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I-TASSER results for job id Rv2042c

[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
10.52 55 1ogxA EQU Rep, Mult 16,40,84,86,88,101,105,118,122
20.03 3 2a15A NCA Rep, Mult 16,28,40,66,86,105,107,118
30.02 2 1oh00 III Rep, Mult 6,7,10,42,43,72,73,74,75,76,77,79,81,83,84,102,103,104,106,121,122,123,124,125,126
40.02 3 3junB AJD Rep, Mult 28,53,56,57,60,64,67,120

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
10.0603d4jB0.4066.080.0630.6914.1.1.33NA
20.0603psgA0.3846.300.0530.6723.4.23.116
30.0604stdA0.4302.590.0910.4914.2.1.9469
40.0602bngC0.4142.120.1520.4573.3.2.8121
50.0601lrwA0.4345.710.0310.6641.1.99.8NA
60.0603i4zA0.4785.550.0600.7662.5.1.34NA
70.0601gpeB0.3596.240.0800.6301.1.3.4194
80.0601w6sC0.4315.710.0390.6571.1.99.871
90.0601fi4A0.4186.200.0580.7064.1.1.3310
100.0601hn0A0.3936.290.0560.6754.2.2.2023
110.0602psgA0.3906.130.0490.6573.4.23.121,110
120.0603lrfA0.3935.540.0730.6152.3.1.4112,75
130.0601kitA0.4135.530.0280.6413.2.1.18NA
140.0602d0vA0.4335.720.0390.6641.1.99.8NA
150.0601e3vB0.4401.840.2130.4725.3.3.140,57,105
160.0601gpeA0.4066.060.0540.6911.1.3.4NA
170.0602w68C0.2476.010.0410.4113.2.1.18NA
180.0601flhA0.3646.200.0770.6263.4.23.1NA
190.0601lrwC0.4335.720.0310.6641.1.99.867

(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
00.370.4212.410.220.471buqA GO:0004769 GO:0005622 GO:0006629 GO:0006810 GO:0008202 GO:0016853
10.300.8752.140.160.974rzmB GO:0016853 GO:0017000
20.210.4422.040.170.483wmdB GO:0016853
30.160.4381.880.180.475cxoB GO:0016787
40.120.4391.940.200.473t8nB GO:0004769 GO:0006629 GO:0008202 GO:0016853
50.070.4735.250.070.714ld7A GO:0009820 GO:0050364
60.070.4785.550.060.773i4zA GO:0009820 GO:0016740 GO:0035835 GO:0050364
70.070.4775.230.070.723o24A GO:0004659 GO:0009820 GO:0016740 GO:0050364
80.060.4395.750.050.714e0tA GO:0009820 GO:0016740 GO:0050364
90.060.4405.440.090.684yzlA GO:0009820 GO:0016740 GO:0050364
100.060.3943.050.110.461m98A GO:0005622 GO:0006810 GO:0007165 GO:0009579 GO:0009881 GO:0016020 GO:0016037 GO:0018298 GO:0030089 GO:0031404 GO:0042651 GO:0050896
110.060.4022.820.140.454xb5A GO:0005622 GO:0006810 GO:0007165 GO:0009579 GO:0009881 GO:0016020 GO:0016037 GO:0018298 GO:0030089 GO:0031404 GO:0042651 GO:0050896
120.060.3275.930.030.551jofA GO:0016853 GO:0017057 GO:0042952 GO:0047768
130.060.2976.480.050.544i5jA GO:0000159 GO:0001754 GO:0005509 GO:0006470 GO:0007525 GO:0008601 GO:0030674 GO:0034047 GO:0045732 GO:0046872 GO:0061053 GO:0090090 GO:0090244 GO:0090249 GO:0090263
140.060.2865.800.040.471moeA
150.060.2716.330.050.484ce0A GO:0008168 GO:0016740 GO:0032259 GO:0046872
160.060.2405.870.070.392l7bA GO:0000302 GO:0001523 GO:0001540 GO:0001937 GO:0002021 GO:0005319 GO:0005543 GO:0005576 GO:0005615 GO:0005634 GO:0005737 GO:0005769 GO:0005783 GO:0005794 GO:0005886 GO:0006629 GO:0006641 GO:0006707 GO:0006810 GO:0006869 GO:0006874 GO:0006898 GO:0006979 GO:0007010 GO:0007186 GO:0007263 GO:0007271 GO:0008201 GO:0008202 GO:0008203 GO:0008289 GO:0010468 GO:0010544 GO:0010873 GO:0010875 GO:0015485 GO:0015909 GO:0016020 GO:0016209 GO:0017038 GO:0017127 GO:0019068 GO:0019433 GO:0019934 GO:0030195 GO:0030425 GO:0030516 GO:0030828 GO:0031012 GO:0031102 GO:0032489 GO:0032805 GO:0033344 GO:0033700 GO:0034361 GO:0034362 GO:0034363 GO:0034364 GO:0034372 GO:0034374 GO:0034375 GO:0034380 GO:0034382 GO:0034384 GO:0034447 GO:0042157 GO:0042158 GO:0042159 GO:0042311 GO:0042627 GO:0042632 GO:0042802 GO:0042803 GO:0043025 GO:0043407 GO:0043524 GO:0043537 GO:0043691 GO:0044794 GO:0045541 GO:0046889 GO:0046907 GO:0046911 GO:0048156 GO:0048168 GO:0048844 GO:0050728 GO:0050750 GO:0051000 GO:0051044 GO:0051055 GO:0051651 GO:0055088 GO:0055089 GO:0060228 GO:0060999 GO:0061000 GO:0070062 GO:0070326 GO:0071682 GO:0071813 GO:0072358 GO:0072562 GO:0090090 GO:0090370 GO:0097113 GO:0097114 GO:0098869 GO:1900221 GO:1901214 GO:1901215 GO:1901216 GO:1901627 GO:1901628 GO:1901630 GO:1901631 GO:1902004 GO:1902430 GO:1902947 GO:1902951 GO:1902952 GO:1902995 GO:1902998 GO:1902999 GO:1903001 GO:1903002 GO:1903561
170.060.2466.370.040.441ww1A GO:0016787 GO:0034414 GO:0042781 GO:0046872
180.060.2094.850.050.302gtlB GO:0005344 GO:0005506 GO:0005576 GO:0005833 GO:0006810 GO:0015671 GO:0019825 GO:0020037 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0004769
GO-Score 0.45
Biological Processes GO:0008202 GO:0006810 GO:0017000
GO-Score 0.45 0.37 0.30
Cellular Component GO:0005622
GO-Score 0.37

(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.