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I-TASSER results for job id Rv2807

[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
10.30 22 3oybA ZZX Rep, Mult 147,208,210,235,237,238,244
20.12 10 3oyiA MN Rep, Mult 147,148,244,247
30.06 6 3os2A QNA Rep, Mult 237,244,245,248,251
40.05 6 3oydA QNA Rep, Mult 123,124,125,126,143,206,230,231,232,233,236,238,239,241,242,245,249,252,284,285
50.04 4 3os1A NUC Rep, Mult 147,150,151,208,209,210,211,235,244,251,379
60.03 3 4bacA MG Rep, Mult 147,208,213
70.02 2 4e7kA NUC Rep, Mult 147,208,209,211,235,244,379
80.02 2 1vseA EPE Rep, Mult 162,165,177,191
90.01 1 1a5wA Y3 Rep, Mult 143,145,206,241,242
100.01 1 1czb0 III Rep, Mult 189,192,195,196,199,200,221,225,267,270,273,274,278

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
10.0603f9kI0.3632.470.1030.3962.7.7.49147,175,208,247,249
20.0601k6yA0.3472.610.1080.3802.7.7.49147,172,175,208,227,229
30.0601c0mA0.4162.870.1150.4642.7.7.49208,210,230,241,244
40.0602hg4C0.3776.930.0560.6432.3.1.94252
50.0601bl3C0.3642.700.1270.4012.7.7.49142,177,197
60.0601zczB0.3596.640.0550.5833.5.4.10,2.1.2.3NA
70.0603l2rA0.7522.480.1470.8182.7.7.7,2.7.7.49,3.1.26.4177
80.0601br2A0.3096.870.0510.5233.6.1.32NA
90.0601ug9A0.3656.900.0470.6203.2.1.70244
100.0602qf7B0.3767.300.0290.6566.4.1.1NA
110.0603l4uA0.3496.990.0280.6043.2.1.20,3.2.1.3NA
120.0602vz9B0.3736.860.0420.6202.3.1.85NA
130.0601vsdA0.3362.300.1580.3622.7.7.49147,208,210
140.0603dy5A0.3466.970.0510.5891.13.11.40,4.2.1.92NA
150.0601eulA0.3087.100.0340.5313.6.3.8208
160.0601hn0A0.3506.970.0310.6024.2.2.20NA
170.0601iwaA0.3496.420.0340.5474.1.1.39170
180.0602vkzG0.3976.830.0570.6562.3.1.38,3.1.2.14212
190.0601ej6A0.3756.790.0580.6282.7.7.50NA

