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I-TASSER results for job id Rv1154c

[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 4 2qv6C CA Rep, Mult 44,45,79,200
20.05 4 3h8aC III Rep, Mult 42,79,82,83
30.04 3 4dh9F NUC Rep, Mult 39,41,92,93,97,100,109,111,112,113,114
40.04 3 3aodC RFP Rep, Mult 42,43,44,80,113
50.04 3 3dsjA HEM Rep, Mult 60,61,64,65,68,95,96,111
60.04 3 3t51A CU Rep, Mult 44,80,138
70.02 2 3dsiA T24 Rep, Mult 92,93,96,97,100,108,109
80.02 2 3fgvB UNL Rep, Mult 138,173,202
90.02 2 2ptz0 III Rep, Mult 8,9,54,56,60,73,74,82,84
100.02 2 3h8aA III Rep, Mult 42,44,47,95,102
110.02 2 3dbmA HO2 Rep, Mult 60,64,104,110
120.02 2 1tkoB FE Rep, Mult 94,97
130.02 2 3dsiB HEM Rep, Mult 79,80,204,207,208
140.01 1 3pm0A HEM Rep, Mult 48,49,56,110,111
150.01 1 3gr3A FMN Rep, Mult 77,78,79,80,191
160.01 1 3ecaA ASP Rep, Mult 80,130
170.01 1 2xctS CPF Rep, Mult 46,47
180.01 1 3damA HEM Rep, Mult 18,22,25,84,85,92,209,210
190.01 1 3pm0A BHF Rep, Mult 118,121,169,205,208,209,213
200.01 1 3fcsC IMD Rep, Mult 156,185

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
10.0602frvD0.4325.960.0330.7651.12.2.1209
20.0602psnC0.4325.540.0360.7284.2.1.11NA
30.0602ptwA0.4375.450.0690.7184.2.1.112
40.0602f9qA0.4236.000.0930.7891.14.14.181
50.0602w0aA0.4235.950.0590.7751.14.13.70NA
60.0603hf2A0.4265.840.0360.7611.14.14.1,1.6.2.4NA
70.0602akzA0.4405.550.0630.7324.2.1.11NA
80.0601nb7A0.4244.830.0500.6383.4.21.98NA
90.0601e9xA0.4255.670.0480.7471.14.13.70NA
100.0601yrqI0.4255.670.0490.7421.12.2.182
110.0603k9vA0.4255.830.0650.7611.14.13.-NA
120.0602vn0A0.4295.620.0710.7611.14.14.1140
130.0601jpzB0.4305.920.0540.7701.14.14.1,1.6.2.4NA
140.0601pdyA0.4395.580.0460.7284.2.1.112
150.0601iyxA0.4385.650.0560.7324.2.1.11NA
160.0601uwkA0.4335.300.0530.7144.2.1.49170
170.0601w0eA0.3446.170.0540.6241.14.13.67,1.14.14.1NA
180.0603hfwA0.4254.790.0580.6533.2.2.19NA
190.0602pa6A0.4395.360.0680.7184.2.1.112

(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
00.070.4934.390.040.724k0eC GO:0005215 GO:0006810 GO:0006812 GO:0008324 GO:0016020 GO:0016021 GO:0098655
10.070.5014.380.040.724k0eA GO:0005215 GO:0006810 GO:0006812 GO:0008324 GO:0016020 GO:0016021 GO:0098655
20.070.4624.820.040.692v50D GO:0005215 GO:0005886 GO:0006810 GO:0006855 GO:0015238 GO:0016020 GO:0016021 GO:0046677
30.070.5034.280.050.714k0eB GO:0005215 GO:0006810 GO:0006812 GO:0008324 GO:0016020 GO:0016021 GO:0098655
40.070.4774.780.060.733w9iF GO:0005215 GO:0005886 GO:0006810 GO:0006855 GO:0015238 GO:0016020 GO:0016021 GO:0046677
50.070.4315.050.030.653d9bA GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015307 GO:0016020 GO:0016021 GO:0042493 GO:0042802 GO:0046618
60.060.4344.760.070.644dnrA GO:0005215 GO:0005375 GO:0005507 GO:0005886 GO:0006810 GO:0006811 GO:0006812 GO:0006825 GO:0006878 GO:0008324 GO:0010272 GO:0010273 GO:0015080 GO:0015673 GO:0015679 GO:0016020 GO:0016021 GO:0046688 GO:0060003 GO:1902601
70.060.4334.970.070.685en5C GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015307 GO:0016020 GO:0016021 GO:0042493 GO:0042802 GO:0046618
80.060.4225.000.060.634r86B GO:0005215 GO:0006810 GO:0016020 GO:0016021
90.060.4375.200.060.724mt1A GO:0005215 GO:0006810 GO:0016020 GO:0016021
100.060.4394.970.060.673nogA GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015307 GO:0016020 GO:0016021 GO:0042493 GO:0042802 GO:0046618
110.060.3705.560.050.634i0wD GO:0004252 GO:0006508 GO:0008233 GO:0008236 GO:0016787
120.060.4005.710.050.693i6sA GO:0004252 GO:0005618 GO:0006508 GO:0008233 GO:0008236 GO:0016787
130.060.3146.060.020.543wxvA GO:0004872 GO:0005886 GO:0006629 GO:0006631 GO:0007186 GO:0009755 GO:0010633 GO:0010719 GO:0010906 GO:0016020 GO:0016021 GO:0019216 GO:0019395 GO:0019901 GO:0030308 GO:0031226 GO:0033210 GO:0033211 GO:0042593 GO:0042802 GO:0046426 GO:0046427 GO:0046628 GO:0046872 GO:0046982 GO:0055100 GO:0097003 GO:1901223
140.060.3076.170.080.583qvjA GO:0006807 GO:0036361
150.060.2894.760.080.454phtY GO:0006810 GO:0008565 GO:0009276 GO:0015031 GO:0016021
160.060.2896.070.050.503qivA
170.060.2845.680.070.493lwkA GO:0005212 GO:0007601 GO:0043010
180.060.2913.770.050.393jb9Y GO:0000166 GO:0000387 GO:0000974 GO:0003676 GO:0003723 GO:0005634 GO:0005681 GO:0006397 GO:0007049 GO:0008380 GO:0017070 GO:0036002 GO:0045292 GO:0046872 GO:0071006 GO:0071007


Consensus prediction of GO terms
 
Molecular Function GO:0015075
GO-Score 0.37
Biological Processes GO:0034220
GO-Score 0.37
Cellular Component GO:0031224
GO-Score 0.46

(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.