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I-TASSER results for job id Rv0040c

[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
10.04 2 3fyeC UNX Rep, Mult 109,110,186,188
20.04 2 3v5mA MA4 Rep, Mult 20,228,265
30.04 2 3dtuC DXC Rep, Mult 178,181,182,185,233
40.04 2 3dtuC DMU Rep, Mult 259,262,263,266
50.02 1 2yl8A MN Rep, Mult 145,178
60.02 1 4oxnB 2NV Rep, Mult 121,271
70.02 1 2odjA C8E Rep, Mult 209,234
80.02 1 1v2bA GLC Rep, Mult 138,139,155,253,260
90.02 1 2gjmA UUU Rep, Mult 200,202
100.02 1 3bjeA R1P Rep, Mult 185,229
110.02 1 4h13A 8K6 Rep, Mult 13,287
120.02 1 2qtkB C8E Rep, Mult 213,245,246
130.02 1 3mjlA 2AI Rep, Mult 185,189,208,303
140.02 1 1nqgA C8E Rep, Mult 213,232,243,245
150.02 1 2vn4A MAN Rep, Mult 103,104
160.02 1 3f7oA HMB Rep, Mult 216,218
170.02 1 1gfmA C8E Rep, Mult 151,168,245
180.02 1 3gyyA ZN Rep, Mult 137,257
190.02 1 3v65C CA Rep, Mult 193,238
200.02 1 3dtuA TRD Rep, Mult 184,187,191

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
10.0603n58A0.3776.200.0460.6163.3.1.1148
20.0603fsnB0.3556.650.0390.6235.2.1.7211,214,245
30.0602vn4A0.3576.240.0300.5943.2.1.3NA
40.0603h9uC0.3716.310.0050.6163.3.1.1NA
50.0603bjuA0.3626.560.0550.6196.1.1.6NA
60.0601v8bA0.3786.190.0550.6163.3.1.1NA
70.0601a7aA0.3696.380.0320.6163.3.1.1NA
80.0603a2pA0.3626.190.0580.5903.5.2.12NA
90.0603lssB0.3695.920.0260.5816.1.1.11NA
100.0602dkiA0.3885.980.0500.6131.14.13.23NA
110.0601fftA0.3656.700.0610.6191.10.3.-NA
120.0603h0lA0.3596.130.0620.5816.3.5.-211
130.0602dq3A0.3576.040.0500.5816.1.1.11NA
140.0601m56A0.3866.470.0600.6451.9.3.1192
150.0601v8bC0.3796.200.0460.6163.3.1.1NA
160.0603d64B0.3156.260.0660.5133.3.1.1148
170.0601gz3A0.3416.530.0320.5711.1.1.38NA
180.0602ow6A0.4055.970.0470.6323.2.1.114189
190.0601peuA0.3686.350.0330.6101.17.4.1NA

(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
00.540.5331.790.970.574ol4A GO:0005576
10.060.3136.650.050.533bubA GO:0000139 GO:0003824 GO:0004553 GO:0004559 GO:0004572 GO:0005783 GO:0005794 GO:0005795 GO:0005975 GO:0006013 GO:0006486 GO:0006487 GO:0006491 GO:0006517 GO:0008152 GO:0008270 GO:0015923 GO:0016020 GO:0016021 GO:0016063 GO:0016787 GO:0016798 GO:0030246 GO:0035010 GO:0046872
20.060.3786.230.060.624av6A GO:0000287 GO:0004427 GO:0005509 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006814 GO:0009678 GO:0015081 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0030955 GO:0035725 GO:0042803 GO:0046872
30.060.3826.510.060.654av3B GO:0000287 GO:0004427 GO:0005509 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006814 GO:0009678 GO:0015081 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0030955 GO:0035725 GO:0042803 GO:0046872
40.060.3935.820.060.624a01A GO:0004427 GO:0005773 GO:0005774 GO:0006810 GO:0006811 GO:0009678 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0046872 GO:0055085
50.060.3846.160.020.615jm0A GO:0000329 GO:0003824 GO:0004553 GO:0004559 GO:0005773 GO:0005975 GO:0006013 GO:0006517 GO:0008152 GO:0008270 GO:0009313 GO:0015923 GO:0016787 GO:0016798 GO:0030246 GO:0044262 GO:0046872
60.060.2915.600.060.451o7dD GO:0003824 GO:0004553 GO:0004559 GO:0005764 GO:0005975 GO:0006013 GO:0006517 GO:0007611 GO:0008152 GO:0008270 GO:0015923 GO:0016787 GO:0016798 GO:0030246 GO:0046872
70.060.2846.400.040.485bofA GO:0000015 GO:0000287 GO:0004634 GO:0005576 GO:0005737 GO:0006096 GO:0009405 GO:0009986 GO:0016829 GO:0046872
80.060.3156.770.020.553zlfA GO:0000015 GO:0000287 GO:0004634 GO:0005576 GO:0005737 GO:0006096 GO:0009405 GO:0009986 GO:0016829 GO:0046872
90.060.2936.010.050.474y25A GO:0006810 GO:0009279 GO:0016020 GO:0016021 GO:0022891 GO:0044010 GO:0055085
100.060.2896.590.060.502ybaB GO:0000122 GO:0000281 GO:0003682 GO:0005634 GO:0005667 GO:0005700 GO:0006281 GO:0006334 GO:0006335 GO:0006342 GO:0006351 GO:0006355 GO:0007307 GO:0007346 GO:0007379 GO:0007517 GO:0008284 GO:0016568 GO:0016571 GO:0016573 GO:0016581 GO:0016584 GO:0016589 GO:0016590 GO:0031491 GO:0031497 GO:0031523 GO:0033186 GO:0035035 GO:0035097 GO:0035098 GO:0042054 GO:0042393 GO:0042766 GO:0042803 GO:0042826 GO:0046974 GO:0046976 GO:0048666 GO:0048812 GO:0048813 GO:0051567 GO:0061085 GO:0070615 GO:0070734 GO:0070822
110.060.2896.370.030.493k5pA GO:0004617 GO:0006564 GO:0008152 GO:0016491 GO:0016597 GO:0016616 GO:0051287 GO:0055114
120.060.2895.750.040.443rd7B GO:0006637 GO:0047617
130.060.2206.270.040.371mzvA GO:0000166 GO:0003999 GO:0009116 GO:0016740 GO:0016757
140.060.2787.090.050.521opeA GO:0005739 GO:0008152 GO:0008260 GO:0008410 GO:0016740 GO:0042803 GO:0046950 GO:0046952
150.060.2587.010.030.473cg1A GO:0005886 GO:0006810 GO:0016020 GO:0046872 GO:1901359
160.060.2416.760.030.431o7dA GO:0003824 GO:0004553 GO:0004559 GO:0005764 GO:0005975 GO:0006013 GO:0006517 GO:0007611 GO:0008152 GO:0008270 GO:0015923 GO:0016787 GO:0016798 GO:0030246 GO:0046872
170.060.2315.980.030.381un2A GO:0003756 GO:0015035 GO:0030288 GO:0042597 GO:0045454 GO:0055114 GO:0071236
180.060.2386.820.040.423om8B GO:0016787 GO:0042952 GO:0047570


Consensus prediction of GO terms
 
Molecular Function GO:0043169 GO:0015405 GO:0016462
GO-Score 0.47 0.36 0.36
Biological Processes GO:0015672 GO:0006818
GO-Score 0.36 0.36
Cellular Component GO:0005576 GO:0031224
GO-Score 0.54 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.