(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
00.270.7572.740.150.834bacA GO:0003676 GO:0003723 GO:0003824 GO:0003887 GO:0003964 GO:0004190 GO:0004518 GO:0004519 GO:0004523 GO:0006278 GO:0006310 GO:0006508 GO:0008152 GO:0008233 GO:0015074 GO:0016740 GO:0016779 GO:0016787 GO:0019012 GO:0030430 GO:0042025 GO:0046718 GO:0046872 GO:0071897 GO:0075713 GO:0075732 GO:0090305 GO:0090502
10.150.3553.000.120.401ex4A GO:0003676 GO:0003677 GO:0003723 GO:0003824 GO:0003887 GO:0003964 GO:0004190 GO:0004518 GO:0004519 GO:0004523 GO:0004533 GO:0005198 GO:0005576 GO:0005654 GO:0005829 GO:0005886 GO:0006278 GO:0006310 GO:0006508 GO:0008152 GO:0008233 GO:0008270 GO:0008289 GO:0008907 GO:0015074 GO:0016020 GO:0016032 GO:0016740 GO:0016779 GO:0016787 GO:0019012 GO:0019013 GO:0019028 GO:0019058 GO:0019061 GO:0019064 GO:0019068 GO:0019072 GO:0019076 GO:0020002 GO:0030260 GO:0030430 GO:0033644 GO:0039526 GO:0039651 GO:0039657 GO:0042025 GO:0042802 GO:0044174 GO:0046718 GO:0046872 GO:0051169 GO:0055036 GO:0072494 GO:0075713 GO:0075732 GO:0090305 GO:0090502 GO:0090503
20.130.3632.260.140.394pa1A GO:0003676 GO:0003677 GO:0003824 GO:0003964 GO:0004170 GO:0004190 GO:0004518 GO:0004519 GO:0004523 GO:0004533 GO:0006278 GO:0006310 GO:0006508 GO:0008152 GO:0008233 GO:0008270 GO:0009117 GO:0015074 GO:0016740 GO:0016779 GO:0016787 GO:0046080 GO:0046718 GO:0046872 GO:0075713 GO:0090305 GO:0090502 GO:0090503
30.130.4433.320.090.515ejkA GO:0003676 GO:0003677 GO:0003723 GO:0003824 GO:0003887 GO:0003964 GO:0004190 GO:0004518 GO:0004519 GO:0004523 GO:0005198 GO:0006278 GO:0006310 GO:0006508 GO:0008152 GO:0008233 GO:0008270 GO:0015074 GO:0016032 GO:0016740 GO:0016779 GO:0016787 GO:0019012 GO:0019013 GO:0019028 GO:0046718 GO:0046872 GO:0075713 GO:0090305 GO:0090502
40.120.4544.000.100.573jcaA GO:0003676 GO:0003677 GO:0003824 GO:0003887 GO:0003964 GO:0004518 GO:0004519 GO:0004523 GO:0006278 GO:0006310 GO:0008152 GO:0008270 GO:0015074 GO:0016740 GO:0016779 GO:0016787 GO:0046718 GO:0046872 GO:0075713 GO:0090305 GO:0090502
50.120.3492.480.110.381k6yB GO:0003676 GO:0003677 GO:0003723 GO:0003824 GO:0003887 GO:0003964 GO:0004190 GO:0004518 GO:0004519 GO:0004523 GO:0004533 GO:0005198 GO:0005546 GO:0006278 GO:0006310 GO:0006508 GO:0008152 GO:0008233 GO:0008270 GO:0008289 GO:0015074 GO:0016020 GO:0016032 GO:0016740 GO:0016779 GO:0016787 GO:0019012 GO:0019013 GO:0019028 GO:0019076 GO:0020002 GO:0030430 GO:0033644 GO:0039526 GO:0039651 GO:0039657 GO:0042025 GO:0042802 GO:0044174 GO:0046718 GO:0046872 GO:0055036 GO:0072494 GO:0075713 GO:0075732 GO:0090305 GO:0090502 GO:0090503
60.100.3552.800.150.393kkrA GO:0003676 GO:0003677 GO:0003723 GO:0003824 GO:0003887 GO:0003964 GO:0004190 GO:0004518 GO:0004519 GO:0004523 GO:0004533 GO:0006278 GO:0006310 GO:0006508 GO:0008152 GO:0008233 GO:0008270 GO:0015074 GO:0016032 GO:0016740 GO:0016779 GO:0016787 GO:0019012 GO:0019013 GO:0019028 GO:0019076 GO:0039660 GO:0046718 GO:0046872 GO:0075521 GO:0075606 GO:0075713 GO:0090305 GO:0090502 GO:0090503
70.070.3632.600.120.401bi4C GO:0003676 GO:0003677 GO:0003723 GO:0003824 GO:0003887 GO:0003964 GO:0004190 GO:0004518 GO:0004519 GO:0004523 GO:0004533 GO:0005198 GO:0005546 GO:0006278 GO:0006310 GO:0006508 GO:0008152 GO:0008233 GO:0008270 GO:0008289 GO:0015074 GO:0016020 GO:0016032 GO:0016740 GO:0016779 GO:0016787 GO:0019012 GO:0019013 GO:0019028 GO:0019076 GO:0020002 GO:0030430 GO:0033644 GO:0039526 GO:0039651 GO:0039657 GO:0042025 GO:0042802 GO:0044174 GO:0046718 GO:0046872 GO:0055036 GO:0072494 GO:0075713 GO:0075732 GO:0090305 GO:0090502 GO:0090503
