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I-TASSER results for job id Rv2306B

[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
10.12 10 3ri5D IVM Rep, Mult 40,43,47,67,70,71,74,78
20.06 5 3re7A CU Rep, Mult 19,32,36
30.04 3 3p4wD DSF Rep, Mult 8,9,46,65,68,69
40.04 3 3a0hM MGE Rep, Mult 41,42,45,46
50.04 3 5d57C 78M Rep, Mult 39,42,43,46,123
60.03 2 3rifB IVM Rep, Mult 16,17,18,21,22,25
70.03 2 3u3cA III Rep, Mult 6,9,10,13
80.02 2 3a0bj MGE Rep, Mult 32,35,36,39,50,51
90.02 2 2yxhA MG Rep, Mult 15,42
100.02 2 1ow7C III Rep, Mult 46,47,51,52,55,69,70
110.01 1 4buoA GLY Rep, Mult 5,50,54
120.01 1 1e3dB FSX Rep, Mult 8,140
130.01 1 3u3fA III Rep, Mult 6,10,14,17,123,130
140.01 1 3k2sA CLR Rep, Mult 5,8,12,42
150.01 1 2rlfD RIM Rep, Mult 5,8
160.01 1 3p4wB DSF Rep, Mult 15,16,72,75
170.01 1 1s5lT CLA Rep, Mult 75,78

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
10.1882ksfA0.5043.440.0870.7082.7.13.313,46,75,123
20.1351wcrA0.4822.490.0470.5972.7.1.6917
30.0601fftA0.5324.270.0620.8331.10.3.-NA
40.0601rqiA0.5333.960.0670.7922.5.1.10NA
50.0603gtdA0.5373.820.0650.7714.2.1.2NA
60.0603kb9A0.5293.680.0170.7784.2.3.3726
70.0602f8zF0.5373.490.0310.7712.5.1.10,2.5.1.1NA
80.0603i9wA0.6723.630.0510.9382.7.13.324,41
90.0602e9fB0.5334.110.0570.7924.3.2.121
100.0602a06C0.5763.760.0380.8121.10.2.213,133
110.0602wbiB0.5213.830.0580.7781.3.99.-NA
120.0601c17M0.5833.680.0570.8333.6.3.1414
130.0603eziA0.5812.580.0580.7222.7.13.3NA
140.0603lomA0.5333.870.0740.7782.5.1.10NA
150.0601k04A0.4763.600.0160.7012.7.10.215
160.0601qleC0.5783.350.0500.8261.9.3.146
170.0601xmeA0.5274.580.0690.9031.9.3.1NA
180.0602v8tA0.5314.340.0520.7851.11.1.635
190.0602frvD0.5234.390.0950.7991.12.2.112
200.0602dh4A0.5354.080.1050.8192.5.1.29NA
210.0601tj7A0.5344.070.0290.7854.3.2.1NA

