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I-TASSER results for job id Rv1204c

[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 2 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
10.09 4 2hcbC MG Rep, Mult 29,30,106,107
20.07 3 1b86A OXY Rep, Mult 309,313
30.05 2 4gpkJ III Rep, Mult 354,356,417,420,421,424,428,458,461,462,496,499,500,530,533,534,537
40.05 2 2bo6B MN Rep, Mult 106,107
50.05 2 2hcbA MG Rep, Mult 30,106,107
60.02 1 2qfcA III Rep, Mult 233,236,239,240,269,272,273,276,306,309,312,350
70.02 1 2qbyA MG Rep, Mult 30,106,195
80.02 1 4f8hA LMD Rep, Mult 353,356
90.02 1 5lcwO III Rep, Mult 153,157,182,185,186,204,210,229,233,240,269,273,276,305,309,312,313,316,320,346,350,354,357,386,387,417,492
100.02 1 2qbyB MG Rep, Mult 30,106,136
110.02 1 5irzD 6OE Rep, Mult 115,119
120.02 1 3cmvH ANP Rep, Mult 310,311,312,313,314,315,316,329,358
130.02 1 3h45O PO4 Rep, Mult 314,317
140.02 1 4i9cA III Rep, Mult 272,309,313,316,320,350,353,354,357,386,417,420,454,455,458

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
10.0602dqmA0.3457.170.0550.5323.4.11.2NA
20.0603h09B0.3517.750.0400.5713.4.21.72NA
30.0603ffzA0.3467.860.0190.5753.4.24.69NA
40.0602eabA0.3846.850.0390.5823.2.1.63NA
50.0603ecqB0.3418.130.0570.5843.2.1.97NA
60.0601ej6A0.3407.770.0460.5602.7.7.50331
70.0602vuaA0.2377.330.0410.3723.4.24.69201
80.0602jgdA0.3488.060.0560.5851.2.4.2415
90.0601dl2A0.3425.740.0380.4703.2.1.113NA
100.0601llwA0.3647.810.0630.5981.4.7.1NA
110.0602gq3A0.3437.790.0550.5782.3.3.9NA
120.0601w6jA0.3746.470.0580.5365.4.99.7NA
130.0602vdcA0.3438.010.0490.5731.4.1.13NA
140.0602pmzQ0.3276.900.0530.4982.7.7.6NA
150.0602gtqA0.3537.340.0480.5573.4.11.2NA
160.0602zxqA0.3408.240.0510.5873.2.1.97181
170.0602cqsA0.3787.420.0630.5962.4.1.20417
180.0602vdcF0.3637.820.0510.6011.4.1.1318,30
190.0602w00B0.3477.390.0540.5413.1.21.3239

