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I-TASSER results for job id Rv3860

[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
10.44 67 1xd9B ADP Rep, Mult 142,144,145,146,147,148,149,312,340,341,342,343,346,366
20.06 11 1xcpB SF4 Rep, Mult 287,288,327,329,330
30.05 7 3la6D CA Rep, Mult 148,173,254
40.04 6 2ynmA ADP Rep, Mult 142,281,283
50.02 3 1m34E ALF Rep, Mult 143,144,147,177,256,257
60.01 1 3ez2A ADP Rep, Mult 152,155,156,168,351
70.01 1 3r9iB III Rep, Mult 181,186,347,348,349,350

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
10.3261cp2A0.5203.660.1490.6211.18.6.1142,147
20.0602z8yD0.3896.470.0680.6131.2.7.4,1.2.99.2289,309
30.0601cp2B0.5203.690.1490.6211.18.6.1143,288
40.0601a82A0.4203.590.1240.5006.3.3.3147
50.0601vcmA0.4184.570.1020.5316.3.4.2194,256
60.0602c4mC0.4255.820.0620.6212.4.1.1142,147
70.0602g3mF0.4036.330.0610.6313.2.1.20NA
80.0601k4yA0.4016.270.0830.6153.1.1.1NA
90.0601mx9D0.4045.810.0520.5903.1.1.1NA
100.0601de0A0.5233.610.1520.6231.18.6.1142,147
110.0602ad5B0.4214.500.0890.5316.3.4.2NA
120.0602jkpB0.4076.270.0440.6383.2.1.20NA
130.0601ofdA0.4186.330.0400.6461.4.7.1NA
140.0601ygpA0.4166.180.0710.6232.4.1.1NA
150.0601ii0B0.4364.800.1280.5543.6.3.16144,147
160.0603bq5A0.3917.100.0470.6722.1.1.14NA
170.0601ua4A0.4125.790.0580.6032.7.1.147NA
180.0601vcnA0.4184.380.1130.5266.3.4.2NA
190.0601bxrA0.4026.010.0470.6036.3.5.5154
200.0601e1yA0.4346.250.0440.6592.4.1.1NA

(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
00.360.4133.790.100.493la6B GO:0000166 GO:0000271 GO:0004713 GO:0005524 GO:0005886 GO:0005887 GO:0009103 GO:0009242 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0016887 GO:0018108 GO:0038083 GO:0045226
10.310.5763.810.140.693ez2B GO:0030541 GO:0042802
20.310.4743.750.150.573kb1A GO:0000166 GO:0005524 GO:0016787 GO:0016887 GO:0046872 GO:0051536
30.310.5272.780.160.593q9lA GO:0000166 GO:0005524 GO:0005829 GO:0005886 GO:0007049 GO:0007059 GO:0009898 GO:0016020 GO:0016887 GO:0031226 GO:0042802 GO:0051301 GO:0051782 GO:0060187
40.260.5262.670.160.591g3qA GO:0000166 GO:0005524 GO:0051301
50.250.5262.850.200.592bejA GO:0000166 GO:0003677 GO:0005524 GO:0007059 GO:0016787
60.240.5013.420.160.593kjeA GO:0000166 GO:0019415
70.180.5052.960.170.571hyqA GO:0000166 GO:0005524 GO:0051301
80.170.5243.580.150.622afhE GO:0000166 GO:0005524 GO:0009399 GO:0016163 GO:0016491 GO:0016612 GO:0018697 GO:0046872 GO:0051536 GO:0051539 GO:0055114
90.170.5153.000.140.584rz2A GO:0000166 GO:0005524
100.160.5102.500.180.564v02A GO:0000166 GO:0005524 GO:0016887
110.160.4663.580.160.562ph1A GO:0000166 GO:0005524 GO:0016787 GO:0016887 GO:0046872 GO:0051536
120.150.4873.220.180.563pg5C GO:0005524 GO:0016491 GO:0055114
130.120.4582.760.140.514dzzA GO:0000166
140.070.5203.660.150.621cp2A GO:0000166 GO:0005524 GO:0009399 GO:0016163 GO:0016491 GO:0016612 GO:0018697 GO:0046872 GO:0051536 GO:0051539 GO:0055114
150.070.5821.410.140.603ea0B GO:0000166 GO:0005524
160.070.5302.750.160.591ionA GO:0000166 GO:0005524 GO:0051301
170.060.3953.330.120.454jlvA GO:0000166 GO:0005576 GO:0006859 GO:0009103 GO:0015542 GO:0015992 GO:0016020 GO:0016021 GO:0045226
180.060.2617.290.020.464cblA GO:0000166 GO:0001172 GO:0003723 GO:0003968 GO:0004175 GO:0004197 GO:0004252 GO:0004386 GO:0005216 GO:0005524 GO:0006508 GO:0006810 GO:0006811 GO:0008026 GO:0008233 GO:0008234 GO:0008236 GO:0016020 GO:0016021 GO:0016032 GO:0016740 GO:0016779 GO:0016787 GO:0016817 GO:0017111 GO:0019012 GO:0019062 GO:0019079 GO:0019082 GO:0030430 GO:0030683 GO:0033644 GO:0033897 GO:0034220 GO:0039503 GO:0039520 GO:0039548 GO:0039654 GO:0039663 GO:0039694 GO:0039707 GO:0042025 GO:0044228 GO:0044385 GO:0046718 GO:0051259 GO:0055036 GO:0070008 GO:0090502 GO:1903608 GO:1990219
190.060.2586.270.050.414mzyA GO:0004514 GO:0004516 GO:0009435 GO:0016740 GO:0016757 GO:0016874 GO:0019358 GO:0019363
200.060.2563.310.110.301mvoA GO:0000160 GO:0003677 GO:0005737 GO:0006351 GO:0006355 GO:0006810 GO:0006817
210.060.2356.770.060.393j79F GO:0003735 GO:0005840 GO:0006412 GO:0022625
220.060.2396.610.090.383ezyA GO:0008152 GO:0016491 GO:0050112 GO:0055114
230.060.3206.840.080.534cmnA GO:0001701 GO:0001750 GO:0004439 GO:0005096 GO:0005634 GO:0005737 GO:0005768 GO:0005769 GO:0005794 GO:0005795 GO:0005798 GO:0005802 GO:0005829 GO:0005886 GO:0005905 GO:0005929 GO:0006629 GO:0006661 GO:0007165 GO:0016020 GO:0016023 GO:0016787 GO:0030030 GO:0030136 GO:0030670 GO:0031410 GO:0031901 GO:0042384 GO:0042995 GO:0043087 GO:0043547 GO:0043647 GO:0046856 GO:0048365 GO:0051056 GO:0052658 GO:0052659 GO:0052745 GO:0070062


Consensus prediction of GO terms
 
Molecular Function GO:0005524 GO:0016887 GO:0042802 GO:0004713 GO:0051536 GO:0046872
GO-Score 0.78 0.70 0.53 0.36 0.31 0.31
Biological Processes GO:0045226 GO:0038083 GO:0009103 GO:0009242 GO:0030541 GO:0007059 GO:0051782 GO:0007049
GO-Score 0.36 0.36 0.36 0.36 0.31 0.31 0.31 0.31
Cellular Component GO:0005887 GO:0005829 GO:0009898 GO:0060187
GO-Score 0.36 0.31 0.31 0.31

(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.