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I-TASSER results for job id Rv3421c

[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
10.07 2 4yduD ADP Rep, Mult 41,42,43,44,76,78,82,122
20.06 2 2vypA RH9 Rep, Mult 99,109,110,111,112,113,139,140,183,184
30.06 2 1yt3A ZN Rep, Mult 13,64
40.06 2 2ivoA WO4 Rep, Mult 77,78,81
50.06 2 3eksA CY9 Rep, Mult 99,101,102,105,109,139,140,184
60.03 1 3mr2A MG Rep, Mult 13,120,125
70.03 1 2iocB MN Rep, Mult 13,120
80.03 1 3i9dL MG Rep, Mult 120,122
90.03 1 3m6gA LO3 Rep, Mult 13,14,80,83,84,87,88
100.03 1 3gocA MG Rep, Mult 13,203
110.03 1 1m1bA MG Rep, Mult 120,200

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
10.0662ivpA0.6693.500.1810.8443.4.24.5715,74
20.0663enoA0.6783.560.1460.8633.4.24.5774
30.0601hkgA0.5544.900.1070.8482.7.1.1NA
40.0603jvpD0.5434.640.0820.7872.7.1.1689
50.0603b8aX0.5614.860.1060.8582.7.1.1NA
60.0602hoeA0.5684.660.1080.8442.7.1.59NA
70.0603flcX0.5744.380.0920.7962.7.1.3054
80.0602w41B0.5414.300.0720.7632.7.1.30NA
90.0602uytA0.5394.730.0650.8202.7.1.5110
100.0602q2rA0.5395.090.1160.8442.7.1.2NA
110.0603f9mA0.5504.630.0810.8252.7.1.2NA
120.0601qhaA0.5624.700.0630.8342.7.1.1NA
130.0603hz6A0.5484.390.1030.7912.7.1.1779,82
140.0601woqA0.5544.680.1880.8252.7.1.63NA
150.0601zc6B0.5634.580.0790.8342.7.1.5913
160.0601q18A0.5454.560.0950.8202.7.1.2NA
170.0603mdqA0.5494.480.0940.8063.6.1.11NA
180.0603htvA0.5644.330.1040.8102.7.1.55NA
190.0602d4wA0.5544.260.1280.7722.7.1.3016,174
200.0603gbtA0.5354.260.0370.7542.7.1.1271
210.0602i7pB0.5364.310.0960.7822.7.1.3378

(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
00.500.8372.020.230.913zeuA GO:0002949
10.470.8601.870.270.925br9C GO:0000408 GO:0002949
20.470.8121.690.300.883r6mA GO:0002949 GO:0005737 GO:0008033
30.460.8432.010.220.924yduC GO:0000408 GO:0002949 GO:0005737 GO:0005829 GO:0006508 GO:0008033 GO:0008237 GO:0042802
40.320.7102.600.270.832a6aA GO:0000408 GO:0002949 GO:0005737 GO:0008033
50.130.6783.560.150.863enoA GO:0000166 GO:0002949 GO:0003824 GO:0004222 GO:0004674 GO:0004712 GO:0005506 GO:0005524 GO:0005737 GO:0006468 GO:0006508 GO:0008033 GO:0008152 GO:0008270 GO:0016301 GO:0016310 GO:0016740 GO:0016746 GO:0016747 GO:0046872 GO:0061711
60.110.6823.350.180.864yduB GO:0000287 GO:0000408 GO:0001948 GO:0002949 GO:0004222 GO:0005506 GO:0005737 GO:0005829 GO:0006508 GO:0008033 GO:0016740 GO:0016746 GO:0016747 GO:0042802 GO:0046872 GO:0061711
70.100.6713.430.180.842ivnA GO:0000049 GO:0000408 GO:0002949 GO:0003727 GO:0005737 GO:0008033 GO:0016740 GO:0016746 GO:0046872 GO:0061711
80.100.6743.670.160.873en9A GO:0000166 GO:0000408 GO:0002949 GO:0003824 GO:0004222 GO:0004672 GO:0004674 GO:0004712 GO:0005506 GO:0005524 GO:0005737 GO:0006468 GO:0006508 GO:0008033 GO:0008152 GO:0008270 GO:0016301 GO:0016310 GO:0016740 GO:0016746 GO:0016747 GO:0046872 GO:0061711
90.070.5924.050.150.783venA GO:0000166 GO:0003824 GO:0005506 GO:0005524 GO:0009058 GO:0016743 GO:0016787 GO:0016874 GO:0017000 GO:0046872 GO:1901121 GO:1901133
100.070.6733.630.160.864k25A GO:0002949 GO:0004222 GO:0005739 GO:0006508 GO:0008033 GO:0016740 GO:0016746 GO:0016747 GO:0046872 GO:0061711 GO:0072670
110.060.3975.230.100.615dwzE GO:0003824 GO:0008152 GO:0044550
120.060.3765.220.070.621f05A GO:0003824 GO:0004801 GO:0005634 GO:0005737 GO:0005829 GO:0005975 GO:0005999 GO:0006002 GO:0006098 GO:0009052 GO:0016740 GO:0019682 GO:0030246 GO:0043231 GO:0048029 GO:0070062
130.060.3585.540.050.604e21B GO:0004616 GO:0006098 GO:0016491 GO:0055114
140.060.2845.470.050.495abbA GO:0005622 GO:0005886 GO:0005887 GO:0006605 GO:0006810 GO:0006886 GO:0015031 GO:0016020 GO:0016021 GO:0043952 GO:0065002
150.060.3065.520.040.534clqA GO:0000447 GO:0000472 GO:0000480 GO:0003723 GO:0003824 GO:0003963 GO:0004521 GO:0005634 GO:0005654 GO:0005730 GO:0006364 GO:0006396 GO:0008047 GO:0030686 GO:0031167 GO:0042254 GO:0043085
160.060.3264.050.030.442du2A GO:0000166 GO:0003824 GO:0010181 GO:0016491 GO:0046872 GO:0055114
170.060.2866.390.050.552yvkA GO:0005737 GO:0008652 GO:0009086 GO:0016853 GO:0019284 GO:0019509 GO:0044237 GO:0044249 GO:0046523
180.060.2515.750.060.454qi1A GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0015992 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
190.060.3014.830.100.473umbA GO:0008152 GO:0016787 GO:0019120


Consensus prediction of GO terms
 
Molecular Function GO:0042802 GO:0008237
GO-Score 0.46 0.46
Biological Processes GO:0002949 GO:0006508
GO-Score 0.95 0.46
Cellular Component GO:0000408 GO:0005829
GO-Score 0.81 0.46

(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.