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I-TASSER results for job id Rv1804c

[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
10.11 6 3qbiB 22B Rep, Mult 31,35,38,51,52,55
20.06 3 3b99A U51 Rep, Mult 48,49,51,52,55,56,72,75,77,91
30.06 3 3b6aD ZCT Rep, Mult 13,16,18,35,49,50,52,54,61,62,65,66,86,89
40.06 3 2jjoA EY5 Rep, Mult 35,48,52,92,95,96,100
50.04 2 2bfnA CA Rep, Mult 27,28
60.04 2 3rovB III Rep, Mult 58,59
70.02 1 3ehbB HEA Rep, Mult 18,90
80.02 1 1o83B PO4 Rep, Mult 95,99,102
90.02 1 2nunA ADP Rep, Mult 28,31,52,72
100.02 1 4bntD 36E Rep, Mult 4,8
110.02 1 4o6mA MPG Rep, Mult 16,31
120.02 1 3serA CA Rep, Mult 36,39
130.02 1 1s32G UUU Rep, Mult 53,54

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
10.0601cleA0.5014.280.0720.8803.1.1.3NA
20.0601vb3A0.5044.140.0400.8704.2.3.1NA
30.0601lpsA0.5004.250.0520.8703.1.1.345
40.0603kb9A0.5074.280.0670.9354.2.3.37NA
50.0603hf2A0.4724.040.1180.7871.14.14.1,1.6.2.436,56
60.0601fsaA0.5004.600.0780.9073.1.3.11NA
70.0601gz7A0.5064.210.0310.8803.1.1.3NA
80.0602wm4A0.5093.670.0980.7961.14.-.-NA
90.0603dsiA0.4964.000.0620.8334.2.1.92NA
100.0602zbzA0.5013.640.1200.7961.14.14.1NA
110.0601gz7C0.5034.380.0410.8983.1.1.3NA
120.0601jpzB0.4893.650.1130.7961.14.14.1,1.6.2.485
130.0601crlA0.5014.210.0210.8703.1.1.3NA
140.0603hxxA0.4933.300.0690.7506.1.1.7NA
150.0602z3tA0.4684.080.0840.8241.-.-.-36,56
160.0601p2yA0.5033.500.0670.7681.14.15.1NA
170.0601osnA0.4954.030.0670.8152.7.1.21NA
180.0603letA0.5233.560.0500.8332.7.7.-62,65
190.0602jjpA0.5143.760.0770.7871.14.-.-49,85

(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
00.070.5304.400.120.944betA GO:0005576 GO:0008152 GO:0009405 GO:0016740 GO:0030430 GO:0043087 GO:0044605
10.070.4634.090.050.772vh3A GO:0005576 GO:0046872
20.070.5603.950.070.905jj6B GO:0000166 GO:0005524 GO:0016020 GO:0016021 GO:0016740 GO:0016779 GO:0018117 GO:0070733
30.060.4183.530.050.633zecB GO:0000166 GO:0000287 GO:0005524 GO:0016740 GO:0016779 GO:0018117 GO:0042803 GO:0070733
40.060.4313.920.050.703zc7A GO:0000166 GO:0000287 GO:0005524 GO:0009405 GO:0016740 GO:0016779 GO:0018117 GO:0042803 GO:0070733
50.060.5014.050.040.864itrA GO:0000166 GO:0003824 GO:0004197 GO:0005524 GO:0005576 GO:0006464 GO:0006508 GO:0008152 GO:0008233 GO:0008234 GO:0009279 GO:0009405 GO:0016020 GO:0016740 GO:0016779 GO:0016787 GO:0018117 GO:0034260 GO:0070733
60.060.3913.630.040.605cklA GO:0000166 GO:0005524 GO:0016740 GO:0016779 GO:0018117 GO:0042803 GO:0070733
70.060.4224.230.030.642vzaA GO:0000166 GO:0005524 GO:0005576 GO:0009405 GO:0016740 GO:0016779 GO:0018117 GO:0070733
80.060.3864.540.060.692ky4A GO:0009579 GO:0015979 GO:0016020 GO:0016829 GO:0018298 GO:0030089 GO:0042651 GO:0055114
90.060.3953.870.060.565a01A GO:0006486 GO:0006493 GO:0008375 GO:0016740 GO:0016757 GO:0035220 GO:0045475
100.060.4024.330.070.692d5kB GO:0005623 GO:0006879 GO:0006950 GO:0008199 GO:0016722 GO:0055114
110.060.3854.610.030.625a31C GO:0004842 GO:0005622 GO:0005654 GO:0005680 GO:0005829 GO:0006511 GO:0007049 GO:0007067 GO:0007080 GO:0007091 GO:0007096 GO:0016567 GO:0030071 GO:0031145 GO:0042787 GO:0043161 GO:0051301 GO:0051436 GO:0051437 GO:0051439 GO:0070979
120.060.5494.060.020.944u0uA GO:0000166 GO:0005524 GO:0016020 GO:0016021 GO:0016740 GO:0016779 GO:0018117 GO:0034260 GO:0070733
130.060.3804.000.060.564xifA GO:0000123 GO:0000791 GO:0001933 GO:0001934 GO:0005547 GO:0005634 GO:0005654 GO:0005737 GO:0005739 GO:0005829 GO:0005886 GO:0006041 GO:0006110 GO:0006486 GO:0006493 GO:0006915 GO:0007165 GO:0007584 GO:0008047 GO:0008134 GO:0008289 GO:0008375 GO:0010628 GO:0010801 GO:0016020 GO:0016262 GO:0016568 GO:0016740 GO:0016757 GO:0019904 GO:0030854 GO:0030900 GO:0031397 GO:0032868 GO:0032869 GO:0032922 GO:0033137 GO:0035020 GO:0042277 GO:0042588 GO:0043005 GO:0043025 GO:0043085 GO:0043981 GO:0043982 GO:0043984 GO:0043995 GO:0043996 GO:0045793 GO:0045862 GO:0045944 GO:0046626 GO:0046972 GO:0048015 GO:0048029 GO:0048312 GO:0048511 GO:0051571 GO:0060548 GO:0061087 GO:0070207 GO:0070208 GO:0070688 GO:0071222 GO:0071300 GO:0071333 GO:0080182 GO:0090315 GO:0090526 GO:0097237 GO:0097363 GO:1900038 GO:1900182 GO:1903428
140.060.3494.340.090.593ooqF GO:0016787 GO:0016810 GO:0019239
150.060.3574.310.080.552fo7A
160.060.3694.710.050.713d8uB GO:0003677 GO:0003700 GO:0006351 GO:0006355
170.060.3524.790.070.672yj4B GO:0000166 GO:0005887 GO:0006812 GO:0008900 GO:0016020 GO:0016021 GO:0016787 GO:0019829 GO:0030001 GO:0035434 GO:0043231 GO:0043682 GO:0046872 GO:0098655 GO:1902600
180.060.3904.000.030.631npdB GO:0000166 GO:0004764 GO:0008652 GO:0009073 GO:0009423 GO:0016491 GO:0030266 GO:0050661 GO:0051287 GO:0052733 GO:0052734 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0035639 GO:0070566 GO:0032559 GO:0032550
GO-Score 0.36 0.36 0.36 0.36
Biological Processes GO:0018175
GO-Score 0.36
Cellular Component GO:0005576 GO:0030430 GO:0016021
GO-Score 0.13 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.