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I-TASSER results for job id Rv0614

[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
10.06 3 3wj8A B2P Rep, Mult 31,33,233,234,235,314,315
20.06 3 2xgxA AKG Rep, Mult 134,138
30.04 2 4dcaA MG Rep, Mult 170,181
40.04 2 1hu9A 4HM Rep, Mult 93,96,97,101,136,282
50.04 2 2wieA CVM Rep, Mult 141,145
60.04 2 4ogqF 3WM Rep, Mult 127,131,134,141
70.02 1 4d2bA 78N Rep, Mult 145,148
80.02 1 1wx2A CU Rep, Mult 112,117
90.02 1 3nz4A TCA Rep, Mult 121,128
100.02 1 3o58Y III Rep, Mult 112,116,125
110.02 1 3attA MG Rep, Mult 181,184
120.02 1 3r4iB CA Rep, Mult 140,181
130.02 1 1dgjA FES Rep, Mult 168,169,170,173,174,175,177,290
140.02 1 2o011 CLA Rep, Mult 36,130
150.02 1 2b0qA MG Rep, Mult 165,181
160.02 1 3d6aA MG Rep, Mult 86,90

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
10.0601jroB0.3726.410.0680.6151.1.1.204NA
20.0603b9jJ0.2296.730.0650.3881.17.1.4,1.17.3.260,141
30.0602e9eA0.3076.600.0550.5001.11.1.7NA
40.0602sqcA0.3436.870.0210.6185.4.99.17NA
50.0603fvyA0.3425.910.0600.5303.4.14.4144,152
60.0601up8A0.3536.260.0710.5761.11.1.18NA
70.0603btaA0.3396.340.0260.5583.4.24.69NA
80.0601fo4A0.3346.380.0720.5581.17.1.4NA
90.0601ygeA0.3736.280.0440.5821.13.11.12NA
100.0601qi9B0.3396.410.0410.5581.11.1.10NA
110.0601rm6A0.3536.650.0530.6001.3.99.20NA
120.0602e1qA0.3516.860.0440.6241.17.3.2,1.17.1.4NA
130.0602iukA0.3706.440.0510.5911.13.11.12NA
140.0603bjxA0.6873.220.1540.8033.8.1.1084
150.0601jrpB0.3726.400.0380.6151.17.1.4148
160.0601vlbA0.3596.500.0290.6001.2.99.7NA
170.0603d2jA0.3446.650.0340.5791.21.3.3176
180.0601h0hA0.3496.590.0350.5911.2.1.2NA
190.0603cmmC0.3706.330.0260.5946.3.2.1963

(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
00.110.7063.280.120.824n2xA GO:0016787 GO:0019120 GO:0033976
10.100.6953.160.150.813bjxA GO:0019120
20.060.2656.650.040.445bxpA GO:0004553 GO:0004563 GO:0005975 GO:0008152 GO:0016020 GO:0016021 GO:0016787 GO:0016798 GO:0047403
30.060.3166.290.050.523gh4A GO:0004553 GO:0004563 GO:0005975
40.060.2966.980.060.544em6A GO:0004347 GO:0005737 GO:0006094 GO:0006096 GO:0016853
50.060.3926.320.050.622cseW GO:0000166 GO:0004386 GO:0005524 GO:0006370 GO:0006397 GO:0016787 GO:0019012 GO:0019028 GO:0039625 GO:0046872
60.060.2906.890.050.513k01A
70.060.2756.950.040.485br4A GO:0004022 GO:0005829 GO:0005975 GO:0006004 GO:0008198 GO:0008912 GO:0016491 GO:0019301 GO:0019317 GO:0042355 GO:0042846 GO:0046872 GO:0051143 GO:0055114
80.060.2766.690.040.474bkqA GO:0004318 GO:0006629 GO:0006631 GO:0006633 GO:0016491 GO:0051287 GO:0055114
90.060.2856.880.030.494m9dB GO:0000166 GO:0000287 GO:0004019 GO:0005525 GO:0005737 GO:0006164 GO:0016874 GO:0044208 GO:0046872
100.060.2736.620.050.464fc6B GO:0005102 GO:0005777 GO:0005778 GO:0006629 GO:0006631 GO:0006636 GO:0008670 GO:0016491 GO:0019166 GO:0044255 GO:0055114
110.060.3006.770.030.513hlfA GO:0016740 GO:0016746 GO:0016787 GO:0017000 GO:0030639 GO:0050832
120.060.2666.770.030.463c8nA GO:0004497 GO:0005618 GO:0005829 GO:0005886 GO:0005975 GO:0016491 GO:0016614 GO:0016705 GO:0045454 GO:0052749 GO:0055114 GO:0070967
130.060.2646.890.050.453txxB GO:0005737 GO:0006520 GO:0006596 GO:0016597 GO:0016740 GO:0016743 GO:0033388 GO:0033390 GO:0050231
140.060.2906.440.070.484c20B GO:0005737 GO:0005975 GO:0005996 GO:0006004 GO:0008736 GO:0016853 GO:0016861 GO:0019317 GO:0030145 GO:0042355 GO:0046872
150.060.2416.730.020.412b69A GO:0005739 GO:0005794 GO:0016020 GO:0016021 GO:0016829 GO:0016831 GO:0032580 GO:0033320 GO:0042803 GO:0048040 GO:0051262 GO:0070062 GO:0070403
160.060.3286.140.060.513iylY GO:0046872
170.060.3516.170.050.563k1qC GO:0046872
180.060.2496.890.030.442amxA GO:0009168 GO:0019239


Consensus prediction of GO terms
 
Molecular Function GO:0016824
GO-Score 0.39
Biological Processes GO:0006096 GO:0006094
GO-Score 0.06 0.06
Cellular Component GO:0016021 GO:0005737
GO-Score 0.06 0.06

(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.