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I-TASSER results for job id Rv1616

[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
10.08 4 2bx2L ZN Rep, Mult 51,54
20.08 4 3mi9C ZN Rep, Mult 41,51,54
30.06 3 4fe1L CLA Rep, Mult 85,113,114,117
40.04 2 2h88D UNL Rep, Mult 78,81,82,85,110,111,114
50.04 2 2elvA ZN Rep, Mult 51,54,61,65
60.04 2 1ijdD BCL Rep, Mult 14,17
70.04 2 1e7bA HLT Rep, Mult 42,44,54,79,82,83,87,107,111
80.02 1 3pfdC IOD Rep, Mult 15,43
90.02 1 3anpD DCC Rep, Mult 57,60,61,65,66,71
100.02 1 2np5C NDS Rep, Mult 48,49,51
110.02 1 3anpA DCC Rep, Mult 80,84,88,89
120.02 1 3rt1C GLC Rep, Mult 20,21,24,64
130.02 1 1qpiA QNA Rep, Mult 67,70,71,74

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
10.0602i2xA0.5444.160.0490.8792.1.1.9027
20.0603etdA0.5094.210.0820.8111.4.1.3NA
30.0601yewB0.6383.460.0630.9091.14.13.2581
40.0601udyA0.5084.660.0960.8711.3.99.3NA
50.0602jkvA0.5123.580.0600.7271.1.1.44NA
60.0602p4qA0.5173.350.0400.7201.1.1.4481
70.0602ebaA0.5124.870.0880.8941.3.99.7NA
80.0601ukwA0.5204.640.0870.8791.3.99.3NA
90.0603d9dA0.4984.860.0740.8641.7.3.1NA
100.0603c20B0.5024.510.0500.8112.7.2.4NA
110.0603g61A0.5534.290.0300.8563.6.3.4455,114
120.0601a5tA0.5413.650.1270.8332.7.7.778
130.0601n63B0.5114.150.0580.8181.2.99.2NA
140.0601hwxA0.5124.090.0170.7801.4.1.3NA
150.0603djlA0.6014.090.0630.9011.3.99.-NA
160.0601m7xB0.5224.170.0590.8792.4.1.18NA
170.0601ivhA0.5084.620.0170.8491.3.99.10NA
180.0601rx0A0.5054.670.0400.8641.3.99.-NA
190.0601ffuB0.5084.300.0580.8261.2.99.2NA

(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
00.160.7862.440.140.964hzuS GO:0016020 GO:0016021
10.150.7352.840.110.954rfsS GO:0005215 GO:0006810 GO:0016020 GO:0016021
20.080.7203.360.061.005do7D GO:0005524 GO:0005886 GO:0006810 GO:0007584 GO:0007588 GO:0010949 GO:0015248 GO:0015914 GO:0015918 GO:0016020 GO:0016021 GO:0016324 GO:0016887 GO:0017127 GO:0030299 GO:0033344 GO:0042493 GO:0042626 GO:0042632 GO:0043190 GO:0043235 GO:0045796 GO:0046982 GO:0055085 GO:0055092
30.070.5134.210.050.804m1mA GO:0000086 GO:0000166 GO:0002481 GO:0002485 GO:0002489 GO:0002591 GO:0005524 GO:0005886 GO:0006810 GO:0006855 GO:0008559 GO:0009986 GO:0015893 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0042623 GO:0042626 GO:0042908 GO:0046581 GO:0055085 GO:0070062 GO:0072089
40.060.4264.410.070.702iw3B GO:0000166 GO:0001933 GO:0003723 GO:0003746 GO:0005524 GO:0005737 GO:0005840 GO:0006412 GO:0006414 GO:0006415 GO:0006469 GO:0010494 GO:0016887 GO:0019843 GO:0022626 GO:0042788
50.060.6363.820.080.985do7A GO:0000166 GO:0005524 GO:0005886 GO:0006810 GO:0007584 GO:0007588 GO:0010212 GO:0010949 GO:0015918 GO:0016020 GO:0016021 GO:0016324 GO:0016887 GO:0017127 GO:0030299 GO:0033344 GO:0042493 GO:0042626 GO:0042632 GO:0043190 GO:0043235 GO:0045177 GO:0045796 GO:0046982 GO:0055085
60.060.3415.230.030.644pl0B GO:0000166 GO:0005524 GO:0005886 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0016887 GO:0030153 GO:0042626 GO:0043213 GO:0055085
70.060.4104.810.060.733qkuA GO:0000166 GO:0005524 GO:0006281 GO:0006302 GO:0006974 GO:0008270 GO:0016787 GO:0016887 GO:0042802 GO:0046872
80.060.3894.370.090.624q4aA GO:0000166 GO:0005524 GO:0006810 GO:0006869 GO:0016020 GO:0016021 GO:0016887 GO:0034040 GO:0042626 GO:0046872 GO:0055085
90.060.3924.540.050.693qktA GO:0000166 GO:0005524 GO:0006281 GO:0006302 GO:0006974 GO:0008270 GO:0016787 GO:0016887 GO:0042802 GO:0046872
100.060.3854.810.050.672zu0C GO:0000166 GO:0005524 GO:0005737 GO:0005829 GO:0006810 GO:0016226 GO:0016887
110.060.3594.610.030.593b5wA GO:0000166 GO:0005319 GO:0005524 GO:0005886 GO:0006810 GO:0006869 GO:0008144 GO:0008289 GO:0015437 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0034040 GO:0042626 GO:0043190 GO:0055085 GO:1901264
120.060.3445.140.030.644wbsB GO:0000166 GO:0005524 GO:0016887 GO:0043190 GO:0055085
130.060.3713.130.050.513wmgA GO:0000166 GO:0005524 GO:0006810 GO:0016020 GO:0016021 GO:0016887 GO:0042626 GO:0055085
140.060.3614.570.030.623gfoA GO:0000166 GO:0005524 GO:0005886 GO:0006810 GO:0006824 GO:0016020 GO:0016787 GO:0016887 GO:0043190
150.060.3794.420.040.635da9B GO:0000723 GO:0005089 GO:0005524 GO:0005634 GO:0006281 GO:0016887 GO:0030870 GO:0035023 GO:0043547
160.060.3893.660.030.584lmaA GO:0004124 GO:0006535 GO:0008652 GO:0016740 GO:0019344
170.060.3704.520.040.611oxuA GO:0000166 GO:0005524 GO:0016887
180.060.3564.850.080.614ymsA GO:0000166 GO:0003333 GO:0005524 GO:0015424 GO:0016887


Consensus prediction of GO terms
 
Molecular Function GO:0032550 GO:0017111 GO:0035639 GO:0032559
GO-Score 0.39 0.39 0.39 0.39
Biological Processes GO:0051234
GO-Score 0.54
Cellular Component GO:0016021
GO-Score 0.39

(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.