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I-TASSER results for job id Rv0349

[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
10.11 5 1bcpC ATP Rep, Mult 205,206
20.02 1 2iyfB UDP Rep, Mult 33,34,64,98,100,119,123,125,128
30.02 1 2uxiA G50 Rep, Mult 132,191
40.02 1 3gsiA MG Rep, Mult 31,161
50.02 1 4u5tA 3CG Rep, Mult 205,212
60.02 1 4gszA ZN Rep, Mult 52,55
70.02 1 2akwB MN Rep, Mult 145,155,158
80.02 1 2q7sA ZN Rep, Mult 46,55,141
90.02 1 2y00A 2CV Rep, Mult 194,200,204
100.02 1 1o5qA MG Rep, Mult 31,113
110.02 1 1kv8A PO4 Rep, Mult 168,188,189
120.02 1 3jskC FE2 Rep, Mult 93,185
130.02 1 4zb0A FRU Rep, Mult 197,198,199
140.02 1 3aj0A ZN Rep, Mult 46,57,132,155
150.02 1 1pnvB UUU Rep, Mult 2,3,14,106
160.02 1 3wmoP BCL Rep, Mult 217,218
170.02 1 2y02B 2CV Rep, Mult 191,194,200
180.02 1 2wyiB PG0 Rep, Mult 174,177

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
10.0602vg8A0.5235.310.0920.8492.4.1.218121,143
20.0601eg7A0.4805.810.0570.8406.3.4.3NA
30.0601ygpA0.5085.380.0700.8312.4.1.1NA
40.0601bu8A0.4535.930.0350.7943.1.1.3NA
50.0602c4mC0.5125.340.1020.8362.4.1.117
60.0601l7aA0.4455.550.0790.7493.1.1.72,3.1.1.4189
70.0602qllA0.4955.270.0320.8042.4.1.1NA
80.0601y8zA0.4855.670.0820.8272.4.1.26NA
90.0601ahpA0.5085.350.1120.8312.4.1.125,134
100.0602azdB0.5035.490.1210.8402.4.1.1121
110.0601sy7A0.4635.120.0570.7441.11.1.6NA
120.0602o6lB0.4614.230.0590.6482.4.1.17121,132
130.0603fvrA0.4525.410.0930.7533.1.1.689
140.0602r60A0.4915.360.0480.7902.4.1.14NA
150.0602c1zA0.4894.890.0540.7582.4.1.115121,145
160.0602gejA0.4895.330.0770.7852.4.1.57125
170.0601l7qA0.4555.500.0430.7443.1.1.1NA
180.0602a3lA0.4715.560.0300.7813.5.4.6NA
190.0601gz5A0.4755.180.0430.7672.4.1.15NA

