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I-TASSER results for job id Rv2255c

[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
10.08 2 3g2wB III Rep, Mult 12,15,18,19,41,44
20.08 2 1o6oA III Rep, Mult 3,15,38,41,44,45
30.08 2 3pz2A GRG Rep, Mult 7,40
40.04 1 3c9iE XE Rep, Mult 45,62
50.04 1 4y18A III Rep, Mult 22,23
60.04 1 3g31B GF1 Rep, Mult 54,55
70.04 1 1f59A III Rep, Mult 29,32,33,36,37,54
80.04 1 3eukA MG Rep, Mult 63,64
90.04 1 4it1D BCT Rep, Mult 12,15
100.04 1 3gwzD CA Rep, Mult 6,12

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
10.0601vcoA0.5492.850.1450.8596.3.4.2NA
20.0601vcnA0.4483.830.0680.7976.3.4.2NA
30.0602uxwA0.5563.380.0160.9691.3.99.-NA
40.0601ho8A0.6143.070.1110.9843.6.3.1415
50.0603d9dA0.5743.240.0780.9691.7.3.1NA
60.0601m7sD0.5653.140.0950.8911.11.1.615,41,46
70.0602jifA0.5623.210.0320.9691.3.99.-42,53
80.0603ihyC0.5513.120.1130.9692.7.1.1372,6,23
90.0601ye9A0.3523.600.1180.5941.11.1.6NA
100.0602o5cA0.5673.030.0830.9385.99.1.2NA
110.0602bneB0.5563.060.0670.9062.7.4.22NA
120.0601vcmA0.4573.370.0190.8126.3.4.2NA
130.0601j33A0.5503.160.1030.8752.4.2.21NA
140.0602va1B0.5683.000.0330.9062.7.4.22NA
150.0603ej6A0.5512.980.0890.8591.11.1.6NA
160.0601ye9M0.4972.470.0780.7341.11.1.638,46
170.0603ismC0.5493.060.0670.9383.6.1.3NA
180.0601jqiA0.5603.480.0950.9691.3.99.2NA
190.0601yn9B0.5572.840.0340.8593.1.3.4828,37,43

