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I-TASSER results for job id Rv1800

[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
10.12 4 1ea0A F3S Rep, Mult 307,308,309,310,313,314,348,351,352
20.03 1 2jstA HLT Rep, Mult 33,71
30.03 1 2wsc4 CLA Rep, Mult 298,301
40.03 1 1utzA PF3 Rep, Mult 401,402
50.03 1 2eigA MN Rep, Mult 373,375,379,401
60.03 1 4sbvA CA Rep, Mult 375,379
70.03 1 4b2nA HEM Rep, Mult 242,340,341,344,345,372,376,377,379,475,476,477,478,480,489,490,491,498,501,502,627,631
80.03 1 2jstB HLT Rep, Mult 33,36,71
90.03 1 3i6sA UUU Rep, Mult 236,250
100.03 1 1siwA SF4 Rep, Mult 314,353,354,358
110.03 1 1lghA DET Rep, Mult 37,44
120.03 1 2g38B MN Rep, Mult 151,154,155
130.03 1 3hdlA UUU Rep, Mult 115,118

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
10.0601fdiA0.3137.810.0470.4951.2.1.2NA
20.0601dgjA0.3078.280.0640.5111.2.-.-NA
30.0603gtgB0.3168.570.0420.5362.7.7.6272
40.0602ivfA0.3087.980.0420.4871.17.99.2NA
50.0602qr5A0.3048.290.0550.5043.4.19.1NA
60.0601t3tA0.3318.070.0530.5366.3.5.3179
70.0601r1jA0.3008.480.0500.5053.4.24.11NA
80.0601ti2A0.3077.990.0330.4931.97.1.2NA
90.0601g8kE0.2648.010.0340.4261.20.98.1NA
100.0601iqcD0.3214.340.0530.3761.11.1.5NA
110.0603lxuX0.3217.810.0730.5133.4.14.10127,138
120.0601q16A0.2987.990.0480.4821.7.99.4NA
130.0603hkzJ0.3208.360.0430.5332.7.7.6187
140.0601ps9A0.3168.070.0600.5141.3.1.34404
150.0603dwbA0.3028.040.0310.4903.4.24.71NA
160.0602vhdA0.3294.130.0660.3821.11.1.5NA
170.0602vdcF0.3137.970.0370.5041.4.1.1386
180.0601g8kA0.3078.230.0600.5051.20.98.1151
190.0601ofdA0.2858.480.0280.4811.4.7.1NA

(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
00.240.8243.120.080.894b2nA GO:0009055 GO:0020037 GO:0046872
10.060.3394.260.050.404fa4B GO:0009055 GO:0016491 GO:0020037 GO:0042597 GO:0046872 GO:0055114
20.060.3304.140.080.384aamA GO:0004130 GO:0004601 GO:0009055 GO:0016491 GO:0020037 GO:0046872 GO:0055114 GO:0098869
30.060.3304.410.070.392c1vA
40.060.3214.350.050.381iqcA GO:0004130 GO:0004601 GO:0009055 GO:0016491 GO:0020037 GO:0042597 GO:0046872 GO:0055114 GO:0098869
50.060.3294.130.070.382vhdA GO:0004130 GO:0004601 GO:0009055 GO:0016491 GO:0020037 GO:0042597 GO:0046872 GO:0055114 GO:0098869
60.060.3234.270.060.383o5cA GO:0004130 GO:0004601 GO:0009055 GO:0016491 GO:0020037 GO:0046872 GO:0055114 GO:0098869
70.060.3154.330.070.373hq6A GO:0004130 GO:0004601 GO:0009055 GO:0016491 GO:0020037 GO:0046872 GO:0055114 GO:0098869
80.060.3114.250.080.361nmlA GO:0009055 GO:0016491 GO:0020037 GO:0046872 GO:0055114
90.060.3024.160.070.353hq7A GO:0004130 GO:0004601 GO:0009055 GO:0016491 GO:0020037 GO:0046872 GO:0055114 GO:0098869
100.060.3034.280.080.354aaoA GO:0004130 GO:0004601 GO:0009055 GO:0016491 GO:0020037 GO:0046872 GO:0055114 GO:0098869
110.060.2994.550.060.351zzhB
120.060.3168.160.040.514lgyA GO:0000166 GO:0004642 GO:0005524 GO:0005737 GO:0006164 GO:0006189 GO:0006541 GO:0009156 GO:0016874 GO:0046872
130.060.3257.720.040.513ikmD GO:0002020 GO:0003676 GO:0003677 GO:0003682 GO:0003887 GO:0005739 GO:0005760 GO:0006259 GO:0006260 GO:0006261 GO:0006264 GO:0006287 GO:0007568 GO:0008408 GO:0009416 GO:0010332 GO:0016740 GO:0016779 GO:0042645 GO:0043195 GO:0043234 GO:0055093 GO:0070062 GO:0071333 GO:0071897 GO:0090305
140.060.2547.890.060.403viuA GO:0000166 GO:0000287 GO:0004642 GO:0005524 GO:0005737 GO:0006164 GO:0006189 GO:0016874 GO:0046872
150.060.2597.930.040.412hs3A GO:0000166 GO:0000287 GO:0004642 GO:0005524 GO:0005737 GO:0006164 GO:0006189 GO:0006541 GO:0009156 GO:0016874 GO:0046872
160.060.2497.890.040.402hruA GO:0000166 GO:0000287 GO:0004642 GO:0005524 GO:0005737 GO:0006164 GO:0006189 GO:0006541 GO:0009156 GO:0016874 GO:0046872
170.060.2338.370.030.391r9jB GO:0003824 GO:0004802 GO:0008152 GO:0016740 GO:0046872
180.060.2057.000.050.304zhtA GO:0000166 GO:0003824 GO:0004553 GO:0005524 GO:0005737 GO:0005829 GO:0006045 GO:0006047 GO:0006054 GO:0007155 GO:0008152 GO:0008761 GO:0009384 GO:0016301 GO:0016310 GO:0016740 GO:0016787 GO:0046835 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0009055 GO:0020037 GO:0046872
GO-Score 0.38 0.38 0.38
Biological Processes GO:0044710
GO-Score 0.36
Cellular Component GO:0042597
GO-Score 0.12

(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.