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I-TASSER results for job id Rv1354c

[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
10.34 30 3pjtA C2E Rep, Mult 375,389,391,392,393,403,404,405,408,420,421,424,449,511,512,569,571,589,590,595
20.21 18 3gg0A MN Rep, Mult 389,449,481,511,532
30.08 6 3n3tA MG Rep, Mult 511,512,534,568
40.03 3 2w27B 5GP Rep, Mult 375,389,391,449,569,570,571,589,590
50.03 4 3gfzB FMN Rep, Mult 194,239,242,243,246,247,265,267,269,281,285,288,290
60.02 3 1lm1A F3S Rep, Mult 305,306,307,329,330,331,334
70.01 1 3qyyA MG Rep, Mult 220,263
80.01 1 3qyyA C2E Rep, Mult 224,225,228,233,236,237,240,259,262,263
90.01 1 3b2xA NA Rep, Mult 228,229,232,236
100.01 1 4afyA MG Rep, Mult 375,389,588

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
10.0601ti6A0.3368.010.0340.5411.97.1.2NA
20.0602wqdA0.3405.400.0480.4382.7.3.9496
30.0602gbcA0.3608.000.0440.5963.4.14.5,3.4.15.5326
40.0603ecqB0.3317.110.0300.4883.2.1.97NA
50.0602dqmA0.3687.480.0570.5683.4.11.2264
60.0601ofdA0.3767.250.0370.5591.4.7.1NA
70.0601z68A0.3337.860.0490.5313.4.21.-NA
80.0602gtqA0.3647.680.0580.5683.4.11.2NA
90.0601qbaA0.3665.730.0550.4833.2.1.52NA
100.0601b0pA0.3147.790.0540.5041.2.7.1NA
110.0602bklB0.3428.260.0430.5683.4.21.26305
120.0602vdcA0.3776.840.0430.5411.4.1.13NA
130.0601rs0A0.2437.790.0490.3883.4.21.47NA
140.0601e5tA0.3468.180.0520.5703.4.21.26NA
150.0602ebsB0.3357.830.0360.5393.2.1.150NA
160.0603bq5A0.4246.790.0590.6122.1.1.14NA
170.0602ok5A0.3437.590.0390.5423.4.21.47NA
180.0601u22A0.4087.110.0520.6052.1.1.14NA
190.0601bxrA0.3498.250.0450.5846.3.5.5191

(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
00.350.3553.660.190.403gfxB GO:0000166 GO:0009785 GO:0009882 GO:0046872 GO:0071949
10.250.2623.270.200.282v0nA GO:0000160 GO:0000166 GO:0004871 GO:0005525 GO:0005737 GO:0007049 GO:0007165 GO:0016740 GO:0030154 GO:0046872 GO:0052621
20.160.2593.160.200.284h54A GO:0000166 GO:0005525 GO:0008270 GO:0016740 GO:0043709 GO:0046872 GO:0051271 GO:0052621 GO:1902209
30.140.2471.790.310.264ursA GO:0000166
40.080.6641.060.360.674rnfA GO:0000155 GO:0000160 GO:0000166 GO:0005622 GO:0016020 GO:0016021 GO:0023014 GO:0042802 GO:0046872
50.060.4404.600.160.523pjwA GO:0000166 GO:0004871 GO:0007165 GO:0016020 GO:0016021
60.060.4373.760.200.493sy8B GO:0000160 GO:0005622 GO:0045892 GO:0046872
70.060.4083.220.210.443sy8D GO:0000160 GO:0005622 GO:0045892 GO:0046872
80.060.3962.190.400.423n3tB GO:0000166 GO:0016020 GO:0016021 GO:0046872
90.060.3992.580.330.434hu3A GO:0000155 GO:0000160 GO:0000287 GO:0005622 GO:0006351 GO:0006355 GO:0016787 GO:0019826 GO:0020037 GO:0023014 GO:0046872 GO:0050896 GO:0070482 GO:0071111
100.060.3972.230.350.424hjfA GO:0000166 GO:0046872
110.060.3902.830.200.424fokA GO:0000166 GO:0046872
120.060.3842.270.290.414y9mA GO:0016020 GO:0016021
130.060.3862.690.310.424kieA GO:0003677 GO:0006355 GO:0016787 GO:0071111
140.060.3732.400.210.403hv9A GO:0000160 GO:0000166 GO:0005622 GO:0006355
150.060.3612.220.240.383pfmA GO:0004871 GO:0007165 GO:0016020 GO:0016021
160.060.3283.510.160.363gfyB GO:0000166 GO:0009785 GO:0009882 GO:0046872 GO:0071949
170.060.3093.170.190.343kzpB GO:0046872
180.060.2522.890.170.273breB GO:0000160 GO:0005622


Consensus prediction of GO terms
 
Molecular Function GO:0052621 GO:0005525 GO:0071949 GO:0009882 GO:0046914
GO-Score 0.37 0.37 0.35 0.35 0.33
Biological Processes GO:0048869 GO:0009785 GO:0090609 GO:1902208 GO:1902116 GO:0051270 GO:0043708 GO:0031345 GO:0000160
GO-Score 0.50 0.35 0.33 0.33 0.33 0.33 0.33 0.33 0.31
Cellular Component GO:0044424
GO-Score 0.50

(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.