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I-TASSER results for job id Rv3733c

[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
10.63 68 2a8pA MN Rep, Mult 42,43,58,62,121
20.07 12 5ansA RX8 Rep, Mult 5,6,7,25,39,40,42,43,82,100,138,140,141
30.04 8 2a8sA GTP Rep, Mult 7,25,40,42,43,44,58,61,62,102,121,140,141,144
40.02 4 3shdI MN Rep, Mult 57,58,61
50.02 3 2qjtB MN Rep, Mult 44,57,58
60.01 1 2o1cC PPV Rep, Mult 42,43,44,58,92
70.01 2 1ktgA AMP Rep, Mult 37,42,102,139
80.01 3 1sz3B GNP Rep, Mult 3,5,42,43,44,98,100,102
90.01 2 1ktgA MG Rep, Mult 19,129
100.00 1 4s2yA NUC Rep, Mult 3,25,34,37,42,43,44,58,62,82,100,121

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
10.3422q9pA0.6152.530.2250.7233.6.1.529,58,62
20.0952w4eA0.5993.060.1630.7593.6.1.1312
30.0671v8mA0.6013.280.2310.7653.6.1.13NA
40.0672yvmA0.6253.010.1930.7953.6.1.-NA
50.0671hx3B0.6423.530.1350.8435.3.3.262
60.0661mqwA0.6243.280.1730.8013.6.1.13NA
70.0662dsbA0.5943.580.1460.7893.6.1.13146
80.0601u60C0.4284.750.0590.7173.5.1.223,25,28
90.0601q33A0.6702.790.1540.8133.6.1.1348,58,61
100.0602a96B0.4094.990.0450.6753.1.3.2NA
110.0601zs6B0.4044.230.0560.6212.7.4.6NA
120.0601viqA0.6582.750.2000.8073.6.1.1358,61,64,124
130.0601viuB0.5993.230.1450.7653.6.1.-NA
140.0602wj2A0.4185.190.0480.7473.5.1.9939
150.0601hbmA0.4145.230.0400.7232.8.4.1NA
160.0603hyqA0.6353.030.1390.8015.3.3.262
170.0601b7bA0.4334.830.0340.7172.7.2.2NA
180.0602r5wB0.6712.590.1270.8072.7.7.138,138
190.0602pnyA0.6623.170.1050.8435.3.3.264
200.0603czdA0.4364.710.0560.7173.5.1.264
210.0601zs6A0.4064.410.0550.6322.7.4.6NA
220.0602e9yA0.4205.040.0480.7172.7.2.2NA
230.0601e6vA0.4215.210.0400.7292.8.4.1NA
240.0602j0lA0.2975.050.0360.4942.7.10.219
250.0601f3yA0.6583.060.2000.8133.6.1.1758,62,105
260.0601xsbA0.7721.990.1700.8493.6.1.1742,62

