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I-TASSER results for job id Rv2571c

[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
10.09 5 1qgrA III Rep, Mult 26,59,63,101,104,105,108,111,115,149,156,160,163,218,222,225,259,262,266
20.09 5 1o6oA III Rep, Mult 132,135,136,140,186,189,190
30.05 3 3w3wA III Rep, Mult 26,27,29,30,33,34,108,111,112,153,156,159,160,163,211,214
40.03 2 2axtM CLA Rep, Mult 163,167
50.03 2 2e75G OPC Rep, Mult 150,154
60.02 1 3t1gA ZN Rep, Mult 189,193
70.02 1 2wycA 3LA Rep, Mult 64,67
80.02 1 1f59A III Rep, Mult 78,81,82,85,86,120,124,128
90.02 1 3arcx CLA Rep, Mult 82,83,86
100.02 1 2ot8A III Rep, Mult 26,56,60,108,152,153,156,163,215,218,222,259,310
110.02 1 2q5dB III Rep, Mult 152,156,221
120.02 1 3gwzD CA Rep, Mult 148,152
130.02 1 1y66A DIO Rep, Mult 187,191
140.02 1 2bptA III Rep, Mult 188,191,192,195,196,246,249
150.02 1 1f59B III Rep, Mult 82,85,86,89,90,122,123,124,125,130
160.02 1 2wieD CVM Rep, Mult 89,92
170.02 1 1pjmB III Rep, Mult 26,52,56,60,62,105,108,112,115,116,156,159,160,163,215,218,222,262,266,268,271,279,284,321,324,325

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
10.0601i8qA0.4775.580.0520.7104.2.2.191
20.0603b95B0.4254.840.0520.5942.1.1.4376,113,115
30.0603btaA0.4186.440.0420.6703.4.24.69NA
40.0603c5wA0.4694.390.1040.6143.1.3.1616
50.0601rw9A0.4575.710.0600.6764.2.2.5NA
60.0601cb8A0.4296.060.0300.6594.2.2.5NA
70.0602g25A0.4246.500.0390.7011.2.4.1NA
80.0602np0A0.4316.420.0370.6993.4.24.69NA
90.0601z0hB0.2547.140.0260.4513.4.24.6973
100.0602uveA0.4166.340.0670.6623.2.1.82NA
110.0602qtcB0.4246.360.0390.6931.2.4.179
120.0601ho8A0.5664.520.0540.7613.6.3.14159,166,214
130.0601dboA0.4346.330.0340.7074.2.2.19NA
140.0602gtqA0.4725.810.0790.7103.4.11.2NA
150.0601gaiA0.4425.630.0630.6623.2.1.3NA
160.0602vn4A0.4395.770.0690.6683.2.1.3NA
170.0602vn7A0.4385.900.0770.6703.2.1.3156
180.0602dqmA0.4316.380.0740.6763.4.11.2NA
190.0601l8aA0.4256.460.0420.7011.2.4.1NA

