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I-TASSER results for job id Rv3912

[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
10.08 4 2zxwN CDL Rep, Mult 53,57,77,81,84,85,88
20.04 2 1gkfB EDO Rep, Mult 13,14,157,163
30.04 2 3g6wA GTP Rep, Mult 55,59,62
40.04 2 3n87J N87 Rep, Mult 26,29
50.04 2 3favC ZN Rep, Mult 22,26
60.02 1 3ag4N CDL Rep, Mult 45,46,85,89,92
70.02 1 5c65A 37X Rep, Mult 53,85
80.02 1 1gm7B EDO Rep, Mult 45,46,96,108,156
90.02 1 1lnyA MG Rep, Mult 184,205
100.02 1 3mdoA CA Rep, Mult 34,67
110.02 1 1um0A FMN Rep, Mult 204,205
120.02 1 1t5bB FMN Rep, Mult 32,41
130.02 1 3e3gB SO4 Rep, Mult 59,78
140.02 1 3wmm7 CRT Rep, Mult 54,64
150.02 1 1gk9B EDO Rep, Mult 47,48,49,144,145,157
160.02 1 1fipA III Rep, Mult 18,19
170.02 1 3ablA CDL Rep, Mult 186,190,193,197
180.02 1 4qjsW MG Rep, Mult 122,184
190.02 1 3bwxA CA Rep, Mult 98,101

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
10.0602pdaA0.3556.380.0430.6421.2.7.1NA
20.0601xc6A0.3706.240.0460.6423.2.1.23NA
30.0601mswD0.3335.790.0400.5552.7.7.6NA
40.0602qtlA0.3436.010.0540.5791.16.1.8NA
50.0602hs4A0.3445.680.0200.5636.3.5.3NA
60.0601b0pA0.3596.510.0560.6531.2.7.1NA
70.0601qlaD0.3446.850.0300.6611.3.99.180,88,122
80.0601kqfA0.3666.230.0320.6461.2.1.2NA
90.0601c4aA0.3065.960.0300.5161.12.7.2NA
100.0602cqsA0.3196.440.0510.5872.4.1.20NA
110.0601b8fA0.3015.950.0640.5044.3.1.3NA
120.0602pmgB0.3376.330.0580.5955.4.2.234
130.0602qubA0.3465.980.0340.5983.1.1.3NA
140.0601aroP0.3235.230.0530.5042.7.7.6NA
150.0602o6yA0.3845.620.0870.6264.3.1.-NA
160.0603c8yA0.3376.200.0540.5981.12.7.2NA
170.0601occA0.3825.450.0540.6021.9.3.1NA
180.0601h2rL0.3656.090.0470.6301.12.2.1NA
190.0601h2aL0.3626.180.0430.6341.12.2.1NA

