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I-TASSER results for job id Rv1367c

[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
10.54 153 3o88A BSH Rep, Mult 34,35,38,104,105,147,149,227,317,318,319,340
20.16 61 2wzzA ZX1 Rep, Mult 35,147,227,315,316,317,318
30.03 12 1l2sA STC Rep, Mult 35,38,149,227,317,318,319,340
40.03 13 2zm7A ACA Rep, Mult 35,147,281,293,316,318,361
50.01 3 2hdsA 4MB Rep, Mult 105,145,147,289,290,292
60.01 3 1scwA CP5 Rep, Mult 34,35,147,293,307,308,309,314,315
70.01 3 2qmiH DO3 Rep, Mult 56,57,93,290
80.01 4 2hdqB C21 Rep, Mult 3,6,8,237,238,241
90.01 5 3s22A 3S2 Rep, Mult 35,106,147,227,289,312,313,314
100.01 5 2hdrB 4A3 Rep, Mult 106,217,218,227,315,316
110.00 1 2hdrA 4A3 Rep, Mult 122,123,219,220,221
120.00 1 1kvlA KCP Rep, Mult 63,64,123,124,125,128,157,160,221
130.00 1 3gv9A GV9 Rep, Mult 112,123,124,128,221,222
140.00 1 2hdqA C21 Rep, Mult 243,244,246,262,307,309,327
150.00 1 2hdrB 4A3 Rep, Mult 265,266,299,300,301,302,303
160.00 1 3gv9A GV9 Rep, Mult 63,160,161
170.00 1 1pi5B SM2 Rep, Mult 278,280,281,284,285,290,295
180.00 1 2hdrA 4A3 Rep, Mult 283,284,285
190.00 1 2hdsA 4MB Rep, Mult 93,94,142,267,268
200.00 1 2hduA F12 Rep, Mult 40,43,44,47

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
10.3841ci8A0.8042.370.3270.8753.1.1.135,38,315
20.2301c3bA0.7162.850.2070.8043.5.2.635,38
30.1182zc7A0.7102.910.1880.8013.5.2.635,38,147
40.1171zkjA0.7072.950.2100.8013.5.2.635,38
50.1151fr1A0.7142.970.1930.8063.5.2.635,38
60.0663bfdA0.4774.180.1070.5843.5.2.6NA
70.0662blmA0.4744.260.1400.5923.5.2.635,38,148
80.0663c4pA0.4834.010.1530.5783.5.2.6238
90.0661g68A0.4884.090.1240.5923.5.2.6NA
100.0661yljA0.4744.150.1160.5813.5.2.6NA
110.0661dy6A0.4774.210.1070.5863.5.2.635,38,148
120.0661iysA0.4764.080.0990.5783.5.2.6NA
130.0661hzoA0.4804.190.1070.5893.5.2.6NA
140.0661bueA0.4764.210.1030.5843.5.2.635,38,148
150.0661mfoA0.4753.980.1340.5763.5.2.6NA
160.0662jc7A0.4533.360.0940.5333.5.2.635
170.0662rl3B0.4513.720.1110.5463.5.2.635
180.0602v2fF0.4824.240.0770.6073.4.16.4NA
190.0601iyqA0.4744.020.1030.5763.5.2.6NA
200.0602qz6A0.7052.920.2130.7933.5.2.6NA
210.0603fwmA0.4934.430.1030.6232.4.1.129,35
220.0601ga0A0.7143.110.2010.8143.5.2.635,38,147
230.0603czdA0.4854.550.1190.6183.5.1.235
240.0603fwlA0.4854.520.1100.6152.4.1.129NA
250.0602qmiA0.7323.050.2210.8253.5.2.635,38
260.0602rcxB0.7142.880.2070.8043.5.2.6238
270.0602e8iA0.6853.340.2010.7903.5.1.46238
280.0602vgkD0.5194.500.1050.6553.4.16.4NA
290.0601u60C0.4904.270.1090.6153.5.1.2NA
300.0601ei5A0.6753.350.1590.7803.4.11.1935,38,147
310.0603a3iA0.5104.430.0920.6523.4.16.4229
320.0601e25A0.4943.950.1210.5923.5.2.635,38
330.0602v1zA0.4884.020.1320.5843.5.2.6NA
340.0601xp4A0.4814.500.1430.6023.4.16.435
350.0602wzxA0.7202.980.2020.8123.5.2.6172,177,179,238
360.0603bydA0.4774.180.0990.5843.5.2.6NA

(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
00.540.8652.320.340.934iviA GO:0016787 GO:0052689
10.370.8042.370.330.881ci8A GO:0005737 GO:0016787
20.360.7053.220.200.801cefA GO:0004180 GO:0005576 GO:0006508 GO:0008233 GO:0008360 GO:0009002 GO:0009252 GO:0016787 GO:0071555
30.330.7142.990.210.815e2hA GO:0008800 GO:0016787 GO:0017001 GO:0030288 GO:0046677
40.330.7213.060.210.824y7pA GO:0004180 GO:0006508
50.320.6593.470.190.764gb7A GO:0016054 GO:0016787 GO:0019875
60.310.7242.660.200.804gdnA GO:0005886 GO:0016020 GO:0016021
70.280.6953.060.210.805eviB GO:0008800 GO:0016787 GO:0017001 GO:0030288 GO:0046677
80.260.7052.920.210.792qz6A GO:0008800 GO:0016787 GO:0017001 GO:0030288 GO:0042597 GO:0046677
90.250.7242.900.180.813o3vA GO:0008800 GO:0016020 GO:0016021 GO:0016787 GO:0017001 GO:0030288 GO:0046677
100.250.6863.360.200.793a65A GO:0016787 GO:0019875 GO:0019876
110.250.7232.960.200.814gzbA GO:0008800 GO:0016787 GO:0017001 GO:0030288 GO:0033252 GO:0042597 GO:0046677
120.250.7173.030.190.813s4xA GO:0008800 GO:0016787 GO:0017001 GO:0030288 GO:0042597 GO:0046677
130.250.7232.790.230.813ws1A GO:0008800 GO:0016787 GO:0017001 GO:0030288 GO:0046677 GO:0046872
140.220.7102.910.190.802zc7A GO:0008800 GO:0016787 GO:0017001 GO:0030288 GO:0046677
150.200.7323.050.220.822qmiA
160.180.8272.830.250.923hlfA GO:0016740 GO:0016746 GO:0016787 GO:0017000 GO:0030639 GO:0050832
170.100.6982.920.230.785e2gA GO:0008800 GO:0016787 GO:0017001 GO:0030288 GO:0046677
180.100.6792.550.190.754e6xA GO:0008800 GO:0016020 GO:0016021 GO:0016787 GO:0017001 GO:0030288 GO:0046677


Consensus prediction of GO terms
 
Molecular Function GO:0052689 GO:0009002 GO:0008800
GO-Score 0.54 0.36 0.33
Biological Processes GO:0006508 GO:0009252 GO:0071555 GO:0008360 GO:0046677 GO:0017001
GO-Score 0.57 0.36 0.36 0.36 0.33 0.33
Cellular Component GO:0005737 GO:0005576 GO:0030288
GO-Score 0.37 0.36 0.33

(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.