(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
00.280.8202.840.080.942x1gF GO:0005737 GO:0006606 GO:0006886 GO:0007270 GO:0008139 GO:0008536 GO:0008565 GO:0031965 GO:0042331 GO:0050804
10.240.7732.990.080.903zkvA GO:0005737 GO:0006606 GO:0006886 GO:0007270 GO:0008139 GO:0008536 GO:0008565 GO:0031965 GO:0042331 GO:0050804
20.230.7842.960.090.913zjyE GO:0005634 GO:0005737 GO:0006606 GO:0006810 GO:0006886 GO:0008139 GO:0008536 GO:0008565 GO:0015031 GO:0031965
30.160.8092.780.080.924ol0B GO:0004872 GO:0005634 GO:0005737 GO:0006810 GO:0008139 GO:0008565 GO:0015031 GO:0031965 GO:0035048 GO:0042802 GO:0043231
40.160.7902.710.080.894c0qA GO:0004872 GO:0005634 GO:0005737 GO:0006810 GO:0008139 GO:0008565 GO:0015031 GO:0031965 GO:0035048 GO:0042802 GO:0043231
50.160.6144.470.060.814c0qB GO:0004872 GO:0005634 GO:0005737 GO:0006810 GO:0008139 GO:0008565 GO:0015031 GO:0031965 GO:0035048 GO:0042802 GO:0043231
60.130.4733.840.070.593tt9A GO:0002159 GO:0005080 GO:0005634 GO:0005654 GO:0005882 GO:0005886 GO:0005911 GO:0005912 GO:0005913 GO:0007155 GO:0007507 GO:0008285 GO:0010765 GO:0014704 GO:0016021 GO:0016264 GO:0016337 GO:0017080 GO:0019215 GO:0030054 GO:0030057 GO:0030336 GO:0032947 GO:0034334 GO:0044325 GO:0045110 GO:0045294 GO:0048496 GO:0055010 GO:0055088 GO:0086001 GO:0086002 GO:0086005 GO:0086019 GO:0086064 GO:0086073 GO:0086083 GO:0086091 GO:0090002 GO:0098641 GO:0098911 GO:2000810
70.120.7144.010.080.905difC GO:0000055 GO:0000776 GO:0005634 GO:0005737 GO:0005816 GO:0006406 GO:0006611 GO:0006810 GO:0006886 GO:0008536 GO:0008565 GO:0015031 GO:0034501 GO:0048471
80.090.6104.820.080.831xm9A GO:0004871 GO:0005521 GO:0005634 GO:0005654 GO:0005882 GO:0005886 GO:0007155 GO:0007165 GO:0007275 GO:0016337 GO:0019215 GO:0030054 GO:0030057 GO:0030280 GO:0043231 GO:0045110 GO:0070062
90.080.7533.310.100.912xwuB GO:0005634 GO:0005737 GO:0006606 GO:0006810 GO:0006886 GO:0008139 GO:0008536 GO:0008565 GO:0015031 GO:0031965
100.070.7164.170.070.913wyfC GO:0000055 GO:0000776 GO:0005634 GO:0005737 GO:0005816 GO:0006406 GO:0006611 GO:0006810 GO:0006886 GO:0008536 GO:0008565 GO:0015031 GO:0034501 GO:0048471
110.070.6284.630.090.853l6xA GO:0005102 GO:0005634 GO:0005737 GO:0005829 GO:0005886 GO:0005911 GO:0005913 GO:0005915 GO:0006351 GO:0006355 GO:0007155 GO:0007420 GO:0016020 GO:0016055 GO:0016337 GO:0019901 GO:0030027 GO:0030426 GO:0030496 GO:0034332 GO:0043197 GO:0045202 GO:0045296 GO:0050839 GO:0070062 GO:0090090 GO:0098641
120.070.4585.870.070.702iw3B GO:0000166 GO:0001933 GO:0003723 GO:0003746 GO:0005524 GO:0005737 GO:0005840 GO:0006412 GO:0006414 GO:0006415 GO:0006469 GO:0010494 GO:0016887 GO:0019843 GO:0022626 GO:0042788
130.060.3336.540.040.543a5vA
140.060.3526.960.050.612hivA GO:0000166 GO:0003677 GO:0003909 GO:0003910 GO:0005524 GO:0005737 GO:0006260 GO:0006273 GO:0006281 GO:0006310 GO:0006974 GO:0007049 GO:0016874 GO:0046872 GO:0051103 GO:0051301 GO:0071897
150.060.3505.650.060.511x87A GO:0005737 GO:0006547 GO:0006548 GO:0016153 GO:0016829 GO:0019556 GO:0019557
160.060.2365.220.070.345bmwB GO:0003824 GO:0004807 GO:0006094 GO:0006096 GO:0006098 GO:0008152 GO:0016853 GO:0042802
170.060.2486.070.040.392gieA GO:0003677 GO:0004518 GO:0004519 GO:0009036 GO:0009307 GO:0016787 GO:0090305
180.060.2526.060.030.394rk9A GO:0005215 GO:0006810
190.060.2235.880.010.341ks4A GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0008810 GO:0016787 GO:0016798
200.060.1996.690.050.332yn3C GO:0005509 GO:0007156 GO:0016020 GO:0016491 GO:0030151 GO:0046872 GO:0055114
210.060.1663.220.040.194exnA GO:0001934 GO:0002376 GO:0005125 GO:0005157 GO:0005576 GO:0005615 GO:0006954 GO:0008083 GO:0008284 GO:0045087 GO:0045651 GO:0045657


Consensus prediction of GO terms
 
Molecular Function GO:0008139 GO:0008565 GO:0060089 GO:0008536
GO-Score 0.70 0.70 0.59 0.58
Biological Processes GO:0006606 GO:0007270 GO:0042331 GO:0050804
GO-Score 0.58 0.45 0.45 0.45
Cellular Component GO:0031965 GO:0005737
GO-Score 0.70 0.70

(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.