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I-TASSER results for job id Rv1888c

[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
10.07 4 1ow6C III Rep, Mult 36,39,40,43,81,84,85
20.05 3 4d2dA 78N Rep, Mult 45,48,51,52,55,163
30.05 3 3luhB 5GP Rep, Mult 74,78
40.05 3 5is0C 6ET Rep, Mult 81,122,129
50.05 3 1cbkA SO4 Rep, Mult 63,74,75,78
60.04 2 4y3bA 49F Rep, Mult 33,36,37,122
70.04 2 1dxoA DQN Rep, Mult 92,111,175
80.04 2 3rifB IVM Rep, Mult 40,41,42,45,46,49
90.02 1 3ri5E IVM Rep, Mult 36,37,40,41,43,44
100.02 1 4ev6E MG Rep, Mult 43,129
110.02 1 3oc4B FAD Rep, Mult 92,93
120.02 1 1uduB MG Rep, Mult 90,176
130.02 1 3riaD IVM Rep, Mult 74,78,127,130,131,134,138
140.02 1 3vh7E MG Rep, Mult 30,33

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
10.0602p3gX0.4335.370.0180.7202.7.11.1NA
20.0603gehA0.5214.470.0370.7693.6.-.-NA
30.0601jtnA0.2695.610.0140.4843.2.1.17NA
40.0601bdgA0.4704.580.0650.7152.7.1.120
50.0601ct9A0.4864.970.0480.7746.3.5.4NA
60.0601occA0.4545.060.0780.7261.9.3.1NA
70.0602ozaA0.4805.510.0240.8062.7.11.1,2.7.11.24NA
80.0603cxhN0.4734.840.0430.7631.10.2.295,97
90.0601hxgA0.5014.520.0430.7424.2.3.9,4.1.99.7NA
100.0601wmwA0.4874.480.0710.7102.5.1.-NA
110.0601ig8A0.3654.940.0880.5702.7.1.1NA
120.0602frvD0.4895.260.0510.7851.12.2.131,40,76
130.0601qhaA0.5105.100.0540.8282.7.1.1NA
140.0603i9wA0.4753.740.0410.6612.7.13.354,144
150.0601frvB0.4745.080.0980.7631.12.2.1NA
160.0602ewgA0.4784.840.0340.7632.5.1.10NA
170.0601cc1L0.4824.880.0710.7901.12.99.6113
180.0602nztA0.4344.830.0330.6942.7.1.1NA
190.0601j36A0.4704.570.0880.6773.4.15.15

(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
00.190.5442.460.070.641oedA 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
10.180.5753.660.090.754aq5E 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
20.160.5562.940.110.682mawA 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
30.140.5502.310.070.641oedB 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
40.140.5512.360.020.641oedE 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
50.110.5322.500.070.631oedC 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
60.110.4993.460.090.672ksrA 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
70.100.5293.130.080.662lm2A 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
80.100.5713.640.040.754aq5A 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
90.100.5543.630.060.734aq5C 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
100.100.5493.480.100.714pirC 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
110.080.4783.520.090.642llyA 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
120.080.5023.490.090.684z90A GO:0005230 GO:0006810 GO:0006811 GO:0016020 GO:0016021 GO:0034220
130.070.5933.490.070.754aq5B 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
140.070.5673.680.040.743jafA GO:0005230 GO:0005254 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006821 GO:0007218 GO:0007417 GO:0008270 GO:0016020 GO:0016021 GO:0016594 GO:0016934 GO:0022824 GO:0030054 GO:0030425 GO:0034220 GO:0034707 GO:0042995 GO:0043200 GO:0043204 GO:0045202 GO:0045211 GO:0045664 GO:0046872 GO:0051260 GO:0060012 GO:0071230 GO:0071294 GO:0071361 GO:0099565 GO:1902476
150.070.5553.810.080.744tnwA GO:0005230 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0008068 GO:0016020 GO:0016021 GO:0016595 GO:0030054 GO:0031987 GO:0045202 GO:0045211 GO:0051259 GO:1902476
160.070.5463.550.070.704ireB GO:0005230 GO:0005267 GO:0005272 GO:0005886 GO:0006810 GO:0006811 GO:0006813 GO:0006814 GO:0016020 GO:0016021 GO:0035725 GO:0071805
170.070.5663.160.030.714cofA GO:0004890 GO:0005216 GO:0005230 GO:0005254 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006821 GO:0007165 GO:0007605 GO:0016020 GO:0016021 GO:0022851 GO:0030054 GO:0034220 GO:0034707 GO:0043523 GO:0043524 GO:0045202 GO:0045211 GO:0048666 GO:0060021 GO:0060080 GO:0060119 GO:0060384 GO:0071420 GO:0090102 GO:1901215 GO:1902476 GO:1902711
180.070.5413.560.070.714yeuA GO:0005230 GO:0005267 GO:0005272 GO:0005886 GO:0006810 GO:0006811 GO:0006813 GO:0006814 GO:0016020 GO:0016021 GO:0034220 GO:0035725 GO:0071805


Consensus prediction of GO terms
 
Molecular Function GO:0004889 GO:0046983 GO:0042277 GO:0042165 GO:0016247 GO:0042802 GO:0070405 GO:0015464 GO:0022824
GO-Score 0.58 0.31 0.31 0.31 0.31 0.31 0.31 0.31 0.31
Biological Processes GO:0098655 GO:1904018 GO:0032680 GO:0014070 GO:0006950 GO:0045765 GO:0006875 GO:1905114 GO:0036293 GO:0055074 GO:0043279 GO:0007268 GO:0070838 GO:0043406 GO:0007611 GO:0042127 GO:0072503 GO:0032147 GO:1903556
GO-Score 0.58 0.31 0.31 0.31 0.31 0.31 0.31 0.31 0.31 0.31 0.31 0.31 0.31 0.31 0.31 0.31 0.31 0.31 0.31
Cellular Component GO:0045211 GO:0030054 GO:0034702 GO:0005887 GO:0098802
GO-Score 0.58 0.58 0.31 0.31 0.31

(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.