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I-TASSER results for job id Rv3650

[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
10.22 61 3is7K HEM Rep, Mult 26,29,30,33,60,64,67,68,70,71
20.07 21 2y01B 2CV Rep, Mult 25,26,63,66,70
30.05 9 4de6A ACD Rep, Mult 33,59,60,63,67
40.04 11 4jolB III Rep, Mult 48,51,52,54,55
50.03 9 3a68B CA Rep, Mult 18,73,76
60.03 7 3uoiX HEM Rep, Mult 19,22,23,26,71,74,75,77,78
70.03 9 4s1xA III Rep, Mult 45,48,49,51,52,55,56,59,62,63,66
80.03 8 1h8aB NUC Rep, Mult 54,57,58,60,61,62
90.02 6 4mbeE III Rep, Mult 55,58,59,62,63,65,66,69
100.02 6 3nmiE PXX Rep, Mult 37,53,56,60
110.01 2 2g381 III Rep, Mult 10,11,14,17,18,20,21,24,25,27,28,31,32,35,54,62,65,73,76,80,87
120.01 2 2j68A GDP Rep, Mult 24,25,26,27,28,29
130.00 1 2w6dA GDP Rep, Mult 35,36,38,39,57
140.00 1 2w6dB CPL Rep, Mult 39,40,41,42,43,51,52,54
150.00 1 3feuA MG Rep, Mult 17,20,22
160.00 1 4dmbA MG Rep, Mult 9,17
170.00 1 3io6A CA Rep, Mult 9,12
180.00 1 3u24A IMD Rep, Mult 31,34,35

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
10.1921cxzB0.5872.330.0270.7552.7.11.1321
20.1491wt6B0.4752.040.1170.5532.7.11.127
30.1431vp7B0.4832.410.0580.6383.1.11.628
40.1421joyA0.4772.450.0980.6282.7.13.318,25
50.1361urfA0.5432.810.0820.7772.7.11.13NA
60.1162h8nA0.4911.470.0360.5433.5.1.9867
70.1121wu0A0.5332.470.0870.7233.6.3.14NA
80.0832w5jA0.5292.670.0670.7343.6.3.14NA
90.0601clqA0.6983.180.1510.9792.7.7.726
100.0601fftA0.6142.570.0660.8081.10.3.-NA
110.0601jtnA0.3083.790.0280.4363.2.1.17NA
120.0603i9wA0.6652.650.0540.9252.7.13.331
130.0602z8yD0.6232.610.0540.7981.2.7.4,1.2.99.230
140.0601m56A0.6013.200.0430.8621.9.3.182
150.0601wleB0.6123.610.0460.8946.1.1.1136
160.0602e9fB0.6342.990.1460.8724.3.2.1NA
170.0601jqkF0.6402.800.0750.8081.2.99.2NA
180.0602iw5A0.6782.840.0790.8941.-.-.-NA
190.0602uxwA0.6082.870.1070.8301.3.99.-22
200.0603g61A0.6652.950.0220.9253.6.3.4439
210.0601is2A0.6133.170.0780.8831.3.3.6NA
220.0602ohyB0.6043.240.0790.9255.4.3.672
230.0601qleA0.5863.090.0690.8721.9.3.1NA
240.0602dq3A0.6572.970.0320.9046.1.1.11NA
250.0603l9oA0.6183.540.0540.8943.6.4.13NA
260.0601z0hB0.3124.870.0110.6173.4.24.6963
270.0602fonB0.6603.210.0540.9361.3.3.6NA

