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I-TASSER results for job id Rv0026

[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
10.07 3 4lq3A 20V Rep, Mult 426,427,430
20.05 2 1m3xL BPH Rep, Mult 424,427,428
30.02 1 1d4m1 MYR Rep, Mult 414,415
40.02 1 3bbxL MG Rep, Mult 380,381
50.02 1 3nbsD HEM Rep, Mult 1,3,13
60.02 1 5sy1A CLR Rep, Mult 431,434
70.02 1 2zt9G III Rep, Mult 418,426
80.02 1 3ufkA NTA Rep, Mult 309,310
90.02 1 2xydB UUU Rep, Mult 365,367,400,401
100.02 1 1n47A UUU Rep, Mult 359,360
110.02 1 4a5tS UUU Rep, Mult 269,271
120.02 1 3pcaM DHB Rep, Mult 369,375
130.02 1 1d6nA MG Rep, Mult 234,235
140.02 1 2wocA MN Rep, Mult 138,140,141
150.02 1 3ufkA FE Rep, Mult 155,309
160.02 1 2c6nB NDG Rep, Mult 373,376,377,380
170.02 1 1s5lL CLA Rep, Mult 428,432
180.02 1 3nbsB HEM Rep, Mult 3,13
190.02 1 2a69A MG Rep, Mult 329,330

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
10.0603fg3A0.2636.910.0290.4134.2.1.92,1.13.11.40NA
20.0603b9jI0.1425.720.0380.2031.17.1.4,1.17.3.2388
30.0601clqA0.2476.780.0480.3862.7.7.7397
40.0601b0pA0.2796.520.0410.4291.2.7.1NA
50.0602vdcA0.2827.140.0520.4641.4.1.13NA
60.0601n63B0.2996.630.0300.4671.2.99.2NA
70.0601cf9A0.3006.700.0740.4691.11.1.6NA
80.0603b9jC0.2607.650.0530.4551.17.3.2,1.17.1.4NA
90.0602gbcA0.2776.970.0190.4463.4.14.5,3.4.15.5292
100.0603g4dA0.2767.180.0470.4554.2.3.13NA
110.0602cseW0.3067.550.0470.5293.6.4.13NA
120.0603b9jJ0.1986.720.0370.3121.17.1.4,1.17.3.2120,131,256,283
130.0601n1hA0.2787.140.0430.4622.7.7.48259
140.0602e1qA0.2657.120.0470.4311.17.3.2,1.17.1.4NA
150.0602w00B0.2907.250.0610.4843.1.21.3432
160.0601u22A0.2757.270.0370.4582.1.1.14NA
170.0602iw5A0.2947.350.0470.4911.-.-.-NA
180.0603g0bB0.2767.080.0310.4493.4.14.5199
190.0602gmhA0.2947.040.0510.4821.5.5.1403,404

