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I-TASSER results for job id Rv3656c

[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 1c61A KR Rep, Mult 26,29,30,33,59,62,63
20.08 4 2axtM CLA Rep, Mult 39,43
30.06 3 3glnA XE Rep, Mult 13,14,29
40.04 2 1jl7A CYN Rep, Mult 39,56,60
50.04 2 2v5kB MG Rep, Mult 28,50
60.04 2 1bjyB CTC Rep, Mult 56,60,63
70.04 2 1vd5A GLY Rep, Mult 39,53
80.02 1 3fk7A 4DM Rep, Mult 63,67
90.02 1 1brrB ARC Rep, Mult 7,64
100.02 1 3jcuZ CLA Rep, Mult 17,21
110.02 1 3x0eA MG Rep, Mult 17,27,29,30
120.02 1 2xquB CVM Rep, Mult 12,16
130.02 1 4rkuJ CLA Rep, Mult 7,10

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
10.0603e6iA0.5273.580.0670.8381.14.13.-NA
20.0602ar0A0.5212.780.0890.8242.1.1.72NA
30.0601yqyA0.4764.230.1030.8683.4.24.8325
40.0601tqgA0.5283.370.0310.9412.7.13.333
50.0601zxvA0.5172.950.0160.8823.4.24.8344
60.0603gqbA0.5452.940.0300.8683.6.3.1456
70.0602wpnB0.5433.300.0780.9261.12.7.2NA
80.0601w27A0.5193.350.0950.8534.3.1.24NA
90.0603d2rB0.5233.620.0450.8532.7.11.2NA
100.0601fftA0.5553.160.0780.8971.10.3.-NA
110.0602zdxA0.5183.700.0600.8532.7.11.2NA
120.0603bhgA0.5293.200.0500.8094.3.2.240
130.0601yfeA0.5223.410.0780.8684.2.1.2NA
140.0602wyeB0.5213.410.1190.8533.5.1.97NA
150.0602nsmA0.5223.940.0450.9413.4.17.3NA
160.0602pdaA0.5272.230.0960.7651.2.7.1NA
170.0601ordA0.5493.280.0830.8824.1.1.17NA
180.0601g4uS0.5653.100.0950.8823.1.3.48NA
190.0601jtnA0.4013.580.0670.6473.2.1.17NA

