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I-TASSER results for job id Rv1004c

[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 1 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
10.22 12 2uv8G FMN Rep, Mult 99,100,101,102,103,151,153,182,206,232,235,236,265,266,295,296,299
20.04 2 3lw51 CLA Rep, Mult 351,354,355
30.04 2 2z6jB TUI Rep, Mult 102,153,155,182,183,206,208,215,231,237,238
40.04 2 1rmgA MAN Rep, Mult 29,30
50.02 1 3ucpA MG Rep, Mult 224,227,230
60.02 1 1o94B SF4 Rep, Mult 123,125,159,160,161,164,165,166
70.02 1 1hri3 S57 Rep, Mult 401,402
80.02 1 3u1iA III Rep, Mult 13,14
90.02 1 1djnA SF4 Rep, Mult 85,88,89,90,91,92,95,96,97
100.02 1 2vc9A CA Rep, Mult 325,328,329,332,334
110.02 1 3pchM CHB Rep, Mult 378,380,384
120.02 1 3pcaM DHB Rep, Mult 365,371
130.02 1 2vn4A MAN Rep, Mult 69,70

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
10.0672z6iB0.5103.100.0690.5801.3.1.9102,121,206
20.0601me7A0.4624.110.0570.5631.1.1.205244,264,343
30.0601bxnE0.4245.190.0570.5784.1.1.39153
40.0602vkzG0.9302.100.0530.9982.3.1.38,3.1.2.14108,124
50.0603bq5A0.4725.700.0490.6712.1.1.14NA
60.0601djnA0.4735.090.0610.6251.5.8.2,1.5.99.7NA
70.0601y8bA0.4455.590.0430.6232.3.3.9NA
80.0601e1cA0.4496.300.0620.6735.4.99.2NA
90.0602uv8G0.9312.100.0480.9982.3.1.86NA
100.0602gjlA0.5173.140.0780.5871.13.12.16296
110.0601bxnA0.4245.200.0570.5784.1.1.39NA
120.0603bw4A0.5113.460.1040.5921.7.3.1245,276
130.0601nvmA0.4564.610.1140.5854.1.3.38NA
140.0603bg3A0.4705.250.0580.6406.4.1.1NA
150.0602tmdA0.4735.030.0610.6231.5.8.2NA
160.0601nf7A0.4684.190.0530.5701.1.1.205NA
170.0602qf7A0.4545.600.0380.6306.4.1.1NA
180.0602epoB0.4505.790.0310.6493.2.1.52NA
190.0601reqA0.4516.230.0540.6715.4.99.2NA
200.0603bicA0.4856.070.0500.7145.4.99.2NA

(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
00.070.5263.080.070.593bo9A GO:0003824 GO:0004318 GO:0016491 GO:0018580 GO:0055114
10.070.5173.140.080.592gjlA GO:0003824 GO:0004497 GO:0016491 GO:0018580 GO:0055114
20.070.5073.380.070.594iqlA GO:0000166 GO:0003824 GO:0018580 GO:0055114
30.070.5203.390.100.614q4kA GO:0000166 GO:0003824 GO:0018580 GO:0055114
40.070.5103.560.110.593bw2A GO:0000166 GO:0003824 GO:0018580 GO:0051213 GO:0055114
50.060.5233.030.070.592z6iB GO:0000166 GO:0003824 GO:0004318 GO:0016491 GO:0018580 GO:0051213 GO:0055114
60.060.3355.960.070.503ihjA GO:0003824 GO:0004021 GO:0005739 GO:0005759 GO:0006103 GO:0008483 GO:0008652 GO:0009058 GO:0016740 GO:0030170 GO:0042851 GO:0042853
70.060.3416.830.040.553etcB GO:0003824 GO:0008152
80.060.2168.000.050.403omlA GO:0003824 GO:0004300 GO:0005777 GO:0006629 GO:0006631 GO:0006635 GO:0008152 GO:0016491 GO:0016616 GO:0016829 GO:0033540 GO:0042803 GO:0055114 GO:0080023
90.060.2877.570.030.511ng9A GO:0000018 GO:0000166 GO:0003677 GO:0003684 GO:0005524 GO:0005829 GO:0006281 GO:0006298 GO:0006974 GO:0008301 GO:0016887 GO:0030983 GO:0032136 GO:0032300 GO:0042802 GO:0043531
100.060.2847.190.030.485flmA GO:0001047 GO:0001055 GO:0003677 GO:0003899 GO:0005665 GO:0005719 GO:0006351 GO:0006366 GO:0016740 GO:0016779
110.060.2577.140.030.424mz0B GO:0003824 GO:0008152 GO:0016740 GO:0031177 GO:0046872
120.060.2917.650.040.535iy6A GO:0000398 GO:0000974 GO:0001055 GO:0001172 GO:0003677 GO:0003899 GO:0003968 GO:0005634 GO:0005654 GO:0005665 GO:0005730 GO:0006283 GO:0006351 GO:0006353 GO:0006355 GO:0006366 GO:0006367 GO:0006368 GO:0006370 GO:0008543 GO:0010467 GO:0016740 GO:0016779 GO:0031047 GO:0031625 GO:0033120 GO:0035019 GO:0042795 GO:0044822 GO:0046872 GO:0050434
130.060.2596.550.050.413b4xA GO:0004497 GO:0005506 GO:0005737 GO:0016491 GO:0016705 GO:0020037 GO:0046872 GO:0055114
140.060.2547.670.040.451pxyB GO:0003779 GO:0005737 GO:0005856 GO:0007623 GO:0046872
150.060.2517.100.050.424mz0A GO:0003824 GO:0008152 GO:0016740 GO:0031177 GO:0046872
160.060.2756.920.040.452pffB GO:0003824 GO:0004312 GO:0004313 GO:0004314 GO:0004318 GO:0004319 GO:0004320 GO:0004321 GO:0005811 GO:0005829 GO:0005835 GO:0006629 GO:0006631 GO:0006633 GO:0008152 GO:0016295 GO:0016296 GO:0016297 GO:0016409 GO:0016491 GO:0016740 GO:0016787 GO:0016829 GO:0019171 GO:0042759 GO:0047451 GO:0055114
170.060.2446.950.050.413tzwA GO:0003824 GO:0005618 GO:0005829 GO:0005886 GO:0008152 GO:0009058 GO:0016740 GO:0016747 GO:0016788 GO:0019367 GO:0031177 GO:0034081 GO:0040007 GO:0051260 GO:0071768 GO:0071769
180.060.2537.200.030.434ryaA GO:0005215 GO:0006810
190.060.2297.460.020.404qbuA GO:0003824 GO:0008152 GO:0016740 GO:0031177
200.060.2987.600.050.524hnxA GO:0004596 GO:0005737 GO:0006474 GO:0017196 GO:0022626 GO:0031415 GO:0031416
210.060.2225.590.040.312ghiA GO:0000166 GO:0005524 GO:0006810 GO:0016020 GO:0016021 GO:0016887 GO:0042626 GO:0055085
220.060.2267.270.060.384trtA GO:0003677 GO:0003887 GO:0005737 GO:0006260 GO:0008408 GO:0009360 GO:0016740 GO:0016779 GO:0071897 GO:0090305
230.060.2387.400.030.422g6gA GO:0004553 GO:0009254 GO:0019867


Consensus prediction of GO terms
 
Molecular Function GO:0016703 GO:0036094 GO:1901265
GO-Score 0.58 0.37 0.37
Biological Processes GO:0044710
GO-Score 0.58
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.