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I-TASSER results for job id Rv1993c

[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 11 3mjwA WYF Rep, Mult 44,46,54,65
20.07 6 3fggB ZN Rep, Mult 67,71
30.04 3 3pg9A AZI Rep, Mult 37,71
40.03 3 3q43A D66 Rep, Mult 44,45,64,67,68,71,72,75
50.03 3 2chwA 039 Rep, Mult 45,46,49,54,55
60.03 3 3tl5A 980 Rep, Mult 20,23,27,30
70.02 2 1a0aA NUC Rep, Mult 52,59,62
80.02 2 1e8wA QUE Rep, Mult 72,73,76,77
90.02 2 3l08A ZIG Rep, Mult 48,54,70,71,72
100.01 1 3q44A D50 Rep, Mult 38,41,45,46,49
110.01 1 3t8mA 3T8 Rep, Mult 14,25,65,70
120.01 1 1e7uA KWT Rep, Mult 33,35,37,41,76,77
130.01 1 3nzuA NZU Rep, Mult 8,24,52,56,66
140.01 1 3dbsA GD9 Rep, Mult 20,23,30,43,49
150.01 1 3dpdA 41A Rep, Mult 24,56,66
160.01 1 1e7vA LY2 Rep, Mult 64,68,69
170.01 1 3csfA DW2 Rep, Mult 9,10,11,15,16
180.01 1 3atsA CA Rep, Mult 77,79

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
10.0602x6fA0.5733.340.0710.8892.7.1.137,2.7.1.153,2.7.1.15420,31
20.0601fmiA0.5613.520.0360.8893.2.1.113NA
30.0601f1sA0.5743.590.0580.9224.2.2.1NA
40.0602vn4A0.5493.530.0600.9113.2.1.3NA
50.0601h12A0.5533.860.0710.9333.2.1.8NA
60.0601is9A0.5533.390.0370.8893.2.1.4NA
70.0601ujkB0.4923.610.0760.8003.4.23.466
80.0602j2fA0.5493.530.0470.8671.14.19.2,1.14.99.667
90.0601lwtA0.5663.290.0840.8673.6.3.14NA
100.0601cb8A0.5593.670.0720.9114.2.2.573
110.0603d9dA0.5383.680.1570.8781.7.3.1NA
120.0602rd0A0.5863.180.0490.9002.7.1.153NA
130.0601i8qA0.5783.550.0600.9114.2.2.110
140.0603ismC0.5603.420.0800.9113.6.1.312,52
150.0603dpyA0.5332.810.0380.7562.5.1.58,2.5.1.5924
160.0602vtbA0.5593.460.0820.8674.1.99.3NA
170.0601dfaA0.5683.290.0710.8783.6.3.14,3.6.1.34NA
180.0601s5jA0.5523.960.0340.9332.7.7.7NA
190.0601fo2A0.5603.680.0360.9003.2.1.113NA