(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
00.240.9461.840.070.985fmwA GO:0002376 GO:0005576 GO:0005579 GO:0005737 GO:0005886 GO:0005887 GO:0006955 GO:0006957 GO:0006958 GO:0016020 GO:0016021 GO:0019835 GO:0019836 GO:0030449 GO:0045087 GO:0070062 GO:0072562
10.070.6103.940.060.733ojyB GO:0002376 GO:0005576 GO:0005579 GO:0005615 GO:0006955 GO:0006956 GO:0006957 GO:0006958 GO:0016020 GO:0019835 GO:0030449 GO:0032403 GO:0045087 GO:0070062 GO:1903561
20.070.5984.360.050.734e0sB GO:0001701 GO:0001970 GO:0002376 GO:0005576 GO:0005579 GO:0006955 GO:0006956 GO:0006958 GO:0019835 GO:0030449 GO:0045087 GO:0045766 GO:0045917 GO:0070062
30.070.6054.300.040.743t5oA GO:0001701 GO:0001970 GO:0002376 GO:0005576 GO:0005579 GO:0006955 GO:0006956 GO:0006958 GO:0019835 GO:0030449 GO:0045087 GO:0045766 GO:0045917 GO:0070062
40.070.5734.170.080.693ojyA GO:0001848 GO:0002376 GO:0005576 GO:0005579 GO:0005615 GO:0005886 GO:0006955 GO:0006956 GO:0006957 GO:0006958 GO:0016020 GO:0016021 GO:0019835 GO:0030449 GO:0032403 GO:0045087 GO:0070062 GO:0072562
50.070.5664.290.050.694a5wB GO:0001701 GO:0001970 GO:0002376 GO:0005576 GO:0005579 GO:0006955 GO:0006956 GO:0006958 GO:0019835 GO:0030449 GO:0045087 GO:0045766 GO:0045917 GO:0070062
60.060.4394.020.050.533nsjA GO:0001771 GO:0002357 GO:0002418 GO:0005509 GO:0005576 GO:0005768 GO:0005886 GO:0016020 GO:0016021 GO:0016023 GO:0019835 GO:0022829 GO:0031904 GO:0044194 GO:0046872 GO:0051260 GO:0051607 GO:0055085
70.060.3944.900.050.512qp2A GO:0046872
80.060.4013.510.070.462qqhA GO:0001848 GO:0002376 GO:0005576 GO:0005579 GO:0005615 GO:0005886 GO:0006955 GO:0006956 GO:0006957 GO:0006958 GO:0016020 GO:0016021 GO:0019835 GO:0030449 GO:0032403 GO:0045087 GO:0070062 GO:0072562
90.060.3843.800.060.462rd7A GO:0001848 GO:0002376 GO:0005576 GO:0005579 GO:0005615 GO:0005886 GO:0006955 GO:0006956 GO:0006957 GO:0006958 GO:0016020 GO:0016021 GO:0019835 GO:0030449 GO:0032403 GO:0045087 GO:0070062 GO:0072562
100.060.3684.850.060.475j67C GO:0005509 GO:0005768 GO:0016020 GO:0016021 GO:0043533 GO:0060187 GO:2000009
110.060.2197.900.030.392xrcB GO:0002376 GO:0004252 GO:0005044 GO:0005576 GO:0005615 GO:0006508 GO:0006898 GO:0006958 GO:0008233 GO:0008236 GO:0016020 GO:0016787 GO:0030449 GO:0045087 GO:0046872 GO:0070062
120.060.2177.800.020.382xrcC GO:0002376 GO:0004252 GO:0005044 GO:0005576 GO:0005615 GO:0006508 GO:0006898 GO:0006958 GO:0008233 GO:0008236 GO:0016020 GO:0016787 GO:0030449 GO:0045087 GO:0046872 GO:0070062
130.060.2097.900.030.383ki9A GO:0006508 GO:0008152 GO:0008233 GO:0008237 GO:0008270 GO:0016787 GO:0016805 GO:0046872
140.060.2056.420.060.313vywD GO:0016645 GO:0046872 GO:0051536 GO:0051539 GO:0055114
150.060.2007.400.010.341n7dA GO:0001618 GO:0001948 GO:0002020 GO:0004872 GO:0005041 GO:0005509 GO:0005764 GO:0005768 GO:0005769 GO:0005770 GO:0005794 GO:0005886 GO:0005887 GO:0005905 GO:0006629 GO:0006810 GO:0006869 GO:0006897 GO:0006898 GO:0008202 GO:0008203 GO:0009897 GO:0009986 GO:0010008 GO:0010867 GO:0010899 GO:0012505 GO:0015914 GO:0016020 GO:0016021 GO:0016032 GO:0016323 GO:0030169 GO:0030229 GO:0030299 GO:0030301 GO:0030669 GO:0032050 GO:0034362 GO:0034383 GO:0042157 GO:0042159 GO:0042632 GO:0042802 GO:0043235 GO:0045177 GO:0046718 GO:0070508 GO:1990666 GO:2000188
160.060.1975.840.030.285fttA GO:0005886 GO:0006915 GO:0007165 GO:0007275 GO:0007411 GO:0009986 GO:0016020 GO:0016021 GO:0021859 GO:0098609 GO:2001222
170.060.1965.780.060.284v2aA GO:0005886 GO:0006915 GO:0007165 GO:0007275 GO:0007411 GO:0016020 GO:0016021 GO:0031175 GO:0031226 GO:0032589 GO:0032809 GO:0033564 GO:0038007 GO:0042995 GO:0045121
180.060.1747.450.030.303vn4A GO:0004175 GO:0004222 GO:0005178 GO:0005509 GO:0005576 GO:0005578 GO:0005615 GO:0005788 GO:0006508 GO:0007160 GO:0007229 GO:0007596 GO:0007599 GO:0008233 GO:0008237 GO:0008270 GO:0009100 GO:0009636 GO:0009986 GO:0016485 GO:0016787 GO:0030168 GO:0034341 GO:0034612 GO:0036066 GO:0043171 GO:0046872 GO:0070670


Consensus prediction of GO terms
 
Molecular Function GO:0032403 GO:0001848
GO-Score 0.13 0.07
Biological Processes GO:0052331 GO:0001897 GO:0030449 GO:0006958 GO:0006957
GO-Score 0.48 0.48 0.42 0.42 0.34
Cellular Component GO:0005615 GO:0044424 GO:0070062 GO:0005579
GO-Score 0.58 0.48 0.42 0.42

(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.