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I-TASSER results for job id Rv0199

[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
10.06 3 1t2kD NUC Rep, Mult 13,14,20,21,24
20.04 2 2a6eD MG Rep, Mult 205,207,210
30.04 2 4ev6D MG Rep, Mult 14,18
40.04 2 2w6dA GDP Rep, Mult 89,90,93,94,125
50.04 2 3r6nB D1D Rep, Mult 103,104,107,118,121
60.04 2 2onk2 III Rep, Mult 105,106,107,108,110,111,112,120,124
70.04 2 4eotA NUC Rep, Mult 21,22,26,29,30,33
80.04 2 3a0bZ CLA Rep, Mult 54,57
90.02 1 1m34A SF4 Rep, Mult 91,92
100.02 1 2p9i3 III Rep, Mult 46,48,49,51,53,54,56,58
110.02 1 1zyrN STD Rep, Mult 45,48,49,53
120.02 1 2w6dB CPL Rep, Mult 94,95,128,129,131
130.02 1 3ojaB MAN Rep, Mult 29,32
140.02 1 3wmn2 BCL Rep, Mult 44,48
150.02 1 2a69A MG Rep, Mult 215,216
160.02 1 1cb2A MAN Rep, Mult 112,116
170.02 1 3hd7F GGG Rep, Mult 71,74
180.02 1 3swfB ZN Rep, Mult 18,22

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
10.0603i9wA0.3934.830.0560.5522.7.13.3120,137,214
20.0603b8eC0.3934.900.0560.5753.6.3.984,144
30.0602iw5A0.3805.420.0340.6261.-.-.-NA
40.0603a1cB0.2525.720.0370.4293.6.3.-205
50.0602nztA0.3635.300.0380.5622.7.1.1NA
60.0601o7hB0.3764.280.0730.5301.14.12.1283,96
70.0602np0A0.3225.090.0340.4933.4.24.69NA
80.0603btaA0.3965.930.0400.6903.4.24.69NA
90.0603errA0.3815.790.0210.6216.1.1.11NA
100.0603b8eA0.3685.880.0740.6443.6.3.9NA
110.0602vuaA0.3265.410.0330.5393.4.24.69NA
120.0603e99A0.3793.710.0650.5071.14.12.10NA
130.0601qhaA0.3515.480.0340.5662.7.1.1NA
140.0601mc0A0.3514.980.0650.5523.1.4.17118
150.0601y2mB0.4094.830.0500.6214.3.1.24147
160.0602uv8G0.3556.330.0540.6712.3.1.86NA
170.0603g61A0.3735.830.0560.6213.6.3.4495,106,108
180.0601serB0.3316.040.0410.5756.1.1.11NA
190.0603b8cB0.3855.100.0550.5983.6.3.6111