(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
00.070.5235.310.090.852vg8A GO:0006805 GO:0008152 GO:0008194 GO:0009636 GO:0009651 GO:0009813 GO:0016740 GO:0016757 GO:0016758 GO:0035251 GO:0042178 GO:0043231 GO:0050505 GO:0052696 GO:0080043 GO:0080044
10.070.5184.900.070.793hbjA GO:0008152 GO:0009698 GO:0009813 GO:0016740 GO:0016757 GO:0016758
20.070.5144.360.080.742iyaA GO:0000166 GO:0008152 GO:0016740 GO:0016757 GO:0016758 GO:0016999
30.070.5034.770.090.753ia7A GO:0008152 GO:0016758 GO:0016999 GO:0046872
40.070.5044.940.050.794relA GO:0000166 GO:0008152 GO:0016740 GO:0016757 GO:0016758
50.070.4894.890.050.762c1zA GO:0008152 GO:0009718 GO:0016740 GO:0016757 GO:0016758 GO:0033303 GO:0033330 GO:0033485 GO:0047213
60.070.5074.490.110.744m7pA GO:0008152 GO:0016740 GO:0016757 GO:0016758 GO:0016999 GO:0046677
70.070.4744.610.060.702o6lB GO:0001972 GO:0005783 GO:0005789 GO:0006629 GO:0008152 GO:0008202 GO:0008209 GO:0009813 GO:0015020 GO:0016020 GO:0016021 GO:0016740 GO:0016757 GO:0016758 GO:0031090 GO:0043231 GO:0052695 GO:0052696 GO:0070062
80.060.5015.040.050.792acvA GO:0000166 GO:0008152 GO:0016740 GO:0016757 GO:0016758
90.060.4944.750.070.752pq6A GO:0008152 GO:0016740 GO:0016757 GO:0016758
100.060.2646.430.040.513rpnA GO:0004364 GO:0004602 GO:0005102 GO:0005622 GO:0005739 GO:0005743 GO:0005759 GO:0005777 GO:0006749 GO:0015035 GO:0016020 GO:0016740 GO:0030855 GO:0043231 GO:0055114 GO:0070062 GO:0098869 GO:1901687
110.060.3085.270.010.513or5A GO:0005623 GO:0016491 GO:0045454 GO:0055114
120.060.2696.110.060.502l4hA GO:0001525 GO:0001933 GO:0001934 GO:0001954 GO:0002931 GO:0005509 GO:0005634 GO:0005654 GO:0005737 GO:0005783 GO:0005794 GO:0005813 GO:0005815 GO:0005856 GO:0005886 GO:0006302 GO:0006469 GO:0006915 GO:0006974 GO:0007026 GO:0007049 GO:0007113 GO:0007155 GO:0007283 GO:0007286 GO:0008022 GO:0008284 GO:0008285 GO:0008427 GO:0010977 GO:0016020 GO:0016324 GO:0017016 GO:0019901 GO:0030027 GO:0030154 GO:0030220 GO:0030291 GO:0030307 GO:0030335 GO:0030424 GO:0030425 GO:0030426 GO:0031122 GO:0031982 GO:0032433 GO:0032587 GO:0033630 GO:0038163 GO:0042127 GO:0042383 GO:0042995 GO:0043005 GO:0043025 GO:0043066 GO:0043085 GO:0043495 GO:0044325 GO:0045653 GO:0046872 GO:0048471 GO:0051092 GO:0051301 GO:0051302 GO:0051898 GO:0070062 GO:0070374 GO:0070886 GO:0071356 GO:0071363 GO:0071901 GO:0071902 GO:0071944 GO:0090004 GO:0090050 GO:0090314 GO:0097191 GO:1900026 GO:1990090 GO:2000256
130.060.2726.320.040.501cs6A GO:0001764 GO:0005886 GO:0007155 GO:0007158 GO:0007409 GO:0007411 GO:0007417 GO:0016020 GO:0031225 GO:0050839 GO:0071205 GO:0097090
140.060.2194.710.020.332lw4A GO:0003676 GO:0003677 GO:0005634 GO:0005654 GO:0005813 GO:0006351 GO:0006354 GO:0006355 GO:0006357 GO:0008023 GO:0008270 GO:0032784 GO:0045944 GO:0046872
150.060.2404.920.060.372e9kA GO:0001947 GO:0003779 GO:0004497 GO:0005634 GO:0007010 GO:0007507 GO:0008270 GO:0010735 GO:0016491 GO:0016709 GO:0019417 GO:0030042 GO:0043914 GO:0046872 GO:0055114 GO:0071949
160.060.1944.510.070.284v8mBZ GO:0002181 GO:0003735 GO:0005840 GO:0006412 GO:0015934 GO:0022625 GO:0042273
170.060.1955.440.040.334v8pBS GO:0002181 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0015934 GO:0022625 GO:0030529 GO:0042273
180.060.2233.620.090.293f51A GO:0003677 GO:0043565


Consensus prediction of GO terms
 
Molecular Function GO:0016757
GO-Score 0.58
Biological Processes GO:0009813 GO:0016999 GO:0009636 GO:0042178 GO:0052696 GO:0009651 GO:0009698
GO-Score 0.13 0.13 0.07 0.07 0.07 0.07 0.07
Cellular Component GO:0043231
GO-Score 0.07

(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.