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I-TASSER results for job id Rv3746c

[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
10.10 10 1hrsA PP9 Rep, Mult 18,21,22,25,69,70,73,77
20.08 8 2dysN DCW Rep, Mult 25,70
30.08 9 2jd68 FE Rep, Mult 17,72,75
40.08 9 3j7y8 NUC Rep, Mult 58,61,62,65,69
50.03 3 4rqeA NUC Rep, Mult 58,69,72,75,78
60.03 3 4n7kL LDA Rep, Mult 16,17,79
70.03 3 3wuuB III Rep, Mult 55,58,62,69
80.02 2 1fbmA RTL Rep, Mult 61,68,71
90.02 2 2i0mA ZN Rep, Mult 70,74
100.02 2 2c9nY NUC Rep, Mult 47,50,53,54,57,58
110.02 2 3wutB III Rep, Mult 51,54,65,68,72
120.01 1 2j9tA BO3 Rep, Mult 81,82,86,93,94,97
130.01 1 3ar3A PTY Rep, Mult 71,74,78,82
140.01 1 3da3A MG Rep, Mult 40,54
150.01 1 1tygA PO4 Rep, Mult 13,14,41,42,61,65,70
160.01 1 3cr3A MG Rep, Mult 7,12
170.01 1 1wuuA MG Rep, Mult 45,47
180.01 1 2g380 III Rep, Mult 9,16,20,23,27,31,35,37,38,39,40,41,42,43,44,45,46,47,50,53,54,57,58,61,64,67,68,71,72,75,79
190.01 1 3l26B MG Rep, Mult 39,40,42
200.01 1 3b6aD ZCT Rep, Mult 98,99

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
10.3872w5jA0.4683.150.1280.6493.6.3.1470
20.1781urfA0.4552.840.0390.6312.7.11.1311,17,69
30.1561cxzB0.4813.010.0400.6312.7.11.1325,31
40.1381wu0A0.5281.960.0850.6403.6.3.14NA
50.1031a91A0.4982.630.0640.6493.6.3.14NA
60.0601j3uA0.5693.370.0670.8384.3.1.1NA
70.0602uxwA0.5893.250.1040.8651.3.99.-NA
80.0601qleC0.5603.660.0520.8381.9.3.157
90.0601biqB0.5573.860.0640.8741.17.4.1NA
100.0602pfmA0.5763.360.0570.8474.3.2.2NA
110.0601cc1L0.5863.550.1000.8741.12.99.697
120.0601k62B0.5853.500.0380.8654.3.2.136
130.0602z1qB0.5633.730.0610.8831.3.99.370
140.0603no9A0.6363.420.1030.9194.2.1.228,65
150.0601k7wD0.5853.430.0470.8564.3.2.1NA
160.0601tj7A0.5933.480.1040.8834.3.2.136
170.0602wpnB0.5573.300.0740.8021.12.7.2NA
180.0603i9wA0.6582.890.0560.8922.7.13.373,77
190.0601w07B0.6463.640.1110.9461.3.3.6NA
200.0601mo7A0.2944.930.0440.5593.6.3.914
210.0601rsrB0.5603.760.0650.8651.17.4.163
220.0601eulA0.5993.960.0470.9553.6.3.8NA
230.0601c3cA0.5843.560.0480.8474.3.2.2NA
240.0602b5uA0.5693.000.0990.7933.1.-.-NA