(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
00.130.4043.840.080.533v6iA GO:0005524 GO:0006754 GO:0006810 GO:0006811 GO:0015991 GO:0015992 GO:0033178 GO:0042777 GO:0046933 GO:0046961
10.060.4195.120.050.644i5sB GO:0000155 GO:0000160 GO:0000166 GO:0005524 GO:0005622 GO:0006355 GO:0007165 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0023014
20.060.3555.400.040.584gczB GO:0000155 GO:0000160 GO:0000166 GO:0004673 GO:0005524 GO:0005622 GO:0006351 GO:0006355 GO:0007165 GO:0009399 GO:0009881 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0018106 GO:0018298 GO:0023014 GO:0046872 GO:0050896
30.060.3006.100.040.553ndaA GO:0005615
40.060.3224.170.030.434ctiD GO:0000155 GO:0000160 GO:0000166 GO:0004673 GO:0004721 GO:0004871 GO:0005524 GO:0005622 GO:0005886 GO:0005887 GO:0006470 GO:0007165 GO:0009898 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0018106 GO:0023014 GO:0046777 GO:0047484
50.060.3144.750.040.474bivA GO:0000155 GO:0000160 GO:0000166 GO:0004673 GO:0004871 GO:0005524 GO:0005622 GO:0005886 GO:0007165 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0018106 GO:0023014 GO:0043708 GO:0046777
60.060.2335.370.040.372zdxA GO:0000166 GO:0002230 GO:0004672 GO:0004740 GO:0005524 GO:0005739 GO:0005743 GO:0005759 GO:0005975 GO:0006006 GO:0006468 GO:0006885 GO:0008286 GO:0009267 GO:0010510 GO:0010565 GO:0010906 GO:0016301 GO:0016310 GO:0016740 GO:0042304 GO:0042593 GO:0042594 GO:0045124 GO:0046320 GO:0071398 GO:0072593 GO:0098792 GO:2000811
70.060.2605.510.020.433crlB GO:0000166 GO:0004674 GO:0004740 GO:0005524 GO:0005739 GO:0005759 GO:0005967 GO:0005975 GO:0006006 GO:0006111 GO:0006468 GO:0006885 GO:0008286 GO:0010510 GO:0010565 GO:0010906 GO:0016301 GO:0016310 GO:0016740 GO:0018105 GO:0031670 GO:0032403 GO:0042593 GO:0042803 GO:0045254 GO:0046982
80.060.2715.390.050.433d36B
90.060.2435.850.030.413d2rB GO:0000166 GO:0002230 GO:0004672 GO:0004740 GO:0005524 GO:0005739 GO:0005743 GO:0005759 GO:0005975 GO:0006006 GO:0006468 GO:0006885 GO:0008286 GO:0009267 GO:0010510 GO:0010565 GO:0010906 GO:0016301 GO:0016310 GO:0016740 GO:0042304 GO:0042593 GO:0042594 GO:0045124 GO:0046320 GO:0071398 GO:0072593 GO:0098792 GO:2000811
100.060.2605.680.040.441hynQ GO:0003779 GO:0005215 GO:0005452 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006820 GO:0006821 GO:0006873 GO:0008022 GO:0008509 GO:0015106 GO:0015108 GO:0015301 GO:0015701 GO:0016020 GO:0016021 GO:0016323 GO:0019899 GO:0030018 GO:0030506 GO:0030863 GO:0042803 GO:0043495 GO:0051453 GO:0070062 GO:0072562 GO:1902476
110.060.2725.560.030.451y8pA GO:0000166 GO:0004672 GO:0004674 GO:0004740 GO:0005524 GO:0005739 GO:0005759 GO:0005975 GO:0006006 GO:0010510 GO:0010906 GO:0016301 GO:0016310 GO:0016740 GO:0018105 GO:0035357 GO:0071333 GO:0071398 GO:0097411 GO:2000377
120.060.2225.380.050.364kp4A GO:0000155 GO:0000160 GO:0000166 GO:0004673 GO:0004721 GO:0004871 GO:0005524 GO:0005622 GO:0005886 GO:0005887 GO:0006470 GO:0007165 GO:0009898 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0018106 GO:0023014 GO:0046777 GO:0047484
130.060.2315.620.030.373lmmD GO:0005524
140.060.2865.250.070.444lrxC GO:0000166 GO:0003677 GO:0005524 GO:0006071 GO:0006351 GO:0006355 GO:0008134 GO:0043565
150.060.2334.580.040.321l0oA GO:0000166 GO:0004672 GO:0004674 GO:0005524 GO:0006468 GO:0010468 GO:0016301 GO:0016310 GO:0016740 GO:0016989 GO:0030435 GO:0030436 GO:0045892
160.060.2485.710.050.423a0rA GO:0000155 GO:0000160 GO:0000166 GO:0005524 GO:0005622 GO:0006355 GO:0007165 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0023014
170.060.2216.590.050.424p7aA GO:0000289 GO:0000712 GO:0000793 GO:0000794 GO:0000795 GO:0001673 GO:0002204 GO:0003682 GO:0003697 GO:0005524 GO:0005634 GO:0005654 GO:0005694 GO:0005712 GO:0006281 GO:0006298 GO:0006303 GO:0006974 GO:0007049 GO:0007060 GO:0007126 GO:0007129 GO:0007131 GO:0007140 GO:0007283 GO:0008630 GO:0016020 GO:0016321 GO:0016446 GO:0016447 GO:0016887 GO:0030983 GO:0032137 GO:0032389 GO:0032407 GO:0043060 GO:0045132 GO:0045141 GO:0045143 GO:0045190 GO:0045950 GO:0048477 GO:0051257
180.060.2264.900.070.343cgzA GO:0000155 GO:0000160 GO:0000166 GO:0004673 GO:0004721 GO:0004871 GO:0005524 GO:0005622 GO:0005886 GO:0006470 GO:0007165 GO:0009405 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0016787 GO:0018106 GO:0023014 GO:0040008 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0032550 GO:0035639 GO:0032559 GO:0038023 GO:0004673
GO-Score 0.57 0.57 0.57 0.36 0.36
Biological Processes GO:0044710 GO:0006468 GO:0035556
GO-Score 0.36 0.36 0.36
Cellular Component GO:0005623
GO-Score 0.36

(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.