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

I-TASSER results for job id Rv0394c

[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
10.06 3 1iw7F MG Rep, Mult 164,204
20.06 3 3k6sC CA Rep, Mult 63,64,65,68,69,71
30.04 2 2yx4A GLN Rep, Mult 97,104,105
40.04 2 1tyeA UUU Rep, Mult 27,42,59
50.02 1 2qfnB OXY Rep, Mult 122,126
60.02 1 3psqB ZN Rep, Mult 186,190
70.02 1 3hycA MG Rep, Mult 22,236
80.02 1 1f61A MG Rep, Mult 56,119
90.02 1 3h7vA MG Rep, Mult 102,119,138
100.02 1 1o5qA MG Rep, Mult 102,144
110.02 1 2pjtA CA Rep, Mult 121,122
120.02 1 2ie7A CA Rep, Mult 180,181
130.02 1 4b92A ZN Rep, Mult 194,198
140.02 1 1bpyA MG Rep, Mult 138,140
150.02 1 2akaA III Rep, Mult 115,116,117,118
160.02 1 3v94F MG Rep, Mult 101,122
170.02 1 1aiiA ETA Rep, Mult 182,183
180.02 1 2c25A SIA Rep, Mult 11,25,57,58
190.02 1 3t1gA ZN Rep, Mult 102,106

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
10.0602ac1A0.4495.580.0490.7413.2.1.26NA
20.0601lrwC0.4695.500.0700.7571.1.99.831
30.0601y9mA0.4545.230.0790.7163.2.1.80NA
40.0601qksB0.5025.150.0300.7911.7.2.176
50.0603elqB0.4585.850.0850.7912.8.2.22125,130
60.0601jofA0.4655.480.0310.7615.5.1.5NA
70.0601cvmA0.4465.650.0200.7453.1.3.8NA
80.0601vcuB0.4345.990.0440.7573.2.1.18NA
90.0602vk6A0.4545.160.0340.7203.2.1.1824
100.0601z68A0.4795.370.0470.7613.4.21.-122
110.0602d0vA0.4715.580.0770.7871.1.99.8NA
120.0602agsA0.4525.470.0390.7413.2.1.18205
130.0602ecfA0.4535.320.0820.7283.4.14.5122
140.0602bixA0.4745.690.0600.7951.14.99.-7,210
150.0602h47H0.4525.840.0440.7821.4.99.4NA
160.0601kb0A0.4805.350.0560.7781.1.99.-NA
170.0602bklB0.4575.240.0390.7243.4.21.26NA
180.0601yniB0.4745.910.0500.8203.5.3.232
190.0601y4wA0.4545.170.0740.7113.2.1.80NA

(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
00.070.4795.610.050.803mvdL GO:0000793 GO:0003682 GO:0005085 GO:0005087 GO:0005634 GO:0005737 GO:0006607 GO:0007049 GO:0007067 GO:0007076 GO:0007346 GO:0007417 GO:0007419 GO:0022008 GO:0043547 GO:0046822 GO:0050767 GO:0051301
10.070.4905.490.050.822cn3A GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030245 GO:0033946 GO:0043263 GO:2000899
20.070.5045.620.070.844d9sA GO:0000785 GO:0003682 GO:0005085 GO:0005634 GO:0005737 GO:0005829 GO:0007165 GO:0009411 GO:0009649 GO:0009881 GO:0010224 GO:0018298 GO:0042803 GO:0043547 GO:0050896
30.070.4514.900.090.692cn2A GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030245 GO:0033946 GO:0043263 GO:2000899
40.070.4835.590.090.823b7fA GO:0016787
50.070.5025.250.050.815jwzA GO:0004553 GO:0005975 GO:0030246 GO:0030247
60.070.4444.760.070.672ebsB GO:0000272 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030245 GO:0033945
70.070.5155.410.080.841a12A GO:0000082 GO:0000790 GO:0000794 GO:0003677 GO:0003682 GO:0005085 GO:0005087 GO:0005634 GO:0005654 GO:0005737 GO:0007049 GO:0007052 GO:0007059 GO:0007067 GO:0007088 GO:0016032 GO:0031492 GO:0031965 GO:0042393 GO:0043547 GO:0051225 GO:0051301
80.070.4895.540.010.803of7A GO:0000054 GO:0000790 GO:0004871 GO:0005085 GO:0005087 GO:0005634 GO:0006407 GO:0006810 GO:0007049 GO:0007067 GO:0007165 GO:0019236 GO:0043547 GO:0051301
90.070.5075.280.070.825fkqA GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246 GO:0030247 GO:0030248
100.070.4795.120.080.753kciA GO:0004842 GO:0005085 GO:0005634 GO:0005654 GO:0005737 GO:0005743 GO:0005814 GO:0005856 GO:0006281 GO:0006303 GO:0006886 GO:0006974 GO:0007283 GO:0008270 GO:0016020 GO:0016567 GO:0016874 GO:0016925 GO:0031625 GO:0032183 GO:0042787 GO:0043547 GO:0046872
110.070.5055.340.050.824lgnA GO:0004553 GO:0005975 GO:0030246 GO:0030247 GO:0030248
120.070.4795.280.090.764o2wA GO:0004842 GO:0005085 GO:0005086 GO:0005737 GO:0005794 GO:0005829 GO:0006810 GO:0010507 GO:0016020 GO:0016567 GO:0016874 GO:0021702 GO:0031175 GO:0043547 GO:0050885
130.070.4985.070.050.774l1mA GO:0004842 GO:0005085 GO:0005634 GO:0005654 GO:0005737 GO:0005743 GO:0005814 GO:0005856 GO:0006281 GO:0006303 GO:0006886 GO:0006974 GO:0007283 GO:0008270 GO:0016020 GO:0016567 GO:0016874 GO:0016925 GO:0031625 GO:0032183 GO:0042787 GO:0043547 GO:0046872
140.070.4765.060.060.754qamA GO:0001750 GO:0005085 GO:0005737 GO:0005794 GO:0005813 GO:0005815 GO:0005856 GO:0005929 GO:0006886 GO:0007601 GO:0030030 GO:0036064 GO:0036126 GO:0042073 GO:0042384 GO:0042995 GO:0043547 GO:0044822 GO:0050896 GO:0072372
150.070.4525.470.120.741jtdB GO:0046872
160.070.4445.880.050.774d4oA GO:0000226 GO:0002098 GO:0005506 GO:0005634 GO:0005737 GO:0007017 GO:0007117 GO:0008270 GO:0009055 GO:0017183 GO:0046872
170.060.4155.810.060.704kc7A GO:0004553 GO:0005576 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0031222 GO:0046558 GO:0046872
180.060.3666.320.070.662f02A GO:0000166 GO:0005524 GO:0005975 GO:0005988 GO:0009024 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0019512 GO:2001059


Consensus prediction of GO terms
 
Molecular Function GO:0033946 GO:0003682 GO:0005087 GO:0009881 GO:0042803
GO-Score 0.13 0.13 0.07 0.07 0.07
Biological Processes GO:2000899 GO:0043547 GO:0030245 GO:0010224 GO:0007419 GO:0007076 GO:0050767 GO:0018298 GO:0006607 GO:0007165 GO:0046822 GO:0009649 GO:0051301 GO:0007346
GO-Score 0.13 0.13 0.13 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07
Cellular Component GO:0043263 GO:0005634 GO:0000785 GO:0005829 GO:0000793
GO-Score 0.13 0.13 0.07 0.07 0.07

(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.