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I-TASSER results for job id Rv2372c

[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
10.68 24 2cx8A SAH Rep, Mult 175,176,177,198,199,200,201,202,203,220,222,223,225,226,227,229,232
20.04 2 1vhk0 III Rep, Mult 93,96,97,100,101,102,136,137,140,141,143,224,225,226,227,228,230,231,235,238,239,241,242,248,249
30.02 1 1v2xA PO4 Rep, Mult 87,89,90,201,228
40.02 1 2z8yO XE Rep, Mult 82,158,197,211
50.02 1 1v6z0 III Rep, Mult 96,100,101,102,141,143,177,178,180,182,184,222,223,227,228,231,235,238,239,241
60.02 1 1z850 III Rep, Mult 100,184,238,239,243

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
10.1771zjrA0.5153.560.1020.6372.1.1.3487,89,94,101,203
20.0603gyqA0.5594.400.1070.7412.1.1.66101,135
30.0601b0pA0.3696.700.0720.6911.2.7.1NA
40.0603hm7B0.4654.680.0480.6603.5.2.5230
50.0602pdaA0.4195.890.0870.6991.2.7.1NA
60.0602vvnA0.5204.890.0590.7563.2.1.5244
70.0601m7jA0.4684.550.0610.6603.5.1.8121
80.0601c7sA0.5564.620.0690.7793.2.1.52NA
90.0603gipA0.4734.520.0810.6643.5.1.82NA
100.0603gh4A0.5724.740.0600.8093.2.1.52NA
110.0601e9yB0.4594.760.0330.6643.5.1.5NA
120.0603giqA0.4744.520.0810.6643.5.1.82132,138
130.0603d6nA0.4644.790.0920.6683.5.2.3NA
140.0601ie7C0.4594.700.0580.6603.5.1.5NA
150.0602vr2A0.4465.130.0490.6643.5.2.2NA
160.0602pffA0.5064.990.1000.7372.3.1.41,2.3.1.86NA
170.0601xc6A0.4764.580.0370.6643.2.1.2330
180.0602gjxA0.5554.670.0770.7793.2.1.52NA
190.0601xrtA0.4524.910.0810.6533.5.2.344
200.0602ftwA0.4455.340.0420.6953.5.2.2NA

(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
00.700.9200.671.000.934l69A GO:0005737 GO:0006364 GO:0008168 GO:0016740 GO:0032259 GO:0070042 GO:0070475
10.480.8082.570.240.931nxzA GO:0005737 GO:0006364 GO:0008168 GO:0016740 GO:0032259 GO:0070042 GO:0070475
20.470.8272.130.240.924e8bA GO:0005737 GO:0006364 GO:0008168 GO:0016740 GO:0032259 GO:0070042 GO:0070475
30.420.7792.510.220.894j3cB GO:0005737 GO:0006364 GO:0008168 GO:0016740 GO:0032259
40.420.7872.120.230.872egvA GO:0005737 GO:0006364 GO:0008168 GO:0016740 GO:0032259 GO:0070042 GO:0070475
50.410.5732.730.240.651v6zA GO:0005737 GO:0006364 GO:0008168 GO:0016740 GO:0032259 GO:0046872 GO:0051536 GO:0051539
60.380.7732.740.260.893kw2A GO:0005737 GO:0006364 GO:0008168 GO:0016740 GO:0032259
70.360.6592.270.320.731vhkB GO:0005737 GO:0006364 GO:0008168 GO:0016740 GO:0032259 GO:0070042 GO:0070475
80.340.7762.750.290.901vhkC GO:0005737 GO:0006364 GO:0008168 GO:0016740 GO:0032259 GO:0070042 GO:0070475
90.250.7012.590.250.811z85B GO:0005737 GO:0006364 GO:0008168 GO:0016740 GO:0032259 GO:0070042 GO:0070475
100.060.4304.840.050.622icsA GO:0016787 GO:0016810 GO:0046872
110.060.3154.930.060.451qpnA GO:0003824 GO:0004514 GO:0005618 GO:0005737 GO:0005886 GO:0009435 GO:0016740 GO:0016757 GO:0016763 GO:0019363 GO:0034213
120.060.2725.560.060.421ev4A GO:0004364 GO:0005634 GO:0005640 GO:0005737 GO:0005829 GO:0007568 GO:0008144 GO:0008152 GO:0016740 GO:0031667 GO:0042178 GO:0042493 GO:0043295
130.060.2874.130.070.383cfyA GO:0000160 GO:0000166 GO:0003677 GO:0005524 GO:0005622 GO:0006351 GO:0006355 GO:0008134 GO:0043565
140.060.2426.670.060.455et5A GO:0003824 GO:0005634 GO:0005737 GO:0005829 GO:0005975 GO:0006000 GO:0006094 GO:0008152 GO:0016311 GO:0016787 GO:0030018 GO:0030054 GO:0042132 GO:0042578 GO:0046872 GO:0070062
150.060.2255.790.110.391v2bB GO:0005509 GO:0009507 GO:0009523 GO:0009535 GO:0009536 GO:0009579 GO:0009654 GO:0015979 GO:0016020 GO:0019898
160.060.1914.400.040.262dlyA GO:0000122 GO:0000166 GO:0004672 GO:0004713 GO:0004715 GO:0005102 GO:0005524 GO:0005634 GO:0005737 GO:0005886 GO:0006468 GO:0007169 GO:0016301 GO:0016310 GO:0016740 GO:0030154 GO:0031234 GO:0038083 GO:0042127 GO:0043231 GO:0045087 GO:0070062
170.060.1313.520.030.161q08A GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0008270 GO:0045893 GO:0046872
180.060.1332.880.050.152e5qA GO:0005634 GO:0005654 GO:0006351 GO:0006355 GO:0008270 GO:0016568 GO:0035064 GO:0035098 GO:0045814 GO:0046872 GO:0061087


Consensus prediction of GO terms
 
Molecular Function GO:0070042
GO-Score 0.95
Biological Processes GO:0070475
GO-Score 0.95
Cellular Component GO:0005737
GO-Score 0.97

(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.