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I-TASSER results for job id Rv1841c

[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
10.56 35 4eagC ATP Rep, Mult 218,224,249,250,251,253,311,312,325,327,328,329,330
20.06 5 3kh5A ADP Rep, Mult 251,264,266,268,269,286,289,290,310,311,312
30.01 1 2y94E III Rep, Mult 255,257,260,289,291,315,319,321,322
40.01 1 3b2xA NA Rep, Mult 63,64,65,66,69

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
10.0601gq2A0.3696.640.0580.6201.1.1.40NA
20.0603n2oA0.3716.080.0490.5864.1.1.19135,300
30.0601gpeA0.3746.560.0660.6201.1.3.4NA
40.0602fqfA0.3467.100.0660.6171.-.-.-NA
50.0602o36A0.3866.640.0210.6583.4.24.15300
60.0603b9jI0.1715.430.0460.2521.17.1.4,1.17.3.268,116
70.0601fo4A0.3616.750.0540.6151.17.1.4NA
80.0603hhsA0.4026.620.0640.6701.14.18.1NA
90.0601ofdA0.3556.610.0390.5971.4.7.1NA
100.0603ig5A0.3946.450.0520.6386.3.2.2310
110.0601o0sA0.3716.540.0400.6151.1.1.38NA
120.0601galA0.3666.580.0660.6091.1.3.4NA
130.0601ea0A0.3296.800.0310.5651.4.1.13NA
140.0601asqA0.3577.080.0490.6411.10.3.3326
150.0603hhsB0.4036.670.0610.6721.14.18.1NA
160.0602vdcF0.3907.120.0330.6901.4.1.13NA
170.0601cf3A0.3666.350.0480.6031.1.3.4NA
180.0601llwA0.3826.990.0560.6721.4.7.1NA
190.0601gpeB0.3696.600.0310.6151.1.3.463,70,332

(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
00.200.3372.040.290.363lfrB GO:0000166 GO:0003824 GO:0016614 GO:0050660 GO:0055114
10.130.4084.100.100.503ddjA GO:0000166 GO:0003824
20.120.3202.820.230.362j9lC GO:0000139 GO:0000166 GO:0005216 GO:0005247 GO:0005254 GO:0005524 GO:0005765 GO:0005768 GO:0005794 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006821 GO:0007588 GO:0010008 GO:0015297 GO:0016020 GO:0016021 GO:0031404 GO:0034220 GO:0045177 GO:0055085 GO:1902476 GO:1903959
30.100.4264.350.170.542v8qE GO:0000166 GO:0004679 GO:0005524 GO:0005654 GO:0006468 GO:0006629 GO:0006631 GO:0006633 GO:0016208 GO:0019901 GO:0031588 GO:0042304 GO:0043234 GO:0043531 GO:0050790 GO:0051291
40.100.4024.340.120.503lfzA
50.090.3172.550.200.353kpcA GO:0003824
60.080.4314.550.110.552ooxE GO:0000166 GO:0003824 GO:0005524 GO:0005634 GO:0005737 GO:0005829 GO:0005975 GO:0006351 GO:0006355 GO:0006357 GO:0007165 GO:0016208 GO:0030295 GO:0031588 GO:0032147
70.070.3163.580.110.383k6eB
80.060.4204.310.140.533tdhC GO:0000166 GO:0001302 GO:0003824 GO:0004679 GO:0005524 GO:0005634 GO:0005641 GO:0005737 GO:0005886 GO:0005975 GO:0006351 GO:0006355 GO:0006357 GO:0006468 GO:0007031 GO:0031588 GO:0043539 GO:0045722 GO:0071902
90.060.3714.080.160.464qfsC GO:0000166 GO:0004679 GO:0005524 GO:0005654 GO:0006468 GO:0006629 GO:0006631 GO:0006633 GO:0016208 GO:0019901 GO:0031588 GO:0042304 GO:0043234 GO:0043531 GO:0050790 GO:0051291
100.060.3754.030.100.472yzqA GO:0003824 GO:0046872 GO:0051536 GO:0051539
110.060.3586.740.060.614uvmA GO:0005215 GO:0006810 GO:0006857 GO:0015197 GO:0015833 GO:0016020 GO:0016021
120.060.4535.050.110.633orgA
130.060.2966.880.040.523nd0A GO:0005216 GO:0005247 GO:0006821 GO:0016020 GO:0016021 GO:0034220 GO:0055085 GO:1903959
140.060.3326.830.050.571kplB GO:0005216 GO:0005247 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006821 GO:0015108 GO:0015297 GO:0016020 GO:0016021 GO:0034220 GO:0055085 GO:1902476 GO:1903959
150.060.3197.090.060.573updA GO:0004585 GO:0005737 GO:0006520 GO:0006526 GO:0006591 GO:0008652 GO:0016597 GO:0016740 GO:0016743
160.060.3364.970.080.454l3vA GO:0003824 GO:0004122 GO:0004124 GO:0005634 GO:0005737 GO:0005829 GO:0006535 GO:0006563 GO:0006565 GO:0008152 GO:0008652 GO:0016829 GO:0019343 GO:0019344 GO:0019346 GO:0019448 GO:0019825 GO:0019899 GO:0020037 GO:0030170 GO:0031625 GO:0042262 GO:0042802 GO:0042803 GO:0043418 GO:0046872 GO:0050421 GO:0050667 GO:0055114 GO:0070025 GO:0070026 GO:0070814 GO:0072341 GO:1904047
170.060.3202.430.150.354fryB GO:0000166
180.060.3266.570.070.551kpkA GO:0005216 GO:0005247 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006821 GO:0015108 GO:0015297 GO:0015299 GO:0015706 GO:0016020 GO:0016021 GO:0031404 GO:0043168 GO:0055085 GO:1902476 GO:1902600 GO:1903959


Consensus prediction of GO terms
 
Molecular Function GO:0032550 GO:0035639 GO:0032559 GO:0016491 GO:0050662
GO-Score 0.42 0.42 0.42 0.40 0.40
Biological Processes GO:0044710
GO-Score 0.40
Cellular Component GO:0005887 GO:0045177 GO:0005765 GO:0000139 GO:0010008 GO:0031588 GO:0005654
GO-Score 0.12 0.12 0.12 0.12 0.12 0.10 0.10

(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.