[Home] [Server] [About] [Statistics] [Annotation]

I-TASSER results for job id Rv2489c

[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
10.12 4 5kc8A CA Rep, Mult 6,9
20.06 2 1i1aA UUU Rep, Mult 44,45,71,72,76
30.06 2 4f8hB LMD Rep, Mult 4,5,8
40.03 1 4c7rA PGT Rep, Mult 10,14
50.03 1 2z1qA FAD Rep, Mult 29,34,37,90,91
60.03 1 1zagD UUU Rep, Mult 47,60,62
70.03 1 3m17A III Rep, Mult 30,31,59,60,91,92
80.03 1 1ohfA MG Rep, Mult 7,43
90.03 1 2o8mB III Rep, Mult 44,46
100.03 1 3b8iB MG Rep, Mult 36,38
110.03 1 1swiC BNZ Rep, Mult 3,7

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
10.0601hv8A0.4514.260.0340.7883.6.4.13NA
20.0602vgrD0.4334.320.0720.7981.3.7.236
30.0601dioA0.3334.970.0570.7174.2.1.28NA
40.0602ywfA0.4544.500.0800.8593.6.5.-NA
50.0602z1qB0.4754.520.0420.8491.3.99.3NA
60.0602d1eA0.4704.050.0690.8181.3.7.537
70.0601y42X0.4544.180.0760.8086.1.1.1NA
80.0602gxaE0.4504.660.0540.8993.6.4.1246
90.0601dl5A0.4484.260.0820.7982.1.1.77NA
100.0601q50A0.2974.920.1090.6165.3.1.9NA
110.0601w2cA0.4674.370.0530.8792.7.1.127NA
120.0603djlA0.4734.250.0720.8281.3.99.-NA
130.0603kb9A0.4684.710.1040.9094.2.3.3790
140.0601bi9D0.3075.020.0690.6461.2.1.36,1.2.1.-NA
150.0603jz4A0.4454.720.0750.8691.2.1.16NA
160.0601o9jA0.4594.540.0780.8791.2.1.3NA
170.0601xnvA0.4454.350.0570.7986.4.1.3NA
180.0602wu8A0.4484.490.0870.8385.3.1.9NA
190.0601ezfB0.4474.430.0940.8382.5.1.2149,92

