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I-TASSER results for job id Rv3090

[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
10.10 5 2e50P TRE Rep, Mult 238,241,242,245
20.06 3 4tt0B IOD Rep, Mult 243,244,247
30.04 2 3jv2B III Rep, Mult 122,123,124,125,126
40.04 2 2xalA PB Rep, Mult 191,203,205
50.04 2 3i8hW MG Rep, Mult 242,243,246
60.04 2 1qiyL IPH Rep, Mult 158,161
70.02 1 3c63D CA Rep, Mult 218,219
80.02 1 4dlmA ZN Rep, Mult 191,228
90.02 1 2h8pC GOA Rep, Mult 79,80
100.02 1 1vdfB CL Rep, Mult 235,238
110.02 1 3wmoP BCL Rep, Mult 251,252
120.02 1 2npiA MG Rep, Mult 36,61
130.02 1 3k3gA MMU Rep, Mult 122,163,166
140.02 1 1dlqB LIO Rep, Mult 208,211
150.02 1 3kiy7 MG Rep, Mult 148,150
160.02 1 3b9zA CO2 Rep, Mult 154,157,203,206

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
10.0602xalA0.3716.130.0550.6102.7.1.158NA
20.0602g25A0.3636.210.0480.6001.2.4.1NA
30.0602vdcA0.3626.170.0470.5901.4.1.13NA
40.0601pg0A0.3526.820.0580.6376.1.1.10NA
50.0602hnhA0.3426.340.0580.5932.7.7.7158
60.0601itkB0.3556.020.0270.5701.11.1.6,1.11.1.7NA
70.0603hhsA0.3516.590.0300.6301.14.18.1NA
80.0601ileA0.3736.540.0310.6616.1.1.5NA
90.0601mo7A0.2286.140.0630.3733.6.3.9175
100.0603fn9C0.3546.800.0560.6613.2.1.23NA
110.0602b3xA0.3696.780.0410.6714.2.1.3NA
120.0602cseW0.3526.670.0270.6103.6.4.13NA
130.0602vdcF0.3646.120.0430.5861.4.1.13NA
140.0602zufA0.3516.620.0320.6006.1.1.19NA
150.0602qtcB0.3656.620.0430.6471.2.4.1183
160.0601pfuA0.3506.920.0440.6416.1.1.10NA
170.0602cnvA0.3676.050.0440.5866.3.2.6NA
180.0601ca1A0.3706.110.0450.6003.1.4.3NA
190.0603b8eA0.3276.310.0580.5663.6.3.9NA

(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
00.060.4125.360.070.614w8yA GO:0000166 GO:0003723 GO:0005737 GO:0046872 GO:0051607
10.060.2976.920.030.543x1lA GO:0000166 GO:0003723 GO:0005737 GO:0046872 GO:0051607
20.060.2706.960.040.493ju8A GO:0004029 GO:0006525 GO:0006527 GO:0008152 GO:0016491 GO:0016620 GO:0019544 GO:0019545 GO:0043824 GO:0055114
30.060.2656.870.030.492ts1A GO:0000166 GO:0003723 GO:0004812 GO:0004831 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006437 GO:0016874
40.060.2666.850.040.491jilA GO:0000166 GO:0003723 GO:0004812 GO:0004831 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006437 GO:0016874
50.060.2875.930.030.463w2wA GO:0000166 GO:0003723 GO:0005737 GO:0046872 GO:0051607
60.060.2646.800.060.484jo0A GO:0046872
70.060.2876.660.030.524dozA GO:0000166 GO:0003723 GO:0005737 GO:0046872 GO:0051607
80.060.2276.550.030.392ol2A GO:0001972 GO:0002020 GO:0002080 GO:0004867 GO:0005539 GO:0005576 GO:0005615 GO:0006810 GO:0006869 GO:0007283 GO:0007338 GO:0007342 GO:0007596 GO:0008201 GO:0009897 GO:0010466 GO:0010951 GO:0016020 GO:0030414 GO:0031091 GO:0031094 GO:0031210 GO:0032190 GO:0036024 GO:0036025 GO:0036026 GO:0036027 GO:0036028 GO:0036029 GO:0036030 GO:0043234 GO:0045861 GO:0051346 GO:0070062 GO:0097181 GO:0097182 GO:0097183
90.060.2496.080.040.412q3sA GO:0003676 GO:0005634 GO:0005737 GO:0005773 GO:0005774 GO:0006139 GO:0008408 GO:0090305
100.060.2425.210.060.361yyaA GO:0003824 GO:0004807 GO:0005737 GO:0006094 GO:0006096 GO:0006098 GO:0008152 GO:0016853
110.060.2576.330.040.444xeaA GO:0003824 GO:0046872
120.060.2216.000.040.363bw8A GO:0005576 GO:0006471 GO:0009405 GO:0016740 GO:0016757 GO:0016763
130.060.2406.200.080.413eu7A GO:0000724 GO:0000731 GO:0000732 GO:0001701 GO:0001756 GO:0001833 GO:0003677 GO:0005634 GO:0005654 GO:0006281 GO:0006310 GO:0006974 GO:0007498 GO:0009887 GO:0031052 GO:0035264 GO:0036342 GO:0043066 GO:0048568
140.060.1744.490.040.251i1gA GO:0003677 GO:0003700 GO:0005622 GO:0006351 GO:0006355 GO:0043565
150.060.1835.920.060.304pooB GO:0008168 GO:0032259 GO:0046872 GO:0051536 GO:0051539
160.060.1834.990.050.271ob8B GO:0003676 GO:0003677 GO:0004518 GO:0004519 GO:0006281 GO:0006310 GO:0006974 GO:0008821 GO:0016787 GO:0046872 GO:0090305
170.060.1975.500.050.302ojzH
180.060.1665.010.030.244dpzX GO:0005737 GO:0006629 GO:0016020 GO:0016021 GO:0016042 GO:0016740 GO:0016746 GO:0016787


Consensus prediction of GO terms
 
Molecular Function GO:0036094 GO:0003676 GO:1901265
GO-Score 0.46 0.46 0.46
Biological Processes GO:0051607 GO:0006437 GO:0055114 GO:0019544 GO:0019545
GO-Score 0.12 0.12 0.06 0.06 0.06
Cellular Component GO:0044424
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.