(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
00.120.4863.240.120.852l7aA GO:0001726 GO:0003779 GO:0005178 GO:0005200 GO:0005737 GO:0005815 GO:0005856 GO:0005886 GO:0005925 GO:0007016 GO:0007044 GO:0007155 GO:0009986 GO:0016020 GO:0017166 GO:0030054 GO:0030274 GO:0030866 GO:0032403 GO:0032587 GO:0042995 GO:0051015 GO:0070062 GO:0070527
10.070.3163.800.060.561sgfA GO:0004175 GO:0004252 GO:0005057 GO:0005615 GO:0005634 GO:0006508 GO:0007264 GO:0008083 GO:0016811 GO:0043234 GO:0043552 GO:0046872 GO:0070062
20.070.6282.760.110.962o8eB GO:0000166 GO:0000228 GO:0000287 GO:0000400 GO:0000710 GO:0000790 GO:0003677 GO:0003682 GO:0003684 GO:0003690 GO:0005524 GO:0005634 GO:0005654 GO:0005694 GO:0005737 GO:0005794 GO:0005886 GO:0006281 GO:0006298 GO:0006974 GO:0007131 GO:0008340 GO:0008630 GO:0009411 GO:0016032 GO:0016446 GO:0016447 GO:0016887 GO:0030983 GO:0032137 GO:0032142 GO:0032143 GO:0032301 GO:0032357 GO:0032405 GO:0035064 GO:0042803 GO:0043231 GO:0043531 GO:0043570 GO:0045190 GO:0045830 GO:0045910 GO:0051096 GO:0097193
30.070.5862.980.080.961ng9A GO:0000018 GO:0000166 GO:0003677 GO:0003684 GO:0005524 GO:0005829 GO:0006281 GO:0006298 GO:0006974 GO:0008301 GO:0016887 GO:0030983 GO:0032136 GO:0032300 GO:0042802 GO:0043531
40.070.5433.070.050.911ewrB GO:0000166 GO:0003677 GO:0003684 GO:0005524 GO:0006281 GO:0006298 GO:0006974 GO:0030983
50.070.5413.450.050.943thxA GO:0000166 GO:0000287 GO:0000400 GO:0000403 GO:0000404 GO:0000406 GO:0000710 GO:0000784 GO:0001701 GO:0002204 GO:0003677 GO:0003684 GO:0003690 GO:0003697 GO:0005524 GO:0005634 GO:0005654 GO:0006119 GO:0006281 GO:0006298 GO:0006301 GO:0006302 GO:0006311 GO:0006974 GO:0007050 GO:0007131 GO:0007281 GO:0008022 GO:0008340 GO:0008584 GO:0008630 GO:0010165 GO:0010224 GO:0016020 GO:0016446 GO:0016447 GO:0016887 GO:0019237 GO:0019724 GO:0019899 GO:0019901 GO:0030183 GO:0030983 GO:0031573 GO:0032137 GO:0032139 GO:0032142 GO:0032143 GO:0032181 GO:0032300 GO:0032301 GO:0032302 GO:0032357 GO:0032405 GO:0042771 GO:0042803 GO:0043524 GO:0043531 GO:0043570 GO:0045128 GO:0045190 GO:0045910 GO:0051096
60.070.6102.450.080.933thwB GO:0000166 GO:0000228 GO:0000710 GO:0003677 GO:0003684 GO:0003697 GO:0005524 GO:0005654 GO:0006281 GO:0006298 GO:0006974 GO:0007131 GO:0016020 GO:0019899 GO:0030983 GO:0032137 GO:0032139 GO:0032142 GO:0032181 GO:0032302 GO:0032357 GO:0042803 GO:0043570 GO:0045910 GO:0051096
70.070.5332.740.130.885akbE GO:0000018 GO:0000166 GO:0003677 GO:0003684 GO:0005524 GO:0005829 GO:0006281 GO:0006298 GO:0006974 GO:0008301 GO:0016887 GO:0030983 GO:0032136 GO:0032300 GO:0042802 GO:0043531
80.070.5403.030.070.881ewqA GO:0000166 GO:0003677 GO:0003684 GO:0005524 GO:0006281 GO:0006298 GO:0006974 GO:0030983
90.070.3954.350.030.823f6tB GO:0003824 GO:0004069 GO:0008483 GO:0009058 GO:0016740 GO:0030170 GO:0080130
100.070.4693.640.070.844ymsA GO:0000166 GO:0003333 GO:0005524 GO:0015424 GO:0016887
110.070.5133.400.080.931u89A GO:0001726 GO:0003779 GO:0005178 GO:0005200 GO:0005737 GO:0005815 GO:0005856 GO:0005886 GO:0005925 GO:0007016 GO:0007044 GO:0007155 GO:0009986 GO:0016020 GO:0017166 GO:0030054 GO:0030274 GO:0030866 GO:0032403 GO:0032587 GO:0042995 GO:0051015 GO:0070062 GO:0070527
120.070.3983.720.060.711ewrA GO:0000166 GO:0003677 GO:0003684 GO:0005524 GO:0006281 GO:0006298 GO:0006974 GO:0030983
130.070.4403.200.040.753p3qB GO:0000160 GO:0005622
140.070.4113.440.060.653nd2A GO:0000059 GO:0000060 GO:0000176 GO:0005087 GO:0005634 GO:0005643 GO:0005737 GO:0006606 GO:0006607 GO:0006610 GO:0006612 GO:0006656 GO:0006810 GO:0006886 GO:0008139 GO:0008536 GO:0008565 GO:0015031 GO:0031965 GO:0034399 GO:0043547 GO:0051028 GO:0051292 GO:0060188
150.060.4204.270.040.781us2A GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0009279 GO:0016020 GO:0016787 GO:0016798 GO:0031176 GO:0045493
160.060.3593.660.080.623k8kA GO:0000272 GO:0000287 GO:0003824 GO:0004556 GO:0005509 GO:0005975 GO:0005983 GO:0008152 GO:0009279 GO:0016020 GO:0016787 GO:0016798 GO:0019867 GO:0046872 GO:2001070
170.060.3623.950.080.653e82D GO:0008152 GO:0016491 GO:0055114
180.060.3854.220.090.815a07A GO:0000026 GO:0000030 GO:0000032 GO:0005794 GO:0006486 GO:0006487 GO:0006493 GO:0016020 GO:0016021 GO:0016740 GO:0016757 GO:0097502


Consensus prediction of GO terms
 
Molecular Function GO:0035639 GO:0032559 GO:0032550 GO:0003690
GO-Score 0.37 0.37 0.37 0.37
Biological Processes GO:0006281
GO-Score 0.37
Cellular Component GO:0031988 GO:1903561 GO:0044424 GO:0071944
GO-Score 0.37 0.37 0.36 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.