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I-TASSER results for job id Rv2955c

[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
10.38 19 4m37A SAH Rep, Mult 112,133,134,135,136,137,141,154,155,156,160,182,183,184,241,248
20.04 2 2jgoB ZN Rep, Mult 242,245
30.04 2 2x2vA DPV Rep, Mult 238,242
40.02 1 3ke6A MN Rep, Mult 133,134,138,139
50.02 1 3ke6A MN Rep, Mult 133,240,296
60.02 1 2hneA MG Rep, Mult 133,155,186

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
10.0601v6sA0.4655.890.0470.7042.7.2.3NA
20.0602vz8B0.4825.110.0690.6702.3.1.85NA
30.0601e3lA0.4695.550.0720.6921.1.1.1251
40.06013pkA0.4915.360.0640.7172.7.2.3NA
50.0601a71A0.4825.230.0630.6851.1.1.1142
60.0602dphA0.4665.160.0630.6671.2.99.4NA
70.0602w98B0.4705.150.0410.6601.3.1.48207
80.0603c6kD0.4675.080.0760.6512.5.1.22NA
90.0601cdoA0.4785.220.0710.6791.1.1.1NA
100.0601tehA0.4855.150.0710.6821.1.1.284,1.1.1.1262,265
110.0601cdoB0.4745.480.0510.6851.1.1.1164,177
120.0602j3jB0.4715.550.0350.6891.3.1.74139
130.0601f8fA0.4805.370.0680.6891.1.1.90NA
140.0601d1tA0.4815.370.0810.6921.1.1.1262
150.0602vz8A0.4815.110.0770.6702.3.1.85NA
160.0601p0fA0.4765.230.0570.6821.1.1.2246,263
170.0602as0A0.4764.790.1160.6422.1.1.-NA
180.0601m6hA0.4835.150.0740.6821.1.1.284,1.1.1.1NA
190.0603cosD0.4795.340.0560.6891.1.1.1NA

(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
00.320.7122.630.140.792py6A GO:0008168 GO:0016740 GO:0032259
10.130.4253.450.100.512ipxA GO:0000494 GO:0001094 GO:0001649 GO:0001651 GO:0001652 GO:0003723 GO:0005634 GO:0005654 GO:0005730 GO:0006364 GO:0006396 GO:0008033 GO:0008168 GO:0008649 GO:0015030 GO:0016020 GO:0016074 GO:0016740 GO:0030529 GO:0031167 GO:0031428 GO:0032040 GO:0032259 GO:0044822 GO:0048254 GO:0051117 GO:0070062 GO:1990258 GO:1990259
20.100.5084.590.110.672yxlA GO:0003723 GO:0006364 GO:0008168 GO:0008757 GO:0032259
30.090.5174.430.100.671sqfA GO:0003723 GO:0005737 GO:0005829 GO:0006355 GO:0006364 GO:0008168 GO:0008649 GO:0009383 GO:0016434 GO:0016740 GO:0031167 GO:0032259 GO:0070475
40.080.4183.130.090.493mb5A GO:0008033 GO:0008168 GO:0016429 GO:0016740 GO:0030488 GO:0031515 GO:0032259
50.070.4924.160.120.634fzvA GO:0003723 GO:0005739 GO:0005762 GO:0006364 GO:0008168 GO:0016740 GO:0019843 GO:0031167 GO:0032259 GO:0042254 GO:0042256 GO:0070131 GO:0070181
60.070.4684.290.160.613m6wA GO:0003723 GO:0005737 GO:0006364 GO:0008168 GO:0016740 GO:0032259
70.070.4864.170.090.631ixkA GO:0003723 GO:0006364 GO:0008168 GO:0008757 GO:0032259
80.070.4724.560.130.624dmgA GO:0003723 GO:0008168 GO:0016740 GO:0032259 GO:0046872 GO:0051536 GO:0051539
90.070.4764.160.120.602frxA GO:0003723 GO:0005737 GO:0006364 GO:0008168 GO:0008649 GO:0008757 GO:0009383 GO:0016434 GO:0016740 GO:0031167 GO:0032259 GO:0070475
100.070.4734.200.140.603m4xA GO:0003723 GO:0005737 GO:0006364 GO:0008168 GO:0008757 GO:0016740 GO:0032259
110.070.4045.380.090.603m6uB GO:0003723 GO:0005737 GO:0006364 GO:0008168 GO:0016740 GO:0032259
120.060.4193.220.090.504pooB GO:0008168 GO:0032259 GO:0046872 GO:0051536 GO:0051539
130.060.4433.060.140.511m6yA GO:0005737 GO:0006364 GO:0008168 GO:0016740 GO:0032259 GO:0070475 GO:0071424
140.060.4203.690.140.513tmaA GO:0003723 GO:0008168 GO:0016740 GO:0032259
150.060.4283.540.110.513eeyA GO:0008168 GO:0032259 GO:0046872 GO:0051536 GO:0051539
160.060.4223.270.140.504df3A GO:0003723 GO:0006364 GO:0008033 GO:0008168 GO:0016740 GO:0032259
170.060.4083.070.100.481eizA GO:0000027 GO:0000453 GO:0001510 GO:0005737 GO:0005829 GO:0006364 GO:0008168 GO:0008650 GO:0016436 GO:0016740 GO:0032259
180.060.4183.150.150.492gpyB GO:0008168 GO:0008171 GO:0016740 GO:0032259 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0003676 GO:0008173 GO:0008757
GO-Score 0.58 0.42 0.42
Biological Processes GO:0001510 GO:0000154 GO:0006399
GO-Score 0.42 0.42 0.40
Cellular Component GO:0015030 GO:0031428 GO:0032040 GO:0001651 GO:0001652 GO:0070062 GO:0016020 GO:0005829 GO:0031515
GO-Score 0.13 0.13 0.13 0.13 0.13 0.13 0.13 0.09 0.08

(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.