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I-TASSER results for job id Rv2990c

[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
10.49 31 1kpgA SAH Rep, Mult 28,29,58,59,60,79,80,84,106,107,108,124,125,126,129,130
20.02 1 1p91A SAM Rep, Mult 26,58,59,60,61,62,63,64,124,125,159,160,277
30.02 1 4er6A AW2 Rep, Mult 41,56,58,59,60,64,79,80,81,105,106,107,122,124,130,156,157,279

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
10.2062p35A0.6233.570.1210.7832.1.1.14458,76
20.1703g5tA0.7243.420.0900.8852.1.1.145133
30.1572iftA0.4683.230.1240.5522.1.1.5263,124
40.1523e05D0.5292.960.1010.6122.1.1.13292,102
50.1432h11B0.5853.570.1010.7172.1.1.6725,129
60.0952pxxA0.5473.160.1510.6433.4.24.71NA
70.0872ex4A0.5913.340.1270.7102.1.1.-128
80.0671f38A0.5233.020.1190.6082.1.1.-NA
90.0673e05B0.5282.920.1000.6082.1.1.132NA
100.0673hnrA0.5343.580.1430.6472.1.1.-NA
110.0672cl5A0.5263.080.1300.6192.1.1.6NA
120.0673bwmA0.5253.150.1300.6192.1.1.6NA
130.0663grzB0.4892.740.1630.5592.1.1.-NA
140.0601xxlA0.5973.850.1300.7452.1.1.-NA
150.0602qyoA0.5244.250.0840.6922.1.1.46NA
160.0602fk8A0.6444.550.1200.8572.1.1.-NA
170.0602o06A0.5423.910.0890.6852.5.1.1658,60,105
180.0603bgdA0.5813.730.1060.7202.1.1.67109,129
190.0601wznA0.5863.480.1000.6922.1.1.-NA
200.0601ri1A0.5943.640.1270.7272.1.1.5658
210.0601kpiA0.6734.430.1180.8882.1.1.79NA
220.0603lccA0.5743.260.1450.6892.1.1.-5,58,129
230.0601kyzE0.5643.940.1160.7172.1.1.68NA
240.0601im8A0.5833.470.1070.6992.1.1.-NA
250.0603c6mD0.5373.920.1090.6752.5.1.22NA
260.0601xcjA0.5693.850.1490.7132.1.1.25,124
270.0601kpgA0.6484.510.0940.8642.1.1.79NA
280.0602aovA0.6414.380.0640.8642.1.1.887
290.0601kywC0.5593.920.1020.7102.1.1.68NA
300.0603c6kD0.5373.910.1090.6752.5.1.2286,126
310.0601fp1D0.5523.670.0890.6892.1.1.-NA
320.0601ri5A0.5953.650.1270.7272.1.1.56NA

