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I-TASSER results for job id Rv1167c

[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
10.08 10 1jt0C QNA Rep, Mult 19,50,51,52,53,54,57,58
20.07 11 4dw6A 0MN Rep, Mult 78,89,90,93,94,97,101,126,131,137,138,141,165,168,169,172,173,188
30.06 10 2uxhB QUE Rep, Mult 90,93,94,109,113,138,164,168,169,172
40.06 7 2yvhD NUC Rep, Mult 15,40,41,52,56,61,62
50.05 9 3whbA DCC Rep, Mult 67,70,71,74,97,100,109,114,123,126,127,131,132,134,135,158,159,161,162,165,169
60.05 9 3anpD DCC Rep, Mult 166,169,170,174,175,178
70.04 6 3angA DCC Rep, Mult 73,111,115,125,126,129,134,156,159,162,166,169
80.03 5 2uxpB CLM Rep, Mult 75,78,80,90,97,134,137,138,168
90.02 3 1jt00 III Rep, Mult 109,113,163,166,167,169,170,171,183,186,187,190,191,193,194
100.02 4 1jt6B DEQ Rep, Mult 108,173,174
110.02 4 3br5A RHQ Rep, Mult 67,70,71,74,77,100,101,104,109,134,168
120.01 2 5cw8B 55X Rep, Mult 28,100,101,106,113,134,162,165,168,172
130.01 1 2i10B NPO Rep, Mult 131,132,162
140.01 2 3q0wA LL5 Rep, Mult 77,81,89,90,93,94,97,137,138,141,145,165,191
150.01 1 2id3A CA Rep, Mult 82,144
160.01 1 3locA URA Rep, Mult 174
170.01 2 3angB DCC Rep, Mult 170,174,178,179,182,186
180.01 1 2uxiA G50 Rep, Mult 115,173
190.01 1 3lsjB COA Rep, Mult 89,150,189,192,193
200.01 1 2id3B CA Rep, Mult 43,47

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
10.0601v6yA0.3974.740.0840.6223.2.1.8NA
20.0602eqdA0.4695.160.0830.7663.2.1.151NA
30.0603c46B0.4925.330.0530.8312.7.7.6144,190
40.0602zuwC0.4554.370.0500.6772.4.1.21163
50.0602pziA0.4675.580.0630.7962.7.11.142
60.0601uasA0.4514.830.0670.7023.2.1.22NA
70.0602i2xA0.4985.060.0560.8162.1.1.9037
80.0603l4uA0.4524.960.0490.7113.2.1.20,3.2.1.3NA
90.0602e8yA0.4834.450.0670.7413.2.1.4121,25
100.0601b1yA0.4594.760.0430.7163.2.1.2NA
110.0601m7xB0.4555.030.0570.7212.4.1.1832
120.0601txzA0.4654.370.0480.6773.1.3.-69
130.0602c8nA0.4535.190.0540.7163.2.1.55NA
140.0603gbdA0.4835.010.0460.7715.4.99.1163
150.0602aaaA0.4645.230.0240.7563.2.1.1NA
160.0602ze0A0.4915.100.0450.7863.2.1.20NA
170.0603k1dA0.4525.540.0630.7712.4.1.1881,85,87
180.0601s46A0.4615.170.0770.7512.4.1.4NA
190.0603czkA0.4685.110.0440.7663.2.1.48NA

(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
00.400.9070.880.190.932zb9A GO:0003677 GO:0006351 GO:0006355
10.390.6403.610.140.863vuqC GO:0003677 GO:0006351 GO:0006355
20.290.7292.950.170.892fq4A GO:0003677 GO:0006351 GO:0006355
30.290.6783.180.140.883mnlA GO:0000976 GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355 GO:0042803
40.280.6393.610.180.874jl3C GO:0003677 GO:0006351 GO:0006355
50.260.6003.910.170.823b81A GO:0003677 GO:0006351 GO:0006355
60.250.6873.480.180.922id3A GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0046872
70.250.5624.380.130.822oerB GO:0003677 GO:0006351 GO:0006355
80.250.6443.570.150.864za6A GO:0003677
90.250.6454.000.090.893qbmA GO:0003677 GO:0003700 GO:0006351 GO:0006355
100.240.6973.070.170.862g3bA GO:0003677 GO:0006351 GO:0006355
110.240.6463.460.150.853whcA GO:0003677 GO:0005737 GO:0006351 GO:0006355 GO:0006629 GO:0006631 GO:0016042
120.240.6004.210.120.863c2bA GO:0003677 GO:0006351 GO:0006355
130.220.6793.140.060.863lwjA GO:0003677 GO:0006351 GO:0006355
140.220.6843.480.110.912f07A GO:0003677 GO:0006351 GO:0006355
150.210.6593.470.140.863bjbB GO:0003677 GO:0006351 GO:0006355
160.210.6413.630.120.882qibA GO:0003677 GO:0003700 GO:0006351 GO:0006355
170.200.6793.440.130.923angC GO:0003677 GO:0006351 GO:0006355
180.190.5924.180.080.853he0C GO:0003677 GO:0006351 GO:0006355
190.190.6693.500.120.885d1wD GO:0003677 GO:0006351 GO:0006355
200.180.5444.400.110.802q24B GO:0003677 GO:0006351 GO:0006355
210.180.5394.210.170.792qwtA GO:0003677 GO:0006351 GO:0006355
220.170.5954.310.130.864jykA GO:0000976 GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355 GO:0045892 GO:0045893
230.160.5754.280.170.852oi8A GO:0003677 GO:0006351 GO:0006355
240.150.5584.270.050.813ppbA GO:0003677 GO:0006351 GO:0006355
250.140.5264.010.120.723vvxA GO:0003677 GO:0006351 GO:0006355
260.130.5614.000.080.803egqA GO:0003677 GO:0006351 GO:0006355
270.130.5714.170.120.865f1jA GO:0003677 GO:0006351 GO:0006355
280.100.6393.920.140.884cgrA GO:0003677 GO:0006351 GO:0006355
290.090.5184.670.060.802o7tA GO:0003677 GO:0006351 GO:0006355
300.090.5894.340.060.873g7rB GO:0003677 GO:0003700 GO:0006351 GO:0006355
310.090.6363.770.140.862hyjA GO:0003677 GO:0003700 GO:0006351 GO:0006355
320.080.6463.620.100.893hggA GO:0003677 GO:0006351 GO:0006355
330.080.6143.860.080.841sgmA GO:0003677 GO:0006351 GO:0006355
340.080.6194.060.120.862uxhA GO:0003677 GO:0006351 GO:0006355
350.070.5634.070.120.792qkoB GO:0003677 GO:0006351 GO:0006355
360.070.5723.820.090.802raeA GO:0003677 GO:0006351 GO:0006355
370.070.5864.010.090.804gclB GO:0003677 GO:0005737 GO:0007049 GO:0009295 GO:0010974 GO:0043565 GO:0043590 GO:0051301 GO:0051302
380.070.5534.140.090.784pxiB GO:0003677 GO:0006351 GO:0006355
390.070.5663.810.080.774gctC GO:0000976 GO:0003677 GO:0003700 GO:0005737 GO:0005829 GO:0006355 GO:0007049 GO:0009295 GO:0010974 GO:0043565 GO:0043590 GO:0051301 GO:0051302


Consensus prediction of GO terms
 
Molecular Function GO:0044212 GO:0001071 GO:0042802 GO:0046983 GO:1990837
GO-Score 0.57 0.57 0.57 0.57 0.57
Biological Processes GO:0006355
GO-Score 0.87
Cellular Component GO:0044444
GO-Score 0.57

(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.