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I-TASSER results for job id Rv3558

[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 2 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
10.08 4 4ue5D NUC Rep, Mult 208,209,210
20.04 2 1af0A CA Rep, Mult 430,431,432,435,447,450,451,455
30.04 2 2quaA CA Rep, Mult 447,450,451,452,454,470,475,476,479
40.02 1 3tu5A CA Rep, Mult 267,269
50.02 1 3cigA UUU Rep, Mult 318,337,339,341,357
60.02 1 2z64A UUU Rep, Mult 353,377,379,381,401
70.02 1 2vn4A MAN Rep, Mult 381,382
80.02 1 1wmrB NDG Rep, Mult 226,274,294
90.02 1 1g9kA CA Rep, Mult 362,364,366,382,387,388,395
100.02 1 2g38B MN Rep, Mult 150,153,154
110.02 1 1rmgA MAN Rep, Mult 435,436
120.02 1 1dbgA UUU Rep, Mult 322,325,345,346,363,364,394
130.02 1 3p4gA CA Rep, Mult 455,456,457,459,470,475,476,479
140.02 1 3huzP MG Rep, Mult 430,432
150.02 1 4ujjF OHX Rep, Mult 422,425
160.02 1 5klbA CA Rep, Mult 320,342
170.02 1 3ciyA UUU Rep, Mult 149,246,264,265,314
180.02 1 3fcsC IMD Rep, Mult 474,525
190.02 1 4hzvA FUC Rep, Mult 311,312
200.02 1 2wieE CVM Rep, Mult 302,303,323

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
10.0601jtaA0.3594.230.0470.4294.2.2.2NA
20.0602fhbA0.3637.790.0570.6013.2.1.41NA
30.0601llwA0.3437.630.0470.5521.4.7.1NA
40.0603jurD0.4284.640.0800.5333.2.1.15315
50.0602e9bA0.3517.880.0310.5833.2.1.41415
60.0601ib4A0.3953.890.0970.4673.2.1.15270
70.0603k1dA0.3527.730.0610.5822.4.1.18NA
80.0601bn8A0.3574.240.0760.4274.2.2.2NA
90.0601kcdA0.3793.370.1040.4353.2.1.15435,486
100.0601hg8A0.3834.290.0870.4663.2.1.15NA
110.0602qx3A0.3524.370.0850.4274.2.2.2NA
120.0601xg2A0.3533.810.0470.4133.1.1.11463
130.0602o1dA0.3584.340.0680.4314.2.2.2239,243
140.0601ia5A0.3863.550.0930.4493.2.1.15NA
150.0603h09B0.6393.890.0790.7413.4.21.72NA
160.0602uveA0.4404.010.0730.5243.2.1.82NA
170.0602fhcA0.3677.920.0600.6143.2.1.41NA
180.0601ofdA0.3427.600.0420.5521.4.7.1NA
190.0601k5cA0.3783.450.1040.4373.2.1.15NA

