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I-TASSER results for job id Rv1476

[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
10.14 7 3ka4A CO Rep, Mult 111,114
20.06 3 5i50A NUC Rep, Mult 104,107
30.04 2 1qbgB FAD Rep, Mult 105,106
40.04 2 3fa4A MG Rep, Mult 20,22
50.02 1 1lg2A EDO Rep, Mult 126,129,147
60.02 1 3etdB B1T Rep, Mult 107,154
70.02 1 4ro2B GLY Rep, Mult 148,151
80.02 1 3w9fD I3P Rep, Mult 71,75,113,122,124,169
90.02 1 1q0kE THJ Rep, Mult 107,110
100.02 1 3zukA 211 Rep, Mult 166,167,180
110.02 1 3d5bF MG Rep, Mult 75,77,90
120.02 1 1h2u0 III Rep, Mult 49,55,56,94,95,97
130.02 1 1bagA CA Rep, Mult 56,58
140.02 1 3owaB FAD Rep, Mult 132,137,138,144,147

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
10.0661ujkB0.4544.020.0400.6563.4.23.46NA
20.0602bs9E0.5624.340.0750.8333.2.1.37NA
30.0602cygA0.5254.540.1070.7853.2.1.39NA
40.0602z1sA0.5284.670.0510.8123.2.1.21157
50.0601qoxA0.5234.450.0380.7903.2.1.21NA
60.0601gowA0.5424.360.0750.8013.2.1.23NA
70.0602cerA0.5364.390.0920.8063.2.1.2394
80.0601hkiA0.5334.310.0460.7803.2.1.1465
90.0601k6wA0.5254.320.0460.7803.5.4.119
100.0601w9pA0.5434.390.0770.7903.2.1.14NA
110.0601ps9A0.5304.860.0590.8281.3.1.34NA
120.0601b1yA0.5244.990.0360.8553.2.1.2NA
130.0601d2kA0.5394.350.0650.7853.2.1.1465
140.0601jqoA0.5294.810.0750.8284.1.1.31NA
150.0601itxA0.5314.530.0450.7903.2.1.1465
160.0603fxyA0.5354.290.0720.7803.2.1.1465
170.0602a3eA0.5394.310.0840.7853.2.1.1488
180.0602pe4A0.5334.860.0480.8603.2.1.35105
190.0601ra0A0.5234.350.0390.7853.5.4.1NA
200.0601ll6A0.5394.350.0650.7853.2.1.14121