(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
00.260.8382.960.090.935g05O GO:0005634 GO:0005654 GO:0005680 GO:0005829 GO:0007049 GO:0007067 GO:0016567 GO:0019903 GO:0031145 GO:0042787 GO:0043161 GO:0051301 GO:0051436 GO:0051437 GO:0051439 GO:0070979
10.090.5735.170.070.734xdnA GO:0000790 GO:0005634 GO:0006302 GO:0007049 GO:0007059 GO:0007064 GO:0007067 GO:0007076 GO:0032116 GO:0051301 GO:0070550 GO:0071169
20.070.5915.070.060.755c6gA GO:0000790 GO:0006302 GO:0007064 GO:0007076 GO:0032116 GO:0070550 GO:0071169
30.070.5645.460.080.755a31Y GO:0005634 GO:0005654 GO:0005680 GO:0005829 GO:0007049 GO:0007067 GO:0016567 GO:0019903 GO:0031145 GO:0042787 GO:0043161 GO:0051301 GO:0051436 GO:0051437 GO:0051439 GO:0070979
40.070.5065.870.080.715a31F GO:0005634 GO:0005654 GO:0005680 GO:0005737 GO:0005813 GO:0005819 GO:0005829 GO:0005876 GO:0007091 GO:0008283 GO:0016567 GO:0019903 GO:0031145 GO:0042787 GO:0043161 GO:0051436 GO:0051437 GO:0051439 GO:0070979
50.070.4795.800.060.655a31C GO:0004842 GO:0005622 GO:0005654 GO:0005680 GO:0005829 GO:0006511 GO:0007049 GO:0007067 GO:0007080 GO:0007091 GO:0007096 GO:0016567 GO:0030071 GO:0031145 GO:0042787 GO:0043161 GO:0051301 GO:0051436 GO:0051437 GO:0051439 GO:0070979
60.060.3945.600.080.531w3bB GO:0000123 GO:0000791 GO:0001933 GO:0001934 GO:0005547 GO:0005634 GO:0005654 GO:0005737 GO:0005739 GO:0005829 GO:0005886 GO:0006041 GO:0006110 GO:0006486 GO:0006493 GO:0006915 GO:0007165 GO:0007584 GO:0008047 GO:0008134 GO:0008289 GO:0008375 GO:0010628 GO:0010801 GO:0016020 GO:0016262 GO:0016568 GO:0016740 GO:0016757 GO:0019904 GO:0030854 GO:0030900 GO:0031397 GO:0032868 GO:0032869 GO:0032922 GO:0033137 GO:0035020 GO:0042277 GO:0042588 GO:0043005 GO:0043025 GO:0043085 GO:0043981 GO:0043982 GO:0043984 GO:0043995 GO:0043996 GO:0045793 GO:0045862 GO:0045944 GO:0046626 GO:0046972 GO:0048015 GO:0048029 GO:0048312 GO:0048511 GO:0051571 GO:0060548 GO:0061087 GO:0070207 GO:0070208 GO:0070688 GO:0071222 GO:0071300 GO:0071333 GO:0080182 GO:0090315 GO:0090526 GO:0097237 GO:0097363 GO:1900038 GO:1900182 GO:1903428
70.060.4055.260.080.531w3bA GO:0000123 GO:0000791 GO:0001933 GO:0001934 GO:0005547 GO:0005634 GO:0005654 GO:0005737 GO:0005739 GO:0005829 GO:0005886 GO:0006041 GO:0006110 GO:0006486 GO:0006493 GO:0006915 GO:0007165 GO:0007584 GO:0008047 GO:0008134 GO:0008289 GO:0008375 GO:0010628 GO:0010801 GO:0016020 GO:0016262 GO:0016568 GO:0016740 GO:0016757 GO:0019904 GO:0030854 GO:0030900 GO:0031397 GO:0032868 GO:0032869 GO:0032922 GO:0033137 GO:0035020 GO:0042277 GO:0042588 GO:0043005 GO:0043025 GO:0043085 GO:0043981 GO:0043982 GO:0043984 GO:0043995 GO:0043996 GO:0045793 GO:0045862 GO:0045944 GO:0046626 GO:0046972 GO:0048015 GO:0048029 GO:0048312 GO:0048511 GO:0051571 GO:0060548 GO:0061087 GO:0070207 GO:0070208 GO:0070688 GO:0071222 GO:0071300 GO:0071333 GO:0080182 GO:0090315 GO:0090526 GO:0097237 GO:0097363 GO:1900038 GO:1900182 GO:1903428
80.060.3776.620.060.554i2wA GO:0005886 GO:0005938 GO:0009792 GO:0018991 GO:0031625 GO:0032154 GO:0040011 GO:0042802 GO:0045214
90.060.3886.110.050.534xifA GO:0000123 GO:0000791 GO:0001933 GO:0001934 GO:0005547 GO:0005634 GO:0005654 GO:0005737 GO:0005739 GO:0005829 GO:0005886 GO:0006041 GO:0006110 GO:0006486 GO:0006493 GO:0006915 GO:0007165 GO:0007584 GO:0008047 GO:0008134 GO:0008289 GO:0008375 GO:0010628 GO:0010801 GO:0016020 GO:0016262 GO:0016568 GO:0016740 GO:0016757 GO:0019904 GO:0030854 GO:0030900 GO:0031397 GO:0032868 GO:0032869 GO:0032922 GO:0033137 GO:0035020 GO:0042277 GO:0042588 GO:0043005 GO:0043025 GO:0043085 GO:0043981 GO:0043982 GO:0043984 GO:0043995 GO:0043996 GO:0045793 GO:0045862 GO:0045944 GO:0046626 GO:0046972 GO:0048015 GO:0048029 GO:0048312 GO:0048511 GO:0051571 GO:0060548 GO:0061087 GO:0070207 GO:0070208 GO:0070688 GO:0071222 GO:0071300 GO:0071333 GO:0080182 GO:0090315 GO:0090526 GO:0097237 GO:0097363 GO:1900038 GO:1900182 GO:1903428
100.060.3056.000.080.433cv0A GO:0005052 GO:0005778 GO:0005829 GO:0016560
110.060.3836.170.060.535a01A GO:0006486 GO:0006493 GO:0008375 GO:0016740 GO:0016757 GO:0035220 GO:0045475
120.060.2815.090.060.362y4uA GO:0004860 GO:0005737 GO:0005783 GO:0005788 GO:0005790 GO:0005829 GO:0006417 GO:0006986 GO:0016020 GO:0019901 GO:0031205 GO:0036494 GO:0036498 GO:0043066 GO:0051087 GO:0051603 GO:0051607 GO:0051787 GO:0070062 GO:0070417 GO:1903561 GO:1903912 GO:1904030
130.060.2813.540.090.332pl2A
140.060.2088.190.050.351xl7B GO:0005102 GO:0005739 GO:0005777 GO:0006091 GO:0006629 GO:0006631 GO:0006635 GO:0006810 GO:0008458 GO:0009437 GO:0010243 GO:0015908 GO:0015936 GO:0016740 GO:0016746 GO:0042493 GO:0043231 GO:0051791
150.060.2444.900.080.314houA GO:0002376 GO:0003723 GO:0005737 GO:0005829 GO:0009615 GO:0016032 GO:0019060 GO:0032091 GO:0043657 GO:0045070 GO:0045071 GO:0045087 GO:0050688 GO:0050689 GO:0051097 GO:0051607 GO:0060337 GO:0071357 GO:0071360
160.060.2304.480.090.282q7fA
170.060.2314.030.130.272e2eA
180.060.2116.710.060.323vylA GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0019903
GO-Score 0.36
Biological Processes GO:0051301 GO:0070979 GO:0031145 GO:0051437 GO:0051436 GO:0000070 GO:0071168 GO:0007062 GO:0030261 GO:0070199 GO:0006281
GO-Score 0.37 0.36 0.36 0.36 0.36 0.30 0.30 0.30 0.30 0.30 0.30
Cellular Component GO:0005654 GO:0005829 GO:0005680 GO:0044454 GO:0000785
GO-Score 0.36 0.36 0.36 0.30 0.30

(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.