[Home] [Server] [About] [Statistics] [Annotation]

I-TASSER results for job id Rv1948c

[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 2ei3A BPY Rep, Mult 24,28,32,52
20.06 3 2p7pA MN Rep, Mult 67,97,109
30.04 2 1c9bQ NUC Rep, Mult 76,83
40.04 2 1lkdA BP6 Rep, Mult 14,46,47,49
50.04 2 2ehzA MCT Rep, Mult 69,70,71,96,110,111,113
60.04 2 2p7qC GG6 Rep, Mult 65,67,97,109,116
70.02 1 1lnyA MG Rep, Mult 14,39
80.02 1 3fpvA FE Rep, Mult 70,98
90.02 1 4llhA CM5 Rep, Mult 22,26
100.02 1 2ehzA MCT Rep, Mult 4,14,16,17
110.02 1 1z2oX MG Rep, Mult 100,102
120.02 1 3m4oA C7P Rep, Mult 31,32,35
130.02 1 3amrA CA Rep, Mult 89,95
140.02 1 1cgpA CMP Rep, Mult 81,85
150.02 1 2qvmA CA Rep, Mult 44,74
160.02 1 1f8iB MG Rep, Mult 14,60
170.02 1 2jfkD COA Rep, Mult 53,54
180.02 1 2vk6A MG Rep, Mult 8,9

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
10.0661npbA0.6093.240.0990.8532.5.1.1818
20.0661f9zA0.5693.040.0630.8024.4.1.5NA
30.0601bsgA0.4684.640.0850.8713.5.2.638,81
40.0601fa7B0.5723.020.0630.8024.4.1.517
50.0601mpyA0.6143.000.1260.8451.13.11.2NA
60.0602ehzA0.6023.120.0970.8531.13.11.-NA
70.0602j9pA0.4674.680.0560.8713.4.16.4NA
80.0602pbyA0.4984.180.0750.8363.5.1.2NA
90.0601eilA0.6262.950.1080.8621.13.11.39NA
100.0602p25A0.5373.320.0740.8024.4.1.5NA
110.0603f2bA0.4664.310.0720.7672.7.7.7NA
120.0601cjxA0.4964.280.0670.8711.13.11.2784
130.0602zi8A0.6252.910.0880.8531.13.11.39NA
140.0601lqkA0.6163.060.1080.8622.5.1.18NA
150.0601sqiA0.5673.280.0660.8361.13.11.27NA
160.0602e8iA0.4744.470.0830.8533.5.1.4625,31,35
170.0603lm4D0.6092.870.0670.8191.13.11.2NA
180.0603brmB0.4684.380.0380.8283.5.1.231,38
190.0601lqoB0.6113.090.1080.8622.5.1.1818
200.0601djaA0.4535.080.0720.8883.5.2.6NA
210.0601g68A0.4595.050.0450.8973.5.2.6NA

(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
00.250.6332.650.120.831r9cA GO:0005737 GO:0046677 GO:0046872
10.210.5842.940.030.822c21A GO:0004462 GO:0016829 GO:0046872
20.180.6222.670.110.832p7pA GO:0005737 GO:0046677 GO:0046872
30.180.6163.060.110.861lqkA GO:0004364 GO:0005737 GO:0016740 GO:0046677 GO:0046872
40.160.6642.680.090.874qb5D GO:0051213 GO:0055114
50.120.6003.160.090.873ct8A GO:0046872
60.110.5972.960.070.814nazA GO:0000287 GO:0005737 GO:0016740 GO:0016765 GO:0046677 GO:0046872
70.100.5653.300.090.831qipB GO:0004462 GO:0005737 GO:0005829 GO:0005975 GO:0006090 GO:0006357 GO:0006749 GO:0008270 GO:0009438 GO:0016829 GO:0030316 GO:0043066 GO:0046872 GO:0070062
80.090.6462.730.080.844z04A GO:0046872 GO:0051213 GO:0055114
90.090.6433.140.130.913zi1A GO:0005739 GO:0005913 GO:0070062 GO:0098609 GO:0098641
100.080.5693.040.060.801f9zA GO:0004462 GO:0005829 GO:0016151 GO:0016829 GO:0019243 GO:0046872
110.070.5593.020.040.793l7tA GO:0004462 GO:0046872
120.070.6053.000.070.844jd1B GO:0000287 GO:0004364 GO:0005737 GO:0016740 GO:0016765 GO:0046677 GO:0046872
130.070.5603.050.090.793ey7A GO:0003824 GO:0051213 GO:0055114
140.070.6463.350.080.911zswA GO:0046872
150.070.6443.260.070.913oajA GO:0005737 GO:0009636 GO:0016491 GO:0019439 GO:0046872 GO:0051213 GO:0055114
160.070.5823.100.090.834mtsA GO:0004462 GO:0016829 GO:0046872
170.070.5653.310.090.834kykA GO:0004462 GO:0005975 GO:0006357 GO:0006749 GO:0008270 GO:0009438 GO:0016829 GO:0019243 GO:0030316 GO:0043066 GO:0046872 GO:0070062
180.070.6163.110.110.843kolA GO:0004462 GO:0046872 GO:0051213 GO:0055114
190.070.5513.220.110.813hnqA GO:0009405
200.070.6593.090.050.914huzA GO:0016491 GO:0046872 GO:0051213 GO:0055114
210.070.6093.240.100.851npbA GO:0004364 GO:0005737 GO:0016740 GO:0046677 GO:0046872
220.070.6483.020.070.905d7zA GO:0004462 GO:0016829 GO:0046872
230.070.5264.090.090.902r5vA GO:0003868 GO:0005506 GO:0009072 GO:0016491 GO:0016701 GO:0017000 GO:0033072 GO:0046872 GO:0050585 GO:0055114
240.070.6082.960.080.844jh1A GO:0000287 GO:0005737 GO:0016740 GO:0016765 GO:0046677 GO:0046872
250.070.5423.310.080.803g12B GO:0016829
260.060.3654.630.050.652xclA GO:0000166 GO:0000287 GO:0003824 GO:0004637 GO:0005524 GO:0006164 GO:0006189 GO:0009113 GO:0016874 GO:0030145 GO:0046872
270.060.3944.590.060.712cgjA GO:0000166 GO:0005524 GO:0005737 GO:0005975 GO:0008993 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0019299 GO:0019301 GO:0046835


Consensus prediction of GO terms
 
Molecular Function GO:0046872 GO:0016846 GO:0016765 GO:0016491
GO-Score 0.60 0.41 0.35 0.31
Biological Processes GO:0046677 GO:0044710
GO-Score 0.50 0.31
Cellular Component GO:0005737
GO-Score 0.50

(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.