(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
00.070.4325.810.040.701m56A GO:0004129 GO:0005506 GO:0005507 GO:0005886 GO:0006119 GO:0006810 GO:0006811 GO:0009055 GO:0009060 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0020037 GO:0022900 GO:0046872 GO:0055114 GO:0070469 GO:1902600
10.060.3905.560.030.611qleA GO:0004129 GO:0005506 GO:0005507 GO:0005886 GO:0006119 GO:0006810 GO:0006811 GO:0009055 GO:0009060 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0020037 GO:0022900 GO:0046872 GO:0055114 GO:0070469 GO:1902600
20.060.3766.700.050.701e1dA GO:0003824 GO:0005737 GO:0016491 GO:0016661 GO:0046872 GO:0050418 GO:0051536 GO:0051539 GO:0055114
30.060.4265.510.060.673eh3A GO:0004129 GO:0005506 GO:0005886 GO:0006119 GO:0006811 GO:0009055 GO:0009060 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0020037 GO:0046872 GO:0055114 GO:0070469 GO:1902600
40.060.4155.600.080.662yevA GO:0004129 GO:0005506 GO:0005507 GO:0005886 GO:0006119 GO:0006810 GO:0006811 GO:0009055 GO:0009060 GO:0015002 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0020037 GO:0022900 GO:0022904 GO:0046872 GO:0055114 GO:0070469 GO:1902600
50.060.3825.450.050.601occA GO:0004129 GO:0005506 GO:0005739 GO:0005743 GO:0006119 GO:0009055 GO:0009060 GO:0016020 GO:0016021 GO:0016491 GO:0020037 GO:0045277 GO:0046872 GO:0055114 GO:0070469 GO:1902600
60.060.3865.460.050.631w27A GO:0003824 GO:0005737 GO:0006559 GO:0009698 GO:0009800 GO:0016829 GO:0016841 GO:0045548
70.060.3905.570.030.621fftA GO:0004129 GO:0005506 GO:0005507 GO:0005886 GO:0005887 GO:0006811 GO:0009055 GO:0009060 GO:0009319 GO:0009486 GO:0015078 GO:0015453 GO:0015990 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0016682 GO:0019646 GO:0020037 GO:0046872 GO:0048039 GO:0055114 GO:0070469
80.060.3386.200.050.611h6dA GO:0006061 GO:0008152 GO:0016491 GO:0042597 GO:0047061 GO:0055114
90.060.3356.250.040.593czoB GO:0003824 GO:0004397 GO:0005737 GO:0009072 GO:0009698 GO:0009699 GO:0009800 GO:0016829 GO:0016841 GO:0045548 GO:0051289
100.060.3405.780.090.563nz4B GO:0003824 GO:0005737 GO:0006558 GO:0006559 GO:0009698 GO:0009800 GO:0009820 GO:0009821 GO:0016829 GO:0016841 GO:0016853 GO:0016869 GO:0042617 GO:0045548 GO:0051289
110.060.3236.780.040.613kdyA GO:0003824 GO:0009403 GO:0016829 GO:0016841 GO:0016853 GO:0017000 GO:0050368 GO:0052883
120.060.3835.570.040.622nyfA GO:0003824 GO:0005737 GO:0009072 GO:0009698 GO:0009699 GO:0009800 GO:0016829 GO:0016841 GO:0045548 GO:0051289
130.060.3815.570.040.624v2rB GO:0003824 GO:0005737 GO:0006558 GO:0006559 GO:0009698 GO:0009800 GO:0009820 GO:0009821 GO:0016829 GO:0016841 GO:0016853 GO:0016869 GO:0042617 GO:0045548 GO:0051289
140.060.3875.350.040.604c6gB GO:0003824 GO:0005737 GO:0006558 GO:0006559 GO:0009698 GO:0009800 GO:0009820 GO:0009821 GO:0016829 GO:0016841 GO:0016853 GO:0016869 GO:0042617 GO:0045548 GO:0051289
150.060.2976.370.040.533bkkA GO:0001822 GO:0001974 GO:0002003 GO:0002005 GO:0002019 GO:0002446 GO:0002474 GO:0003081 GO:0003779 GO:0004175 GO:0004180 GO:0005576 GO:0005615 GO:0005737 GO:0005764 GO:0005768 GO:0005886 GO:0006508 GO:0007283 GO:0008144 GO:0008217 GO:0008233 GO:0008237 GO:0008238 GO:0008240 GO:0008241 GO:0008270 GO:0009897 GO:0014910 GO:0016020 GO:0016021 GO:0016787 GO:0019229 GO:0031404 GO:0031434 GO:0031711 GO:0032943 GO:0042312 GO:0042447 GO:0043171 GO:0046872 GO:0050435 GO:0050482 GO:0051019 GO:0060047 GO:0060177 GO:0060218 GO:0061098 GO:0070062 GO:0070573 GO:0071838 GO:1900086 GO:1902033 GO:1903597 GO:2000170
160.060.3035.730.030.492rjqA GO:0004222 GO:0005178 GO:0005576 GO:0005578 GO:0005615 GO:0005788 GO:0006508 GO:0008201 GO:0008233 GO:0008237 GO:0008270 GO:0016787 GO:0022617 GO:0031012 GO:0036066 GO:0042742 GO:0046872 GO:0050840
170.060.3735.350.080.591gk2A GO:0003824 GO:0004397 GO:0005737 GO:0006547 GO:0006548 GO:0016829 GO:0016841 GO:0019556 GO:0019557
180.060.3876.330.070.691gnlA GO:0003824 GO:0005737 GO:0016491 GO:0016661 GO:0046872 GO:0050418 GO:0051536 GO:0051539 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0015002 GO:0046914 GO:0015078 GO:0016676 GO:0046906
GO-Score 0.47 0.47 0.47 0.47 0.47
Biological Processes GO:0015672 GO:0045333 GO:0098662 GO:0006818 GO:0046034 GO:0016310
GO-Score 0.47 0.47 0.47 0.47 0.47 0.47
Cellular Component GO:0071944 GO:0031224
GO-Score 0.47 0.38

(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.