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I-TASSER results for job id Rv1920

[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
10.07 3 2x2vH DPV Rep, Mult 255,263
20.07 3 2x2vB DPV Rep, Mult 259,263,266,270
30.05 2 3a0bK CLA Rep, Mult 167,168,170
40.05 2 3bk9C TRP Rep, Mult 252,255
50.02 1 3qs0D NAG Rep, Mult 59,165
60.02 1 2ofwA ADX Rep, Mult 54,55
70.02 1 1r9cB MN Rep, Mult 66,68
80.02 1 2zyqB TAR Rep, Mult 133,134
90.02 1 2onkE MG Rep, Mult 83,100,104
100.02 1 3mtgB NAD Rep, Mult 69,91,92,93,94,97,133,134,154
110.02 1 3phxA ZN Rep, Mult 230,234
120.02 1 3jpyA ZN Rep, Mult 66,231
130.02 1 3h9uB NAD Rep, Mult 119,161,166
140.02 1 1iuqA GOL Rep, Mult 148,149,151,249,252,253,256
150.02 1 1llrD UUU Rep, Mult 135,137
160.02 1 1m34A SF4 Rep, Mult 62,63

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
10.0601hwxA0.4245.920.0770.6791.4.1.3NA
20.0601z45A0.4175.030.1110.6035.1.3.2,5.1.3.3NA
30.0601v8bC0.4805.620.0950.7633.3.1.1180,185
40.0601kzhB0.4395.540.0570.6792.7.1.90NA
50.0602pffD0.4335.850.0430.6902.3.1.8670,74
60.0602pffA0.4335.670.0480.6792.3.1.41,2.3.1.86NA
70.0601v8bA0.4815.640.1000.7633.3.1.1NA
80.0601wvgA0.4135.350.0910.6134.2.1.45NA
90.0603m07A0.4136.320.0770.6933.2.1.141132,133
100.0603d64A0.4775.590.0950.7563.3.1.1NA
110.0603g1uC0.4825.360.0770.7493.3.1.1NA
120.0603ifgA0.4045.900.0340.6381.2.1.16231
130.0603k92A0.4166.190.0450.7001.4.1.2139
140.0601kerB0.4145.430.0790.6104.2.1.46113
150.0601i24A0.3565.880.0560.5823.13.1.1NA
160.0602o2rC0.4126.130.0430.6721.5.1.6NA
170.0603n58A0.4745.640.0880.7533.3.1.193,183
180.0602ph5A0.4175.580.0910.6412.5.1.44131
190.0601k30A0.7362.940.1050.8542.3.1.1566

(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
00.130.7362.940.100.851k30A GO:0004366 GO:0006629 GO:0006650 GO:0008152 GO:0008654 GO:0009507 GO:0009536 GO:0009570 GO:0016024 GO:0016740 GO:0016746
10.070.5015.540.090.795jpiA GO:0004013 GO:0006730 GO:0016787
20.070.4815.640.100.761v8bA GO:0004013 GO:0005829 GO:0006730 GO:0016787 GO:0033353
30.070.4905.640.090.783ce6A GO:0004013 GO:0005576 GO:0005618 GO:0005737 GO:0005829 GO:0005886 GO:0006730 GO:0009087 GO:0016787 GO:0033353 GO:0040007 GO:0046085 GO:0070403
40.070.4955.670.070.793ondB GO:0004013 GO:0006730 GO:0016787
50.070.4805.740.090.771a7aA GO:0000096 GO:0001666 GO:0002439 GO:0004013 GO:0005634 GO:0005737 GO:0005829 GO:0006730 GO:0007584 GO:0016787 GO:0019510 GO:0030554 GO:0032259 GO:0033353 GO:0042470 GO:0042745 GO:0042802 GO:0043005 GO:0051287 GO:0070062 GO:0071268
60.070.4775.590.100.763d64A GO:0004013 GO:0005737 GO:0006730 GO:0016787
70.070.4925.580.100.783h9uC GO:0000166 GO:0004013 GO:0005829 GO:0006730 GO:0016787 GO:0033353
80.070.4765.570.080.763n58B GO:0004013 GO:0005737 GO:0006730 GO:0016787
90.070.4805.900.050.783gvpA GO:0004013 GO:0005737 GO:0005783 GO:0005829 GO:0006730 GO:0016787 GO:0033353 GO:0043005 GO:0043231
100.070.4825.360.080.753g1uC GO:0000166 GO:0004013 GO:0005829 GO:0006730 GO:0016787 GO:0033353
110.070.4445.640.090.703x2fA GO:0004013 GO:0005737 GO:0005829 GO:0006730 GO:0016787 GO:0033353
120.060.3425.890.060.544ijuB GO:0003845 GO:0005783 GO:0005789 GO:0006629 GO:0006704 GO:0008202 GO:0016020 GO:0016021 GO:0016491 GO:0030324 GO:0055114 GO:0070524
130.060.3546.120.050.593vpxB GO:0006520 GO:0016491 GO:0016639 GO:0055114
140.060.3734.920.120.533d3wB GO:0005634 GO:0005881 GO:0005886 GO:0005902 GO:0005903 GO:0005975 GO:0005997 GO:0006006 GO:0006739 GO:0016020 GO:0016491 GO:0016614 GO:0016655 GO:0019640 GO:0042732 GO:0050038 GO:0051289 GO:0055114 GO:0070062
150.060.3685.850.050.575a2aA GO:0003824 GO:0004556 GO:0005975 GO:0008152 GO:0016020 GO:0016021 GO:0016787 GO:0016798
160.060.3885.110.120.563awdA GO:0016491 GO:0055114
170.060.3406.100.040.575dt9A GO:0004617 GO:0005737 GO:0008152 GO:0008615 GO:0009070 GO:0016491 GO:0016616 GO:0033711 GO:0046983 GO:0051287 GO:0055114
180.060.3435.070.070.523dttB GO:0000166


Consensus prediction of GO terms
 
Molecular Function GO:0016802
GO-Score 0.48
Biological Processes GO:0044281 GO:0044763 GO:0044237
GO-Score 0.48 0.48 0.40
Cellular Component GO:0005829 GO:0009570 GO:0005886 GO:0005618 GO:0005576
GO-Score 0.13 0.13 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.