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I-TASSER results for job id Rv2369c

[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
10.19 7 5lopA MG Rep, Mult 19,20
20.08 3 4ixmA ZN Rep, Mult 15,22,58
30.06 2 2hgq5 III Rep, Mult 14,47,59,60
40.06 2 2bs2A NA Rep, Mult 23,28,29,30
50.06 2 1x1cA ZN Rep, Mult 14,18
60.03 1 1qvo8 III Rep, Mult 34,35,44,45,47,60
70.03 1 3g8rA ZN Rep, Mult 9,34

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
10.0601d8yA0.4914.060.0830.8302.7.7.728
20.0602gv9B0.4664.690.0710.9202.7.7.750
30.0602rc4A0.4553.420.0120.7202.3.1.48,NA
40.0601yt3A0.4614.120.0550.8203.1.13.5NA
50.0601whvA0.2695.390.0290.5803.1.13.4NA
60.0602q2rA0.4544.110.0580.7802.7.1.2NA
70.0602p0mB0.3485.080.0710.7601.13.11.3323,33
80.0601kflA0.4484.620.0320.8402.5.1.54NA
90.0601of6A0.4633.810.0610.8002.5.1.54,4.1.2.159
100.0602qf7B0.4494.330.0540.8306.4.1.1NA
110.0602p51A0.5064.280.0200.9103.1.13.4NA
120.0601ubuS0.4544.180.0960.7501.12.2.162
130.0602pq8A0.4633.370.0510.7102.3.1.48NA
140.0602a1rB0.3884.470.0270.6803.1.13.443,85
150.0601s0kA0.3914.040.0130.6903.2.1.1865
160.0601a39A0.4454.110.0610.7403.2.1.4NA
170.0601jnrA0.4614.430.0320.8801.8.99.2NA
180.0601yqwA0.4504.190.0840.7501.12.2.1NA
190.0603h0lA0.4554.450.0520.8306.3.5.-54

