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I-TASSER results for job id Rv3395c

[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
10.33 37 2zriA ADP Rep, Mult 61,62,63,88,91,201
20.12 13 3cmvD MG Rep, Mult 61,62,129
30.05 5 4j7cD ATP Rep, Mult 62,200
40.04 5 3cmwA NUC Rep, Mult 140,141,144,148,167,168,169,170,171,186,187
50.02 2 3cmtA ALF Rep, Mult 191
60.02 2 3cmxD NUC Rep, Mult 140,141,144,186,187
70.01 1 2g88A DTP Rep, Mult 40,43
80.01 1 2zrcA PO4 Rep, Mult 108,110,111,114,115,116
90.01 1 2gblB MG Rep, Mult 61,85,166
100.01 1 1xmvA MG Rep, Mult 19,24,27,28
110.01 1 3s99A IOD Rep, Mult 72,124,125,160

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
10.0661g64B0.5383.280.0860.6672.5.1.17NA
20.0603gqbA0.6423.030.1080.7943.6.3.14NA
30.0601w36C0.3656.370.0750.7113.1.11.599
40.0602r9vA0.6313.280.0650.7943.6.3.14145
50.0601xfkA0.5234.990.0440.8193.5.3.8NA
60.0602zrpA0.8531.550.2270.9073.4.99.37168
70.0603crvA0.5173.930.0590.7113.6.4.12NA
80.0602qe7D0.6463.020.0760.7943.6.1.34NA
90.0603l9oA0.5504.360.0500.7943.6.4.1361
100.0602dpyB0.6243.310.0750.7993.6.3.14NA
110.0601w4rA0.5092.810.1110.6082.7.1.21197
120.0602ocaA0.5594.020.0690.7843.6.4.1263
130.0601pq3D0.5134.680.1000.7843.5.3.1NA
140.0601cbuB0.5133.510.0720.6422.7.1.156,2.7.7.6260,63,197
150.0602aebA0.5144.630.0770.7843.5.3.186
160.0601w36D0.5464.500.0700.7743.1.11.5119,163
170.0601fx0A0.6443.070.0650.7993.6.3.14NA
180.0603kx2B0.5364.100.0860.7503.6.4.13NA
190.0603fksF0.6213.620.0810.8043.6.3.14NA
200.0603b2qA0.5973.800.0590.7893.6.3.14191