(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
00.190.5542.940.030.973g2sA GO:0005622 GO:0005654 GO:0005768 GO:0005794 GO:0006810 GO:0006886 GO:0010008 GO:0015031 GO:0016020 GO:0016192 GO:0030131 GO:0043231 GO:0044267 GO:0045732 GO:1901998
10.180.5883.030.020.981qgkA GO:0000059 GO:0000060 GO:0005634 GO:0005635 GO:0005643 GO:0005654 GO:0005737 GO:0005829 GO:0006309 GO:0006606 GO:0006607 GO:0006610 GO:0006810 GO:0006886 GO:0007079 GO:0007080 GO:0008139 GO:0008270 GO:0008536 GO:0008565 GO:0015031 GO:0016020 GO:0016032 GO:0019054 GO:0019899 GO:0019904 GO:0030953 GO:0031291 GO:0031965 GO:0034399 GO:0040001 GO:0043234 GO:0044822 GO:0045184 GO:0051879 GO:0070062 GO:0071782 GO:0075733 GO:0090307
20.080.5952.980.060.981dvpA GO:0001933 GO:0005737 GO:0005768 GO:0005769 GO:0005770 GO:0005829 GO:0005938 GO:0006886 GO:0006887 GO:0006897 GO:0007269 GO:0007275 GO:0007298 GO:0008021 GO:0008293 GO:0008333 GO:0008593 GO:0016050 GO:0016079 GO:0016082 GO:0016197 GO:0016322 GO:0031398 GO:0032509 GO:0033565 GO:0033619 GO:0042059 GO:0043130 GO:0045743 GO:0045752 GO:0046872 GO:0048471 GO:0051726 GO:1990182 GO:2000274
30.070.5883.120.060.983nd2A GO:0000059 GO:0000060 GO:0000176 GO:0005087 GO:0005634 GO:0005643 GO:0005737 GO:0006606 GO:0006607 GO:0006610 GO:0006612 GO:0006656 GO:0006810 GO:0006886 GO:0008139 GO:0008536 GO:0008565 GO:0015031 GO:0031965 GO:0034399 GO:0043547 GO:0051028 GO:0051292 GO:0060188
40.070.5513.570.050.922l0tB GO:0005654 GO:0005737 GO:0005768 GO:0005829 GO:0006810 GO:0006886 GO:0006914 GO:0015031 GO:0016020 GO:0016197 GO:0031901 GO:0033565 GO:0036258 GO:0042059 GO:0043231
50.070.5553.410.120.942qk1A GO:0000776 GO:0000778 GO:0005200 GO:0005737 GO:0005816 GO:0005819 GO:0005856 GO:0005874 GO:0005876 GO:0005938 GO:0007020 GO:0008017 GO:0030472
60.070.5852.840.020.971jplA GO:0005622 GO:0005768 GO:0005794 GO:0005802 GO:0006810 GO:0006886 GO:0010008 GO:0015031 GO:0016020 GO:0016192 GO:0030131 GO:0030306 GO:0044267 GO:0045732
70.070.5933.100.031.003rruA GO:0005622 GO:0005737 GO:0005764 GO:0005768 GO:0005794 GO:0005795 GO:0005829 GO:0006810 GO:0006886 GO:0007165 GO:0010008 GO:0015031 GO:0016020 GO:0017124 GO:0019901 GO:0030276 GO:0030295 GO:0031954 GO:0032147 GO:0043130 GO:0043162 GO:0045839 GO:0070062 GO:2000278
80.070.5793.080.050.981elkA GO:0005622 GO:0005737 GO:0005768 GO:0005769 GO:0005829 GO:0006810 GO:0006886 GO:0006897 GO:0015031 GO:0016020 GO:0016197 GO:0030276 GO:0070062
90.070.5443.330.080.971ialA GO:0005634 GO:0005643 GO:0005654 GO:0005737 GO:0005829 GO:0006606 GO:0006607 GO:0006810 GO:0008139 GO:0008565 GO:0015031 GO:0016020 GO:0042826 GO:0044822
100.070.5963.170.021.002q5dB GO:0000059 GO:0000060 GO:0005634 GO:0005635 GO:0005643 GO:0005654 GO:0005737 GO:0005829 GO:0006309 GO:0006606 GO:0006607 GO:0006610 GO:0006810 GO:0006886 GO:0007079 GO:0007080 GO:0008139 GO:0008270 GO:0008536 GO:0008565 GO:0015031 GO:0016020 GO:0016032 GO:0019054 GO:0019899 GO:0019904 GO:0030953 GO:0031291 GO:0031965 GO:0034399 GO:0040001 GO:0043234 GO:0044822 GO:0045184 GO:0051879 GO:0070062 GO:0071782 GO:0075733 GO:0090307
110.070.5913.080.160.971qbkB GO:0000059 GO:0000060 GO:0005634 GO:0005737 GO:0005829 GO:0006607 GO:0006610 GO:0006810 GO:0006886 GO:0008139 GO:0008536 GO:0008565 GO:0015031 GO:0016032 GO:0031965 GO:0034399 GO:0043488 GO:0044822 GO:0070062 GO:0072372
120.070.6232.900.080.984xriA GO:0005622 GO:0006886 GO:0008536
130.070.5722.910.060.973ldzA GO:0005070 GO:0005737 GO:0005768 GO:0005829 GO:0006810 GO:0006886 GO:0006914 GO:0007165 GO:0009967 GO:0015031 GO:0016020 GO:0016197 GO:0031901 GO:0033565 GO:0036258 GO:0042059 GO:1903543 GO:1903551
140.070.5752.810.030.951mhqB GO:0005622 GO:0005768 GO:0005794 GO:0005802 GO:0006810 GO:0006886 GO:0010008 GO:0015031 GO:0016020 GO:0016192 GO:0030131 GO:0030136 GO:0030306 GO:0044267
150.070.5923.120.031.004avxA GO:0005737 GO:0005768 GO:0005769 GO:0005829 GO:0006622 GO:0006810 GO:0006886 GO:0006914 GO:0007165 GO:0008285 GO:0010324 GO:0010628 GO:0015031 GO:0016020 GO:0016197 GO:0019904 GO:0031901 GO:0032585 GO:0033565 GO:0036258 GO:0042059 GO:0042176 GO:0043231 GO:0043405 GO:0046426 GO:0046872 GO:0070062 GO:0072657 GO:1903543
160.070.5553.380.120.953w3zA GO:0000059 GO:0000060 GO:0005634 GO:0005737 GO:0006406 GO:0006606 GO:0006607 GO:0006610 GO:0006810 GO:0007088 GO:0008139 GO:0008565 GO:0015031 GO:0031965 GO:0034399 GO:0060188
170.070.5543.260.070.953w3uA GO:0000059 GO:0000060 GO:0005634 GO:0005737 GO:0006406 GO:0006606 GO:0006607 GO:0006610 GO:0006810 GO:0007088 GO:0008139 GO:0008565 GO:0015031 GO:0031965 GO:0034399 GO:0060188
180.070.5863.020.120.954jlqA GO:0000059 GO:0000060 GO:0005634 GO:0005737 GO:0005829 GO:0006607 GO:0006610 GO:0006810 GO:0006886 GO:0008139 GO:0008536 GO:0008565 GO:0015031 GO:0016032 GO:0031965 GO:0034399 GO:0043488 GO:0044822 GO:0070062 GO:0072372


Consensus prediction of GO terms
 
Molecular Function GO:0017016 GO:0005048 GO:0022892 GO:0003723 GO:0031072 GO:0046914
GO-Score 0.48 0.48 0.48 0.37 0.37 0.37
Biological Processes GO:0043623 GO:0006606 GO:0042176 GO:0051247 GO:0009896 GO:0000070 GO:0030262 GO:0000737 GO:0019048 GO:0046794 GO:1902850 GO:0051293 GO:0051225 GO:0007265 GO:1902583 GO:0051310 GO:0031122 GO:0051305 GO:0019058 GO:0044068
GO-Score 0.48 0.48 0.38 0.38 0.38 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37
Cellular Component GO:0005635 GO:0005654 GO:0030119 GO:0044440 GO:0005774 GO:0030118 GO:0031988 GO:0098827 GO:1903561 GO:0005829
GO-Score 0.48 0.38 0.38 0.38 0.38 0.38 0.37 0.37 0.37 0.30

(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.