(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
00.170.5723.360.100.771ug3A GO:0000184 GO:0000289 GO:0001662 GO:0003723 GO:0003743 GO:0005737 GO:0005829 GO:0005913 GO:0006412 GO:0006413 GO:0006417 GO:0006446 GO:0008135 GO:0008190 GO:0016020 GO:0016032 GO:0016281 GO:0043488 GO:0044822 GO:0045666 GO:0098609 GO:0098641
10.130.5072.920.020.652iosA GO:0003723 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0006915 GO:0007569 GO:0034393 GO:0043066 GO:0043508 GO:0045892 GO:0051246 GO:1904761
20.120.5893.740.060.823juiA GO:0001541 GO:0003743 GO:0005085 GO:0005634 GO:0005737 GO:0005829 GO:0005851 GO:0006412 GO:0006413 GO:0006417 GO:0007568 GO:0009408 GO:0009749 GO:0014002 GO:0014003 GO:0031369 GO:0032057 GO:0034976 GO:0035690 GO:0042552 GO:0043434 GO:0043547 GO:0045948 GO:0048708
30.120.5942.990.060.751paqA GO:0003743 GO:0005085 GO:0005851 GO:0006412 GO:0006413 GO:0006417 GO:0006446 GO:0009058 GO:0016779 GO:0032045 GO:0043547
40.100.5763.630.070.792iu1A GO:0000166 GO:0003743 GO:0003924 GO:0005525 GO:0005634 GO:0005737 GO:0005829 GO:0005886 GO:0005913 GO:0006412 GO:0006413 GO:0006446 GO:0008135 GO:0044822 GO:0098609 GO:0098641
50.100.5663.740.070.792fulE GO:0000166 GO:0001732 GO:0003743 GO:0005092 GO:0005096 GO:0005525 GO:0006412 GO:0006413 GO:0006446 GO:0022627 GO:0031369 GO:0033290 GO:0042256 GO:0043547 GO:0043614 GO:0045947 GO:0050790
60.080.5493.380.040.732zu6B GO:0003723 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0006915 GO:0007569 GO:0034393 GO:0043066 GO:0043508 GO:0045786 GO:0045892 GO:0051246 GO:1904761
70.070.5993.990.090.875fu7A 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
80.070.5823.650.080.802fulA GO:0000166 GO:0001732 GO:0003743 GO:0005092 GO:0005096 GO:0005525 GO:0006412 GO:0006413 GO:0006446 GO:0022627 GO:0031369 GO:0033290 GO:0042256 GO:0043547 GO:0043614 GO:0045947 GO:0050790
90.070.5803.470.090.783l6aA GO:0003723 GO:0003743 GO:0005829 GO:0005913 GO:0006412 GO:0006413 GO:0006417 GO:0006446 GO:0007050 GO:0008135 GO:0008219 GO:0016020 GO:0016281 GO:0044822 GO:0098609 GO:0098641
100.070.4904.880.070.771xdmB GO:0001889 GO:0003824 GO:0004332 GO:0005634 GO:0005737 GO:0005764 GO:0005815 GO:0005829 GO:0005856 GO:0005886 GO:0006000 GO:0006094 GO:0006096 GO:0006116 GO:0008092 GO:0009743 GO:0009750 GO:0010043 GO:0014070 GO:0016829 GO:0030388 GO:0030867 GO:0030868 GO:0031210 GO:0031668 GO:0032781 GO:0032869 GO:0034451 GO:0042493 GO:0042594 GO:0042802 GO:0043200 GO:0043231 GO:0043434 GO:0046688 GO:0048471 GO:0051117 GO:0051384 GO:0051591 GO:0061609 GO:0061621 GO:0061624 GO:0070061 GO:0070062 GO:0070072 GO:0070741
110.070.5074.690.040.804by6A GO:0046872
120.060.4024.750.050.631ujpA GO:0000162 GO:0003824 GO:0004834 GO:0006568 GO:0008152 GO:0008652 GO:0009073 GO:0016829
130.060.4014.570.090.614wjiA GO:0000166 GO:0004665 GO:0006571 GO:0008977 GO:0055114
140.060.4005.640.050.693wpnA 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
150.060.4384.900.110.721v4vA GO:0008761 GO:0016853
160.060.3195.320.030.544x0tA GO:0004029 GO:0004043 GO:0005634 GO:0005737 GO:0005739 GO:0005759 GO:0005829 GO:0006081 GO:0006554 GO:0007605 GO:0008152 GO:0008802 GO:0016491 GO:0016620 GO:0019285 GO:0042426 GO:0055114 GO:0070062
170.060.3356.290.050.651frvB GO:0008901 GO:0016151 GO:0016491 GO:0042597 GO:0046872 GO:0047806 GO:0055114
180.060.4404.540.050.672bklB GO:0004252 GO:0006508 GO:0008236 GO:0070008


Consensus prediction of GO terms
 
Molecular Function GO:0045296 GO:0098632 GO:0098772 GO:0003743 GO:0031369
GO-Score 0.51 0.51 0.46 0.43 0.34
Biological Processes GO:0007155 GO:0051345 GO:0043087 GO:0006446 GO:0050769 GO:0042596 GO:0002209 GO:0045664 GO:0044764 GO:0000288 GO:0044708 GO:0044403 GO:0043487
GO-Score 0.51 0.46 0.46 0.35 0.34 0.34 0.34 0.34 0.34 0.34 0.34 0.34 0.34
Cellular Component GO:0005911 GO:0005912 GO:0043234 GO:0005829 GO:0005634
GO-Score 0.51 0.51 0.46 0.43 0.32

(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.