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I-TASSER results for job id Rv1417

[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
10.04 2 4f4sN EFO Rep, Mult 58,59,62
20.04 2 5l1gB GYB Rep, Mult 28,29
30.04 2 1jh0L BPH Rep, Mult 22,25,26,30,57
40.04 2 3ar3A PTY Rep, Mult 102,141,145,148,149
50.04 2 3huxH MG Rep, Mult 36,129,130
60.04 2 2c88A NA Rep, Mult 61,62,63,64,65,86
70.04 2 1pt8A ACO Rep, Mult 105,106,126
80.02 1 1k77A MG Rep, Mult 128,129
90.02 1 3ar3A PTY Rep, Mult 61,64,68,72,121
100.02 1 3n92A BGC Rep, Mult 95,96,104,105
110.02 1 3wmnA MQ8 Rep, Mult 33,37
120.02 1 2agvA PTY Rep, Mult 61,132,136,139,140
130.02 1 2h9dD CA Rep, Mult 49,52
140.02 1 3akkA MG Rep, Mult 86,116
150.02 1 1vf5S III Rep, Mult 68,69
160.02 1 2eauA PTY Rep, Mult 139,143,147
170.02 1 4fnnA STE Rep, Mult 64,67
180.02 1 3wmoP BCL Rep, Mult 70,71
190.02 1 2gjpA GLC Rep, Mult 95,109
200.02 1 3a0bZ CLA Rep, Mult 30,33

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
10.0602imcB0.4474.260.0500.6883.4.24.69NA
20.0603i39X0.5215.180.0260.9031.2.99.2101,120,122
30.0602vkzG0.4615.130.0600.8122.3.1.38,3.1.2.1466,96
40.0601mhsA0.5094.410.0590.7663.6.3.6NA
50.0603b8eC0.5054.750.0460.8313.6.3.923,66,94
60.0602r8qA0.4594.780.1010.7533.1.4.1730
70.0601eulA0.5034.470.0520.7663.6.3.8NA
80.0601q50A0.4555.210.0900.8255.3.1.9NA
90.0602w2dA0.4484.220.0500.6953.4.24.69NA
100.0602f89F0.4633.720.0480.6562.5.1.1,2.5.1.1076,103
110.0602o2dB0.4594.980.0760.8125.3.1.9NA
120.0601t3cA0.4484.160.0500.6823.4.24.69NA
130.0601z0hB0.3605.170.0650.6433.4.24.69NA
140.0601hbmA0.4594.330.0930.6952.8.4.1NA
150.0603b8eA0.5064.860.0400.8253.6.3.9NA
160.0603ffzA0.4764.510.0490.7603.4.24.69NA
170.0601zn3A0.4474.170.0500.6823.4.24.69NA
180.0601e1hC0.3155.330.0780.5973.4.24.69133,136
190.0601jqkF0.5195.080.0650.8771.2.99.264,100,142