(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
00.220.6762.870.030.892mawA GO:0000187 GO:0001540 GO:0001666 GO:0004889 GO:0005216 GO:0005230 GO:0005886 GO:0005892 GO:0006810 GO:0006811 GO:0006816 GO:0006874 GO:0007165 GO:0007271 GO:0007613 GO:0008284 GO:0015276 GO:0015464 GO:0015643 GO:0016020 GO:0016021 GO:0017081 GO:0022848 GO:0030054 GO:0032720 GO:0034220 GO:0035094 GO:0042166 GO:0042803 GO:0045202 GO:0045211 GO:0045766 GO:0050890 GO:0098655 GO:0099565
10.210.6603.080.070.882ksrA GO:0001508 GO:0001661 GO:0001666 GO:0004889 GO:0005216 GO:0005230 GO:0005886 GO:0005892 GO:0006810 GO:0006811 GO:0006816 GO:0006939 GO:0007165 GO:0007271 GO:0007274 GO:0007601 GO:0007605 GO:0007612 GO:0007613 GO:0007626 GO:0008144 GO:0008306 GO:0008542 GO:0009897 GO:0014059 GO:0015276 GO:0015464 GO:0016020 GO:0016021 GO:0019233 GO:0021562 GO:0021631 GO:0021771 GO:0021952 GO:0021955 GO:0030054 GO:0030890 GO:0032225 GO:0032226 GO:0033603 GO:0035094 GO:0035095 GO:0035176 GO:0042053 GO:0042113 GO:0042166 GO:0042220 GO:0042320 GO:0042391 GO:0045188 GO:0045202 GO:0045211 GO:0045471 GO:0045759 GO:0046982 GO:0048814 GO:0050877 GO:0050890 GO:0051291 GO:0051899 GO:0051963 GO:0060084 GO:0098655 GO:0099565
20.200.6623.070.050.874pirC GO:0004889 GO:0004993 GO:0005230 GO:0005232 GO:0005886 GO:0005892 GO:0006810 GO:0006811 GO:0007210 GO:0007271 GO:0015276 GO:0015464 GO:0016020 GO:0016021 GO:0022850 GO:0030054 GO:0034220 GO:0042166 GO:0045202 GO:0045211 GO:0051378 GO:0098655 GO:1904602
30.190.6583.400.090.913o1jA GO:0000155 GO:0000160 GO:0000166 GO:0004673 GO:0004871 GO:0005524 GO:0005622 GO:0007165 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0018106 GO:0023014
40.190.6573.580.040.914aq5C GO:0004889 GO:0005216 GO:0005230 GO:0005886 GO:0006810 GO:0006811 GO:0016020 GO:0016021 GO:0030054 GO:0034220 GO:0045202 GO:0045211 GO:0098655
50.170.6462.560.040.821oedB GO:0004889 GO:0005216 GO:0005230 GO:0005886 GO:0006810 GO:0006811 GO:0016020 GO:0016021 GO:0030054 GO:0034220 GO:0045202 GO:0045211 GO:0098655
60.170.6583.530.050.924aq5A GO:0004889 GO:0005216 GO:0005230 GO:0005886 GO:0006810 GO:0006811 GO:0016020 GO:0016021 GO:0030054 GO:0034220 GO:0045202 GO:0045211 GO:0098655
70.160.6412.540.050.811oedA GO:0004889 GO:0005216 GO:0005230 GO:0005886 GO:0006810 GO:0006811 GO:0016020 GO:0016021 GO:0030054 GO:0034220 GO:0045202 GO:0045211 GO:0098655
80.160.6272.820.040.812lm2A GO:0001508 GO:0001661 GO:0001666 GO:0004889 GO:0005216 GO:0005230 GO:0005886 GO:0005892 GO:0006810 GO:0006811 GO:0006816 GO:0006939 GO:0007165 GO:0007271 GO:0007274 GO:0007601 GO:0007605 GO:0007612 GO:0007613 GO:0007626 GO:0008144 GO:0008306 GO:0008542 GO:0009897 GO:0014059 GO:0015276 GO:0015464 GO:0016020 GO:0016021 GO:0019233 GO:0021562 GO:0021631 GO:0021771 GO:0021952 GO:0021955 GO:0030054 GO:0030890 GO:0032225 GO:0032226 GO:0033603 GO:0035094 GO:0035095 GO:0035176 GO:0042053 GO:0042113 GO:0042166 GO:0042220 GO:0042320 GO:0042391 GO:0045188 GO:0045202 GO:0045211 GO:0045471 GO:0045759 GO:0046982 GO:0048814 GO:0050877 GO:0050890 GO:0051291 GO:0051899 GO:0051963 GO:0060084 GO:0098655 GO:0099565
90.150.7062.960.070.903i9yA GO:0000155 GO:0000160 GO:0000166 GO:0004673 GO:0004871 GO:0005524 GO:0005622 GO:0007165 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0018106 GO:0023014
100.140.6372.730.030.821oedE GO:0004889 GO:0005216 GO:0005230 GO:0005886 GO:0006810 GO:0006811 GO:0016020 GO:0016021 GO:0030054 GO:0034220 GO:0045202 GO:0045211 GO:0098655
110.140.6683.360.070.904aq5E GO:0004889 GO:0005216 GO:0005230 GO:0005886 GO:0006810 GO:0006811 GO:0016020 GO:0016021 GO:0030054 GO:0034220 GO:0045202 GO:0045211 GO:0098655
120.130.6212.760.080.801oedC GO:0004889 GO:0005216 GO:0005230 GO:0005886 GO:0006810 GO:0006811 GO:0016020 GO:0016021 GO:0030054 GO:0034220 GO:0045202 GO:0045211 GO:0098655
130.130.6723.630.050.943i9wA GO:0000155 GO:0000160 GO:0000166 GO:0004673 GO:0004721 GO:0004871 GO:0005524 GO:0005622 GO:0005886 GO:0006470 GO:0007165 GO:0009061 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0016868 GO:0018106 GO:0023014 GO:0046777 GO:0071310
140.110.6893.240.040.924aq5B GO:0004889 GO:0005216 GO:0005230 GO:0005886 GO:0006810 GO:0006811 GO:0016020 GO:0016021 GO:0030054 GO:0034220 GO:0045202 GO:0045211 GO:0098655
150.110.5803.210.020.792llyA GO:0001508 GO:0001666 GO:0004889 GO:0005216 GO:0005230 GO:0005886 GO:0005892 GO:0006281 GO:0006810 GO:0006811 GO:0006816 GO:0006979 GO:0007165 GO:0007268 GO:0007271 GO:0007274 GO:0007585 GO:0007626 GO:0009897 GO:0014059 GO:0015276 GO:0015464 GO:0016020 GO:0016021 GO:0019233 GO:0030054 GO:0030425 GO:0034220 GO:0035094 GO:0035095 GO:0035640 GO:0042113 GO:0042166 GO:0042391 GO:0043025 GO:0045202 GO:0045211 GO:0050877 GO:0050890 GO:0051899 GO:0060080 GO:0098655
160.070.7142.770.090.894akkA GO:0003723 GO:0006351 GO:0006355 GO:0031564
170.070.6553.910.060.972d4yA GO:0005198 GO:0005576 GO:0009288 GO:0009424 GO:0044780 GO:0071973
180.070.6793.700.060.984ut1A GO:0005198 GO:0009424 GO:0044780


