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I-TASSER results for job id Rv2205c

[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 2 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 1zjjA MG Rep, Mult 8,10,270
20.05 3 1l7xA 700 Rep, Mult 181,184,199,203
30.05 3 1rd4C L08 Rep, Mult 3,5,22,35,263,265,294,296,297,298,316,317,318,341,344,346
40.04 2 1gfzA CFF Rep, Mult 17,42,44,48
50.04 2 3m0kA MN Rep, Mult 136,141,170,172
60.04 2 5m7oA MG Rep, Mult 7,8,16,267,320
70.02 1 1zdmB XE Rep, Mult 6,7,19,266,267,298
80.02 1 3cejB AVF Rep, Mult 319,320,321,337
90.02 1 1to60 III Rep, Mult 1,262,294,296,301,302,304,309,315,316,317,318,319,321,322,323,324,327,344,347,348,349
100.02 1 1kgzB MN Rep, Mult 66,112,273
110.02 1 3mboC MG Rep, Mult 268,278
120.02 1 3qqsA MG Rep, Mult 272,273
130.02 1 3mboE MG Rep, Mult 268,271
140.02 1 1bk5B CO Rep, Mult 114,170
150.02 1 1exvB 700 Rep, Mult 182,202,206
160.02 1 1o5qA MG Rep, Mult 170,240

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
10.0601ahpA0.4466.680.0770.7512.4.1.1NA
20.0602qr5A0.4166.250.0800.6593.4.19.1NA
30.0602azdB0.4426.670.0610.7462.4.1.1270
40.0602epoA0.4116.240.0710.6593.2.1.52NA
50.0601e3xA0.4036.890.0260.6933.2.1.1129
60.0601djnA0.4196.840.0530.7181.5.8.2,1.5.99.7170
70.0602tmdA0.4206.840.0530.7211.5.8.2333
80.0602c4mC0.4386.610.0380.7262.4.1.1NA
90.0602bs9E0.4066.620.0600.6843.2.1.37NA
100.0601ps9A0.4056.250.0530.6481.3.1.34NA
110.0601qbaA0.4186.990.0490.7373.2.1.52NA
120.0602epoB0.3547.010.0500.6153.2.1.52NA
130.0601to6B0.9271.430.3040.9642.7.1.3195,136,171,185,270,279
140.0602cftA0.4315.130.0890.5983.1.3.74NA
150.0602bfgA0.4156.650.0660.7013.2.1.37NA
160.0602pbgA0.4156.680.0660.6793.2.1.85NA
170.0602r4uA0.4106.390.0680.6542.4.1.2188
180.0603gpbA0.4466.450.0630.7212.4.1.1NA
190.0601c7sA0.4166.810.0620.7183.2.1.52NA

(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
00.460.7713.800.340.943cwcB GO:0008887 GO:0016301 GO:0016310 GO:0016740 GO:0031388
10.440.9411.170.300.961to6A GO:0000166 GO:0005524 GO:0008887 GO:0016301 GO:0016310 GO:0016740 GO:0031388
20.070.4515.970.060.683kc2B GO:0046474
30.070.4385.030.090.604bx2A GO:0000287 GO:0004647 GO:0004721 GO:0005737 GO:0005829 GO:0005856 GO:0005886 GO:0005911 GO:0006470 GO:0007088 GO:0008152 GO:0015629 GO:0016020 GO:0016787 GO:0016791 GO:0030027 GO:0030496 GO:0030836 GO:0031072 GO:0031247 GO:0031258 GO:0032154 GO:0032361 GO:0032465 GO:0032587 GO:0033883 GO:0042803 GO:0042995 GO:0046872 GO:0070062 GO:0070938 GO:0071318
40.070.4415.060.100.613hltA GO:0016311 GO:0016791 GO:0019899 GO:0046872 GO:0070062
50.070.4525.960.050.683rf6B GO:0046474
60.070.4375.290.080.614bkmA GO:0000121 GO:0000287 GO:0004647 GO:0004721 GO:0004725 GO:0005737 GO:0005829 GO:0005856 GO:0005886 GO:0005911 GO:0005975 GO:0006114 GO:0006470 GO:0006650 GO:0007088 GO:0008152 GO:0008967 GO:0015629 GO:0016020 GO:0016311 GO:0016787 GO:0016791 GO:0030027 GO:0030496 GO:0030836 GO:0031072 GO:0031247 GO:0031258 GO:0032154 GO:0032361 GO:0032465 GO:0032587 GO:0033883 GO:0035335 GO:0042803 GO:0042995 GO:0043136 GO:0045721 GO:0046872 GO:0070062 GO:0070938 GO:0071318 GO:0098519
70.070.4404.790.090.602ho4B GO:0016311 GO:0016791 GO:0019899 GO:0046872 GO:0070062
80.070.4355.210.110.611zjjB GO:0046872
90.060.4215.090.130.592c4nA GO:0000287 GO:0005829 GO:0005975 GO:0008253 GO:0016311 GO:0016787 GO:0046050 GO:0046872
100.060.4304.990.100.593eprA GO:0016787
110.060.4235.010.150.581ydfA GO:0016787
120.060.4295.090.090.591vjrA GO:0016311 GO:0016791 GO:0046872
130.060.4155.640.080.612hx1A GO:0046872
140.060.4255.080.080.591yv9A GO:0016787
150.060.4235.080.100.593pdwA GO:0016311 GO:0016787 GO:0016791 GO:0046872
160.060.4265.200.130.601wviA
170.060.4225.210.140.591ys9A
180.060.3566.140.060.565hbrA GO:0048037


Consensus prediction of GO terms
 
Molecular Function GO:0008887 GO:0005524
GO-Score 0.70 0.44
Biological Processes GO:0031388
GO-Score 0.70
Cellular Component GO:0070062 GO:0032587 GO:0030496 GO:0005829 GO:0070938 GO:0032154 GO:0005911 GO:0031258 GO:0015629
GO-Score 0.13 0.07 0.07 0.07 0.07 0.07 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.