(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
00.090.6443.220.030.964pjwA GO:0000775 GO:0000785 GO:0005634 GO:0005654 GO:0005694 GO:0005730 GO:0005829 GO:0005886 GO:0007049 GO:0007059 GO:0007062 GO:0007067 GO:0015629 GO:0016020 GO:0016925 GO:0032876 GO:0045111 GO:0051301 GO:0051321
10.090.6093.160.150.934kf7A GO:0005643 GO:0006406 GO:0006606 GO:0006999 GO:0017056 GO:0031990 GO:0044611
20.070.6332.810.100.904d10D GO:0000338 GO:0000715 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0006283 GO:0008021 GO:0008180 GO:0010388 GO:0019784 GO:0030054 GO:0031410 GO:0045202 GO:0070062
30.070.5663.220.090.883jcoP GO:0000502 GO:0006511 GO:0008180 GO:0008541 GO:0010388 GO:0031595 GO:0034515 GO:0043161
40.070.5922.730.040.833txmA GO:0000502 GO:0005838 GO:0005875 GO:0008541 GO:0043161
50.070.6582.890.120.934cemB GO:0000184 GO:0001889 GO:0003723 GO:0005634 GO:0005737 GO:0005829 GO:0006406 GO:0031100 GO:0035145 GO:0042162 GO:0048471
60.070.5643.610.090.934cekA GO:0000184 GO:0001889 GO:0003723 GO:0005634 GO:0005737 GO:0005829 GO:0006406 GO:0031100 GO:0035145 GO:0042162 GO:0048471
70.070.5693.550.100.885a9qA GO:0000972 GO:0005215 GO:0005634 GO:0005635 GO:0005643 GO:0006405 GO:0006406 GO:0006409 GO:0006606 GO:0006810 GO:0006913 GO:0006998 GO:0007077 GO:0010827 GO:0015031 GO:0016020 GO:0016032 GO:0016925 GO:0017056 GO:0019083 GO:0031047 GO:0031965 GO:0036228 GO:0044611 GO:0051028 GO:0075733 GO:0086014 GO:1900034
80.070.5223.820.090.894lunU GO:0000184 GO:0003723 GO:0005737 GO:0005844 GO:0006310 GO:0006452 GO:0070478
90.070.5013.610.100.834f5xB GO:0003723 GO:0019013
100.070.6233.120.080.875haxA GO:0005634 GO:0005643 GO:0006810 GO:0006913 GO:0015031 GO:0016020 GO:0017056 GO:0031965 GO:0051028
110.070.5333.530.110.914uvkA GO:0000755 GO:0003682 GO:0005634 GO:0005829 GO:0006473 GO:0007064 GO:0009847 GO:0031505 GO:0031618 GO:0031934 GO:0034990 GO:1990707
120.070.4763.890.100.844d10C GO:0000715 GO:0001701 GO:0005634 GO:0005654 GO:0005737 GO:0006283 GO:0006511 GO:0007165 GO:0008180 GO:0009416 GO:0010388
130.070.6343.030.080.885hb1A GO:0005634 GO:0005643 GO:0006810 GO:0006913 GO:0015031 GO:0016020 GO:0017056 GO:0031965 GO:0051028
140.070.4044.620.060.794ghnA GO:0006508 GO:0008236 GO:0016020 GO:0016021
150.060.4283.980.130.734ijcA GO:0005737 GO:0005829 GO:0016491 GO:0044262 GO:0045290 GO:0055114
160.060.4353.880.040.742kwiA GO:0000145 GO:0000166 GO:0000910 GO:0001928 GO:0001934 GO:0003924 GO:0005525 GO:0005622 GO:0005776 GO:0005886 GO:0006915 GO:0007049 GO:0007165 GO:0007264 GO:0007265 GO:0009267 GO:0016020 GO:0019003 GO:0030496 GO:0031625 GO:0032091 GO:0032092 GO:0051117 GO:0051301 GO:0060178 GO:0070062 GO:0071360 GO:0071902 GO:2000786
170.060.4784.070.060.865aijA GO:0016787 GO:0042802 GO:0046872 GO:0046983
180.060.4143.990.030.721nikA GO:0001055 GO:0001172 GO:0003677 GO:0003899 GO:0003968 GO:0005634 GO:0005665 GO:0006351 GO:0006366 GO:0016740 GO:0016779 GO:0019985 GO:0043566 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0017056 GO:0019784
GO-Score 0.09 0.07
Biological Processes GO:0010388 GO:0043161 GO:0032876 GO:0051321 GO:0007067 GO:0016925 GO:0007062 GO:0051301 GO:0006606 GO:0031990 GO:0006999 GO:0006283 GO:0000715
GO-Score 0.13 0.13 0.09 0.09 0.09 0.09 0.09 0.09 0.09 0.09 0.09 0.07 0.07
Cellular Component GO:0005654 GO:0008180 GO:0008541 GO:0000785 GO:0005886 GO:0015629 GO:0005730 GO:0045111 GO:0000775 GO:0044611 GO:0008021 GO:0070062 GO:0030054 GO:0031595 GO:0005875 GO:0034515
GO-Score 0.15 0.13 0.13 0.09 0.09 0.09 0.09 0.09 0.09 0.09 0.07 0.07 0.07 0.07 0.07 0.07

(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.