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

I-TASSER results for job id Rv1231c

[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
10.09 5 2grr1 III Rep, Mult 71,72,75,76,79
20.05 3 3n0gA MG Rep, Mult 101,105,152,155
30.04 2 1oya0 III Rep, Mult 70,71,72,119,120,123,124,127,130,134,162,163
40.04 2 1h2u0 III Rep, Mult 82,88,89
50.04 2 4wmrA 865 Rep, Mult 70,74,75,96,99,100,103,104,114,117,118,121,122,149
60.04 2 4bo0D FXE Rep, Mult 90,93,94,97,147,148,151
70.02 1 2ql2C NUC Rep, Mult 96,100
80.02 1 3ahxD 7PE Rep, Mult 76,77,78,86
90.02 1 2io31 III Rep, Mult 95,98,101,102,105
100.02 1 3prqX CLA Rep, Mult 46,53
110.02 1 2ie40 III Rep, Mult 16,66,69,72,111,112,113,116,117
120.02 1 3c62B CA Rep, Mult 118,120
130.02 1 1z5s3 III Rep, Mult 80,84,87
140.02 1 3c2mA MN Rep, Mult 115,118
150.02 1 1z83B ZN Rep, Mult 120,171
160.02 1 3pyoY MG Rep, Mult 91,138
170.02 1 2nr9A PA6 Rep, Mult 56,60
180.02 1 1xrmA III Rep, Mult 126,129

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
10.0661ujkB0.4934.230.0660.7443.4.23.4678,82,125
20.0601bgaA0.5854.310.0370.8613.2.1.21NA
30.0601px8A0.5543.960.0600.7833.2.1.37NA
40.0602e9lA0.5784.210.0930.8283.2.1.21NA
50.0601h7aA0.5574.220.0670.8221.17.4.2NA
60.0601qoxM0.5884.160.0560.8503.2.1.2177
70.0601bwlA0.5753.750.0260.8171.6.99.1NA
80.0601gowA0.5784.460.0620.8503.2.1.23NA
90.0601tr1D0.5844.330.0370.8563.2.1.21NA
100.0603gnoA0.5304.850.0760.8443.2.1.2176
110.0602zoxA0.5804.200.0930.8283.2.1.21NA
120.0602bfgA0.5673.920.0530.7893.2.1.37NA
130.0603cmjA0.5744.320.0500.8443.2.1.21NA
140.0602jieA0.5844.240.0560.8443.2.1.21NA
150.0602z1sA0.5854.250.0560.8443.2.1.21NA
160.0602dgaA0.5754.380.0300.8673.2.1.21NA
170.0601b1yA0.5614.160.0460.8113.2.1.2101,125
180.0601np2A0.5714.410.0930.8563.2.1.21NA
190.0601gonA0.5844.340.0610.8613.2.1.21129
200.0601qoxA0.5884.160.0560.8503.2.1.21NA

