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

I-TASSER results for job id Rv1356c

[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
10.18 13 1qsrA ACO Rep, Mult 69,146,147,148,149,150,157,158,159,160,161,162,183,184,186,188,191,192,194
20.14 10 2g0bA NLT Rep, Mult 66,71,145,146,147,148,165,169,183,184,185,186,192,199,208,211,212,213,219
30.03 2 2jddA 3PG Rep, Mult 69,70,78,146,147,186,211,214
40.01 1 2hbkA MN Rep, Mult 76,153
50.01 1 5icvB III Rep, Mult 69,71,72,73,144,146,208,209
60.01 1 1hizA GLA Rep, Mult 10,144,192
70.01 1 1kfvA NUC Rep, Mult 104,116,130,131,132,140
80.01 1 1aniA PO4 Rep, Mult 191,192,214
90.01 1 2ch1A LLP Rep, Mult 213,215
100.01 1 3p2hA MTA Rep, Mult 78,79,118,131,147
110.01 1 2i14A ZN Rep, Mult 187,221,247
120.01 1 3gwzD CA Rep, Mult 210,212
130.01 1 3mflB DHY Rep, Mult 52,66

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
10.1631ro5A0.5753.230.0920.7002.3.1.184NA
20.0672cntD0.4632.770.1130.5362.3.1.128150,188
30.0662vqyA0.4833.530.1120.6082.3.1.8243,167,188
40.0661yghA0.4663.340.1630.5702.3.1.48NA
50.0661cm0A0.4543.060.1510.5472.3.1.4890,106
60.0601qsmD0.4223.500.0860.5252.3.1.4866
70.0601mj9A0.4303.800.0800.5442.3.1.4874,155,189
80.0603iu2A0.4593.960.1030.6082.3.1.97NA
90.0603b9jI0.2135.630.0230.3421.17.1.4,1.17.3.264,70,77,83
100.0601k4jA0.5253.800.1150.6732.3.1.18482,93,150
110.0601p4nA0.4283.870.0790.5472.3.2.10200,202
120.0601yvoB0.4513.400.1590.5552.3.-.-143
130.0603b9jC0.4156.300.0380.7111.17.3.2,1.17.1.4NA
140.0602e1qA0.3406.750.0470.6271.17.3.2,1.17.1.4NA
150.0601vhsA0.4503.570.1410.5632.3.1.183NA
160.0602rc4A0.4293.750.0600.5442.3.1.48,NA
170.0601yleA0.5164.360.1040.6962.3.1.10944,46,77
180.0601dgjA0.4336.290.0630.7531.2.-.-NA
190.0601t3tA0.4286.010.0710.7156.3.5.361
200.0603d2pB0.4243.460.0510.5132.3.1.1170,175
210.0601q2yA0.4512.600.1170.5212.3.1.-NA
220.0601nmtA0.4383.800.0460.5702.3.1.9766,144,161,189
230.0602p0wA0.4303.910.0340.5402.3.1.48NA
240.0601z4rA0.4543.090.1540.5472.3.1.4890,106

(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
00.160.4752.570.120.551xebA GO:0004596 GO:0006474 GO:0008080 GO:0031248
10.120.4573.360.080.573ld2B GO:0008080 GO:0016740
20.120.5463.400.090.684fd7A GO:0008080
30.110.5363.400.140.664fd4A GO:0008080
40.100.4832.950.090.581tiqA GO:0004145 GO:0004596 GO:0006474 GO:0008080 GO:0016740 GO:0016746 GO:0030435 GO:0031248 GO:0043939
50.100.4482.860.110.521y9kB GO:0004596 GO:0006474 GO:0008080 GO:0016740 GO:0016746 GO:0031248
60.090.5633.000.120.673p2hA GO:0009372 GO:0016740 GO:0061579
70.090.4503.470.100.564rs2B GO:0008080 GO:0016740 GO:0016746
80.080.4883.310.040.602oh1A GO:0008080 GO:0016740
90.070.4512.600.120.521q2yA GO:0008080 GO:0016740 GO:0016746
100.070.4572.980.070.553efaA GO:0008080 GO:0016740 GO:0016746
110.070.4823.090.120.592qecA GO:0008080 GO:0016740
120.070.4542.760.060.532bswA GO:0008080 GO:0016740
130.070.5753.230.090.701ro5A GO:0007165 GO:0009372 GO:0016740 GO:0061579
140.070.4572.970.100.542r7hB GO:0008080 GO:0016740
150.070.5253.770.120.671kzfA GO:0009372 GO:0009405 GO:0016740 GO:0061579
160.070.5403.480.130.674fd6A GO:0008080
170.070.5233.360.080.653te4A GO:0004059 GO:0004060 GO:0005737 GO:0006584 GO:0008080 GO:0016740 GO:0016746 GO:0030187 GO:0030431 GO:0042420 GO:0042429 GO:0045187 GO:0046334 GO:0048066
180.070.4483.900.130.591u6mA GO:0008080 GO:0016740
190.070.4613.370.110.572jlmD GO:0008080 GO:0016740
200.060.4543.310.130.564mbuA GO:0008080 GO:0016740
210.060.4233.840.130.535f47B GO:0008080
220.060.4033.620.070.512beiB GO:0004145 GO:0005737 GO:0008080 GO:0009447 GO:0016740 GO:0016746 GO:0032918 GO:0032919 GO:0032920 GO:0046204 GO:0070062
230.060.2955.550.040.474my0C GO:0008080 GO:0016740
240.060.4053.880.120.515hmnB GO:0008080
250.060.3983.880.070.513t90A GO:0004343 GO:0005783 GO:0005789 GO:0006044 GO:0006048 GO:0008080 GO:0016020 GO:0016740 GO:0016746
260.060.3972.730.130.464qusB GO:0004596 GO:0006474 GO:0008080 GO:0016740 GO:0016746 GO:0016747 GO:0031248


Consensus prediction of GO terms
 
Molecular Function GO:0034212
GO-Score 0.48
Biological Processes GO:0031365 GO:0006473
GO-Score 0.48 0.48
Cellular Component GO:1902493 GO:0044424
GO-Score 0.48 0.48

(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.