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I-TASSER results for job id Rv0420c

[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
10.09 4 1ijdD BCL Rep, Mult 109,112
20.07 4 4dq1A UMP Rep, Mult 98,99
30.04 2 2wieB CVM Rep, Mult 117,118,121
40.04 2 2xquA CVM Rep, Mult 99,103
50.04 2 1t5tA CA Rep, Mult 40,41,44,110,113
60.04 2 3orcA NUC Rep, Mult 70,71
70.04 2 2bl2A NA Rep, Mult 33,34,35,36,37,74,106
80.02 1 2r5bA III Rep, Mult 118,121,122,125
90.02 1 3ar7A PTY Rep, Mult 113,117,120
100.02 1 2q7mC 2CS Rep, Mult 28,29,99,106,107,110
110.02 1 5kb2A ZN Rep, Mult 122,125,126
120.02 1 2agvA PTY Rep, Mult 7,35,39,42,43
130.02 1 1kf6O CE1 Rep, Mult 46,51
140.02 1 3s8gA OLC Rep, Mult 34,38,71,72,75
150.02 1 2q68A CA Rep, Mult 65,71
160.02 1 2vt4D SOG Rep, Mult 56,99,100

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
10.0601y2mB0.5754.370.0450.9264.3.1.24NA
20.0601occA0.5494.250.1000.8751.9.3.1NA
30.0601fgjA0.5343.460.0450.7431.7.3.4NA
40.0602occN0.5343.860.0710.8161.9.3.1NA
50.0603bnjA0.5334.300.0580.8311.7.2.282
60.0601m56A0.5513.950.0540.8531.9.3.1NA
70.0603fedA0.5433.610.0600.8163.4.17.21NA
80.0601k7wD0.4444.700.0850.7504.3.2.1NA
90.0603dwwA0.5513.170.0870.7655.3.99.342,69,106
100.0602bl2A0.6243.320.1000.8683.6.3.1437,42,63,75
110.0602o6yA0.5594.090.0610.8604.3.1.-NA
120.0601dcnB0.4404.720.0850.7504.3.2.1NA
130.0602ix6E0.5284.710.0570.8901.3.3.6104
140.0601i0aA0.4454.730.0930.7504.3.2.1NA
150.0603ixzA0.5314.630.0600.9043.6.3.10NA
160.0602pnoL0.5923.290.1180.8164.4.1.207,75,111
170.0602qb0B0.3084.480.0680.5223.2.1.1753
180.0602ohyB0.5224.180.0390.7945.4.3.6NA
190.0603d9dA0.5433.870.0590.8241.7.3.1NA

