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

I-TASSER results for job id Rv2733c

[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 2 1cgvA MAL Rep, Mult 69,70,83,101
20.06 2 3ke6A MN Rep, Mult 121,122,123,125
30.04 1 4jc0A FS5 Rep, Mult 33,34,36,37,70,71,72,73,104,178,180,182,184,185,187,188,191,222,265
40.03 1 2vl1B III Rep, Mult 295,296
50.03 1 2hufA 1BO Rep, Mult 39,227
60.03 1 3qf1A PZE Rep, Mult 191,194
70.03 1 3vmmA MG Rep, Mult 411,418
80.03 1 1kclA GLC Rep, Mult 88,91,95,96
90.03 1 2cxgA GLC Rep, Mult 73,74,75,78,106
100.03 1 1oltA UUU Rep, Mult 182,184,185,186,222,223,224,264,265,267,290,292,304,330,332,361,362,363,364
110.03 1 2a5hA UUU Rep, Mult 398,407
120.03 1 3ke6A MN Rep, Mult 121,271,330
130.03 1 1v3mA GAL Rep, Mult 70,71,72,77,124
140.03 1 1r3nF BIB Rep, Mult 304,419
150.03 1 4dwrA SO4 Rep, Mult 255,263,265,297

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
10.0601ojnA0.3877.220.0610.6214.2.2.1NA
20.0601edqA0.4036.420.0780.5903.2.1.14NA
30.0603k1dA0.3866.320.0360.5552.4.1.18NA
40.0602fhcA0.4176.460.0470.6153.2.1.4181,109,114
50.0609cgtA0.4096.330.0650.5942.4.1.1988
60.0601bf2A0.4006.550.0190.5963.2.1.68395
70.0603c46B0.3947.470.0460.6392.7.7.6NA
80.0601b0pA0.4066.920.0310.6131.2.7.1NA
90.0601eh9A0.3936.120.0310.5603.2.1.141121
100.0603b9eA0.3956.310.0840.5743.2.1.14NA
110.0602e9bA0.4006.220.0440.5763.2.1.41193
120.0601d7fA0.4066.530.0670.6042.4.1.19NA
130.0601cdgA0.4126.410.0640.6072.4.1.19NA
140.0601ciuA0.3926.770.0620.5902.4.1.1982,112
150.0601tz7A0.3846.500.0480.5652.4.1.25NA
160.0602w5fB0.3876.330.0290.5623.2.1.8175
170.0601rw9A0.3847.260.0750.6194.2.2.537
180.0602vncB0.3856.760.0430.5843.2.1.-NA
190.0601tiwA0.3445.850.0360.4801.5.1.12,1.5.99.8177

(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
00.450.8161.030.300.834jc0A GO:0003824 GO:0005506 GO:0005737 GO:0005829 GO:0009451 GO:0016740 GO:0018339 GO:0035599 GO:0035600 GO:0043412 GO:0046872 GO:0051536 GO:0051539
10.060.4434.760.120.551oltA GO:0003824 GO:0004109 GO:0005737 GO:0006779 GO:0006782 GO:0016491 GO:0046872 GO:0051536 GO:0051539 GO:0051989 GO:0055114
20.060.4056.340.020.583amlA GO:0003824 GO:0003844 GO:0004553 GO:0005975 GO:0005978 GO:0005982 GO:0009501 GO:0009507 GO:0009536 GO:0016740 GO:0016757 GO:0019252 GO:0043169
30.060.3466.840.050.543m07A GO:0003824 GO:0004553 GO:0005737 GO:0005975 GO:0005992 GO:0008152 GO:0016787 GO:0016798 GO:0033942 GO:0046872
40.060.4006.540.040.592vr5A GO:0003824 GO:0004133 GO:0004177 GO:0004553 GO:0005975 GO:0005980 GO:0006508
50.060.4016.330.050.583wdhA GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0046872 GO:0051060
60.060.3996.140.050.572e8yA GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0051060
70.060.3906.880.050.594okdA GO:0003824 GO:0004553 GO:0005975
80.060.3996.330.040.585cltA GO:0003824 GO:0003844 GO:0004553 GO:0005829 GO:0005975 GO:0005977 GO:0005978 GO:0006091 GO:0016740 GO:0016757 GO:0043169 GO:0070062
90.060.3936.140.030.562bhzA GO:0003824 GO:0004553 GO:0005737 GO:0005975 GO:0005992 GO:0008152 GO:0016787 GO:0016798 GO:0033942
100.060.3936.120.030.561eh9A GO:0003824 GO:0004553 GO:0005737 GO:0005975 GO:0005992 GO:0008152 GO:0016787 GO:0016798 GO:0033942
110.060.4006.550.020.601bf2A GO:0003824 GO:0004553 GO:0005576 GO:0005975 GO:0005977 GO:0008152 GO:0016787 GO:0016798 GO:0019156 GO:0046872
120.060.3856.390.040.565e70B GO:0003824 GO:0003844 GO:0004553 GO:0005975 GO:0005977 GO:0005978 GO:0016740 GO:0016757 GO:0043169
130.060.4136.350.050.614aioA GO:0003824 GO:0004553 GO:0005975 GO:0046872 GO:0051060
140.060.3896.570.040.582wskA GO:0003824 GO:0004133 GO:0004135 GO:0004553 GO:0005975 GO:0005977 GO:0005980 GO:0006974 GO:0008152 GO:0016787 GO:0016798
150.060.3766.360.050.545e70C GO:0003824 GO:0003844 GO:0004553 GO:0005975 GO:0005977 GO:0005978 GO:0016740 GO:0016757 GO:0043169
160.060.3726.490.040.554lxfA GO:0003824 GO:0005975 GO:0046872
170.060.3856.760.040.582vncB GO:0003824 GO:0004133 GO:0004177 GO:0004553 GO:0005975 GO:0005980 GO:0006508
180.060.3786.390.030.564lxfB GO:0003824 GO:0005975 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0051539 GO:0035599 GO:0005506 GO:0016798
GO-Score 0.49 0.45 0.45 0.36
Biological Processes GO:0035600 GO:0018339
GO-Score 0.45 0.45
Cellular Component GO:0005829
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.