(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
00.260.6561.670.210.764kxrA GO:0005576 GO:0009405
10.220.6832.870.050.942d1lA 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
20.200.7042.610.070.923pltA GO:0005737 GO:0005938 GO:0006469 GO:0006897 GO:0008289 GO:0009408 GO:0032126
30.170.6913.020.100.954nqiD 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
40.070.5653.740.080.891y2oA 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
50.070.6753.140.060.954akvB GO:0000281 GO:0005737 GO:0005768 GO:0005829 GO:0006810 GO:0006886 GO:0006897 GO:0007032 GO:0007049 GO:0007067 GO:0015031 GO:0016020 GO:0016023 GO:0016050 GO:0016197 GO:0017038 GO:0019898 GO:0030659 GO:0031410 GO:0035091 GO:0036089 GO:0042802 GO:0044351 GO:0045806 GO:0051044 GO:0051301 GO:0097320 GO:2000009 GO:2000010
60.070.6453.060.040.931i49A GO:0001726 GO:0005525 GO:0005737 GO:0005829 GO:0005886 GO:0005913 GO:0005938 GO:0006928 GO:0007264 GO:0019904 GO:0030032 GO:0030036 GO:0030742 GO:0031529 GO:0032588 GO:0034315 GO:0048365 GO:0070273 GO:0098609 GO:0098641
70.070.5463.540.060.794ecgA GO:0046872
80.070.6983.030.100.952rajA GO:0000281 GO:0001726 GO:0005545 GO:0005737 GO:0005768 GO:0005794 GO:0005802 GO:0005886 GO:0005913 GO:0006810 GO:0006886 GO:0006897 GO:0006898 GO:0007049 GO:0007067 GO:0008289 GO:0015031 GO:0016020 GO:0016023 GO:0016050 GO:0016197 GO:0030136 GO:0030659 GO:0031234 GO:0031410 GO:0031625 GO:0032461 GO:0035091 GO:0036089 GO:0042803 GO:0042995 GO:0043547 GO:0045860 GO:0051044 GO:0051301 GO:0060988 GO:0070062 GO:0071933 GO:0097320 GO:0098609 GO:0098641
90.070.4094.220.070.682o36A GO:0004222 GO:0005737 GO:0005758 GO:0006508 GO:0006518 GO:0008233 GO:0008237 GO:0016787 GO:0042277 GO:0046872
100.070.4074.210.070.681i1iP GO:0004222 GO:0005737 GO:0005739 GO:0005758 GO:0005829 GO:0006508 GO:0006518 GO:0008233 GO:0008237 GO:0016787 GO:0046872 GO:0070012
110.070.4813.350.050.684y21A GO:0000149 GO:0005737 GO:0005886 GO:0006887 GO:0007268 GO:0007269 GO:0016020 GO:0016082 GO:0017075 GO:0019904 GO:0019992 GO:0030054 GO:0030154 GO:0030507 GO:0035556 GO:0042734 GO:0042803 GO:0043005 GO:0043195 GO:0043234 GO:0045202 GO:0046872 GO:0046982 GO:0047485 GO:0060076 GO:0060291
120.060.3974.690.100.662xdqB GO:0000166 GO:0005524 GO:0015979 GO:0015995 GO:0016491 GO:0016636 GO:0016730 GO:0019685 GO:0036068 GO:0046148 GO:0046872 GO:0051536 GO:0051539 GO:0055114
130.060.3764.130.060.611ocuA GO:0000139 GO:0000407 GO:0005737 GO:0005768 GO:0005794 GO:0005829 GO:0006810 GO:0006897 GO:0006914 GO:0008104 GO:0008289 GO:0015031 GO:0016020 GO:0016050 GO:0019898 GO:0031902 GO:0032258 GO:0032266 GO:0034499 GO:0035091
140.060.3984.930.050.683tqeA GO:0003824 GO:0004314 GO:0008152 GO:0016740 GO:0016746
150.060.3852.560.060.504egxA GO:0000166 GO:0003774 GO:0003777 GO:0005524 GO:0005737 GO:0005856 GO:0005871 GO:0005874 GO:0007018 GO:0008017 GO:0008089 GO:0016887 GO:1904115
160.060.3393.830.010.502frhA GO:0003677 GO:0005737 GO:0006351 GO:0006355 GO:0009405 GO:0046872
170.060.3952.940.040.493oa7A GO:0003677 GO:0005200 GO:0005737 GO:0005816 GO:0005824 GO:0005856 GO:0007020 GO:0007049 GO:0007052 GO:0019076 GO:0030435 GO:0046806 GO:0051301 GO:0051321
180.060.3235.190.060.652dybA GO:0002479 GO:0005737 GO:0005768 GO:0005829 GO:0006955 GO:0008289 GO:0010008 GO:0016020 GO:0016176 GO:0032010 GO:0032266 GO:0035091 GO:0043020 GO:0043085 GO:0045454 GO:0046983 GO:0048010 GO:0055114
190.060.3473.850.010.532cskA GO:0005769 GO:0006810 GO:0008289 GO:0010629 GO:0010955 GO:0015031 GO:0016020 GO:0016050 GO:0019898 GO:0019899 GO:0030100 GO:0035091 GO:0042177 GO:0051224 GO:0070062 GO:2000642


Consensus prediction of GO terms
 
Molecular Function GO:0003779 GO:0032403 GO:0046983 GO:0005543
GO-Score 0.43 0.43 0.34 0.34
Biological Processes GO:0034331 GO:0032231 GO:0055065 GO:0061061 GO:0050678 GO:0060562 GO:0008154 GO:0051495 GO:0008285 GO:0072507 GO:0072080 GO:0034405 GO:0043009 GO:0016236 GO:0001503 GO:0035850 GO:0034332 GO:0031214 GO:0051258 GO:0050691 GO:0032835 GO:0044089 GO:0001933 GO:0009266 GO:0033673 GO:0045859 GO:0007009 GO:0006884 GO:0071470 GO:0044765 GO:0006971 GO:0006898 GO:1903047 GO:0030031 GO:0061640 GO:0030104 GO:0055082 GO:0031154
GO-Score 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.40 0.40 0.40 0.40 0.40 0.34 0.34 0.34 0.34 0.34 0.34 0.34 0.34 0.34 0.34 0.34
Cellular Component GO:0070161 GO:0099568 GO:0044459 GO:0044430 GO:0012505 GO:0005773 GO:0043234 GO:0030139 GO:0098589
GO-Score 0.43 0.40 0.34 0.34 0.34 0.34 0.34 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.