 GO:0005737 GO:0006364 GO:0008152 GO:0008168 GO:0016740 GO:0032259 GO:0070677
10.340.3722.050.500.403fq6B GO:0000453 GO:0005737 GO:0006364 GO:0008152 GO:0008168 GO:0016740 GO:0032259 GO:0070677
20.310.6642.640.200.761wyzB GO:0008152 GO:0008168 GO:0016740 GO:0032259
30.290.3512.340.370.393hh1A GO:0000453 GO:0005737 GO:0006364 GO:0008152 GO:0008168 GO:0016740 GO:0032259 GO:0070677
40.270.3611.860.480.393ffyA GO:0000453 GO:0005737 GO:0006364 GO:0008152 GO:0008168 GO:0016740 GO:0032259 GO:0070677
50.190.6013.640.190.763nutC GO:0008152 GO:0008168 GO:0009236 GO:0016740 GO:0032259
60.170.5993.860.180.781cbfA GO:0008152 GO:0008168 GO:0009236 GO:0016740 GO:0032259 GO:0046026 GO:0055114
70.140.5823.250.150.722qbuA GO:0008152 GO:0008168 GO:0008757 GO:0009236 GO:0016740 GO:0030788 GO:0032259
80.120.5773.970.170.762yboA GO:0004851 GO:0006779 GO:0008152 GO:0008168 GO:0016740 GO:0032259 GO:0055114
90.110.5673.380.180.711ve2A GO:0006779 GO:0008152 GO:0008168 GO:0016740 GO:0032259 GO:0055114
100.100.6593.660.180.821wdeA GO:0004164 GO:0008152 GO:0008168 GO:0016740 GO:0017183 GO:0032259
110.070.6223.230.120.752dekA GO:0004164 GO:0008152 GO:0008168 GO:0016740 GO:0017183 GO:0032259 GO:0050843
120.070.6263.110.130.751vhvB GO:0004164 GO:0008152 GO:0008168 GO:0016740 GO:0017183 GO:0032259
130.070.6013.330.090.733i4tA GO:0004164 GO:0008152 GO:0008168 GO:0017183 GO:0032259
140.070.5753.810.120.754e16A GO:0008152 GO:0008168 GO:0009236 GO:0016740 GO:0032259 GO:0046026 GO:0055114
150.060.3726.400.060.654fb5A GO:0008152 GO:0016491 GO:0055114
160.060.3126.210.050.531o68B GO:0003824 GO:0003864 GO:0005737 GO:0015940 GO:0016740 GO:0046872
170.060.2706.470.030.453q0qA GO:0003723 GO:0003730 GO:0005737 GO:0006417 GO:0010494 GO:0010608 GO:0031965 GO:0034063 GO:0043488 GO:0044822 GO:0048471 GO:0051983 GO:0060964 GO:1900246 GO:2000637
180.060.2885.800.050.461o66E GO:0003824 GO:0003864 GO:0005737 GO:0015940 GO:0016740 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0070677
GO-Score 0.83
Biological Processes GO:0000453
GO-Score 0.83
Cellular Component GO:0005737
GO-Score 0.83

(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.