80.060.3773.100.100.433hpgB GO:0003676 GO:0003677 GO:0003824 GO:0003964 GO:0004170 GO:0004190 GO:0004518 GO:0004519 GO:0004523 GO:0004533 GO:0006278 GO:0006310 GO:0006508 GO:0008152 GO:0008233 GO:0008270 GO:0009117 GO:0015074 GO:0016740 GO:0016779 GO:0016787 GO:0046080 GO:0046718 GO:0046872 GO:0075713 GO:0090305 GO:0090502 GO:0090503
90.060.3476.350.050.541rblA GO:0000287 GO:0004497 GO:0009853 GO:0015977 GO:0015979 GO:0016491 GO:0016829 GO:0016984 GO:0019253 GO:0046872 GO:0055114
100.060.3632.470.100.403f9kA GO:0003676 GO:0003677 GO:0003723 GO:0003824 GO:0003887 GO:0003964 GO:0004190 GO:0004518 GO:0004519 GO:0004523 GO:0004533 GO:0005198 GO:0006278 GO:0006310 GO:0006508 GO:0008152 GO:0008233 GO:0008270 GO:0008289 GO:0015074 GO:0016020 GO:0016032 GO:0016740 GO:0016779 GO:0016787 GO:0019012 GO:0019013 GO:0019028 GO:0019076 GO:0020002 GO:0030430 GO:0033644 GO:0039657 GO:0042025 GO:0044174 GO:0046718 GO:0046872 GO:0055036 GO:0072494 GO:0075713 GO:0075732 GO:0090305 GO:0090502 GO:0090503
110.060.3422.720.120.381c6vA GO:0003676 GO:0003677 GO:0003723 GO:0003824 GO:0003887 GO:0003964 GO:0004190 GO:0004518 GO:0004519 GO:0004523 GO:0004533 GO:0005198 GO:0006278 GO:0006310 GO:0006508 GO:0008152 GO:0008233 GO:0008270 GO:0015074 GO:0016020 GO:0016032 GO:0016740 GO:0016779 GO:0016787 GO:0019012 GO:0019013 GO:0019028 GO:0019076 GO:0020002 GO:0030430 GO:0033644 GO:0039657 GO:0042025 GO:0046718 GO:0046872 GO:0075713 GO:0075732 GO:0090305 GO:0090502 GO:0090503
120.060.2811.940.110.305cz2F GO:0003676 GO:0003677 GO:0003824 GO:0003887 GO:0003964 GO:0004518 GO:0004519 GO:0004523 GO:0006278 GO:0006310 GO:0008152 GO:0008270 GO:0015074 GO:0016740 GO:0016779 GO:0016787 GO:0046718 GO:0046872 GO:0075713 GO:0090305 GO:0090502
130.060.2235.720.030.334pfxA GO:0000166 GO:0016740
140.060.2696.630.030.443ctzA GO:0004177 GO:0005737 GO:0006508 GO:0008233 GO:0008237 GO:0010815 GO:0016787 GO:0030145 GO:0042803 GO:0046872 GO:0070006 GO:0070062
150.060.1704.790.070.232anvA GO:0003796 GO:0003824 GO:0008152 GO:0009253 GO:0016787 GO:0016798 GO:0016998 GO:0019076 GO:0019835 GO:0030430 GO:0042742
160.060.1795.860.050.281ckvA GO:0004497 GO:0006725 GO:0015049 GO:0015050 GO:0015947 GO:0016491 GO:0055114
170.060.1275.340.020.181gxeA GO:0001671 GO:0003007 GO:0003779 GO:0005829 GO:0005863 GO:0006942 GO:0007155 GO:0008307 GO:0014705 GO:0017022 GO:0030017 GO:0030049 GO:0031432 GO:0031672 GO:0032036 GO:0032781 GO:0032971 GO:0032982 GO:0042802 GO:0046872 GO:0055010 GO:0060048
180.060.1142.940.020.131wjbA GO:0003676 GO:0003677 GO:0003723 GO:0003824 GO:0003887 GO:0003964 GO:0004190 GO:0004518 GO:0004519 GO:0004523 GO:0004533 GO:0005198 GO:0005546 GO:0006278 GO:0006310 GO:0006508 GO:0008152 GO:0008233 GO:0008270 GO:0008289 GO:0015074 GO:0016020 GO:0016032 GO:0016740 GO:0016779 GO:0016787 GO:0019012 GO:0019013 GO:0019028 GO:0019076 GO:0020002 GO:0030430 GO:0033644 GO:0039526 GO:0039651 GO:0039657 GO:0042025 GO:0042802 GO:0044174 GO:0046718 GO:0046872 GO:0055036 GO:0072494 GO:0075713 GO:0075732 GO:0090305 GO:0090502 GO:0090503


Consensus prediction of GO terms
 
Molecular Function GO:0004523 GO:0003964 GO:0004190 GO:0016896 GO:0003887 GO:0003723 GO:0003677 GO:0008270 GO:0005515
GO-Score 0.59 0.59 0.53 0.53 0.53 0.46 0.43 0.43 0.30
Biological Processes GO:0006278 GO:0015074 GO:0006310 GO:0075713 GO:0090502 GO:0075732 GO:0039656 GO:0039712 GO:0043280 GO:0019051 GO:0022607 GO:0039663 GO:0010629
GO-Score 0.59 0.59 0.59 0.59 0.59 0.38 0.30 0.30 0.30 0.30 0.30 0.30 0.30
Cellular Component GO:0019028 GO:0042025 GO:0044444 GO:0044184 GO:0071944 GO:0031981 GO:0044218
GO-Score 0.52 0.38 0.30 0.30 0.30 0.30 0.30

(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.