(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
00.220.9072.860.130.984om9A GO:0004175 GO:0004252 GO:0005576 GO:0006508 GO:0008233 GO:0008236 GO:0009279 GO:0009405 GO:0009986 GO:0016020 GO:0016021 GO:0016787 GO:0019867 GO:0042597
10.210.8912.910.100.973szeA GO:0004175 GO:0004252 GO:0005576 GO:0006508 GO:0008233 GO:0008236 GO:0009279 GO:0009405 GO:0009986 GO:0016020 GO:0016021 GO:0016787 GO:0019867 GO:0042597
20.160.7783.980.090.921wxrA GO:0004175 GO:0004252 GO:0005576 GO:0006508 GO:0008233 GO:0008236 GO:0009279 GO:0009405 GO:0009986 GO:0016020 GO:0016021 GO:0016787 GO:0019867 GO:0042597
30.160.7794.000.090.923ak5A GO:0004175 GO:0004252 GO:0005576 GO:0006508 GO:0008233 GO:0008236 GO:0009279 GO:0009405 GO:0009986 GO:0016020 GO:0016021 GO:0016787 GO:0019867 GO:0042597
40.120.6094.060.070.721dabA GO:0005576 GO:0007155 GO:0009279 GO:0009405 GO:0009986 GO:0016020 GO:0016021 GO:0019867 GO:0042597
50.100.6983.760.080.813syjA GO:0004175 GO:0004252 GO:0005576 GO:0006508 GO:0007155 GO:0008233 GO:0008236 GO:0009279 GO:0009986 GO:0016020 GO:0016021 GO:0016787 GO:0019867 GO:0042597 GO:0042802
60.070.6393.890.080.743h09B GO:0004175 GO:0004252 GO:0005576 GO:0006508 GO:0008233 GO:0008236 GO:0009279 GO:0009405 GO:0009986 GO:0016020 GO:0016021 GO:0016787 GO:0042597
70.060.2236.920.060.343h2zA GO:0003824 GO:0008152 GO:0008926 GO:0016491 GO:0019594 GO:0050662 GO:0055114
80.060.2247.460.030.364kkdB GO:0001867 GO:0002376 GO:0004252 GO:0005509 GO:0005576 GO:0005615 GO:0006508 GO:0006898 GO:0006956 GO:0008233 GO:0008236 GO:0016787 GO:0042803 GO:0045087 GO:0045916 GO:0046872 GO:0048306
90.060.2076.900.010.312qkdA GO:0000226 GO:0001833 GO:0001834 GO:0005634 GO:0005654 GO:0005730 GO:0005737 GO:0006397 GO:0007275 GO:0008270 GO:0008380 GO:0010628 GO:0015030 GO:0021510 GO:0030154 GO:0030424 GO:0030426 GO:0030576 GO:0030971 GO:0031369 GO:0031641 GO:0032797 GO:0033120 GO:0042023 GO:0042307 GO:0042995 GO:0043025 GO:0043204 GO:0045927 GO:0046872 GO:0048471 GO:0061564 GO:0071364 GO:0071931 GO:0097504 GO:1902742 GO:1990261 GO:2000672
100.060.2237.150.060.351gpzA GO:0002376 GO:0004252 GO:0005509 GO:0005576 GO:0006508 GO:0006955 GO:0006956 GO:0006958 GO:0008233 GO:0008236 GO:0016787 GO:0045087 GO:0070062 GO:0072562
110.060.2146.840.040.321w62A GO:0005576 GO:0005737 GO:0007275 GO:0016020 GO:0016853 GO:0018112
120.060.1926.260.060.283bliA GO:0003824 GO:0003852 GO:0008652 GO:0009082 GO:0009098 GO:0016740 GO:0019752 GO:0046872 GO:0046912
130.060.2267.260.060.361zjkA GO:0001855 GO:0001867 GO:0002376 GO:0004252 GO:0005509 GO:0005576 GO:0006508 GO:0006956 GO:0006958 GO:0008233 GO:0008236 GO:0016787 GO:0045087 GO:0046872 GO:0048306 GO:0070062
140.060.1937.320.030.314f7kA GO:0005507 GO:0016491 GO:0052716 GO:0055114
150.060.1985.890.040.271tiaA GO:0006629 GO:0016042 GO:0016787
160.060.1717.200.040.275it9g GO:0000747 GO:0001403 GO:0001965 GO:0004871 GO:0005080 GO:0005092 GO:0005737 GO:0007186 GO:0010255 GO:0017148 GO:0022627 GO:0031139 GO:0031954 GO:0032995 GO:0034613 GO:0035556 GO:0043022 GO:0050790 GO:0060733
170.060.1666.120.040.241h8vA GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0008810 GO:0016787 GO:0016798
180.060.1597.220.040.253he3A GO:0000166 GO:0008767


Consensus prediction of GO terms
 
Molecular Function GO:0004252
GO-Score 0.57
Biological Processes GO:0009405 GO:0006508
GO-Score 0.62 0.57
Cellular Component GO:0042597 GO:0009986 GO:0016021 GO:0009279 GO:0005576
GO-Score 0.62 0.62 0.62 0.62 0.62

(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.