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I-TASSER results for job id Rv0047c

[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
10.04 2 2h23A M3L Rep, Mult 6,7,8,11,12,13,52,70
20.04 2 2cbjA OAN Rep, Mult 4,5,83
30.04 2 3bvdA XE Rep, Mult 113,116,166,167
40.04 2 1nf4C FEC Rep, Mult 120,127,128,131,135,150,157,158,161
50.04 2 3b6aD ZCT Rep, Mult 153,154
60.04 2 3f8fA DM1 Rep, Mult 4,80,83,84,87
70.02 1 5dnmG RAX Rep, Mult 125,128
80.02 1 5da5E GOA Rep, Mult 122,126,156
90.02 1 3q8mA NUC Rep, Mult 40,119
100.02 1 3f38A 2MY Rep, Mult 35,36,77
110.02 1 2bkoA CA Rep, Mult 124,157,161
120.02 1 4brbB 78N Rep, Mult 102,109,112
130.02 1 3rf3A III Rep, Mult 6,17,21
140.02 1 3hd7F GGG Rep, Mult 158,161
150.02 1 2rb1X 261 Rep, Mult 67,70
160.02 1 2idkB C2F Rep, Mult 38,40
170.02 1 3u24A IMD Rep, Mult 45,48,49
180.02 1 5l8gT CA Rep, Mult 130,152,156
190.02 1 2cbjB OAN Rep, Mult 24,25,34
200.02 1 4mteA NUC Rep, Mult 18,40,54,70

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
10.0601bg7A0.3242.440.0130.3721.16.3.1124
20.0601g8mA0.4443.570.0790.6003.5.4.10,2.1.2.3NA
30.0601xzpA0.4374.390.1060.6003.6.5.-69
40.0601z0hB0.2645.730.0410.4833.4.24.6919
50.0601yqwR0.4435.080.0430.7391.12.2.1117
60.0602wyhA0.4354.810.0350.6443.2.1.24NA
70.0602htnG0.4473.480.1650.5671.16.3.132
80.0601syyA0.4495.110.0440.7441.17.4.1NA
90.0602rccA0.4335.120.0300.7281.17.4.1NA
100.0601xjjA0.4354.940.0320.7061.17.4.126
110.0602d0tB0.4534.300.0500.6331.13.11.52NA
120.0602frvD0.4544.960.0490.7441.12.2.16,8
130.0601mhyD0.4425.350.0290.7611.14.13.25NA
140.0601p4rA0.4393.640.0860.6002.1.2.3,3.5.4.10NA
150.0603gehA0.4373.640.0340.5783.6.-.-NA
160.0601mfrW0.4294.160.0540.5941.16.3.183
170.0602bq1I0.4395.100.0630.7331.17.4.1NA
180.0602j62A0.5004.020.0420.6893.2.1.5239
190.0603ee4A0.4803.720.0820.6281.17.4.1NA

(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
00.190.6323.060.150.812rkhA
10.110.4083.450.170.503bpxA GO:0003677 GO:0003700 GO:0006351 GO:0006355
20.070.5324.460.050.771ozvB GO:0008168 GO:0009507 GO:0009536 GO:0016740 GO:0030785 GO:0032259
30.070.4554.770.120.753qxyA GO:0005634 GO:0005737 GO:0008168 GO:0016279 GO:0016740 GO:0018026 GO:0019827 GO:0032088 GO:0032259 GO:0034968 GO:0048863 GO:0050727 GO:0051059
40.070.4824.850.080.813smtA GO:0000790 GO:0001102 GO:0003713 GO:0005634 GO:0005654 GO:0006351 GO:0006355 GO:0008168 GO:0010452 GO:0016568 GO:0016740 GO:0018022 GO:0018023 GO:0018024 GO:0018026 GO:0018027 GO:0032259 GO:0042800 GO:0045893 GO:0045944 GO:0046975 GO:0051149 GO:0051568
50.060.3792.760.150.444a5nB GO:0003677 GO:0006351 GO:0006355
60.060.3675.870.030.681p5jA GO:0003941 GO:0004794 GO:0005737 GO:0005739 GO:0006094 GO:0006520 GO:0006565 GO:0016829 GO:0030170 GO:0042803 GO:0042866
70.060.2915.680.030.552brrY
80.060.3075.200.080.522zwrB GO:0046872
90.060.3042.900.160.382gmgA
100.060.3135.230.080.531fj1B
110.060.2686.590.040.561dbaH GO:0001788 GO:0001798 GO:0001812 GO:0002455 GO:0003823 GO:0005576 GO:0005615 GO:0006910 GO:0006911 GO:0006958 GO:0009897 GO:0016064 GO:0019731 GO:0042571 GO:0042742 GO:0050766 GO:0050778
120.060.2725.900.060.503k60A GO:0005524 GO:0006457 GO:0006950 GO:0006986 GO:0009408 GO:0016887 GO:0051082
130.060.3045.520.050.543ojdB
140.060.3665.110.050.633ka7A GO:0000166 GO:0016491 GO:0055114
150.060.2645.830.050.482jkiB GO:0000166 GO:0005524 GO:0006457 GO:0006950 GO:0051082
160.060.2655.740.010.483bzwA
170.060.2144.980.040.361cl7H
180.060.2224.820.060.344v6wAR GO:0000028 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0022627 GO:0030529


Consensus prediction of GO terms
 
Molecular Function GO:0016741
GO-Score 0.37
Biological Processes GO:1903506 GO:2000112 GO:0010468 GO:0006351
GO-Score 0.34 0.34 0.34 0.34
Cellular Component GO:0009507 GO:0000790 GO:0005654
GO-Score 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.