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I-TASSER results for job id Rv2283

[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
10.11 6 1ea0A F3S Rep, Mult 5,6,7,8,9,10,11,12,17,18
20.08 5 4u4mC URE Rep, Mult 27,30
30.07 4 3du4A PLP Rep, Mult 56,58
40.05 3 2z6iB CA Rep, Mult 33,36
50.05 3 1gahA MAN Rep, Mult 49,51,52
60.03 2 4d2bA 78N Rep, Mult 41,44
70.03 2 4bjwB I3C Rep, Mult 26,27
80.02 1 2wpdF ATP Rep, Mult 52,59
90.02 1 2pywB EDO Rep, Mult 33,37,41,52
100.02 1 2gbxA FES Rep, Mult 12,16,17,59,60,62
110.02 1 1uwcA FER Rep, Mult 24,29
120.02 1 4y283 CLA Rep, Mult 29,32
130.02 1 3bbxL MG Rep, Mult 58,60

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
10.0602excX0.4523.260.0560.8122.7.11.24,2.7.1.3734
20.0601yqjA0.4493.580.0180.8282.7.11.24,2.7.1.3734
30.0602z02B0.4583.280.0530.8286.3.2.642,51,53
40.0602esmA0.4613.230.0520.8122.7.11.138
50.0602h96A0.4563.180.0570.7972.7.11.24NA
60.0601o0sA0.4553.330.0360.8121.1.1.38NA
70.0602w4oA0.4583.460.0360.8122.7.11.17NA
80.0602ozoA0.4653.330.0860.8442.7.10.2NA
90.0602vdcA0.4613.910.0660.8911.4.1.13NA
100.0601jegA0.2593.800.0450.5312.7.10.220
110.0601fvrB0.4693.450.0710.8442.7.10.123,25,29
120.0602wb8A0.4763.560.0680.8442.7.11.113,21
130.0603d7uA0.4063.610.0710.8122.7.10.227
140.0603itzA0.4613.510.0180.8282.7.11.244
150.0602z7rA0.4353.840.0000.7972.7.11.1NA
160.0603g51A0.4533.430.0180.8122.7.11.1NA
170.0603h9fA0.4603.260.0560.8122.7.12.133,59
180.0601ea0A0.4613.910.0660.8911.4.1.13NA
190.0602evaA0.4683.710.0540.8592.7.11.2538,40