(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
00.340.8470.990.270.904kxrA GO:0005576 GO:0009405
10.260.5732.920.030.783k9aA
20.240.6642.520.030.932d1lA GO:0001701 GO:0002230 GO:0003779 GO:0003785 GO:0005102 GO:0005737 GO:0005856 GO:0005912 GO:0007009 GO:0007015 GO:0007399 GO:0007517 GO:0010960 GO:0015629 GO:0030036 GO:0030041 GO:0030282 GO:0032233 GO:0034334 GO:0042802 GO:0050680 GO:0051015 GO:0061333 GO:0071498 GO:0072001 GO:0072102 GO:0072160 GO:0098792 GO:2001013
30.230.6652.320.090.904nqiD GO:0000281 GO:0000331 GO:0001891 GO:0005885 GO:0005905 GO:0006909 GO:0007009 GO:0009992 GO:0010324 GO:0031150 GO:0035091 GO:0042803 GO:0045335 GO:0046847 GO:0071476 GO:0072583
40.220.4561.260.000.512x7rC GO:0002223 GO:0005198 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0019064 GO:0019082 GO:0020002 GO:0030683 GO:0033644 GO:0039654 GO:0039663 GO:0044174 GO:0044175 GO:0046718 GO:0055036 GO:0075509 GO:0075512
50.200.6772.760.040.911qbzA GO:0005198 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0020002 GO:0033644 GO:0039663 GO:0044174 GO:0044175 GO:0046718 GO:0055036
60.170.5652.750.030.803p30A
70.150.5813.370.020.871envA GO:0000122 GO:0000790 GO:0000978 GO:0000981 GO:0001080 GO:0001084 GO:0001135 GO:0001190 GO:0001191 GO:0002223 GO:0003677 GO:0003682 GO:0003700 GO:0005198 GO:0005634 GO:0005667 GO:0006351 GO:0006355 GO:0006366 GO:0008652 GO:0010691 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0019064 GO:0019082 GO:0020002 GO:0030683 GO:0033644 GO:0039654 GO:0039663 GO:0042802 GO:0043565 GO:0044174 GO:0044175 GO:0045899 GO:0046718 GO:0055036 GO:0060261 GO:0075509 GO:0075512 GO:1903833
80.150.6183.080.060.892ezoA GO:0005198 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0020002 GO:0033644 GO:0039663 GO:0044174 GO:0044175 GO:0046718 GO:0055036
90.150.5352.600.090.733cp1A GO:0005198 GO:0019031
100.130.7122.910.070.961y2oA GO:0001726 GO:0005737 GO:0005829 GO:0005856 GO:0005886 GO:0005913 GO:0007009 GO:0007409 GO:0008022 GO:0008093 GO:0008286 GO:0008360 GO:0009617 GO:0014069 GO:0015629 GO:0016020 GO:0016358 GO:0030141 GO:0030165 GO:0030175 GO:0030838 GO:0032956 GO:0038096 GO:0042802 GO:0042995 GO:0043005 GO:0043025 GO:0043197 GO:0048010 GO:0048167 GO:0051017 GO:0051764 GO:0061003 GO:0070062 GO:0070064 GO:0097481 GO:0098609 GO:0098641 GO:2000251
110.130.6652.390.040.863wfvA GO:0005198 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0020002 GO:0033644 GO:0039663 GO:0044174 GO:0044175 GO:0046718 GO:0055036
120.100.7732.340.130.984ckgA GO:0005096 GO:0005768 GO:0006810 GO:0015031 GO:0016020 GO:0043547 GO:0046872 GO:0055038
130.100.6092.750.070.824h8sC GO:0005634 GO:0005737 GO:0005768 GO:0007049 GO:0007165 GO:0008283 GO:0010008 GO:0016020 GO:0016581 GO:0031901 GO:0070062
140.080.5863.200.010.892q13A GO:0005634 GO:0005737 GO:0005768 GO:0005829 GO:0007049 GO:0007165 GO:0008283 GO:0008286 GO:0010008 GO:0012506 GO:0016020 GO:0016581 GO:0031901 GO:0042802 GO:0043422 GO:0046324 GO:0070062 GO:0090003 GO:0097192
150.070.6122.690.070.841qsdA GO:0005737 GO:0005856 GO:0005874 GO:0007021 GO:0007023 GO:0015631 GO:0048487
160.060.3523.500.030.484mk0A GO:0000166 GO:0002026 GO:0002029 GO:0003108 GO:0004672 GO:0004674 GO:0004703 GO:0005524 GO:0005737 GO:0005829 GO:0005886 GO:0006468 GO:0007165 GO:0007186 GO:0007213 GO:0007217 GO:0007507 GO:0016020 GO:0016301 GO:0016310 GO:0016740 GO:0018105 GO:0018107 GO:0019079 GO:0031623 GO:0031694 GO:0031755 GO:0033605 GO:0045988 GO:0046718 GO:0047696 GO:0060048 GO:0072372
170.060.3663.770.030.562h1yB GO:0003824 GO:0004314 GO:0008152 GO:0016740 GO:0016746
180.060.3313.760.000.472p51A GO:0000289 GO:0003676 GO:0003723 GO:0003729 GO:0004518 GO:0004527 GO:0004535 GO:0005634 GO:0005737 GO:0005829 GO:0006351 GO:0006355 GO:0016787 GO:0030014 GO:0030015 GO:0046872 GO:0090305 GO:0090503
190.060.3674.550.080.693uzsA GO:0000166 GO:0002029 GO:0002031 GO:0003108 GO:0004672 GO:0004674 GO:0004703 GO:0005524 GO:0005737 GO:0005829 GO:0005886 GO:0006468 GO:0006886 GO:0007165 GO:0007186 GO:0007213 GO:0009966 GO:0016020 GO:0016301 GO:0016310 GO:0016740 GO:0018105 GO:0031694 GO:0031755 GO:0045988 GO:0047696 GO:0060048
200.060.3323.050.030.442dn6A GO:0003677 GO:0005509 GO:0005524 GO:0005634 GO:0005737 GO:0005829 GO:0005856 GO:0005886 GO:0005913 GO:0007204 GO:0008064 GO:0016020 GO:0016444 GO:0030027 GO:0030835 GO:0032233 GO:0032880 GO:0033633 GO:0042995 GO:0045190 GO:0051017 GO:0060754 GO:0098609 GO:0098641 GO:1902309
210.060.3503.750.030.493ljuX GO:0005096 GO:0005634 GO:0005737 GO:0005886 GO:0007166 GO:0043087 GO:0043533 GO:0043547 GO:0046872
220.060.3362.070.100.404hhvA GO:0000902 GO:0001701 GO:0003007 GO:0004672 GO:0005654 GO:0005737 GO:0005739 GO:0005783 GO:0005789 GO:0005794 GO:0005829 GO:0006468 GO:0006672 GO:0006810 GO:0006869 GO:0006936 GO:0006955 GO:0007029 GO:0007165 GO:0008283 GO:0008289 GO:0016301 GO:0016310 GO:0030148 GO:0034976 GO:0035620 GO:0035621 GO:0048471 GO:0055088 GO:0070273 GO:0070584 GO:0097001
230.060.3333.270.040.482da0A GO:0005096 GO:0005546 GO:0005547 GO:0005737 GO:0005829 GO:0005913 GO:0016020 GO:0030030 GO:0043197 GO:0043547 GO:0046872 GO:0060271 GO:0061000 GO:0098609 GO:0098641
240.060.3142.910.000.401fb8A GO:0005543 GO:0005547 GO:0005737 GO:0005829 GO:0005886 GO:0006470 GO:0007165 GO:0016020 GO:0043325
250.060.3023.840.090.451v89A GO:0005096 GO:0005829 GO:0007165 GO:0043547 GO:0051056
260.060.3203.670.140.461eazA GO:0001553 GO:0005634 GO:0005654 GO:0005737 GO:0005886 GO:0007283 GO:0008209 GO:0008210 GO:0008289 GO:0008585 GO:0009791 GO:0014065 GO:0016020 GO:0030165 GO:0031529 GO:0032587 GO:0033327 GO:0035264 GO:0043325 GO:0045184 GO:0048008 GO:0048705 GO:0050853 GO:0051898 GO:0060021 GO:0060325 GO:0070062 GO:0070301


