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I-TASSER results for job id Rv2632c

[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 9 1mz9B VDY Rep, Mult 65,68,72
20.06 8 3gxvA III Rep, Mult 65,68,71,72,75
30.05 7 1ybkC BEQ Rep, Mult 61,64,65,68,69
40.05 6 2h9dD PYR Rep, Mult 58,61
50.04 5 1pcrM BCL Rep, Mult 56,59,60,63
60.04 5 1hwjB ADP Rep, Mult 39,40,41,64,65,68,69,70,71
70.04 5 1tqqA NCO Rep, Mult 53,57
80.03 4 3i54D CMP Rep, Mult 72,76
90.03 4 3wguB CLR Rep, Mult 77,80
100.02 3 4kt0F CLA Rep, Mult 55,59
110.02 2 4hgaA PC4 Rep, Mult 63,67
120.01 2 2hn2D CA Rep, Mult 79,86
130.01 2 3m9iA 3PE Rep, Mult 74,78
140.01 1 3n3pB AMP Rep, Mult 34,35,57,60,63
150.01 1 2dvp0 III Rep, Mult 19,20,23,25,27,42
160.01 2 1nuiA MG Rep, Mult 19,49
170.01 2 3lk4G III Rep, Mult 23,24,41,43
180.01 2 1hw8C 114 Rep, Mult 23,42,43,46,47,48

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
10.0605coxA0.5493.790.0340.8391.14.99.1NA
20.0601prhA0.5453.860.0110.8501.14.99.1NA
30.0602carA0.5463.380.0910.7533.6.1.19NA
40.0602w90B0.5303.890.0860.7851.1.1.44NA
50.0603etdA0.5353.530.0870.8171.4.1.3NA
60.0601pdyA0.5293.830.0500.7964.2.1.1127
70.0602dw6A0.5462.770.1570.7204.2.1.81NA
80.0601mo7A0.2884.660.0630.5593.6.3.942,61,67
90.0602fuaA0.5282.930.0660.6774.1.2.17NA
100.0603ixzA0.5613.230.0360.8173.6.3.10NA
110.0602psnC0.3493.590.0110.5054.2.1.1127
120.0603b8eC0.5603.460.0360.8393.6.3.973
130.0601kkoA0.5433.080.1770.7744.3.1.2NA
140.0601z6fA0.5043.230.0710.7203.4.16.4NA
150.0603fwnA0.5363.790.0540.7851.1.1.44NA
160.0603b8eA0.5563.290.0240.8173.6.3.9NA
170.0602z3tA0.4843.860.0680.7741.-.-.-NA
180.0602pyuA0.5642.970.0530.7423.6.1.1525
190.0602ptxA0.5283.920.0370.8174.2.1.1127

(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
00.070.6372.330.070.844akrB GO:0000902 GO:0003779 GO:0005737 GO:0005856 GO:0005884 GO:0008290 GO:0009617 GO:0030036 GO:0044351 GO:0045335 GO:0051015 GO:0051016 GO:0051693
10.070.6382.710.070.844kwyA GO:0019867 GO:0043165
20.070.5404.040.080.952v50D GO:0005215 GO:0005886 GO:0006810 GO:0006855 GO:0015238 GO:0016020 GO:0016021 GO:0046677
30.070.6002.440.120.771h2iA GO:0000724 GO:0000730 GO:0003677 GO:0005634 GO:0005654 GO:0006281 GO:0006302 GO:0006310 GO:0006974 GO:0010792 GO:0016925 GO:0034599 GO:0042802 GO:0043234 GO:0045002 GO:2000819
40.070.6363.200.070.854uv3A GO:0005886 GO:0009279 GO:0016020 GO:0022610 GO:0030288 GO:0031246 GO:0042802 GO:0044010 GO:0071806
50.070.5643.710.050.893nogA GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015307 GO:0016020 GO:0016021 GO:0042493 GO:0042802 GO:0046618
60.070.5483.680.060.894mt1A GO:0005215 GO:0006810 GO:0016020 GO:0016021
70.070.5623.880.110.913d9bA GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015307 GO:0016020 GO:0016021 GO:0042493 GO:0042802 GO:0046618
80.070.6502.580.030.875adxL GO:0001669 GO:0003779 GO:0005737 GO:0005903 GO:0008290 GO:0014704 GO:0016020 GO:0030018 GO:0030027 GO:0030030 GO:0030032 GO:0030036 GO:0030863 GO:0031115 GO:0031175 GO:0048487 GO:0048747 GO:0051015 GO:0051016 GO:0090036
90.070.4862.930.010.674moaA GO:0005102 GO:0006952 GO:0009405 GO:0030435
100.070.4543.860.090.692uu7A GO:0000166 GO:0003824 GO:0004351 GO:0004356 GO:0005524 GO:0005737 GO:0005739 GO:0006542 GO:0006807 GO:0016829 GO:0016874
110.070.5733.140.090.842i9iA GO:0009279
120.070.5523.780.050.883w9iF GO:0005215 GO:0005886 GO:0006810 GO:0006855 GO:0015238 GO:0016020 GO:0016021 GO:0046677
130.070.3934.590.100.753u0oB GO:0000166 GO:0000287 GO:0004756 GO:0005524 GO:0005829 GO:0016260 GO:0016301 GO:0016310 GO:0016740 GO:0070329
140.070.6192.670.100.843bghA GO:0009279
150.060.4152.900.010.573b55A GO:0046677 GO:0046872
160.060.3934.420.060.704metA GO:0005737 GO:0016829 GO:0016831 GO:0030288 GO:0033609 GO:0045735 GO:0046564 GO:0046872
170.060.5323.730.110.874dnrA GO:0005215 GO:0005375 GO:0005507 GO:0005886 GO:0006810 GO:0006811 GO:0006812 GO:0006825 GO:0006878 GO:0008324 GO:0010272 GO:0010273 GO:0015080 GO:0015673 GO:0015679 GO:0016020 GO:0016021 GO:0046688 GO:0060003 GO:1902601
180.060.5263.940.090.884k0eB GO:0005215 GO:0006810 GO:0006812 GO:0008324 GO:0016020 GO:0016021 GO:0098655


Consensus prediction of GO terms
 
Molecular Function GO:0042802 GO:0051015 GO:0003677 GO:0015238
GO-Score 0.13 0.07 0.07 0.07
Biological Processes GO:0043165 GO:0009617 GO:0044351 GO:0000902 GO:0051016 GO:0071806 GO:0000730 GO:2000819 GO:0016925 GO:0006855 GO:0034599 GO:0010792 GO:0046677 GO:0022610 GO:0044010
GO-Score 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07
Cellular Component GO:0005886 GO:0045335 GO:0008290 GO:0005884 GO:0005654 GO:0031246 GO:0016021 GO:0030288
GO-Score 0.13 0.07 0.07 0.07 0.07 0.07 0.07 0.07

(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.