(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
00.070.4914.060.080.831d8yA GO:0003676 GO:0003677 GO:0003824 GO:0003887 GO:0004518 GO:0004527 GO:0005737 GO:0005829 GO:0006139 GO:0006260 GO:0006261 GO:0006281 GO:0006284 GO:0006974 GO:0008408 GO:0008409 GO:0016740 GO:0016779 GO:0016787 GO:0071897 GO:0090305
10.070.4963.960.130.821kfdA GO:0003676 GO:0003677 GO:0003824 GO:0003887 GO:0004518 GO:0004527 GO:0005737 GO:0005829 GO:0006139 GO:0006260 GO:0006261 GO:0006281 GO:0006284 GO:0006974 GO:0008408 GO:0008409 GO:0016740 GO:0016779 GO:0016787 GO:0071897 GO:0090305
20.070.4824.430.010.904gmjB GO:0000175 GO:0000289 GO:0000290 GO:0000932 GO:0003676 GO:0003700 GO:0003723 GO:0004518 GO:0004527 GO:0004532 GO:0004535 GO:0004871 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0005975 GO:0006351 GO:0006355 GO:0006417 GO:0006977 GO:0007165 GO:0008284 GO:0008285 GO:0010629 GO:0016020 GO:0016787 GO:0030014 GO:0031047 GO:0033962 GO:0035195 GO:0043928 GO:0045944 GO:0046872 GO:0060213 GO:0061014 GO:0090305 GO:0090503 GO:1900153
30.070.4744.140.100.834xviA GO:0000724 GO:0003676 GO:0003677 GO:0003887 GO:0005634 GO:0005654 GO:0005730 GO:0005737 GO:0006260 GO:0006261 GO:0006281 GO:0006974 GO:0008409 GO:0016740 GO:0016779 GO:0019985 GO:0030332 GO:0036297 GO:0090305
40.070.4903.940.010.824x0pA GO:0000166 GO:0000724 GO:0003676 GO:0003677 GO:0003682 GO:0003684 GO:0003887 GO:0005524 GO:0005634 GO:0005654 GO:0005694 GO:0006260 GO:0006261 GO:0006281 GO:0006284 GO:0006302 GO:0006974 GO:0016446 GO:0016740 GO:0016779 GO:0043142 GO:0051260 GO:0051575 GO:0071897 GO:0097681 GO:2000042
50.070.4724.390.030.884b8cA GO:0000175 GO:0000289 GO:0000932 GO:0003676 GO:0003723 GO:0004518 GO:0004527 GO:0005634 GO:0005737 GO:0006351 GO:0006355 GO:0006357 GO:0006368 GO:0016787 GO:0030015 GO:0032968 GO:0046872 GO:0090305 GO:0090503
60.070.4944.000.030.865fiqA GO:0003676 GO:0003723 GO:0005737 GO:0006139 GO:0008408 GO:0031047 GO:0034587 GO:0042803 GO:0043186 GO:0051321 GO:1990923
70.070.5064.280.020.912p51A GO:0000289 GO:0003676 GO:0003723 GO:0003729 GO:0004518 GO:0004527 GO:0004535 GO:0005634 GO:0005737 GO:0005829 GO:0006351 GO:0006355 GO:0016787 GO:0030014 GO:0030015 GO:0046872 GO:0090305 GO:0090503
80.070.3854.520.030.692a1sC GO:0000166 GO:0000184 GO:0000289 GO:0003676 GO:0003723 GO:0003730 GO:0004518 GO:0004527 GO:0004535 GO:0005634 GO:0005730 GO:0005737 GO:0005829 GO:0006402 GO:0007292 GO:0009451 GO:0016787 GO:0019901 GO:0043488 GO:0044822 GO:0046872 GO:0090305 GO:0090503
90.070.4544.260.020.823d45B GO:0000166 GO:0000184 GO:0000289 GO:0003676 GO:0003723 GO:0004518 GO:0004527 GO:0004535 GO:0005634 GO:0005730 GO:0005737 GO:0006402 GO:0016787 GO:0019901 GO:0044822 GO:0046872 GO:0090305 GO:0090503
100.070.4443.990.060.774dqqD GO:0000166 GO:0003676 GO:0003677 GO:0003824 GO:0003887 GO:0004518 GO:0006139 GO:0006260 GO:0006261 GO:0008408 GO:0016740 GO:0016779 GO:0016787 GO:0046872 GO:0071897 GO:0090305
110.070.4254.600.060.815c51A GO:0002020 GO:0003676 GO:0003677 GO:0003682 GO:0003887 GO:0005739 GO:0005760 GO:0006259 GO:0006260 GO:0006261 GO:0006264 GO:0006287 GO:0007568 GO:0008408 GO:0009416 GO:0010332 GO:0016740 GO:0016779 GO:0042645 GO:0043195 GO:0043234 GO:0055093 GO:0070062 GO:0071333 GO:0071897 GO:0090305
120.070.4804.200.020.863d45A GO:0000166 GO:0000184 GO:0000289 GO:0003676 GO:0003723 GO:0004518 GO:0004527 GO:0004535 GO:0005634 GO:0005730 GO:0005737 GO:0006402 GO:0016787 GO:0019901 GO:0044822 GO:0046872 GO:0090305 GO:0090503
130.070.4304.210.070.794ds4D GO:0000166 GO:0003676 GO:0003677 GO:0003824 GO:0003887 GO:0004518 GO:0006139 GO:0006260 GO:0006261 GO:0008408 GO:0016740 GO:0016779 GO:0016787 GO:0046872 GO:0071897 GO:0090305
140.060.3973.950.060.691sl0A GO:0003676 GO:0003677 GO:0003887 GO:0004518 GO:0004527 GO:0006260 GO:0006261 GO:0008408 GO:0016032 GO:0016740 GO:0016779 GO:0016787 GO:0039693 GO:0071897 GO:0090305
150.060.3964.000.120.652ajqA GO:0003676 GO:0003677 GO:0003887 GO:0004518 GO:0004527 GO:0006260 GO:0006261 GO:0008408 GO:0016032 GO:0016740 GO:0016779 GO:0016787 GO:0039693 GO:0071897 GO:0090305
160.060.3903.960.060.691sksA GO:0003676 GO:0003677 GO:0003887 GO:0004518 GO:0004527 GO:0006260 GO:0006261 GO:0008408 GO:0016032 GO:0016740 GO:0016779 GO:0016787 GO:0039693 GO:0071897 GO:0090305
170.060.4354.320.050.803ikmD GO:0002020 GO:0003676 GO:0003677 GO:0003682 GO:0003887 GO:0005739 GO:0005760 GO:0006259 GO:0006260 GO:0006261 GO:0006264 GO:0006287 GO:0007568 GO:0008408 GO:0009416 GO:0010332 GO:0016740 GO:0016779 GO:0042645 GO:0043195 GO:0043234 GO:0055093 GO:0070062 GO:0071333 GO:0071897 GO:0090305
180.060.4054.300.050.734n56A GO:0001882 GO:0003676 GO:0003677 GO:0003824 GO:0003887 GO:0006260 GO:0006261 GO:0006281 GO:0006974 GO:0016740 GO:0016779 GO:0071897


Consensus prediction of GO terms
 
Molecular Function GO:0097159 GO:1901363 GO:0034061 GO:0004518
GO-Score 0.55 0.55 0.48 0.37
Biological Processes GO:0034645 GO:0006259 GO:0006974 GO:0034654
GO-Score 0.48 0.48 0.48 0.37
Cellular Component GO:0044444 GO:0031981
GO-Score 0.37 0.37

(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.