Consensus prediction of GO terms
 
Molecular Function GO:0003779 GO:0032403 GO:0046983 GO:0005543
GO-Score 0.47 0.47 0.46 0.46
Biological Processes GO:0050678 GO:0016236 GO:0008154 GO:0051258 GO:0034332 GO:0044089 GO:0008285 GO:0001503 GO:0061333 GO:0034405 GO:0032835 GO:0061061 GO:0055065 GO:0051495 GO:0050691 GO:0072080 GO:0032231 GO:0034331 GO:0043009 GO:0072507 GO:0031214 GO:0035850 GO:0031154 GO:0030104 GO:0030031 GO:0006884 GO:0044765 GO:0055082 GO:1903047 GO:0071470 GO:0006971 GO:0061640 GO:0019049 GO:0016485 GO:0019080 GO:0050687 GO:0050690 GO:0020012 GO:0019065 GO:0044800 GO:0044650 GO:0002220 GO:0007009 GO:0009405
GO-Score 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.41 0.34
Cellular Component GO:0070161 GO:0012505 GO:0043234 GO:0044430 GO:0030139 GO:0044459 GO:0098589 GO:0005773 GO:0044174 GO:0033644 GO:0036338 GO:0031224 GO:0005576
GO-Score 0.47 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.43 0.43 0.43 0.34 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.