(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
00.500.7851.290.210.821ktgA GO:0000166 GO:0004081 GO:0005524 GO:0006167 GO:0006172 GO:0006754 GO:0006915 GO:0008796 GO:0015967 GO:0016787 GO:0019693 GO:0043135
10.430.7501.810.160.825cfiA GO:0004081 GO:0008796 GO:0016787
20.420.6222.980.180.783cngC GO:0016787 GO:0046872
30.410.7252.810.150.873sonA GO:0016787
40.350.5652.780.230.683smdA GO:0016020 GO:0016021 GO:0016787
50.340.5203.720.120.721mutA GO:0000287 GO:0006260 GO:0006281 GO:0006974 GO:0008413 GO:0016787 GO:0030145 GO:0035539 GO:0044715 GO:0044716 GO:0046872 GO:0047693
60.330.6952.570.200.832o1cA GO:0000287 GO:0008828 GO:0016787 GO:0019177 GO:0046654 GO:0046656 GO:0046872
70.320.5902.950.140.732b06A GO:0016787
80.320.7132.430.190.824mpoB GO:0016787
90.310.6432.790.220.775hzxA GO:0006281 GO:0008413 GO:0016787
100.310.7092.970.160.872kdvA GO:0005737 GO:0006402 GO:0016787 GO:0016818 GO:0034353 GO:0046872 GO:0050779
110.310.6002.760.150.744v14A GO:0006281 GO:0008413 GO:0016787
120.300.6712.590.130.812r5wB GO:0000166 GO:0000309 GO:0003824 GO:0009058 GO:0016740 GO:0016779 GO:0016787 GO:0046872
130.300.6373.020.180.783gg6A GO:0000287 GO:0005829 GO:0009117 GO:0016787 GO:0034656 GO:0044715 GO:0044716 GO:0044717 GO:0046057 GO:0046067 GO:0046712 GO:0046872
140.300.6402.850.170.812jvbA GO:0000184 GO:0000290 GO:0000932 GO:0003682 GO:0003723 GO:0003729 GO:0005634 GO:0005737 GO:0006397 GO:0016787 GO:0030145 GO:0031087 GO:0034063 GO:0046872 GO:0050072 GO:0060261
150.280.5613.000.200.693id9B GO:0016787
160.260.5853.300.170.774jzsA GO:0016787 GO:0046872
170.260.6182.660.150.742a6tB GO:0000166 GO:0000287 GO:0000290 GO:0000340 GO:0000932 GO:0003723 GO:0003727 GO:0005524 GO:0005634 GO:0005737 GO:0005829 GO:0005845 GO:0006397 GO:0010494 GO:0016787 GO:0030145 GO:0031087 GO:0046872 GO:0050072 GO:0098745
180.260.5803.150.150.743q91B GO:0005737 GO:0005829 GO:0008768 GO:0016787 GO:0016818 GO:0018279 GO:0046872 GO:0047631 GO:0070062
190.250.5863.470.140.773q91D GO:0005737 GO:0005829 GO:0008768 GO:0016787 GO:0016818 GO:0018279 GO:0046872 GO:0047631 GO:0070062
200.250.6412.910.160.792b0vA GO:0016787
210.250.7113.100.150.882fmlA GO:0016787
220.250.6273.100.160.783hhjB GO:0006281 GO:0008413 GO:0016787
230.240.6172.720.160.734s2vA GO:0005737 GO:0006402 GO:0016787 GO:0016818 GO:0034353 GO:0046872 GO:0050779
240.240.6183.110.170.774kyxA GO:0016787
250.230.6152.810.160.753fk9A GO:0016787
260.230.6632.060.260.751vc8A GO:0000166 GO:0005524 GO:0016787 GO:0016818 GO:0046872
270.230.6622.470.130.783dkuA GO:0016787
280.220.6302.810.180.754dywA GO:0016787
290.220.6202.540.170.753f13B GO:0016787
300.210.6622.720.170.803grnA GO:0016787
310.210.6592.530.210.781su2A GO:0000166 GO:0005524 GO:0016787
320.210.6293.070.180.792rrkA GO:0006281 GO:0016787
330.210.6443.180.160.815bonA GO:0005829 GO:0006203 GO:0008413 GO:0016787 GO:0017110 GO:0034656 GO:0035539 GO:0046872
340.210.6312.570.130.763h95A GO:0005634 GO:0005737 GO:0005739 GO:0008083 GO:0016787
350.200.6272.810.130.774hfqA GO:0016787
360.190.5743.350.160.743exqA GO:0016787
370.190.6253.120.160.793o61D GO:0000287 GO:0016787 GO:0016818 GO:0046872 GO:0052751
380.190.6353.030.140.803hyqA GO:0004452 GO:0005737 GO:0008299 GO:0016787 GO:0016853 GO:0046872 GO:0050992
390.170.6123.150.160.773q4iA GO:0016787
400.160.7202.930.160.863fjyB GO:0016787
410.150.7652.000.170.841xsaA GO:0000166 GO:0000302 GO:0004081 GO:0005525 GO:0005739 GO:0005759 GO:0006139 GO:0006915 GO:0008796 GO:0008803 GO:0016787
420.140.6362.890.150.783j9me GO:0003735 GO:0005654 GO:0005739 GO:0005743 GO:0005762 GO:0005840 GO:0016787 GO:0030054 GO:0030529 GO:0070125 GO:0070126
430.140.5962.460.120.713gwyB GO:0016787
440.120.6402.380.180.751nqzA GO:0016787
450.100.6583.060.200.811f3yA GO:0000166 GO:0004081 GO:0005524 GO:0016787
460.090.6782.770.140.832qkmB GO:0000166 GO:0000287 GO:0000290 GO:0000340 GO:0000932 GO:0003723 GO:0003727 GO:0005524 GO:0005634 GO:0005737 GO:0005829 GO:0005845 GO:0006397 GO:0010494 GO:0016787 GO:0030145 GO:0031087 GO:0046872 GO:0050072 GO:0098745
470.090.6632.340.250.773i7uC GO:0000166 GO:0005524 GO:0016787
480.080.6362.930.170.771k2eA GO:0016787
490.070.5833.110.130.752pqvB GO:0016787
500.070.6393.430.130.832b2kB GO:0004452 GO:0005737 GO:0006974 GO:0008299 GO:0016787 GO:0016853 GO:0046872 GO:0050992
510.070.6083.290.130.781vhzA GO:0000287 GO:0005829 GO:0016787 GO:0019144 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0004081 GO:0043135 GO:0005524 GO:0046872
GO-Score 0.71 0.50 0.50 0.42
Biological Processes GO:0015967 GO:0006915 GO:0006172 GO:0006167 GO:0006754
GO-Score 0.50 0.50 0.50 0.50 0.50
Cellular Component GO:0016021
GO-Score 0.35

(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.