(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
00.070.5853.600.120.903j792 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0022625
10.070.4634.530.040.904zfzA GO:0002376 GO:0002474 GO:0006955 GO:0016020 GO:0016021 GO:0019882 GO:0042605 GO:0042612
20.070.5033.990.110.854v8pAO GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0030529
30.070.4804.090.030.844v6xCr GO:0000184 GO:0003723 GO:0003735 GO:0005622 GO:0005737 GO:0005829 GO:0005840 GO:0006364 GO:0006412 GO:0006413 GO:0006614 GO:0016020 GO:0019083 GO:0022625 GO:0030425 GO:0030529 GO:0036464 GO:0044297 GO:0044822 GO:0070062 GO:1903146 GO:1903955
40.070.4534.400.070.842h26A GO:0002250 GO:0002376 GO:0005764 GO:0005765 GO:0005768 GO:0005886 GO:0006955 GO:0009986 GO:0010008 GO:0016020 GO:0016021 GO:0030881 GO:0030883 GO:0030884 GO:0048007 GO:0050776 GO:0071723
50.070.3134.220.140.563jvgB GO:0006955 GO:0016020 GO:0016021
60.070.4594.450.030.883pwuA GO:0002376 GO:0002474 GO:0006955 GO:0016020 GO:0016021 GO:0019882 GO:0042605 GO:0042612
70.070.3104.120.100.564y2dA GO:0001865 GO:0001916 GO:0002376 GO:0005737 GO:0005764 GO:0005765 GO:0005768 GO:0005769 GO:0005770 GO:0005886 GO:0006955 GO:0009897 GO:0009986 GO:0010008 GO:0016020 GO:0016021 GO:0019882 GO:0030881 GO:0030882 GO:0030883 GO:0030884 GO:0033084 GO:0042102 GO:0042393 GO:0042608 GO:0043032 GO:0045059 GO:0045078 GO:0045086 GO:0045087 GO:0045404 GO:0048006 GO:0048007 GO:0050776 GO:0050839 GO:0051135 GO:0051138 GO:0071723
80.070.4794.620.090.893arbA GO:0001865 GO:0001916 GO:0002376 GO:0005737 GO:0005764 GO:0005765 GO:0005768 GO:0005769 GO:0005770 GO:0005886 GO:0006955 GO:0009897 GO:0009986 GO:0010008 GO:0016020 GO:0016021 GO:0019882 GO:0030881 GO:0030882 GO:0030883 GO:0030884 GO:0033084 GO:0042102 GO:0042393 GO:0042608 GO:0043032 GO:0045059 GO:0045078 GO:0045086 GO:0045087 GO:0045404 GO:0048006 GO:0048007 GO:0050776 GO:0050839 GO:0051135 GO:0051138 GO:0071723
90.070.4724.300.060.881frtA GO:0003823 GO:0005886 GO:0006955 GO:0006959 GO:0016020 GO:0016021 GO:0019770 GO:0019864 GO:0019882 GO:0030881 GO:0038094 GO:0042605
100.070.4544.420.030.853jtcB GO:0004872 GO:0005576 GO:0005813 GO:0005886 GO:0005887 GO:0005925 GO:0006955 GO:0007596 GO:0007599 GO:0009986 GO:0016020 GO:0016021 GO:0050819 GO:0050900 GO:0070062
110.070.4864.290.120.874v6wCr GO:0000022 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0007052 GO:0022008 GO:0022625 GO:0030529 GO:0051298
120.070.4664.500.040.871a1mA GO:0000139 GO:0002376 GO:0002474 GO:0002479 GO:0002480 GO:0005783 GO:0005794 GO:0005886 GO:0006955 GO:0009986 GO:0012507 GO:0016020 GO:0016021 GO:0016032 GO:0019882 GO:0030670 GO:0031901 GO:0042605 GO:0042612 GO:0050776 GO:0060333 GO:0060337 GO:0071556
130.070.4494.120.060.804f7eA GO:0006955 GO:0016020 GO:0016021
140.070.4833.950.080.804v8mBc GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0022625
150.070.4684.410.070.901efxA GO:0000139 GO:0002376 GO:0002474 GO:0002479 GO:0002480 GO:0005783 GO:0005794 GO:0005886 GO:0006955 GO:0009986 GO:0012507 GO:0016020 GO:0016021 GO:0016032 GO:0019882 GO:0030670 GO:0031901 GO:0042605 GO:0042612 GO:0045087 GO:0046977 GO:0050776 GO:0060333 GO:0060337 GO:0071556
160.070.4654.350.070.874hwzA GO:0000139 GO:0002376 GO:0002474 GO:0002479 GO:0002480 GO:0005783 GO:0005794 GO:0005886 GO:0006955 GO:0009986 GO:0012507 GO:0016020 GO:0016021 GO:0016032 GO:0019882 GO:0030670 GO:0030881 GO:0031901 GO:0042605 GO:0042612 GO:0044822 GO:0050776 GO:0060333 GO:0060337 GO:0071556
170.070.4734.450.040.901hyrC GO:0001913 GO:0002250 GO:0002376 GO:0002418 GO:0003823 GO:0005615 GO:0005737 GO:0005886 GO:0005887 GO:0006955 GO:0006974 GO:0009408 GO:0009986 GO:0016020 GO:0016021 GO:0016032 GO:0019835 GO:0019882 GO:0030881 GO:0032815 GO:0042267 GO:0042742 GO:0045953 GO:0046629 GO:0046703 GO:0050776 GO:0051607
180.070.4594.520.040.891biiA GO:0001916 GO:0002376 GO:0002474 GO:0002479 GO:0002485 GO:0005102 GO:0005783 GO:0005794 GO:0005797 GO:0005886 GO:0006955 GO:0009897 GO:0009986 GO:0010977 GO:0016020 GO:0016021 GO:0019882 GO:0030670 GO:0030881 GO:0042605 GO:0042608 GO:0042612 GO:0044822 GO:0045121 GO:0046977 GO:0070062 GO:0070971 GO:0071556


Consensus prediction of GO terms
 
Molecular Function GO:0005198
GO-Score 0.37
Biological Processes GO:0043043 GO:0010467 GO:0044267 GO:0034645
GO-Score 0.37 0.37 0.37 0.37
Cellular Component GO:0043232 GO:0044444 GO:0030529
GO-Score 0.37 0.37 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.