(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
00.250.5064.860.040.823b8eA GO:0000166 GO:0002028 GO:0005391 GO:0005524 GO:0005886 GO:0005890 GO:0006810 GO:0006811 GO:0006813 GO:0006814 GO:0006883 GO:0010107 GO:0010248 GO:0015991 GO:0016020 GO:0016021 GO:0016787 GO:0030007 GO:0030955 GO:0031402 GO:0036376 GO:0042383 GO:0043231 GO:0046872 GO:0051117 GO:0086009 GO:0090662 GO:1990573
10.070.4984.510.070.773w5bA GO:0000166 GO:0005388 GO:0005509 GO:0005524 GO:0005783 GO:0005789 GO:0005793 GO:0006810 GO:0006811 GO:0006816 GO:0006942 GO:0016020 GO:0016021 GO:0016529 GO:0016787 GO:0031448 GO:0031673 GO:0031674 GO:0033017 GO:0045988 GO:0046872 GO:0048471 GO:0070588
20.060.5044.750.030.813ixzA GO:0000166 GO:0000287 GO:0005391 GO:0005524 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006813 GO:0006814 GO:0006883 GO:0008900 GO:0010107 GO:0010248 GO:0015991 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0030007 GO:0036376 GO:0043231 GO:0046872
30.060.5225.260.050.903i01A GO:0003824 GO:0006091 GO:0015977 GO:0016151 GO:0016491 GO:0018492 GO:0043885 GO:0046872 GO:0051536 GO:0051539 GO:0055114
40.060.5094.410.060.771mhsA GO:0000166 GO:0005524 GO:0005886 GO:0005887 GO:0006754 GO:0006810 GO:0006811 GO:0008553 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0043231 GO:0046872 GO:0051453 GO:1902600
50.060.5044.810.040.823b8cA GO:0000166 GO:0000287 GO:0005524 GO:0005886 GO:0005887 GO:0006754 GO:0006810 GO:0006811 GO:0008553 GO:0015991 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0046872 GO:0051453
60.060.4684.900.040.773a3yA GO:0000166 GO:0005391 GO:0005524 GO:0006810 GO:0006811 GO:0006813 GO:0006814 GO:0010248 GO:0016020 GO:0016021 GO:0016787 GO:0046872 GO:0090662
70.060.5185.090.070.881jqkA GO:0003824 GO:0005737 GO:0005886 GO:0006091 GO:0016020 GO:0016151 GO:0016491 GO:0018492 GO:0043885 GO:0046872 GO:0051536 GO:0051539 GO:0055114
80.060.4855.100.050.843cf4A GO:0003824 GO:0005506 GO:0006084 GO:0015948 GO:0016151 GO:0016491 GO:0018492 GO:0019385 GO:0043885 GO:0046872 GO:0051536 GO:0051539 GO:0055114
90.060.3674.470.100.554umvA GO:0000166 GO:0005886 GO:0006812 GO:0016020 GO:0016021 GO:0016787 GO:0019829 GO:0030001 GO:0046872 GO:0098655
100.060.5215.180.030.903i39X GO:0003824 GO:0005737 GO:0005886 GO:0006091 GO:0016020 GO:0016151 GO:0016491 GO:0018492 GO:0019415 GO:0043885 GO:0046872 GO:0051536 GO:0051539 GO:0055114
110.060.3705.380.060.671oj7A GO:0000302 GO:0005829 GO:0008106 GO:0008270 GO:0016491 GO:0018455 GO:0033721 GO:0046872 GO:0055114 GO:1990002
120.060.4254.250.120.614bbjA GO:0000166 GO:0005886 GO:0006812 GO:0016020 GO:0016021 GO:0016787 GO:0019829 GO:0046872 GO:0098655
130.060.3374.650.070.552caiB GO:0004364 GO:0016740
140.060.4095.320.080.753j09A GO:0000166 GO:0005507 GO:0005524 GO:0005886 GO:0006810 GO:0006811 GO:0006812 GO:0006825 GO:0016020 GO:0016021 GO:0016787 GO:0019829 GO:0030001 GO:0046872 GO:0098655
150.060.3204.870.060.533hklB GO:0000166 GO:0001934 GO:0004672 GO:0004713 GO:0004714 GO:0005524 GO:0005886 GO:0006468 GO:0007275 GO:0007528 GO:0007613 GO:0008582 GO:0009897 GO:0010628 GO:0010629 GO:0014850 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0018108 GO:0019901 GO:0030054 GO:0030154 GO:0031594 GO:0032224 GO:0042995 GO:0043113 GO:0045202 GO:0045211 GO:0045887 GO:0046777 GO:0046872 GO:0048678 GO:0050731 GO:0051602 GO:0060041 GO:0060291 GO:0090102
160.060.3424.670.050.554v7rAD GO:0000028 GO:0002181 GO:0003723 GO:0003729 GO:0003735 GO:0005737 GO:0005840 GO:0006407 GO:0006412 GO:0006450 GO:0015935 GO:0019843 GO:0022627 GO:0030529
170.060.3264.770.040.531u3iA GO:0004364 GO:0016740
180.060.3363.710.010.481nosA GO:0001542 GO:0001666 GO:0004517 GO:0005102 GO:0005516 GO:0005622 GO:0005737 GO:0005777 GO:0005829 GO:0006527 GO:0006801 GO:0006809 GO:0006954 GO:0007263 GO:0007623 GO:0010181 GO:0010629 GO:0016491 GO:0018119 GO:0020037 GO:0030863 GO:0031284 GO:0032310 GO:0032496 GO:0034617 GO:0034618 GO:0035690 GO:0042127 GO:0042177 GO:0042742 GO:0042803 GO:0045776 GO:0045909 GO:0046872 GO:0048471 GO:0050660 GO:0050796 GO:0051712 GO:0055114 GO:0071222 GO:0071345 GO:0071346 GO:0071407 GO:0072604 GO:0072606 GO:1900015


Consensus prediction of GO terms
 
Molecular Function GO:0008556 GO:0015081 GO:0031420 GO:0019899 GO:0005524
GO-Score 0.59 0.59 0.49 0.49 0.38
Biological Processes GO:0006875 GO:0055075 GO:0055078 GO:0071436 GO:0030004 GO:0090662 GO:0015988 GO:0071805 GO:0098739 GO:0010959 GO:0042391
GO-Score 0.59 0.59 0.59 0.59 0.59 0.59 0.59 0.59 0.49 0.49 0.49
Cellular Component GO:0090533 GO:0098797 GO:0005887 GO:0043231
GO-Score 0.49 0.49 0.49 0.34

(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.