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I-TASSER results for job id Rv3658c

[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
10.06 3 1dy7B HEC Rep, Mult 105,140,142,150,158,159,162,163,167
20.04 2 4pe1A DCD Rep, Mult 210,213
30.04 2 2axtH CLA Rep, Mult 15,18
40.02 1 1s5lk CLA Rep, Mult 215,219
50.02 1 1iw7P MG Rep, Mult 142,146
60.02 1 4xgcC III Rep, Mult 207,208
70.02 1 1lphD IPH Rep, Mult 109,113
80.02 1 1n0wA MG Rep, Mult 91,104,107
90.02 1 1z68B NDG Rep, Mult 229,231,236,237
100.02 1 3ak3D EDO Rep, Mult 13,16
110.02 1 2a68P MG Rep, Mult 197,200,201
120.02 1 4po7A III Rep, Mult 6,10,11,13,244,245,258,265
130.02 1 3b29A LSM Rep, Mult 212,239,243
140.02 1 1jb0M CLA Rep, Mult 208,212
150.02 1 2d0vA CA Rep, Mult 157,158,161,175,177
160.02 1 2wycA 3LA Rep, Mult 72,75
170.02 1 2p9xD ZN Rep, Mult 94,98
180.02 1 3kziX CLA Rep, Mult 104,107
190.02 1 1aofA HEM Rep, Mult 88,89,92,93,97,108,113,118,123,124,125
200.02 1 2dysO CDL Rep, Mult 7,11,14,15,18

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
10.0601sllA0.4276.520.0890.7824.2.2.15105,106
20.0601qksB0.4675.860.0510.7781.7.2.196,120
30.0603g0bB0.4395.520.0550.7143.4.14.5185
40.0601z68A0.5245.610.0510.8463.4.21.-NA
50.0602bixA0.4296.380.0790.7561.14.99.-188
60.0601w6sC0.4286.410.0430.7671.1.99.8NA
70.0601cruB0.4346.150.0760.7481.1.5.2131
80.0602w68C0.2376.250.0570.4103.2.1.1898
90.0602jkbA0.4126.460.0380.7373.2.1.18,4.2.2.15NA
100.0602d0vA0.4656.410.0580.8351.1.99.8NA
110.0601lrwA0.4605.970.0670.7821.1.99.8NA
120.0601kv9A0.4646.240.0790.8041.1.99.-NA
130.0601k3iA0.4026.390.0670.7181.1.3.9NA
140.0601xc6A0.4256.340.0320.7593.2.1.23NA
150.0601e5tA0.4325.960.0680.7333.4.21.26NA
160.0602ebsB0.4246.260.0890.7563.2.1.150NA
170.0603h71B0.4186.390.0310.7333.2.1.18NA
180.0602gbcA0.5215.870.0700.8763.4.14.5,3.4.15.5NA
190.0601oygA0.4136.350.0420.7262.4.1.10NA