(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
00.080.3584.160.020.751eg9A GO:0005506 GO:0006725 GO:0016491 GO:0016705 GO:0016708 GO:0018625 GO:0019439 GO:0046872 GO:0051213 GO:0051536 GO:0051537 GO:0055114
10.070.3634.550.030.772b1xA GO:0005506 GO:0006725 GO:0016491 GO:0016705 GO:0016708 GO:0019439 GO:0046872 GO:0051213 GO:0051536 GO:0051537 GO:0055114
20.070.4903.090.080.804o6bB GO:0000166 GO:0001172 GO:0003723 GO:0003724 GO:0003725 GO:0003824 GO:0003968 GO:0004252 GO:0004386 GO:0004482 GO:0004483 GO:0005198 GO:0005524 GO:0005576 GO:0006351 GO:0006355 GO:0006370 GO:0006397 GO:0006508 GO:0008026 GO:0008152 GO:0008168 GO:0008233 GO:0008236 GO:0016020 GO:0016021 GO:0016032 GO:0016070 GO:0016740 GO:0016779 GO:0016787 GO:0016817 GO:0017111 GO:0019012 GO:0019028 GO:0019031 GO:0019058 GO:0019062 GO:0019079 GO:0030683 GO:0032259 GO:0033644 GO:0036265 GO:0039502 GO:0039503 GO:0039520 GO:0039564 GO:0039574 GO:0039654 GO:0039663 GO:0039694 GO:0042025 GO:0044165 GO:0044167 GO:0046718 GO:0046872 GO:0046983 GO:0055036 GO:0070008 GO:0075509 GO:0075512 GO:0080009
30.070.4952.960.070.804tplB GO:0000166 GO:0001172 GO:0003723 GO:0003724 GO:0003725 GO:0003968 GO:0004252 GO:0004386 GO:0004482 GO:0004483 GO:0005198 GO:0005524 GO:0006370 GO:0006508 GO:0008026 GO:0008168 GO:0008233 GO:0008236 GO:0016020 GO:0016021 GO:0016032 GO:0016070 GO:0016740 GO:0016779 GO:0016787 GO:0016817 GO:0017111 GO:0019012 GO:0019028 GO:0019031 GO:0019058 GO:0019062 GO:0019079 GO:0032259 GO:0033644 GO:0036265 GO:0039520 GO:0039654 GO:0039663 GO:0039694 GO:0046718 GO:0046983 GO:0055036 GO:0070008 GO:0080009
40.060.3434.110.060.735iy3A GO:0000166 GO:0001172 GO:0003723 GO:0003724 GO:0003725 GO:0003968 GO:0004252 GO:0004386 GO:0004482 GO:0004483 GO:0005198 GO:0005524 GO:0006370 GO:0006508 GO:0008026 GO:0008168 GO:0008233 GO:0008236 GO:0016020 GO:0016021 GO:0016032 GO:0016070 GO:0016740 GO:0016779 GO:0016787 GO:0016817 GO:0017111 GO:0019012 GO:0019028 GO:0019031 GO:0019058 GO:0019062 GO:0019079 GO:0032259 GO:0033644 GO:0036265 GO:0039520 GO:0039654 GO:0039663 GO:0039694 GO:0046718 GO:0046983 GO:0055036 GO:0070008 GO:0080009
50.060.3494.440.040.801wqlA GO:0005506 GO:0006725 GO:0016491 GO:0016705 GO:0016708 GO:0019439 GO:0046872 GO:0051213 GO:0051536 GO:0051537 GO:0055114
60.060.4024.480.020.912jopA GO:0004872 GO:0004888 GO:0005044 GO:0005886 GO:0005887 GO:0006898 GO:0008037 GO:0008283 GO:0009897 GO:0016020 GO:0016021 GO:0031295 GO:0097190
70.060.3664.130.070.723n0qA GO:0005506 GO:0006725 GO:0016491 GO:0016705 GO:0016708 GO:0019439 GO:0046872 GO:0051536 GO:0051537 GO:0055114
80.060.3374.370.040.805aeuA GO:0005506 GO:0006725 GO:0016491 GO:0016705 GO:0016708 GO:0018687 GO:0019439 GO:0046872 GO:0051213 GO:0051536 GO:0051537 GO:0055114
90.060.4893.430.020.802gbwA GO:0005506 GO:0006725 GO:0016491 GO:0016705 GO:0016708 GO:0019439 GO:0046872 GO:0051213 GO:0051536 GO:0051537 GO:0055114
100.060.5033.730.000.832ckfE GO:0005506 GO:0006725 GO:0016491 GO:0016705 GO:0016708 GO:0019439 GO:0046872 GO:0051213 GO:0051536 GO:0051537 GO:0055114
110.060.3383.200.020.594qurA GO:0005506 GO:0006725 GO:0016491 GO:0016705 GO:0016708 GO:0019439 GO:0046872 GO:0051213 GO:0051536 GO:0051537 GO:0055114
120.060.3633.930.020.733en1A GO:0005506 GO:0006725 GO:0016491 GO:0016705 GO:0016708 GO:0018619 GO:0018624 GO:0019439 GO:0042184 GO:0042203 GO:0046872 GO:0051213 GO:0051536 GO:0051537 GO:0055114
130.060.3554.270.090.721f37B GO:0003954 GO:0009060 GO:0010181 GO:0046872 GO:0051287 GO:0051536 GO:0051537 GO:0051539 GO:0055114
140.060.4023.760.070.752bmoA GO:0005506 GO:0006725 GO:0016491 GO:0016705 GO:0016708 GO:0019439 GO:0046872 GO:0051536 GO:0051537 GO:0055114
150.060.3783.760.030.733iqtA GO:0000155 GO:0000160 GO:0000166 GO:0004673 GO:0004871 GO:0005524 GO:0005622 GO:0005886 GO:0006351 GO:0006355 GO:0007165 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0018106 GO:0023014
160.060.4263.830.020.801uliC GO:0005506 GO:0006725 GO:0016491 GO:0016705 GO:0016708 GO:0018687 GO:0019439 GO:0046872 GO:0051213 GO:0051536 GO:0051537 GO:0055114
170.060.3734.060.020.673gkqA GO:0016491 GO:0046872 GO:0051213 GO:0051536 GO:0051537 GO:0055114
180.060.3234.090.020.622zylA GO:0005506 GO:0006629 GO:0006694 GO:0006707 GO:0008198 GO:0008202 GO:0009405 GO:0016042 GO:0016491 GO:0036200 GO:0046872 GO:0047086 GO:0050292 GO:0051536 GO:0051537 GO:0055114 GO:0070207 GO:0070723


Consensus prediction of GO terms
 
Molecular Function GO:0043169 GO:0032550 GO:0042623 GO:0008170 GO:0035639 GO:0008171 GO:0008238 GO:0003723 GO:0008174 GO:0032559 GO:0017171 GO:0004175 GO:0070035 GO:0005515 GO:0034062
GO-Score 0.39 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37
Biological Processes GO:0006397 GO:0039703 GO:0010508 GO:0044033 GO:0019538 GO:0039519 GO:0016556 GO:0001510 GO:0009452 GO:0044800 GO:0030260 GO:0044650 GO:0097659
GO-Score 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37
Cellular Component GO:0033643 GO:0036338 GO:0044218
GO-Score 0.37 0.37 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.