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I-TASSER results for job id Rv1913

[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
10.63 255 5ewaB 9BZ Rep, Mult 69,71,150,175,178,185,186,215
20.29 121 1wuoB ZN Rep, Mult 67,69,150,175
30.04 24 1x8gA CO3 Rep, Mult 71,150,175,178,215
40.03 12 2bmiB NA Rep, Mult 22,23,37,71,172
50.02 14 1kr3A 113 Rep, Mult 150,175,178,186,215
60.02 11 3iofA IFS Rep, Mult 20,40,70,71,101,104,105,109,150,175,186,215
70.01 5 2fhxA AZI Rep, Mult 37,66,67,172,174,175
80.00 1 2y87A MG Rep, Mult 70,117
90.00 1 4gyuA IMD Rep, Mult 37,38,65,67,72
100.00 1 4ey2B ZN Rep, Mult 97,188
110.00 2 1jjeA ZN Rep, Mult 23,217
120.00 1 1vgn0 III Rep, Mult 18,21,210,217,218,219,220,222,226
130.00 1 2bgaA AZI Rep, Mult 140,161
140.00 1 1bc20 III Rep, Mult 183,184,186,187,191,192,230,231,232
150.00 1 1m2xA ZN Rep, Mult 226,229
160.00 1 2bflB AZI Rep, Mult 150,186
170.00 1 2cfzA 1DO Rep, Mult 71,106,109,113,115,184
180.00 1 3f9oA CO3 Rep, Mult 201,202,205,206,208
190.00 1 3f9oA CO3 Rep, Mult 106,118

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
10.4291l9yA0.7342.920.1600.8763.5.2.671
20.4131qh3A0.6503.020.1530.7763.1.2.671
30.2191a8tA0.7901.610.1900.8443.5.2.6NA
40.1932q42A0.6442.860.1610.7523.1.2.621,69,71
50.1302qedA0.6253.050.1370.7443.1.2.673
60.1071qh5A0.6512.980.1530.7763.1.2.6NA
70.1022p18A0.6813.030.1670.8123.1.2.671
80.0711xm8A0.6452.840.1670.7523.1.2.671
90.0601ko2A0.7661.540.2210.8163.5.2.6NA
100.0601znbB0.8031.510.1920.8523.5.2.6152,215
110.0602dkfA0.5814.050.1440.7723.1.-.-73
120.0602zo4A0.7403.160.1900.8963.-.-.-NA
130.0602cbnA0.5114.940.1140.7283.1.26.1123,69,71
140.0601x8hA0.8391.590.1750.8923.5.2.671
150.0601zedA0.4395.680.0670.7203.1.3.1148,228
160.0602gmnA0.7223.290.1670.8883.5.2.671
170.0602i7vA0.5714.320.0900.7763.1.27.-71
180.0601ayxA0.4096.160.0390.7123.2.1.3NA
190.0601smlA0.7313.190.1520.8883.5.2.671
200.0603dhaA0.6293.160.1670.7443.1.1.-71
210.0602ohhA0.7363.160.1880.8921.-.-.-71
220.0601p9eA0.6783.790.1700.8483.1.8.1NA
230.0603hnnA0.6913.270.1200.8321.-.-.-NA
240.0601m2xA0.7901.460.1580.8363.5.2.671
250.0601bvtA0.7661.570.2110.8163.5.2.6NA
260.0601ycfA0.7243.010.1610.8721.7.99.771

(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
00.530.7901.460.160.841m2xA GO:0008270 GO:0008800 GO:0016787 GO:0017001 GO:0042597 GO:0046677 GO:0046872
10.520.7403.160.190.902zo4A GO:0046872
20.490.7591.740.190.823l6nA GO:0008270 GO:0008800 GO:0017001 GO:0046872
30.480.7901.610.190.841a8tA GO:0008270 GO:0008800 GO:0016787 GO:0017001 GO:0042597 GO:0046677 GO:0046872
40.470.6353.580.130.792r2dA GO:0016787 GO:0046872 GO:0102007
50.470.6642.920.230.792zwrB GO:0046872
60.410.8361.480.130.883sd9A GO:0008270 GO:0008800 GO:0016787 GO:0017001 GO:0046677 GO:0046872
70.390.7611.580.230.814d1tA GO:0008270 GO:0008800 GO:0017001 GO:0046872
80.380.6213.830.170.783aj3A GO:0016787 GO:0042820 GO:0046872 GO:0047585
90.380.8391.590.170.893faiA GO:0008270 GO:0008800 GO:0016787 GO:0017001 GO:0042597 GO:0046677 GO:0046872
100.380.7551.960.170.824hl2A GO:0008270 GO:0008800 GO:0016787 GO:0017001 GO:0042597 GO:0046677 GO:0046872
110.370.7691.650.180.822yntA GO:0046872
120.360.6293.160.170.743dhaA GO:0016787 GO:0046872 GO:0102007
130.350.7471.800.210.812m5cA GO:0008270 GO:0008800 GO:0016787 GO:0017001 GO:0042597 GO:0046677 GO:0046872
140.340.7571.770.170.824wd6A GO:0046872
150.330.7581.830.180.824ubqA GO:0008270 GO:0008800 GO:0016787 GO:0017001 GO:0046677 GO:0046872
160.320.8392.090.140.924bp0A GO:0008270 GO:0008800 GO:0016787 GO:0017001 GO:0046872
170.310.7233.280.170.893lvzB GO:0046872
180.280.7651.750.170.825ev6B GO:0008270 GO:0008800 GO:0016787 GO:0017001 GO:0042597 GO:0046677 GO:0046872
190.250.7213.110.190.875axoA GO:0046872
200.230.6442.860.160.752q42A GO:0004416 GO:0005506 GO:0005739 GO:0008270 GO:0016787 GO:0019243 GO:0046872
210.230.7362.840.150.871e5dA GO:0009055 GO:0010181 GO:0016491 GO:0022904 GO:0046872 GO:0055114
220.220.7153.320.170.864ad9A GO:0004521 GO:0005739 GO:0005759 GO:0008270 GO:0016787 GO:0046872 GO:0090502
230.170.8012.930.150.945aijA GO:0016787 GO:0042802 GO:0046872 GO:0046983
240.160.7923.000.160.934pdxA GO:0016787 GO:0018741 GO:0030288 GO:0046983


Consensus prediction of GO terms
 
Molecular Function GO:0008270 GO:0008800 GO:0102007
GO-Score 0.88 0.88 0.47
Biological Processes GO:0017001 GO:0046677
GO-Score 0.88 0.75
Cellular Component GO:0042597
GO-Score 0.75

(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.