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I-TASSER results for job id Rv1051c

[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
10.05 3 1fz9A ETI Rep, Mult 99,100,103,104,143
20.05 3 1xvgA BRJ Rep, Mult 100,101,136,139,140
30.04 2 2ql2A NUC Rep, Mult 171,172,175
40.04 2 2qapA PO4 Rep, Mult 177,178,181
50.04 2 2yzeA NOB Rep, Mult 170,171
60.02 1 2z7cD ARG Rep, Mult 122,125
70.02 1 3qoqD NUC Rep, Mult 116,118
80.02 1 3ecnB MG Rep, Mult 65,97
90.02 1 2g9zA MG Rep, Mult 132,134
100.02 1 1cprA ZN Rep, Mult 120,177
110.02 1 1sl0A MG Rep, Mult 65,122
120.02 1 2w9nA ZN Rep, Mult 103,119
130.02 1 3n9vA CA Rep, Mult 68,69,119
140.02 1 2vrzA ZN Rep, Mult 181,184
150.02 1 1xvgA BRJ Rep, Mult 13,17,85
160.02 1 3mliD CA Rep, Mult 97,103
170.02 1 3cr3A MG Rep, Mult 24,65
180.02 1 1xveA 3BB Rep, Mult 103,106,107,115,116,153
190.02 1 2iefB NUC Rep, Mult 228,229
200.02 1 3qu6A ZN Rep, Mult 123,127

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
10.0602eabA0.4465.700.0240.7133.2.1.63NA
20.0601fziA0.4465.740.0380.7171.14.13.2590
30.0601htoA0.4395.810.0440.7336.3.1.2NA
40.0602dgaA0.4126.330.0510.7293.2.1.2198
50.0601mhyD0.4525.650.0310.7251.14.13.25NA
60.0601xnvA0.4095.840.0340.6896.4.1.3NA
70.0602e1qA0.4356.260.0660.7651.17.3.2,1.17.1.4NA
80.0601fo4A0.4405.940.0580.7371.17.1.4NA
90.0601oqzB0.4136.240.0640.7373.5.1.93201
100.0602zzgA0.4255.720.0350.6816.1.1.7124,202
110.0601f1hA0.4325.810.0580.7256.3.1.2NA
120.0601z8lA0.4076.080.0400.6973.4.17.21NA
130.0601lf6A0.4176.010.0630.7173.2.1.3NA
140.0602jg0A0.4175.420.0380.6493.2.1.28146
150.0602je8B0.4146.320.0470.7493.2.1.25246
160.0602e9lA0.4146.380.0560.7413.2.1.21NA
170.0601f1hL0.4325.770.0630.7216.3.1.2NA
180.0601jqnA0.4355.350.0350.6774.1.1.31213
190.0601lgrA0.4115.930.0620.6896.3.1.2NA

(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
00.070.4246.050.040.722okxA GO:0003824
10.070.4605.820.080.763wakA GO:0004576 GO:0006486 GO:0016020 GO:0016021 GO:0016740 GO:0046872
20.070.4605.800.070.763wajA GO:0004576 GO:0006486 GO:0016020 GO:0016021 GO:0016740 GO:0046872
30.070.4815.360.060.743w5mA GO:0003824 GO:0046872
40.070.4575.710.040.742incA GO:0004497 GO:0006725 GO:0016491 GO:0046872 GO:0055114
50.070.4625.730.050.753dhiA GO:0004497 GO:0006725 GO:0016491 GO:0019439 GO:0042203 GO:0046872 GO:0055114
60.070.4525.650.030.731mhyD GO:0004497 GO:0006725 GO:0006730 GO:0015049 GO:0016491 GO:0046872 GO:0055114
70.060.4465.740.040.721fziA GO:0004497 GO:0006725 GO:0006730 GO:0015049 GO:0015050 GO:0015947 GO:0016491 GO:0046872 GO:0055114
80.060.4635.510.040.733cihA GO:0003824
90.060.3306.590.080.603eddA GO:0003824 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0046872 GO:0047798
100.060.3745.790.020.632amxA GO:0009168 GO:0019239
110.060.3226.670.040.615azaA GO:0004576 GO:0005215 GO:0005363 GO:0006486 GO:0006810 GO:0006974 GO:0008643 GO:0015768 GO:0016020 GO:0016021 GO:0016740 GO:0030288 GO:0034289 GO:0042597 GO:0042956 GO:0043190 GO:0055052 GO:0060326 GO:1901982 GO:1990060
120.060.3796.150.040.671lshA GO:0005319 GO:0006869 GO:0045735
130.060.3606.220.040.634j6rG GO:0005198 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0039663 GO:0044174 GO:0044175 GO:0046718 GO:0055036
140.060.2996.250.050.534xmpG GO:0005198 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0020002 GO:0033644 GO:0039663 GO:0044174 GO:0044175 GO:0046718 GO:0055036
150.060.3226.230.040.582y27B GO:0000166 GO:0003824 GO:0005524 GO:0008152 GO:0010124 GO:0016874 GO:0046872 GO:0047475
160.060.3116.360.030.553waiA GO:0004576 GO:0005215 GO:0005363 GO:0006486 GO:0006810 GO:0006974 GO:0008643 GO:0015768 GO:0016020 GO:0016021 GO:0016740 GO:0030288 GO:0034289 GO:0042597 GO:0042956 GO:0043190 GO:0046872 GO:0055052 GO:0060326 GO:1901982 GO:1990060
170.060.3266.340.030.581p8jA GO:0002020 GO:0004175 GO:0004252 GO:0004867 GO:0005576 GO:0005615 GO:0005769 GO:0005783 GO:0005788 GO:0005789 GO:0005794 GO:0005802 GO:0005886 GO:0006465 GO:0006508 GO:0007568 GO:0008233 GO:0008236 GO:0008283 GO:0009966 GO:0009986 GO:0010951 GO:0012510 GO:0016020 GO:0016021 GO:0016485 GO:0016486 GO:0016787 GO:0019058 GO:0030140 GO:0030335 GO:0030511 GO:0030574 GO:0031985 GO:0032455 GO:0032804 GO:0032902 GO:0032911 GO:0032940 GO:0042176 GO:0042277 GO:0043043 GO:0045121 GO:0045714 GO:0046872 GO:0048406 GO:0052548 GO:0070062
180.060.2886.560.040.541mhyB GO:0004497 GO:0006725 GO:0006730 GO:0015049 GO:0016491 GO:0016709 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0043169
GO-Score 0.47
Biological Processes GO:0006486 GO:0006725 GO:0055114
GO-Score 0.13 0.07 0.07
Cellular Component GO:0016021
GO-Score 0.13

(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.