Consensus prediction of GO terms
 
Molecular Function GO:0004889 GO:0015464 GO:0042166 GO:0042277 GO:0016247 GO:0042802 GO:0022824 GO:0046983 GO:0043176 GO:0008227 GO:0099589 GO:0032550 GO:0016775 GO:0004672 GO:0035639 GO:0032559
GO-Score 0.60 0.51 0.51 0.45 0.45 0.45 0.45 0.45 0.41 0.41 0.41 0.39 0.39 0.39 0.39 0.39
Biological Processes GO:0098655 GO:0007271 GO:0032147 GO:0006875 GO:0072503 GO:0055074 GO:1904018 GO:0043406 GO:1903556 GO:0045765 GO:0032680 GO:0045187 GO:0050953 GO:0014046 GO:0050773 GO:0042417 GO:0042747 GO:0050671 GO:0007631 GO:0021794 GO:0033605 GO:0030888 GO:0051259 GO:0051705 GO:0042069 GO:0006936 GO:0007274 GO:0021554 GO:0051703 GO:0007612 GO:0010769 GO:0021602 GO:0050807 GO:0021955 GO:0050954 GO:0042748 GO:0048857 GO:0097305 GO:0032225 GO:0044087 GO:0060073 GO:0048813 GO:0007416 GO:0007632 GO:0050806 GO:0098900 GO:0030534 GO:0050871 GO:0007186 GO:0018202 GO:0001666 GO:0099565 GO:0035094 GO:0006816 GO:0007613
GO-Score 0.60 0.51 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.41 0.39 0.39 0.39 0.39 0.39 0.39
Cellular Component GO:0045211 GO:0030054 GO:0005892 GO:0098552 GO:0009986 GO:0034703
GO-Score 0.60 0.60 0.51 0.42 0.42 0.41

(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.