(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
00.160.6253.580.070.853feyA GO:0000184 GO:0000339 GO:0000398 GO:0003723 GO:0005634 GO:0005654 GO:0005737 GO:0005739 GO:0005829 GO:0005845 GO:0005846 GO:0006366 GO:0006368 GO:0006369 GO:0006370 GO:0006397 GO:0006405 GO:0006406 GO:0006417 GO:0006446 GO:0006810 GO:0008334 GO:0008380 GO:0008543 GO:0010467 GO:0016070 GO:0030307 GO:0030529 GO:0031047 GO:0031124 GO:0031442 GO:0034518 GO:0042795 GO:0044822 GO:0045292 GO:0051028 GO:0051168 GO:0098789 GO:1900363
10.090.6513.830.110.915fu7A GO:0000122 GO:0000289 GO:0000932 GO:0004535 GO:0005615 GO:0005634 GO:0005737 GO:0005778 GO:0005829 GO:0006351 GO:0006355 GO:0006417 GO:0006977 GO:0007275 GO:0010606 GO:0016020 GO:0017148 GO:0019904 GO:0030014 GO:0030015 GO:0030331 GO:0031047 GO:0032947 GO:0033147 GO:0035195 GO:0042974 GO:0043231 GO:0044822 GO:0048387 GO:0060213 GO:0061014 GO:0070016 GO:0090503 GO:1900153 GO:2000036
20.080.6534.130.090.954by6A GO:0046872
30.070.6303.480.080.851h2uA GO:0000184 GO:0000339 GO:0000398 GO:0003723 GO:0005634 GO:0005654 GO:0005737 GO:0005739 GO:0005829 GO:0005845 GO:0005846 GO:0006366 GO:0006368 GO:0006369 GO:0006370 GO:0006397 GO:0006405 GO:0006406 GO:0006417 GO:0006446 GO:0006810 GO:0008334 GO:0008380 GO:0008543 GO:0010467 GO:0016070 GO:0030307 GO:0030529 GO:0031047 GO:0031124 GO:0031442 GO:0034518 GO:0042795 GO:0044822 GO:0045292 GO:0051028 GO:0051168 GO:0098789 GO:1900363
40.070.5144.520.060.784d0jA GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0030245 GO:0102483
50.060.4035.010.070.661z7aA GO:0003824 GO:0005975 GO:0016810
60.060.4274.510.030.662xn0A GO:0003824 GO:0004553 GO:0004557 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0052692
70.060.3644.550.070.571v4vA GO:0008761 GO:0016853
80.060.3965.220.040.663wpnA GO:0000166 GO:0000922 GO:0003777 GO:0005524 GO:0005737 GO:0005819 GO:0005829 GO:0005856 GO:0005871 GO:0005874 GO:0005876 GO:0006890 GO:0007018 GO:0007049 GO:0007051 GO:0007052 GO:0007059 GO:0007067 GO:0007100 GO:0008017 GO:0008574 GO:0016020 GO:0019886 GO:0019901 GO:0032403 GO:0046602 GO:0051225 GO:0051301 GO:0090307
90.060.3435.210.060.584wjiA GO:0000166 GO:0004665 GO:0006571 GO:0008977 GO:0055114
100.060.3095.800.030.574p3lA GO:0006810 GO:0008643 GO:0030288 GO:0042597
110.060.3066.220.040.603l4dB GO:0004497 GO:0005506 GO:0008168 GO:0008398 GO:0016491 GO:0016705 GO:0020037 GO:0032259 GO:0046872 GO:0055114 GO:0070988
120.060.3165.260.120.521y97A GO:0000287 GO:0003676 GO:0004518 GO:0004527 GO:0005634 GO:0006259 GO:0006281 GO:0006974 GO:0008296 GO:0008853 GO:0016787 GO:0042803 GO:0046872 GO:0090305
130.060.4554.780.070.742bklB GO:0004252 GO:0006508 GO:0008236 GO:0070008
140.060.2725.370.060.444gxzA GO:0005623 GO:0015035 GO:0045454 GO:0055114
150.060.2734.020.010.392ktbB GO:0000228 GO:0003677 GO:0003682 GO:0005634 GO:0005654 GO:0006338 GO:0006351 GO:0006355 GO:0007067 GO:0008285 GO:0016568 GO:0090544
160.060.3175.370.050.533iypB GO:0000166 GO:0001172 GO:0003723 GO:0003724 GO:0003968 GO:0004197 GO:0004386 GO:0005198 GO:0005216 GO:0005524 GO:0006351 GO:0006508 GO:0006810 GO:0006811 GO:0008233 GO:0008234 GO:0016020 GO:0016032 GO:0016740 GO:0016779 GO:0016787 GO:0017111 GO:0018144 GO:0019012 GO:0019028 GO:0019062 GO:0030430 GO:0033644 GO:0034220 GO:0039694 GO:0039707 GO:0044161 GO:0044162 GO:0044385 GO:0046718 GO:0051259
170.060.2484.610.020.383idoA GO:0004725 GO:0006470 GO:0035335
180.060.2543.470.060.341qsdA GO:0005737 GO:0005856 GO:0005874 GO:0007021 GO:0007023 GO:0015631 GO:0048487


Consensus prediction of GO terms
 
Molecular Function GO:0003723
GO-Score 0.57
Biological Processes GO:0034248 GO:2000112 GO:0032268 GO:0016458 GO:0010608 GO:0006366 GO:0098787 GO:0045927 GO:0000956 GO:0006413 GO:0006354 GO:0001558 GO:0009301 GO:0050685 GO:0071427 GO:0031440 GO:0006405 GO:0006378 GO:0007169 GO:0000377 GO:0009452 GO:0006353 GO:0044344
GO-Score 0.57 0.57 0.57 0.57 0.57 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44
Cellular Component GO:0044444 GO:1990904 GO:0034518 GO:0031981
GO-Score 0.57 0.44 0.44 0.44

(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.