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I-TASSER results for job id Rv3655c

[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
10.13 9 2fieA A74 Rep, Mult 7,8,10,11,12,14,15,16,19,20,23,24,27,108
20.10 6 2wbbH RO3 Rep, Mult 34,37,38,40,49,50,53,54,55,56
30.06 4 3erzD HG Rep, Mult 41,45,49
40.04 3 5e3kB CO3 Rep, Mult 35,39
50.04 3 2i0mA ZN Rep, Mult 32,36
60.03 2 4khyA CA Rep, Mult 39,42
70.03 2 1h9mA MOO Rep, Mult 76,77,80
80.01 1 1qb4A MN Rep, Mult 2,32
90.01 1 3h0nA ZN Rep, Mult 115,116,117
100.01 1 1htwA MG Rep, Mult 44,45
110.01 1 5jreH ADE Rep, Mult 34,35,91
120.01 1 1nv0A PO4 Rep, Mult 19,20,22,23,86,87
130.01 1 4mhlA ARF Rep, Mult 25,29
140.01 1 5hzzB MN Rep, Mult 29,32

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
10.0601hxgA0.5504.700.0680.9044.2.3.9,4.1.99.79
20.0602j5cB0.5144.460.0340.8244.2.3.-NA
30.0602iw2A0.5573.800.0250.8403.4.13.9NA
40.0601pv9B0.5063.790.0630.7603.4.13.997
50.0602oknA0.5573.800.0250.8403.4.13.9NA
60.0601o0xA0.5333.770.1070.8003.4.11.18NA
70.0601hm7B0.5264.220.0710.8324.2.3.7,4.6.1.5NA
80.0601n1zA0.5234.920.0330.9285.5.1.8NA
90.0601qxyA0.5293.750.0780.8083.4.11.1830,77,125
100.0601fuiA0.5154.340.0620.8725.3.1.2536,51
110.0603kb9A0.5554.790.0970.9524.2.3.37NA
120.0602hb6A0.5254.700.0730.9123.4.11.1NA
130.0602hb6B0.5254.700.0730.9123.4.11.134,39
140.0604matA0.5343.810.0650.8163.4.11.1827
150.0601jawA0.5603.820.0570.8483.4.11.9NA
160.0602qvrA0.5673.690.0620.8483.1.3.11NA
170.0601ftaA0.5553.930.0430.8723.1.3.11NA
180.0603ctzA0.5673.840.0410.8483.4.11.9NA
190.0602zsgA0.5423.640.0690.8083.4.11.997

(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
00.120.5573.800.030.842iw2A GO:0004177 GO:0004181 GO:0006508 GO:0006520 GO:0008233 GO:0008237 GO:0016787 GO:0016805 GO:0030145 GO:0030574 GO:0046872 GO:0070062 GO:0102009
10.080.5063.790.060.761pv9B GO:0005737 GO:0006508 GO:0008233 GO:0008237 GO:0016787 GO:0016805 GO:0046872 GO:0102009
20.070.5733.610.080.864r60B GO:0016787 GO:0046872
30.070.5894.010.070.874s2rP GO:0004177 GO:0006508 GO:0016787 GO:0046872
40.070.5643.800.070.854pv4A GO:0004177 GO:0006508 GO:0016787 GO:0030145 GO:0046872
50.070.5673.840.040.853ctzA GO:0004177 GO:0005737 GO:0006508 GO:0008233 GO:0008237 GO:0010815 GO:0016787 GO:0030145 GO:0042803 GO:0046872 GO:0070006 GO:0070062
60.070.5443.660.030.794zwuA GO:0004063 GO:0006508 GO:0008233 GO:0008235 GO:0008237 GO:0009636 GO:0016311 GO:0016787 GO:0016795 GO:0016805 GO:0046872 GO:0047862 GO:0102009
70.070.5443.660.040.793l24B GO:0004063 GO:0006508 GO:0008233 GO:0008235 GO:0008237 GO:0009636 GO:0016311 GO:0016787 GO:0016795 GO:0016805 GO:0046872 GO:0047862 GO:0102009
80.070.5493.500.030.803rvaA GO:0006508 GO:0008233 GO:0008235 GO:0008237 GO:0016787 GO:0016795 GO:0016805 GO:0046872 GO:0102009
90.070.5193.930.080.801pv9A GO:0005737 GO:0006508 GO:0008233 GO:0008237 GO:0016787 GO:0016805 GO:0046872 GO:0102009
100.070.5463.800.070.854fukA GO:0004177 GO:0005737 GO:0006508 GO:0008233 GO:0008235 GO:0016787 GO:0022626 GO:0046872 GO:0070006 GO:0070084
110.070.4943.920.070.744fkcA GO:0004177 GO:0006508 GO:0016787 GO:0046872
120.070.5383.670.090.804egeA GO:0016787 GO:0046872
130.070.5643.730.040.843ig4A GO:0004177 GO:0006508 GO:0016787 GO:0030145 GO:0046872
140.070.4365.020.060.793ct9B GO:0006508 GO:0006526 GO:0008152 GO:0008237 GO:0008270 GO:0008777 GO:0016787 GO:0043171 GO:0070573
150.060.5533.650.080.823q6dA GO:0006508 GO:0016787 GO:0016805 GO:0046872 GO:0102009
160.060.3204.750.030.584m05B GO:0016491 GO:0046872 GO:0050587 GO:0055114
170.060.5443.610.060.812howA GO:0016787
180.060.5623.800.060.852bh3A GO:0004177 GO:0005737 GO:0005829 GO:0006508 GO:0008233 GO:0008235 GO:0008237 GO:0016787 GO:0030145 GO:0042802 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0008238 GO:0046914
GO-Score 0.46 0.36
Biological Processes GO:0019538
GO-Score 0.59
Cellular Component GO:0070062 GO:0005737
GO-Score 0.12 0.08

(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.