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

I-TASSER results for job id Rv0580c

[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
10.49 19 3r5wM F42 Rep, Mult 41,48,49,50,51,55,57,58,59,60,71,72,74,75,76,78,79,140
20.02 1 2iab0 III Rep, Mult 41,43,45,46,47,48,49,52,53,54,55,56,58,83,85,87,88,89,92,94
30.02 1 1vl70 III Rep, Mult 40,41,43,45,48,52,53,54,55,56,58,60,73,74,85,87,89,119,139,140
40.02 1 2ou5A FMN Rep, Mult 45,88,90,95,97
50.02 1 2i51A FMN Rep, Mult 61,70,72,157

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
10.0601ky9B0.4264.830.0600.6563.4.21.-NA
20.0601rtkA0.4074.870.0650.6323.4.21.4783
30.0601s4fA0.4355.290.0390.7792.7.7.48NA
40.0603iu2A0.4265.290.0620.7972.3.1.97NA
50.0602wj2A0.4445.750.0390.8903.5.1.9975
60.0601jnwA0.4943.420.0720.6441.4.3.5NA
70.0603fimB0.4375.270.0610.7791.1.3.7NA
80.0603d35A0.4465.350.0730.8162.3.1.4841
90.0601p4nA0.4485.130.0770.7972.3.2.1057,60,86
100.0601bdaA0.4314.680.0280.6633.4.21.68NA
110.0601nrgA0.5033.600.0920.6631.4.3.5NA
120.0602qubA0.4264.820.0390.6993.1.1.3NA
130.0602aj4A0.4234.400.0790.6502.7.1.6NA
140.0601hylA0.4314.830.0870.6563.4.21.49NA
150.0601hi8A0.4345.590.0450.8162.7.7.48101,113
160.0601wv4A0.4642.750.0830.5521.4.3.5NA
170.0601ci0A0.5003.500.0970.6561.4.3.5NA
180.0602gwdA0.4124.880.0720.6936.3.2.2NA
190.0601ikpA0.4394.580.0530.6812.4.2.-NA

(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
00.290.7791.290.160.833r5yD GO:0010181 GO:0016491 GO:0055114
10.260.7111.480.140.773r5zA GO:0016491 GO:0055114
20.250.6672.110.180.773h96C GO:0016491 GO:0055114
30.200.5132.680.100.613db0B GO:0010181 GO:0016491 GO:0055114
40.170.5122.730.070.622i02A GO:0000166 GO:0010181 GO:0016491 GO:0055114
50.170.5811.830.140.644y9iA GO:0016491 GO:0055114
60.150.5223.100.140.642hq9B GO:0000166 GO:0010181 GO:0016491 GO:0055114
70.130.5333.410.100.674qvbB GO:0004733 GO:0010181 GO:0016491 GO:0030170 GO:0042803 GO:0042816 GO:0042823 GO:0055114
80.090.5472.450.070.643tgvA GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
90.080.5122.650.100.613f7eA GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
100.080.5303.100.110.651rfeA GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
110.070.5053.650.070.681t9mA GO:0000166 GO:0002047 GO:0004733 GO:0008615 GO:0010181 GO:0016491 GO:0016638 GO:0042823 GO:0055114
120.070.5122.630.130.603ec6A GO:0000166 GO:0003677 GO:0010181 GO:0016491 GO:0055114
130.070.5362.370.080.635bncA GO:0010181 GO:0016491 GO:0055114
140.070.5472.510.130.633r5lA GO:0005618 GO:0005886 GO:0010181 GO:0016020 GO:0016491 GO:0055114 GO:0070967
150.070.5252.830.060.653gasA GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0046872 GO:0055114
160.070.5502.490.110.641vl7A GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
170.070.5462.320.120.632arzA GO:0010181 GO:0016491 GO:0055114
180.070.5273.090.040.663swjA GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
190.070.5113.240.120.654hmtB GO:0002047 GO:0004733 GO:0008615 GO:0009405 GO:0010181 GO:0016491 GO:0016638 GO:0017000 GO:0042823 GO:0055114
200.070.4713.370.090.613dmbA GO:0010181 GO:0016491 GO:0055114
210.060.3525.490.060.675anbK GO:0000166 GO:0003924 GO:0005525 GO:0005622 GO:0006412 GO:0042254 GO:0042256 GO:0043022
220.060.3755.360.050.673uw1A GO:0004751 GO:0006098 GO:0009052 GO:0016853
230.060.3005.830.060.563ag6A GO:0000166 GO:0004592 GO:0005524 GO:0005737 GO:0015940 GO:0016874


Consensus prediction of GO terms
 
Molecular Function GO:0016491 GO:0010181
GO-Score 0.74 0.53
Biological Processes GO:0055114
GO-Score 0.74
Cellular Component
GO-Score

(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.