(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
00.260.5494.250.100.881occA GO:0004129 GO:0005506 GO:0005739 GO:0005743 GO:0006119 GO:0009055 GO:0009060 GO:0016020 GO:0016021 GO:0016491 GO:0020037 GO:0045277 GO:0046872 GO:0055114 GO:0070469 GO:1902600
10.250.5513.950.050.851m56A GO:0004129 GO:0005506 GO:0005507 GO:0005886 GO:0006119 GO:0006810 GO:0006811 GO:0009055 GO:0009060 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0020037 GO:0022900 GO:0046872 GO:0055114 GO:0070469 GO:1902600
20.180.6163.580.100.903j9tR GO:0000220 GO:0005773 GO:0005774 GO:0006623 GO:0006810 GO:0006811 GO:0006878 GO:0006879 GO:0006897 GO:0007033 GO:0007035 GO:0015078 GO:0015991 GO:0015992 GO:0016020 GO:0016021 GO:0033177 GO:0033179 GO:0046961
30.120.3593.360.090.504bemA GO:0005886 GO:0006810 GO:0006811 GO:0015078 GO:0015986 GO:0015991 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0033177 GO:0045263
40.100.3773.160.070.512wieA GO:0006810 GO:0006811 GO:0015078 GO:0015986 GO:0015991 GO:0015992 GO:0016020 GO:0016021 GO:0033177 GO:0045263
50.070.5574.520.060.913o0rB GO:0004129 GO:0005506 GO:0005886 GO:0009055 GO:0009060 GO:0016020 GO:0016021 GO:0016491 GO:0016966 GO:0019333 GO:0020037 GO:0046872 GO:0055114 GO:0070469 GO:1902600
60.070.6393.910.070.953eh3A GO:0004129 GO:0005506 GO:0005886 GO:0006119 GO:0006811 GO:0009055 GO:0009060 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0020037 GO:0046872 GO:0055114 GO:0070469 GO:1902600
70.070.6243.440.080.873aouA GO:0005886 GO:0006810 GO:0006811 GO:0006814 GO:0015078 GO:0015991 GO:0016020 GO:0016021 GO:0033177 GO:0033179
80.070.5643.940.090.865djqA GO:0004129 GO:0005506 GO:0005507 GO:0005886 GO:0005887 GO:0006119 GO:0009055 GO:0009060 GO:0015078 GO:0015990 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0016705 GO:0019411 GO:0019646 GO:0019825 GO:0020037 GO:0045154 GO:0045278 GO:0046872 GO:0055114 GO:0070069 GO:0070469 GO:0070470 GO:1902600
90.070.5814.230.130.911fftA GO:0004129 GO:0005506 GO:0005507 GO:0005886 GO:0005887 GO:0006811 GO:0009055 GO:0009060 GO:0009319 GO:0009486 GO:0015078 GO:0015453 GO:0015990 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0016682 GO:0019646 GO:0020037 GO:0046872 GO:0048039 GO:0055114 GO:0070469
100.070.5383.880.060.821qleA GO:0004129 GO:0005506 GO:0005507 GO:0005886 GO:0006119 GO:0006810 GO:0006811 GO:0009055 GO:0009060 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0020037 GO:0022900 GO:0046872 GO:0055114 GO:0070469 GO:1902600
110.070.5873.740.140.884bemJ GO:0005886 GO:0006810 GO:0006811 GO:0015078 GO:0015986 GO:0015991 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0033177 GO:0045263
120.070.3833.260.060.533zk1A GO:0005886 GO:0006754 GO:0006810 GO:0006811 GO:0008289 GO:0015078 GO:0015986 GO:0015991 GO:0015992 GO:0016020 GO:0016021 GO:0033177 GO:0045263
130.070.5394.000.040.842yevA GO:0004129 GO:0005506 GO:0005507 GO:0005886 GO:0006119 GO:0006810 GO:0006811 GO:0009055 GO:0009060 GO:0015002 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0020037 GO:0022900 GO:0022904 GO:0046872 GO:0055114 GO:0070469 GO:1902600
140.060.3105.120.030.574n1yB GO:0003677 GO:0003700 GO:0003707 GO:0005496 GO:0005634 GO:0006351 GO:0006355 GO:0008270 GO:0043401 GO:0043565 GO:0046872
150.060.3803.340.050.532wgmA GO:0005886 GO:0006754 GO:0006810 GO:0006811 GO:0006814 GO:0008289 GO:0015078 GO:0015986 GO:0015991 GO:0015992 GO:0016020 GO:0016021 GO:0033177 GO:0045263
160.060.3025.170.070.572ldxA GO:0003824 GO:0004459 GO:0005634 GO:0005737 GO:0005929 GO:0005975 GO:0006090 GO:0006754 GO:0016491 GO:0016616 GO:0019244 GO:0019516 GO:0019752 GO:0030317 GO:0031514 GO:0055114 GO:0070062
170.060.3804.770.070.675aca2 GO:0000166 GO:0001172 GO:0003723 GO:0003724 GO:0003968 GO:0004197 GO:0004386 GO:0005198 GO:0005216 GO:0005524 GO:0006351 GO:0006508 GO:0006810 GO:0006811 GO:0008233 GO:0008234 GO:0016020 GO:0016032 GO:0016740 GO:0016779 GO:0016787 GO:0019012 GO:0019028 GO:0019030 GO:0019062 GO:0019082 GO:0030430 GO:0033644 GO:0034220 GO:0039694 GO:0039707 GO:0044161 GO:0044162 GO:0044385 GO:0046718 GO:0051259
180.060.3863.100.040.515garO GO:0015078 GO:0015991 GO:0016020 GO:0016021 GO:0033177 GO:0033179


Consensus prediction of GO terms
 
Molecular Function GO:0020037 GO:0004129 GO:0005506 GO:0044769 GO:0036442
GO-Score 0.44 0.44 0.44 0.36 0.36
Biological Processes GO:0009060 GO:0006119 GO:0015985 GO:0006754 GO:0046916 GO:0007034 GO:0072666 GO:0055070 GO:0055072 GO:0016192 GO:0006996 GO:0051452 GO:0006605 GO:0015991
GO-Score 0.44 0.44 0.42 0.42 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.35
Cellular Component GO:0016021 GO:0019866 GO:0070069 GO:0098803 GO:0031966 GO:0045259 GO:0016471 GO:0033177 GO:0005886
GO-Score 0.64 0.51 0.51 0.51 0.51 0.42 0.36 0.35 0.34

(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.