(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
00.220.8821.870.220.951mo4A GO:0000150 GO:0000166 GO:0000287 GO:0000400 GO:0000725 GO:0000730 GO:0003677 GO:0003690 GO:0003697 GO:0004518 GO:0004519 GO:0004520 GO:0005524 GO:0005737 GO:0005829 GO:0006259 GO:0006281 GO:0006310 GO:0006312 GO:0006314 GO:0006974 GO:0008094 GO:0009432 GO:0009650 GO:0010212 GO:0016539 GO:0016787 GO:0016887 GO:0030145 GO:0042148 GO:0046677 GO:0090305
10.190.8442.100.170.943hr8A GO:0000150 GO:0000166 GO:0000400 GO:0000730 GO:0003677 GO:0003684 GO:0003690 GO:0003697 GO:0004520 GO:0005524 GO:0005737 GO:0005829 GO:0006259 GO:0006281 GO:0006310 GO:0006312 GO:0006974 GO:0008094 GO:0009432 GO:0010212 GO:0042148
20.190.8532.000.220.922g88A GO:0000166 GO:0003677 GO:0003697 GO:0005524 GO:0006259 GO:0006281 GO:0006310 GO:0006974 GO:0008094 GO:0009432
30.190.8401.560.200.901xp8A GO:0000150 GO:0000166 GO:0000400 GO:0000730 GO:0003677 GO:0003684 GO:0003690 GO:0003697 GO:0004520 GO:0005524 GO:0005737 GO:0005829 GO:0006259 GO:0006281 GO:0006302 GO:0006310 GO:0006312 GO:0006974 GO:0008094 GO:0009432 GO:0010212 GO:0042148
40.190.8462.430.170.943cmvA GO:0000150 GO:0000166 GO:0000400 GO:0000730 GO:0003677 GO:0003684 GO:0003690 GO:0003697 GO:0004520 GO:0005524 GO:0005737 GO:0005829 GO:0006259 GO:0006281 GO:0006310 GO:0006312 GO:0006974 GO:0008094 GO:0009432 GO:0010212 GO:0042148 GO:0048870
50.180.8201.890.180.893cmvG GO:0000150 GO:0000166 GO:0000400 GO:0000730 GO:0003677 GO:0003684 GO:0003690 GO:0003697 GO:0004520 GO:0005524 GO:0005737 GO:0005829 GO:0006259 GO:0006281 GO:0006310 GO:0006312 GO:0006974 GO:0008094 GO:0009432 GO:0010212 GO:0042148 GO:0048870
60.170.8101.800.170.871xmvA GO:0000150 GO:0000166 GO:0000400 GO:0000730 GO:0003677 GO:0003684 GO:0003690 GO:0003697 GO:0004520 GO:0005524 GO:0005737 GO:0005829 GO:0006259 GO:0006281 GO:0006310 GO:0006312 GO:0006974 GO:0008094 GO:0009432 GO:0010212 GO:0042148 GO:0048870
70.130.6682.900.100.801szpA GO:0000150 GO:0000166 GO:0000228 GO:0000400 GO:0000709 GO:0000722 GO:0000724 GO:0000730 GO:0000794 GO:0003677 GO:0003690 GO:0003697 GO:0004520 GO:0005524 GO:0005634 GO:0005654 GO:0005694 GO:0006259 GO:0006281 GO:0006310 GO:0006974 GO:0007131 GO:0008094 GO:0010212 GO:0030491 GO:0042148 GO:0042802 GO:0045002 GO:0070192 GO:1990426
80.100.6883.020.090.823ew9A GO:0000166 GO:0003677 GO:0003684 GO:0005524 GO:0006259 GO:0006281 GO:0006310 GO:0006974 GO:0008094
90.100.6933.190.100.841xu4A GO:0000166 GO:0003677 GO:0003684 GO:0005524 GO:0006259 GO:0006281 GO:0006310 GO:0006974 GO:0008094
100.100.6673.020.110.802zucB GO:0000150 GO:0000166 GO:0000400 GO:0000730 GO:0003677 GO:0003684 GO:0003690 GO:0003697 GO:0004520 GO:0005524 GO:0006259 GO:0006281 GO:0006310 GO:0006312 GO:0006974 GO:0008094 GO:0010212 GO:0042148
110.090.6443.070.070.801fx0A GO:0000166 GO:0005524 GO:0006754 GO:0006810 GO:0006811 GO:0009507 GO:0009535 GO:0009536 GO:0009579 GO:0015986 GO:0015991 GO:0015992 GO:0016020 GO:0016787 GO:0016820 GO:0033178 GO:0045261 GO:0046034 GO:0046933 GO:0046961
120.090.6572.800.140.792cvfA GO:0000166 GO:0003677 GO:0003684 GO:0005524 GO:0006281 GO:0006310 GO:0006974 GO:0008094 GO:0016887
130.090.6782.820.070.804hyyA GO:0000150 GO:0000166 GO:0000400 GO:0000730 GO:0000781 GO:0000794 GO:0001541 GO:0001556 GO:0003677 GO:0003690 GO:0003697 GO:0004520 GO:0005524 GO:0005634 GO:0005654 GO:0005694 GO:0006259 GO:0006281 GO:0006312 GO:0007049 GO:0007126 GO:0007129 GO:0007131 GO:0007141 GO:0007276 GO:0007283 GO:0007286 GO:0007292 GO:0008094 GO:0010212 GO:0042148 GO:0051321 GO:0070192
140.080.6532.420.140.753io5B GO:0000166 GO:0003677 GO:0003697 GO:0005524 GO:0006259 GO:0006260 GO:0006281 GO:0006310 GO:0006974 GO:0008094
150.070.6502.880.100.773fyhA GO:0000166 GO:0003677 GO:0003684 GO:0005524 GO:0006259 GO:0006281 GO:0006310 GO:0006974 GO:0008094
160.070.6262.530.090.731n0wA GO:0000150 GO:0000166 GO:0000228 GO:0000400 GO:0000722 GO:0000724 GO:0000730 GO:0000731 GO:0000732 GO:0000784 GO:0000785 GO:0000790 GO:0000793 GO:0000794 GO:0000800 GO:0001932 GO:0003677 GO:0003682 GO:0003690 GO:0003697 GO:0004520 GO:0005524 GO:0005634 GO:0005654 GO:0005730 GO:0005737 GO:0005739 GO:0005759 GO:0005815 GO:0005856 GO:0006259 GO:0006268 GO:0006281 GO:0006310 GO:0006312 GO:0006974 GO:0007126 GO:0007127 GO:0007131 GO:0008022 GO:0008094 GO:0009636 GO:0010165 GO:0010569 GO:0010833 GO:0014070 GO:0016605 GO:0031297 GO:0032200 GO:0035861 GO:0042148 GO:0042493 GO:0042802 GO:0043142 GO:0048471 GO:0051106 GO:0051260 GO:0070182 GO:0070192 GO:0071312 GO:0071479 GO:0071480 GO:0072711 GO:0072719 GO:0072757 GO:1902521 GO:1990414 GO:1990426
170.070.6243.020.090.764wiaA GO:0000166 GO:0005524 GO:0097589
180.070.6162.840.110.742w0mA GO:0000150 GO:0000400 GO:0000730 GO:0003690 GO:0003697 GO:0004520 GO:0005524 GO:0006312 GO:0008094 GO:0010212 GO:0042148 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0005524 GO:0008094 GO:0003697 GO:0003690 GO:0000150 GO:0000400 GO:0004520 GO:0003684 GO:0046914
GO-Score 0.67 0.67 0.67 0.59 0.59 0.59 0.59 0.47 0.44
Biological Processes GO:0009432 GO:0000730 GO:0042148 GO:0010212 GO:0006312 GO:0042221 GO:0030908 GO:0009411 GO:0051674 GO:0006928 GO:0040011
GO-Score 0.67 0.59 0.59 0.59 0.59 0.44 0.44 0.44 0.38 0.38 0.38
Cellular Component GO:0005829
GO-Score 0.59

(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.