(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
00.270.7043.400.120.853mggB GO:0008168 GO:0016740 GO:0032259
10.270.7433.230.120.892yqzA GO:0008152 GO:0008168 GO:0032259 GO:0046872 GO:0051536 GO:0051539
20.270.6413.560.110.803ccfB GO:0008152 GO:0008168 GO:0016740 GO:0030798 GO:0032259
30.250.6583.340.120.793egeA GO:0008152 GO:0008168 GO:0032259
40.230.5453.640.160.673h2bB GO:0008168 GO:0016740 GO:0032259
50.220.5492.870.150.644qtuB GO:0000056 GO:0000447 GO:0005634 GO:0005730 GO:0005737 GO:0006364 GO:0008152 GO:0008168 GO:0008757 GO:0016435 GO:0016740 GO:0032259 GO:0070476
60.210.5823.750.160.711ve3B GO:0046872 GO:0051536 GO:0051539
70.210.6534.240.120.853kkzA GO:0046872 GO:0051536 GO:0051539
80.210.4963.070.100.585cm2Z GO:0000049 GO:0002098 GO:0005634 GO:0005737 GO:0005829 GO:0008152 GO:0008168 GO:0008198 GO:0016300 GO:0016706 GO:0030488 GO:0032259 GO:0055114
90.210.6663.910.100.834pneB GO:0008152 GO:0008168 GO:0016740 GO:0032259
100.200.5343.580.140.653hnrA GO:0008152 GO:0008168 GO:0008757 GO:0016740 GO:0032259
110.200.5713.470.130.692gs9A GO:0008152 GO:0008168 GO:0032259
120.190.4842.460.120.544iscA GO:0008168 GO:0008757 GO:0009312 GO:0009877 GO:0016740 GO:0032259
130.190.5233.020.120.611f38A GO:0006479 GO:0008168 GO:0008276 GO:0009236 GO:0016740 GO:0032259 GO:0046140
140.190.6434.360.110.834ineA GO:0000773 GO:0005737 GO:0006656 GO:0008152 GO:0008168 GO:0016740 GO:0032259 GO:0080101
150.190.6013.890.110.752gluA GO:0005737 GO:0008152 GO:0008168 GO:0008757 GO:0016740 GO:0032259
160.190.6384.550.100.843f4kA GO:0005737 GO:0008168 GO:0008757 GO:0016740 GO:0032259 GO:0046872 GO:0051536 GO:0051539
170.180.6514.330.100.843e7pA GO:0046872 GO:0051536 GO:0051539
180.180.6103.810.140.765je1A GO:0008168 GO:0016740 GO:0032259
190.180.5983.240.140.724qdkA GO:0005737 GO:0008168 GO:0008757 GO:0015979 GO:0015995 GO:0016740 GO:0032259 GO:0036068 GO:0046406
200.180.5903.910.130.724htfB GO:0008033 GO:0008168 GO:0016740 GO:0032259
210.170.5653.340.150.673sm3A GO:0008152 GO:0008168 GO:0016740 GO:0032259 GO:0046872
220.170.6213.810.150.794hg2B GO:0008152 GO:0008168 GO:0016740 GO:0032259
230.170.6093.660.140.741vl5A GO:0008152 GO:0008168 GO:0016740 GO:0032259
240.160.4913.430.130.593cggA GO:0008168 GO:0016740 GO:0032259
250.160.6943.680.090.883b5iA GO:0000287 GO:0008168 GO:0009944 GO:0010252 GO:0016740 GO:0032259 GO:0042802 GO:0046872 GO:0051749
260.160.6224.290.120.803busA GO:0008152 GO:0008168 GO:0016740 GO:0032259
270.150.5863.480.100.691wznA
280.150.5663.490.100.673dlcA GO:0008152 GO:0008168 GO:0016740 GO:0032259 GO:0046872 GO:0051536 GO:0051539
290.150.5923.750.110.722avnA GO:0008152 GO:0008168 GO:0016740 GO:0032259
300.140.5703.310.120.671vlmA GO:0005737 GO:0008152 GO:0008168 GO:0008757 GO:0032259
310.140.7443.680.100.951m6eX GO:0008168 GO:0016740 GO:0032259 GO:0046872
320.130.7303.430.120.912eg5E GO:0008168 GO:0009820 GO:0016740 GO:0032259
330.130.7393.690.080.945f2kA GO:0008168 GO:0032259
340.130.7403.470.100.932efjA GO:0008168 GO:0009820 GO:0016740 GO:0032259
350.130.5632.950.130.653dh0B GO:0005737 GO:0008757 GO:0032259 GO:0046872 GO:0051536 GO:0051539
360.080.6533.560.090.791p91A GO:0005737 GO:0006364 GO:0008168 GO:0008270 GO:0008989 GO:0016740 GO:0032259 GO:0046872 GO:0052911 GO:0070475
370.080.6644.500.100.881kpgA GO:0005737 GO:0005886 GO:0006629 GO:0008168 GO:0008610 GO:0008825 GO:0016740 GO:0032259 GO:0046500 GO:0071768
380.070.4832.880.110.563i9fB GO:0008152 GO:0008168 GO:0032259 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0051540 GO:0043169 GO:0008757
GO-Score 0.53 0.53 0.53
Biological Processes GO:0032259
GO-Score 0.77
Cellular Component
GO-Score

(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.