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I-TASSER results for job id Rv1387

[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
10.10 5 2cjeA MG Rep, Mult 46,49
20.06 3 1x70A UUU Rep, Mult 151,155,157,158
30.06 3 1l0vO MQ7 Rep, Mult 54,55
40.04 2 3ak3D EDO Rep, Mult 50,53
50.04 2 3pt7B UUU Rep, Mult 118,122
60.02 1 2bgrA UUU Rep, Mult 39,46,82,83
70.02 1 2bgrB UUU Rep, Mult 145,156,157,161
80.02 1 3k3wA CA Rep, Mult 131,139
90.02 1 3fk7A 4DM Rep, Mult 163,167
100.02 1 1tk3B NDG Rep, Mult 173,175,182,185
110.02 1 3kziX CLA Rep, Mult 17,20
120.02 1 3iilA MG Rep, Mult 10,11
130.02 1 2rh1A CLR Rep, Mult 50,78
140.02 1 1u8eA UUU Rep, Mult 135,138,142
150.02 1 3c9iC XE Rep, Mult 110,113
160.02 1 2a2rB CA Rep, Mult 22,92

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
10.0601clqA0.3128.020.0220.5272.7.7.7NA
20.0601z68A0.3627.490.0270.5963.4.21.-14
30.0602ok5A0.3347.360.0140.5293.4.21.4713,165
40.0602np0A0.2858.080.0340.4883.4.24.69156
50.0601llwA0.3438.080.0480.5881.4.7.1NA
60.0602ckjA0.2917.190.0540.4531.17.1.4,1.17.3.2NA
70.0603b9jJ0.2066.230.0570.2931.17.1.4,1.17.3.218,37,83
80.0602j5wA0.3727.750.0480.6311.16.3.1NA
90.0602pdaA0.2707.890.0450.4531.2.7.139,138
100.0601orvA0.3577.610.0280.5943.4.14.514
110.0603ebgA0.3377.760.0320.5553.4.11.-NA
120.0601r9mB0.3547.720.0380.5943.4.14.514
130.0603b9jC0.2757.840.0440.4621.17.3.2,1.17.1.4NA
140.0601tgoA0.3398.200.0730.5862.7.7.796
150.0602gtqA0.3327.550.0550.5443.4.11.2NA
160.0601b0pA0.2547.990.0150.4301.2.7.1NA
170.0601fo4A0.3927.570.0700.6401.17.1.4NA
180.0601z1wA0.3347.800.0470.5513.4.11.-NA
190.0602eabA0.3547.510.0360.5713.2.1.63NA

(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
00.210.8782.820.100.951ciyA GO:0005102 GO:0006952 GO:0009405 GO:0030435
10.180.8343.060.090.924w8jA GO:0005102 GO:0006952 GO:0009405 GO:0030435
20.170.8233.280.060.921dlcA GO:0005102 GO:0006952 GO:0009405 GO:0030435
30.170.8023.460.070.913eb7A GO:0005102 GO:0006952 GO:0009405 GO:0030435
40.160.8223.390.060.931ji6A GO:0005102 GO:0006952 GO:0009405 GO:0030435
50.160.7963.620.060.912c9kA GO:0005102 GO:0006952 GO:0009405 GO:0030435
60.150.7893.760.040.914moaA GO:0005102 GO:0006952 GO:0009405 GO:0030435
70.110.7044.540.060.861i5pA GO:0005102 GO:0006952 GO:0009405 GO:0030435
80.100.6864.560.060.844d8mA GO:0009405 GO:0030435
90.060.2357.830.030.405e24E GO:0000122 GO:0000978 GO:0000980 GO:0000982 GO:0001077 GO:0001078 GO:0001709 GO:0003677 GO:0003700 GO:0005634 GO:0005700 GO:0005737 GO:0006351 GO:0006355 GO:0006366 GO:0007219 GO:0007252 GO:0007275 GO:0007451 GO:0007616 GO:0008356 GO:0008586 GO:0016360 GO:0017053 GO:0030097 GO:0042683 GO:0042688 GO:0043234 GO:0043565 GO:0045892 GO:0045893 GO:0045944 GO:0046331 GO:0048190 GO:1900087
100.060.2136.820.040.325an9A GO:0000027 GO:0003735 GO:0005615 GO:0005622 GO:0005737 GO:0005840 GO:0006412 GO:0022625 GO:0030529
110.060.2126.740.040.321t5cA GO:0000166 GO:0000278 GO:0000775 GO:0000776 GO:0000777 GO:0000779 GO:0000940 GO:0003777 GO:0005524 GO:0005634 GO:0005694 GO:0005737 GO:0005819 GO:0005829 GO:0005856 GO:0005871 GO:0005874 GO:0006890 GO:0007018 GO:0007049 GO:0007059 GO:0007062 GO:0007067 GO:0007079 GO:0007080 GO:0007275 GO:0008017 GO:0015630 GO:0016020 GO:0016887 GO:0019886 GO:0030071 GO:0030496 GO:0043515 GO:0045860 GO:0051301 GO:0051315 GO:0051382 GO:1990023
120.060.2237.490.030.373j8gX GO:0000027 GO:0000166 GO:0003924 GO:0005525 GO:0005829 GO:0032794 GO:0042254 GO:0043022
130.060.1976.870.030.303n9sA GO:0003824 GO:0004332 GO:0005975 GO:0006096 GO:0008270 GO:0016829 GO:0016832 GO:0030388 GO:0046872
140.060.1756.450.020.262iewA GO:0000122 GO:0000166 GO:0000821 GO:0000823 GO:0000824 GO:0000825 GO:0000827 GO:0005524 GO:0005634 GO:0006351 GO:0006355 GO:0006525 GO:0008440 GO:0016236 GO:0016301 GO:0016310 GO:0016740 GO:0030674 GO:0032958 GO:0035004 GO:0045944 GO:0046854 GO:0046872 GO:0050821
150.060.1973.700.060.233km5A GO:0006508 GO:0008233 GO:0008234 GO:0009405 GO:0016787
160.060.1243.520.010.143ajwA GO:0003774 GO:0005886 GO:0006810 GO:0006935 GO:0009288 GO:0015031 GO:0016020 GO:0044781 GO:0071973
170.060.1334.350.030.164wpeA GO:0000142 GO:0000144 GO:0000281 GO:0000917 GO:0005737 GO:0005856 GO:0005935 GO:0007049 GO:0007067 GO:0008092 GO:0044697 GO:0051301 GO:0090339
180.060.1195.950.030.172mf6A GO:0005576


Consensus prediction of GO terms
 
Molecular Function GO:0005102
GO-Score 0.62
Biological Processes GO:0006952 GO:0030435 GO:0009405
GO-Score 0.62 0.62 0.62
Cellular Component
GO-Score

(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.