(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
00.070.3986.100.060.682ecfA GO:0006508 GO:0008236
10.070.5545.420.060.893wsxA GO:0000042 GO:0001540 GO:0004888 GO:0005576 GO:0005615 GO:0005641 GO:0005768 GO:0005769 GO:0005783 GO:0005794 GO:0005802 GO:0005887 GO:0006605 GO:0006622 GO:0006629 GO:0006810 GO:0006869 GO:0006892 GO:0006897 GO:0006898 GO:0007165 GO:0008202 GO:0008203 GO:0014910 GO:0016020 GO:0016021 GO:0030169 GO:0030306 GO:0031985 GO:0032091 GO:0032460 GO:0034362 GO:0043407 GO:0045053 GO:0045732 GO:0050768 GO:0051604 GO:0055037 GO:0070062 GO:0070863 GO:1901215 GO:1902430 GO:1902771 GO:1902948 GO:1902953 GO:1902955 GO:1902960 GO:1902963 GO:1902966 GO:1902997 GO:2001137
20.070.5055.930.040.854wjlB GO:0005886 GO:0006508 GO:0008236 GO:0008239 GO:0015459 GO:0016020 GO:0016021 GO:0072659 GO:0090004 GO:1901379
30.070.5665.370.050.893wsyA GO:0000042 GO:0001540 GO:0004888 GO:0005576 GO:0005615 GO:0005641 GO:0005768 GO:0005769 GO:0005783 GO:0005794 GO:0005802 GO:0005887 GO:0006605 GO:0006622 GO:0006629 GO:0006810 GO:0006869 GO:0006892 GO:0006897 GO:0006898 GO:0007165 GO:0008202 GO:0008203 GO:0014910 GO:0016020 GO:0016021 GO:0030169 GO:0030306 GO:0031985 GO:0032091 GO:0032460 GO:0034362 GO:0043407 GO:0045053 GO:0045732 GO:0050768 GO:0051604 GO:0055037 GO:0070062 GO:0070863 GO:1901215 GO:1902430 GO:1902771 GO:1902948 GO:1902953 GO:1902955 GO:1902960 GO:1902963 GO:1902966 GO:1902997 GO:2001137
40.070.5245.610.050.851z68A GO:0001525 GO:0002020 GO:0004175 GO:0004222 GO:0004252 GO:0005178 GO:0005576 GO:0005615 GO:0005737 GO:0005886 GO:0005925 GO:0006508 GO:0006915 GO:0007155 GO:0008233 GO:0008236 GO:0008239 GO:0009986 GO:0010710 GO:0010716 GO:0016020 GO:0016021 GO:0016787 GO:0030027 GO:0030054 GO:0031258 GO:0032587 GO:0042803 GO:0042995 GO:0043542 GO:0045177 GO:0045178 GO:0046983 GO:0051603 GO:0051917 GO:0060244 GO:0071158 GO:0071438 GO:0071850 GO:0097325 GO:1900119 GO:1902362 GO:1903054
50.070.4926.280.090.884po7A GO:0001503 GO:0005634 GO:0005764 GO:0005765 GO:0005768 GO:0005769 GO:0005783 GO:0005789 GO:0005794 GO:0005829 GO:0005886 GO:0005905 GO:0006810 GO:0006895 GO:0006897 GO:0007186 GO:0007218 GO:0007275 GO:0008333 GO:0008625 GO:0009986 GO:0010008 GO:0010465 GO:0010468 GO:0014902 GO:0016020 GO:0016021 GO:0016023 GO:0016050 GO:0019899 GO:0030136 GO:0030140 GO:0030154 GO:0030379 GO:0030425 GO:0031965 GO:0032509 GO:0032580 GO:0032868 GO:0038180 GO:0043025 GO:0043231 GO:0045599 GO:0046323 GO:0048011 GO:0048227 GO:0048406 GO:0048471 GO:0051005 GO:1904037
60.070.5295.660.050.862aj8A GO:0001618 GO:0001662 GO:0001666 GO:0002020 GO:0004177 GO:0004252 GO:0005102 GO:0005576 GO:0005765 GO:0005886 GO:0005925 GO:0006508 GO:0007155 GO:0008233 GO:0008236 GO:0008239 GO:0008284 GO:0009986 GO:0010716 GO:0016020 GO:0016021 GO:0016324 GO:0016787 GO:0030027 GO:0030054 GO:0030139 GO:0031258 GO:0031295 GO:0033632 GO:0035641 GO:0036343 GO:0042110 GO:0042802 GO:0042803 GO:0042995 GO:0043542 GO:0045121 GO:0046581 GO:0046718 GO:0070062 GO:0071438
70.070.4576.380.040.814q1vA GO:0006508 GO:0008236 GO:0016787 GO:0046872
80.070.4855.560.080.772bklB GO:0004252 GO:0006508 GO:0008236 GO:0070008
90.070.4496.080.080.773azoA GO:0004177 GO:0006508 GO:0008236
100.070.3986.340.040.712d5lA GO:0004177 GO:0006508 GO:0008233 GO:0008236 GO:0016787
110.070.4436.010.080.745fkqA GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246 GO:0030247 GO:0030248
120.070.4326.270.070.753o4jC GO:0005737 GO:0006508 GO:0008236 GO:0016787
130.070.3916.600.070.724hxgF GO:0006508 GO:0008236 GO:0046872
140.070.5215.870.070.882gbcA GO:0002020 GO:0002709 GO:0004177 GO:0004252 GO:0005102 GO:0005518 GO:0005576 GO:0005783 GO:0005794 GO:0005886 GO:0006508 GO:0007155 GO:0008233 GO:0008236 GO:0008239 GO:0008284 GO:0009986 GO:0010716 GO:0016020 GO:0016021 GO:0016324 GO:0016787 GO:0030027 GO:0030054 GO:0030139 GO:0031258 GO:0031295 GO:0042277 GO:0042803 GO:0042995 GO:0043542 GO:0045121 GO:0051234 GO:0071438
150.060.4426.400.050.794amyA GO:0004252 GO:0005737 GO:0006508 GO:0008233 GO:0008236 GO:0016787 GO:0070008
160.060.5275.940.090.894n8eB GO:0001618 GO:0001662 GO:0001666 GO:0002020 GO:0004177 GO:0004252 GO:0005102 GO:0005576 GO:0005765 GO:0005886 GO:0005925 GO:0006508 GO:0007155 GO:0008233 GO:0008236 GO:0008239 GO:0008284 GO:0009986 GO:0010716 GO:0016020 GO:0016021 GO:0016324 GO:0016787 GO:0030027 GO:0030054 GO:0030139 GO:0031258 GO:0031295 GO:0033632 GO:0035641 GO:0036343 GO:0042110 GO:0042802 GO:0042803 GO:0042995 GO:0043542 GO:0045121 GO:0046581 GO:0046718 GO:0070062 GO:0071438
170.060.5295.840.080.881xfdA GO:0005886 GO:0006508 GO:0008076 GO:0008236 GO:0008239 GO:0009986 GO:0015459 GO:0016020 GO:0016021 GO:0043025 GO:0043268 GO:0070062 GO:0072659 GO:1901379
180.060.4556.200.060.782xe4A GO:0004252 GO:0005737 GO:0005829 GO:0006508 GO:0008236 GO:0016787 GO:0070008 GO:0070012


Consensus prediction of GO terms
 
Molecular Function GO:0070011 GO:0017171
GO-Score 0.37 0.37
Biological Processes GO:0019538
GO-Score 0.37
Cellular Component GO:0031224 GO:0044421
GO-Score 0.38 0.37

(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.