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I-TASSER results for job id Rv1888A

[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
10.35 7 1rjeB SAH Rep, Mult 4,5,6,7,30,31,32,35
20.12 3 4ro2B GLY Rep, Mult 45,48
30.11 2 2uyqA SAM Rep, Mult 5,6,7
40.04 1 1wb1C DXC Rep, Mult 50,51,54,56
50.04 1 3rt1A GLC Rep, Mult 35,40

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
10.0602f9zC0.6082.420.0190.9303.1.1.61,3.5.1.44NA
20.0601kywC0.5912.210.1040.7892.1.1.68NA
30.0603cjcA0.6182.560.0730.9653.1.21.119
40.0602atmA0.6872.500.0531.0003.2.1.35NA
50.0602a0mA0.5952.350.0380.9123.5.3.8NA
60.0602ashA0.5962.610.0740.9302.4.2.29NA
70.0601mzhA0.5922.450.0750.8954.1.2.4NA
80.0603figB0.6012.680.0930.9472.3.3.1320
90.0602iipA0.6152.230.1920.9122.1.1.15,34
100.0601af7A0.6472.020.1600.8772.1.1.80NA
110.0601j2wA0.6072.880.0580.8954.1.2.4NA
120.0602opbB0.6072.360.2590.9302.1.1.28NA
130.0601cz1A0.5972.590.0910.9653.2.1.58NA
140.0601w3hA0.6142.700.0910.9653.2.1.8NA
150.0602pxxA0.5962.280.2240.8603.4.24.71NA
160.0601tw2B0.6162.290.1800.8252.1.1.-6
170.0601h1nA0.6002.860.0740.9473.2.1.4NA
180.0601fp1D0.6042.150.1250.7892.1.1.-NA
190.0602ggeD0.5932.430.0190.9125.-.-.-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
00.180.8021.360.500.982ckdA GO:0008168 GO:0016740 GO:0032259
10.150.7951.500.541.002uyoA GO:0008168 GO:0016740 GO:0032259
20.150.7641.620.191.003p71T GO:0003880 GO:0005829 GO:0006464 GO:0006479 GO:0006481 GO:0008168 GO:0008276 GO:0008757 GO:0010906 GO:0016740 GO:0018423 GO:0031333 GO:0032259 GO:0042981 GO:0090266
30.150.7561.550.160.981rjdC GO:0005829 GO:0006481 GO:0008168 GO:0010506 GO:0016740 GO:0018423 GO:0032259 GO:0043623
40.140.7811.540.191.003o7wA GO:0003880 GO:0005829 GO:0006464 GO:0006479 GO:0006481 GO:0008168 GO:0008276 GO:0008757 GO:0010906 GO:0016740 GO:0018423 GO:0031333 GO:0032259 GO:0042981 GO:0090266
50.130.7481.600.160.981rjgA GO:0005829 GO:0006481 GO:0008168 GO:0010506 GO:0016740 GO:0018423 GO:0032259 GO:0043623
60.110.6872.500.051.002atmA GO:0003824 GO:0004415 GO:0005576 GO:0005975 GO:0006952 GO:0008152 GO:0016787 GO:0016798
70.090.6572.580.071.001fcuA GO:0003824 GO:0004415 GO:0005576 GO:0005975 GO:0006952 GO:0008152 GO:0016787 GO:0016798
80.080.6642.070.180.982zwaB GO:0005737 GO:0005739 GO:0005829 GO:0006400 GO:0008033 GO:0008168 GO:0008175 GO:0008757 GO:0016740 GO:0030488 GO:0031591 GO:0032259
90.070.5083.150.110.932pe4A GO:0000302 GO:0001618 GO:0003824 GO:0004415 GO:0005576 GO:0005615 GO:0005737 GO:0005764 GO:0005975 GO:0006954 GO:0008134 GO:0008152 GO:0009615 GO:0010634 GO:0016787 GO:0016798 GO:0030207 GO:0030212 GO:0030213 GO:0030214 GO:0030307 GO:0030308 GO:0031410 GO:0036117 GO:0036120 GO:0043202 GO:0044344 GO:0045766 GO:0045785 GO:0045927 GO:0046677 GO:0050501 GO:0050679 GO:0051216 GO:0060272 GO:0070062 GO:0071347 GO:0071356 GO:0071467 GO:0071493 GO:1900106
100.070.5542.830.110.913ggdA
110.070.4503.560.070.914dcmA GO:0003676 GO:0005737 GO:0006364 GO:0008168 GO:0008990 GO:0016740 GO:0031167 GO:0032259 GO:0052916 GO:0070475
120.070.3633.580.020.651q6aA GO:0006468 GO:0007623 GO:0042802 GO:0048511
130.070.4743.250.060.861j1zA GO:0000166 GO:0004055 GO:0005524 GO:0005737 GO:0006526 GO:0008652 GO:0016874
140.070.4953.330.070.933lyhB GO:0009236 GO:0016852
150.070.4362.770.040.812yc3A GO:0003824 GO:0008299 GO:0009507 GO:0009536 GO:0009570 GO:0016740 GO:0016779 GO:0019288 GO:0050518
160.060.3822.800.040.544f4wA GO:0000287 GO:0003677 GO:0003684 GO:0003887 GO:0005737 GO:0006260 GO:0006261 GO:0006281 GO:0006974 GO:0016740 GO:0016779 GO:0046872 GO:0071897
170.060.3953.180.060.612zi8A GO:0003824 GO:0005506 GO:0006629 GO:0006707 GO:0006725 GO:0008198 GO:0008202 GO:0008203 GO:0009405 GO:0016042 GO:0016491 GO:0019439 GO:0046872 GO:0047071 GO:0051213 GO:0055114 GO:0070723
180.060.4123.320.060.673qdlA GO:0016491 GO:0046677 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0018423
GO-Score 0.38
Biological Processes GO:0006006 GO:0006915 GO:0043254 GO:0043067 GO:0007094 GO:1903504 GO:0010675 GO:0006481
GO-Score 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.38
Cellular Component GO:0005829
GO-Score 0.38

(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.