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I-TASSER results for job id Rv2880c

[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
10.48 7 5hr6A SF4 Rep, Mult 126,128,130,133,136,221
20.10 2 1mw0A UUU Rep, Mult 92,93,94,96,159,160
30.06 1 3rfaA UUU Rep, Mult 126,128,130,132,133,136,174,175,177,178,179,215,220,246,266,268,269

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
10.0603aboA0.4445.800.0550.7064.3.1.7152,172,177,219,226
20.0603b2qA0.4455.800.0520.7133.6.3.14270
30.0601icpA0.4524.880.0740.6441.3.1.42NA
40.0601bwkA0.4055.150.0610.5961.6.99.1168
50.0601gowA0.4585.270.0680.6913.2.1.23NA
60.0601bf2A0.4615.100.0540.6653.2.1.68NA
70.0601b1yA0.4504.920.0550.6513.2.1.2148
80.0603b9eA0.4486.260.0560.7643.2.1.14NA
90.0601z41A0.4534.650.0340.6401.6.99.1,1.-.-.-NA
100.0601jphA0.4425.050.0480.6444.1.1.37NA
110.0601t7lA0.4665.020.0380.6872.1.1.14NA
120.0601iwpA0.4635.510.0540.7134.2.1.30NA
130.0601bwlA0.4065.130.0510.6001.6.99.1NA
140.0602nq5A0.4615.090.0530.6842.1.1.14NA
150.0601dioA0.4595.530.0580.7094.2.1.28NA
160.0603kruA0.4574.390.0390.6331.6.99.1NA
170.0601djnA0.4534.420.0430.6331.5.8.2,1.5.99.7NA
180.0601wkvB0.4475.600.0940.7062.5.1.47NA
190.0601u22A0.4595.020.0390.6802.1.1.1446,76

(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
00.310.7752.780.220.875hr7A GO:0000049 GO:0002935 GO:0003824 GO:0005737 GO:0005829 GO:0006364 GO:0008033 GO:0008168 GO:0008173 GO:0016740 GO:0019843 GO:0030488 GO:0032259 GO:0046677 GO:0046872 GO:0051536 GO:0051539 GO:0070040 GO:0070475
10.090.4295.840.050.692bhzA GO:0003824 GO:0004553 GO:0005737 GO:0005975 GO:0005992 GO:0008152 GO:0016787 GO:0016798 GO:0033942
20.070.4974.940.060.723amlA GO:0003824 GO:0003844 GO:0004553 GO:0005975 GO:0005978 GO:0005982 GO:0009501 GO:0009507 GO:0009536 GO:0016740 GO:0016757 GO:0019252 GO:0043169
30.070.4754.930.040.693ucqA GO:0003824 GO:0005975
40.070.4994.760.040.715cltA GO:0003824 GO:0003844 GO:0004553 GO:0005829 GO:0005975 GO:0005977 GO:0005978 GO:0006091 GO:0016740 GO:0016757 GO:0043169 GO:0070062
50.070.4676.070.070.773eddA GO:0003824 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0046872 GO:0047798
60.070.4665.320.030.694aioA GO:0003824 GO:0004553 GO:0005975 GO:0046872 GO:0051060
70.070.4285.840.040.692vncB GO:0003824 GO:0004133 GO:0004177 GO:0004553 GO:0005975 GO:0005980 GO:0006508
80.070.4615.100.050.671bf2A GO:0003824 GO:0004553 GO:0005576 GO:0005975 GO:0005977 GO:0008152 GO:0016787 GO:0016798 GO:0019156 GO:0046872
90.070.4106.060.040.692ya1A GO:0003824 GO:0004553 GO:0005576 GO:0005618 GO:0005975 GO:0016020 GO:0016021 GO:0030246
100.070.4265.570.030.661eh9A GO:0003824 GO:0004553 GO:0005737 GO:0005975 GO:0005992 GO:0008152 GO:0016787 GO:0016798 GO:0033942
110.070.4505.120.070.652wskA GO:0003824 GO:0004133 GO:0004135 GO:0004553 GO:0005975 GO:0005977 GO:0005980 GO:0006974 GO:0008152 GO:0016787 GO:0016798
120.060.4305.760.050.704okdA GO:0003824 GO:0004553 GO:0005975
130.060.3816.600.040.682e8yA GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0051060
140.060.4325.510.070.673m07A GO:0003824 GO:0004553 GO:0005737 GO:0005975 GO:0005992 GO:0008152 GO:0016787 GO:0016798 GO:0033942 GO:0046872
150.060.3556.300.040.614h8vA GO:0003824 GO:0005975 GO:0046872
160.060.3156.570.040.574howA GO:0003824 GO:0005975 GO:0016853 GO:0046872
170.060.4245.910.060.692vr5A GO:0003824 GO:0004133 GO:0004177 GO:0004553 GO:0005975 GO:0005980 GO:0006508
180.060.4255.120.030.624lxfB GO:0003824 GO:0005975 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0016798 GO:0019843 GO:0002935 GO:0000049 GO:0051539 GO:0046872 GO:0070040
GO-Score 0.40 0.31 0.31 0.31 0.31 0.31 0.31
Biological Processes GO:0070475 GO:0030488 GO:0046677
GO-Score 0.31 0.31 0.31
Cellular Component GO:0005829
GO-Score 0.35

(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.