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I-TASSER results for job id Rv1864c

[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
10.05 3 4oicB MN Rep, Mult 95,97
20.05 3 1sijA FES Rep, Mult 70,71,72,74,75,76,77,79
30.03 2 1jp4A MG Rep, Mult 71,116
40.03 2 4uc1A Z0P Rep, Mult 228,231,235
50.03 2 1c3xB CA Rep, Mult 112,116
60.03 2 2wse1 CLA Rep, Mult 172,175
70.02 1 3toyA CA Rep, Mult 238,241
80.02 1 2h2sA SEK Rep, Mult 28,30,188
90.02 1 3zs0C UUU Rep, Mult 117,123
100.02 1 3s7wA AZI Rep, Mult 146,179,181
110.02 1 3fahA GOL Rep, Mult 156,160,161
120.02 1 1g42A CP2 Rep, Mult 74,75
130.02 1 2xb2C III Rep, Mult 87,165
140.02 1 4mjtA ZN Rep, Mult 97,99
150.02 1 2zo5A HEC Rep, Mult 111,113,151,154,155,158,159,162,164,167,168,172
160.02 1 1n1lB III Rep, Mult 46,187,189,191
170.02 1 3bk7A SF4 Rep, Mult 111,117,118,119,120,121
180.02 1 2bq8X ZN Rep, Mult 132,139
190.02 1 3kviA FAH Rep, Mult 228,229
200.02 1 5lopA MG Rep, Mult 236,237

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
10.0602e1qA0.3576.350.0630.6451.17.3.2,1.17.1.4NA
20.0601zj9B0.3926.050.0590.6971.8.7.131
30.0601cb7B0.3835.840.0360.6375.4.99.1144
40.0601k1dA0.3975.930.0410.6693.5.2.-NA
50.0603ebgA0.3836.160.0590.6733.4.11.-NA
60.0601vlbA0.3476.630.0190.6531.2.99.7137,175
70.0601ynyB0.3966.060.0580.6813.5.2.2NA
80.0601ti2A0.3966.050.0450.6731.97.1.2NA
90.0603b9jI0.2785.600.0520.4581.17.1.4,1.17.3.2111,154
100.0601x6vA0.3895.640.0540.6452.7.1.25,2.7.7.495,110,149
110.0603b9jC0.3376.110.0350.6021.17.3.2,1.17.1.4NA
120.0602ftwA0.3986.130.0270.6893.5.2.2NA
130.0603hm7B0.3866.060.0320.6773.5.2.5NA
140.0601gkpA0.3916.080.0450.6733.5.2.2185
150.0601zj8A0.3876.100.0690.6931.8.7.1149,173
160.0602ckjA0.3156.310.0310.5581.17.1.4,1.17.3.2NA
170.0602r9vA0.3845.970.0860.6533.6.3.14171
180.0601ti6A0.3646.560.0290.6731.97.1.2NA
190.0601nfgA0.3956.130.0460.6813.5.2.2NA

(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
00.360.7222.390.240.821o65A GO:0003824 GO:0005829 GO:0009636 GO:0030151 GO:0030170
10.180.5032.900.150.601oruA GO:0003824 GO:0030151 GO:0030170
20.060.4066.430.080.744he8G GO:0005886 GO:0008137 GO:0016020 GO:0016021 GO:0016491 GO:0042773 GO:0048038 GO:0055114
30.060.4326.160.090.754he8I GO:0005886 GO:0006810 GO:0008137 GO:0016020 GO:0016021 GO:0016491 GO:0042773 GO:0048038 GO:0050136 GO:0055114
40.060.3306.240.030.584aahA GO:0005509 GO:0005886 GO:0015945 GO:0016020 GO:0016491 GO:0016614 GO:0030288 GO:0046872 GO:0052930 GO:0052931 GO:0052932 GO:0052933 GO:0055114
50.060.4315.720.040.711yiqA GO:0005509 GO:0009055 GO:0016020 GO:0016491 GO:0016614 GO:0020037 GO:0042597 GO:0046872 GO:0055114 GO:0070968
60.060.3526.250.010.624cvbA GO:0046872
70.060.3276.510.020.591kv9A GO:0005509 GO:0009055 GO:0016020 GO:0016491 GO:0016614 GO:0020037 GO:0030288 GO:0042597 GO:0046872 GO:0055114 GO:0070968
80.060.3006.170.040.542v6gA GO:0000166 GO:0003824 GO:0016491 GO:0047787 GO:0050662 GO:0055114
90.060.3936.030.050.674maeA GO:0005509 GO:0016020 GO:0016491 GO:0016614 GO:0052930 GO:0052931 GO:0052932 GO:0052933 GO:0052934 GO:0052935 GO:0052936 GO:0055114
100.060.3875.800.050.651lrwA GO:0005509 GO:0015945 GO:0016020 GO:0016491 GO:0016614 GO:0030288 GO:0042597 GO:0046872 GO:0052930 GO:0052931 GO:0052932 GO:0052933 GO:0055114
110.060.3786.040.070.651kb0A GO:0005509 GO:0009055 GO:0016020 GO:0016491 GO:0016614 GO:0020037 GO:0030288 GO:0042597 GO:0046872 GO:0055114
120.060.2976.600.030.552wtxD GO:0003824 GO:0003825 GO:0005829 GO:0005992 GO:0006970 GO:0006974 GO:0016740 GO:0016757 GO:0070415
130.060.3865.700.040.644tqoA GO:0005509 GO:0015946 GO:0016020 GO:0016614 GO:0018468 GO:0030288 GO:0046872 GO:0055114
140.060.3875.680.060.632d0vA GO:0005509 GO:0016020 GO:0016614 GO:0030288 GO:0046872 GO:0055114
150.060.3805.930.050.641w6sC GO:0005509 GO:0005886 GO:0015945 GO:0016020 GO:0016491 GO:0016614 GO:0030288 GO:0046872 GO:0052930 GO:0052931 GO:0052932 GO:0052933 GO:0055114
160.060.3496.120.040.611flgA GO:0005509 GO:0006069 GO:0016020 GO:0016491 GO:0016614 GO:0018468 GO:0030288 GO:0042597 GO:0046872 GO:0052934 GO:0052935 GO:0052936 GO:0055114
170.060.3096.600.040.582taaA GO:0003824 GO:0004556 GO:0005509 GO:0005576 GO:0005975 GO:0008152 GO:0009277 GO:0016052 GO:0016787 GO:0016798 GO:0030287 GO:0030428 GO:0031521 GO:0032163 GO:0043169 GO:0046872
180.060.2956.700.040.564pk1A GO:0007155 GO:0009279 GO:0016020 GO:0016021 GO:0019867 GO:0042802 GO:0043165 GO:0051205 GO:0071709 GO:1990063


Consensus prediction of GO terms
 
Molecular Function GO:0030170 GO:0003824 GO:0030151
GO-Score 0.48 0.48 0.48
Biological Processes GO:0044710 GO:0009636
GO-Score 0.36 0.36
Cellular Component GO:0071944 GO:0005829
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.