[Home] [Server] [About] [Statistics] [Annotation]

I-TASSER results for job id Rv1593c

[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 3 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 10 3gz8D APR Rep, Mult 9,11,38,40,52,53,71,91,92,94,99,133
20.15 8 2a8rA POP Rep, Mult 11,38,51,52,53,67,71
30.11 4 3gz6B QNA Rep, Mult 165,182,185,203,207,208,209,211,212
40.06 4 2a8tB UUU Rep, Mult 11,37,38,49,51,52,53,67,71,99,130,132,133,136
50.05 2 3gz6A QNA Rep, Mult 180,182,183,186,187,190,209,210,233,234
60.05 3 2a8sA MN Rep, Mult 51,67,70,71
70.02 1 3i9x0 III Rep, Mult 4,5,7,8,54,56,57,59,60,85,87,89,98,100

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
10.2082yvmA0.4763.020.1420.5683.6.1.-38
20.1111xsbA0.4943.090.1260.6023.6.1.17NA
30.0672w4eA0.4632.770.1320.5423.6.1.1338
40.0602j5wA0.4046.390.0490.7371.16.3.1NA
50.0601h16A0.4205.710.0620.7082.3.1.54NA
60.0602jfgA0.3935.560.0520.6576.3.2.9NA
70.0603ff6A0.4075.850.0460.7086.4.1.2,6.3.4.14NA
80.0601q33A0.5003.380.1120.6023.6.1.138,51
90.0601hx3B0.4693.100.1180.5725.3.3.270
100.0601v8mA0.4593.080.1320.5473.6.1.1338,73
110.0602gb5A0.4442.830.1130.5253.6.1.227,52,58
120.0602pflA0.4175.740.0570.7032.3.1.54137,142
130.0601gqyB0.4005.560.0510.6576.3.2.8NA
140.0602a6tA0.4852.840.1240.5763.6.1.3070
150.0603hyqA0.4542.900.1240.5475.3.3.2NA
160.0602q9pA0.4202.640.1360.4873.6.1.52NA
170.0601gqqA0.3006.100.0460.5346.3.2.8NA
180.0602qb7A0.3915.510.0220.6523.6.1.11NA
190.0601mx9D0.3926.100.0370.6993.1.1.1NA
200.0602pnyA0.4643.360.0810.5895.3.3.237
210.0602ewbA0.4025.470.0290.6573.4.11.1,3.4.11.5NA
220.0601b0pA0.4126.150.0690.7121.2.7.1NA

(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
00.410.7962.600.310.925bs6D GO:0016787
10.370.8691.120.300.903gz6A GO:0016787
20.320.7352.200.260.832fmlA GO:0016787
30.220.4802.700.260.563gg6A GO:0000287 GO:0005829 GO:0009117 GO:0016787 GO:0034656 GO:0044715 GO:0044716 GO:0044717 GO:0046057 GO:0046067 GO:0046712 GO:0046872
40.210.5271.720.330.563gz8C GO:0016787
50.200.4542.320.200.523o8sA
60.170.5502.000.260.613i9xA GO:0016787
70.170.4713.010.180.552yyhA GO:0016787
80.130.4683.450.120.602kdvA GO:0005737 GO:0006402 GO:0016787 GO:0016818 GO:0034353 GO:0046872 GO:0050779
90.120.4703.040.170.575bonA GO:0005829 GO:0006203 GO:0008413 GO:0016787 GO:0017110 GO:0034656 GO:0035539 GO:0046872
100.120.4702.340.130.533dkuA GO:0016787
110.110.4773.170.140.583f13B GO:0016787
120.080.4643.200.150.561su2A GO:0000166 GO:0005524 GO:0016787
130.080.4852.580.150.563q4iA GO:0016787
140.070.5294.050.100.693fjyB GO:0016787
150.070.5063.970.100.643fjyA GO:0016787
160.070.4932.930.130.591xsaA GO:0000166 GO:0000302 GO:0004081 GO:0005525 GO:0005739 GO:0005759 GO:0006139 GO:0006915 GO:0008796 GO:0008803 GO:0016787
170.070.4793.270.120.582qkmB GO:0000166 GO:0000287 GO:0000290 GO:0000340 GO:0000932 GO:0003723 GO:0003727 GO:0005524 GO:0005634 GO:0005737 GO:0005829 GO:0005845 GO:0006397 GO:0010494 GO:0016787 GO:0030145 GO:0031087 GO:0046872 GO:0050072 GO:0098745
180.070.4802.600.160.551k2eA GO:0016787
190.070.4612.890.130.553fcmB GO:0016787


Consensus prediction of GO terms
 
Molecular Function GO:0046872 GO:0017110
GO-Score 0.45 0.45
Biological Processes GO:0046056 GO:0044282 GO:0046066 GO:0009181 GO:0009184 GO:0009154 GO:0046710 GO:0009155 GO:1901069
GO-Score 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45
Cellular Component GO:0044444
GO-Score 0.45

(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.