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I-TASSER results for job id Rv0138

[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
10.43 105 5stdB UNN Rep, Mult 26,46,48,61,62,65,95,97,99,110,112,114,127,129,131
20.04 10 2inxA FFP Rep, Mult 18,22,46,95,112,114,127,129
30.02 6 4xbtC 3ZQ Rep, Mult 46,65,97,99,110,131
40.02 5 5bvbB DOG Rep, Mult 23,26,34,46,61,62,65,69,73,95,108,112,131,137
50.01 2 1oh00 III Rep, Mult 12,16,47,48,79,80,81,82,83,84,85,90,92,94,95,110,111,113,115,131,132,133,134,135,136
60.01 2 3juqA AJD Rep, Mult 31,34,58,61,62,65,69,73,112,129
70.01 2 4xbyC 3ZS Rep, Mult 26,44,62,127
80.00 1 3f8hA CA Rep, Mult 30,32
90.00 1 2bmo0 III Rep, Mult 17,21,24,25,28,29,30,31,32,33,36,37,72,74,75,76,77,78,96,98,100,105,107

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
10.1881hkxA0.6022.900.0990.7662.7.11.1717,25
20.1633e99A0.6312.800.0980.7721.14.12.1018,24
30.1621o7hB0.6562.710.0700.8021.14.12.1226,37
40.1373gzxB0.6512.820.1120.8021.14.12.18NA
50.1134stdA0.7272.640.0890.8744.2.1.9444
60.1111e3vB0.6282.510.1090.7545.3.3.138
70.0961buqA0.5942.650.0970.7315.3.3.1NA
80.0601kb0A0.4494.610.0210.7071.1.99.-96
90.0608choA0.6401.930.1060.7255.3.3.125,35,59
100.0603ecqB0.4525.010.0670.7843.2.1.9734
110.0603i4zA0.4484.590.0970.7372.5.1.34131
120.0601z45A0.4544.980.0210.7435.1.3.2,5.1.3.3109,111
130.0601j0mA0.4665.260.0710.8144.2.2.1258
140.0601i8qA0.4675.300.0810.8084.2.2.1NA
150.0602d0vA0.4974.550.0550.7431.1.99.8NA
160.0601sa3A0.4534.390.0310.7013.1.21.4NA
170.0601kitA0.4454.980.0710.7193.2.1.18NA
180.0601kv9A0.4554.540.0640.6951.1.99.-96
190.0603elqB0.4484.560.0480.6892.8.2.22NA
200.0601cb8A0.4535.220.0690.7724.2.2.5126
210.0602ux0A0.5992.940.0770.7602.7.11.1746
220.0601nu3B0.6312.500.1190.7493.3.2.8NA
230.0601lrwC0.4984.650.0620.7491.1.99.8NA
240.0603en1B0.6492.870.1120.8021.14.12.3,1.14.12.11NA
250.0602wyhA0.4465.000.0510.7493.2.1.2421
260.0602v7oA0.3155.090.0280.5332.7.11.17NA

(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
00.260.6362.280.120.755cxoB GO:0016787
10.240.6732.630.110.814l8pA GO:0016829 GO:0033988
20.230.6922.270.110.803a76B GO:0009636 GO:0016829 GO:0042597
30.230.6792.640.100.814r9kC GO:0016787 GO:0018744
40.200.6162.700.180.751z1sA GO:0017000
50.200.7272.640.090.874stdA GO:0006582 GO:0016829 GO:0030411 GO:0042438 GO:0043581
60.190.6472.460.120.774xbxC GO:0016787 GO:0018744
70.190.6352.430.100.753t8nB GO:0004769 GO:0006629 GO:0008202 GO:0016853
80.170.6092.470.090.742bngC GO:0004301 GO:0005886 GO:0016787 GO:0033963 GO:0097176
90.170.6562.790.110.804l8oA GO:0016829 GO:0033988
100.160.5903.030.100.744cdlA GO:0004769 GO:0006629 GO:0008202 GO:0016853
110.150.6412.370.140.763wmdB GO:0016853
120.140.5942.650.100.731buqA GO:0004769 GO:0005622 GO:0006629 GO:0006810 GO:0008202 GO:0016853
130.060.3435.100.040.572r2iA GO:0001750 GO:0005509 GO:0005886 GO:0007601 GO:0007602 GO:0008048 GO:0030249 GO:0031282 GO:0031284 GO:0046872 GO:0050896 GO:0071277
140.060.3855.410.060.695d80B GO:0000166 GO:0000221 GO:0000329 GO:0003677 GO:0004518 GO:0004519 GO:0005524 GO:0005773 GO:0005774 GO:0006314 GO:0006810 GO:0006811 GO:0007035 GO:0012505 GO:0015991 GO:0015992 GO:0016020 GO:0016539 GO:0016787 GO:0016820 GO:0030908 GO:0033178 GO:0044267 GO:0046034 GO:0046961 GO:0090305
150.060.3065.510.030.533alnA GO:0000165 GO:0000166 GO:0004672 GO:0004674 GO:0004702 GO:0004713 GO:0005524 GO:0005634 GO:0005737 GO:0005829 GO:0006468 GO:0006915 GO:0007165 GO:0007254 GO:0009611 GO:0016301 GO:0016310 GO:0016740 GO:0018108 GO:0035897 GO:0038095 GO:0071260 GO:2000672
160.060.3085.430.050.553bvcA GO:0046872
170.060.2975.470.030.553csqD GO:0003824 GO:0006508 GO:0008152 GO:0008233 GO:0008237 GO:0016787 GO:0016798 GO:0019012 GO:0019076 GO:0019835 GO:0042742 GO:0046718 GO:0046872 GO:0071555 GO:0098023
180.060.3485.770.020.652refA GO:0003824 GO:0008080 GO:0008152 GO:0016740 GO:0031177
190.060.2485.100.010.423qz6A GO:0003824 GO:0046872
200.060.2695.130.030.461xx6A GO:0000166 GO:0004797 GO:0005524 GO:0005737 GO:0006259 GO:0008270 GO:0009157 GO:0016301 GO:0016310 GO:0016740 GO:0046872 GO:0071897


Consensus prediction of GO terms
 
Molecular Function GO:0016836 GO:0004301
GO-Score 0.49 0.45
Biological Processes GO:0042221 GO:0044249 GO:0016999
GO-Score 0.46 0.40 0.40
Cellular Component GO:0044464
GO-Score 0.38

(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.