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I-TASSER results for job id Rv3440c

[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 3 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
10.08 18 1s5lC CLA Rep, Mult 16,83,87,90,91
20.07 14 5e1uA RIR Rep, Mult 28,31,71,74,75,78
30.05 11 3vgxC III Rep, Mult 70,73,74,77,81,84,87,88,91
40.05 10 1t8zE 12P Rep, Mult 59,63,66,70,73,77,80
50.05 10 1gd2E NUC Rep, Mult 52,55,56,59,60,63,67
60.05 10 1dgcA NUC Rep, Mult 60,63,64,67,68,71
70.04 7 4de6A ACD Rep, Mult 20,81,82,85,89
80.04 8 2g38B MN Rep, Mult 87,90,91
90.04 8 2jqkA III Rep, Mult 27,31,34,35,38,64,65,67,68,71,74,75
100.03 5 3f33A PFL Rep, Mult 17,20,21,24,85
110.03 7 3mgnF DTR Rep, Mult 89,90,93,94
120.01 1 2jizG STL Rep, Mult 71,74,75,78,79
130.01 1 2jj1G PIT Rep, Mult 23,26,27,30,31
140.01 3 2ck3G III Rep, Mult 25,73,74,77
150.00 1 1l8d0 III Rep, Mult 36,39,43,46,59,63
160.00 1 2d32A MG Rep, Mult 93,95
170.00 1 1i4d1 III Rep, Mult 28,31,34,35,38,39,41,42,43,45,46,64,67,71,74,75
180.00 1 3favC ZN Rep, Mult 8,12
190.00 1 2id3A CA Rep, Mult 12,76

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
10.2171urfA0.5532.560.0870.6992.7.11.1318,30,79
20.1121wu0A0.5022.440.0560.6503.6.3.14NA
30.0931cxzB0.5602.760.0980.7282.7.11.13NA
40.0601vdkA0.6092.880.0520.8064.2.1.252
50.0601j3uA0.5862.970.0510.8064.3.1.152
60.0602iw5A0.6722.390.0600.8451.-.-.-NA
70.0601u7lA0.6503.260.0990.9133.6.3.14NA
80.0601yfeA0.5903.050.0730.8064.2.1.2NA
90.0601serB0.5213.220.0990.7866.1.1.11NA
100.0603lssB0.6682.510.0390.8256.1.1.1146,48,51
110.0602fonB0.6332.610.0820.7961.3.3.6NA
120.0601dofA0.5923.360.1290.8254.3.2.2NA
130.0602dq3A0.6572.890.0530.8546.1.1.1128,35
140.0601tj7A0.6213.090.0630.8354.3.2.1NA
150.0603no9A0.6083.140.0660.8354.2.1.283
160.0602occN0.6022.820.0220.7961.9.3.1NA
170.0601sesA0.5473.990.1210.9036.1.1.1168
180.0601occA0.6002.810.0220.7961.9.3.165
190.0601k62B0.5973.070.0610.8254.3.2.1NA
200.0601i0aA0.6372.990.0950.8354.3.2.1NA
210.0603gtdA0.5973.010.0320.8064.2.1.2NA
220.0603g61A0.6772.900.0200.9223.6.3.44NA

(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
00.360.8281.850.100.942vrzA GO:0005576 GO:0009405
10.250.7202.430.060.923g67A GO:0004871 GO:0007165 GO:0016020
20.210.7712.460.080.933zx6A GO:0004871 GO:0004888 GO:0005886 GO:0005887 GO:0006935 GO:0007165 GO:0016020 GO:0016021 GO:0043200 GO:0043424 GO:0046872 GO:0048870
30.180.5502.680.040.743p30A
40.180.5191.900.060.623cp1A GO:0005198 GO:0019031
50.170.6232.420.060.803wfvA 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
60.160.5433.060.030.781envA 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
70.150.4591.760.060.534bl6C GO:0003729 GO:0005737 GO:0005794 GO:0005829 GO:0005856 GO:0006810 GO:0007275 GO:0007293 GO:0007294 GO:0007309 GO:0007310 GO:0007312 GO:0007314 GO:0008103 GO:0008298 GO:0016325 GO:0017137 GO:0019233 GO:0030100 GO:0030154 GO:0030669 GO:0030727 GO:0032050 GO:0045502 GO:0048477 GO:0048488 GO:0050658 GO:0051028 GO:0070727 GO:2000302 GO:2000370
80.150.6122.850.080.831qbzA 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
90.140.5873.180.070.882ezoA 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
100.140.5372.750.110.773k9aA
110.130.5692.990.070.772oszA GO:0005487 GO:0005634 GO:0005635 GO:0005643 GO:0006810 GO:0006913 GO:0008139 GO:0015031 GO:0016020 GO:0031965 GO:0042306 GO:0043234 GO:0051028 GO:0051260 GO:0051290 GO:0051291 GO:0070208
120.130.7772.180.080.912ch7A GO:0004871 GO:0005886 GO:0006935 GO:0007165 GO:0016020 GO:0016021
130.120.7542.680.040.941y2oA 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
140.120.6502.960.140.924rsjA GO:0000166 GO:0003677 GO:0005524 GO:0005694 GO:0005737 GO:0006260 GO:0007059 GO:0007062 GO:0030261 GO:0051276
150.070.4651.570.050.522npsD GO:0000139 GO:0005484 GO:0005769 GO:0005794 GO:0005802 GO:0005829 GO:0005886 GO:0006810 GO:0006886 GO:0006906 GO:0007032 GO:0015031 GO:0016020 GO:0016021 GO:0016192 GO:0019905 GO:0030136 GO:0031201 GO:0032456 GO:0032588 GO:0032880 GO:0042147 GO:0043195 GO:0045335 GO:0048193 GO:0048278 GO:0048471 GO:0090161 GO:1903827
160.070.5292.950.090.702c2jA GO:0005737 GO:0006879 GO:0006950 GO:0008199 GO:0016491 GO:0046872 GO:0055114
170.070.5453.170.060.824uxvA GO:0000921 GO:0005886 GO:0005940 GO:0007049 GO:0016020 GO:0016021 GO:0051301 GO:0051781
180.070.5023.710.100.802jesA GO:0019012 GO:0019028 GO:0019076 GO:0046718 GO:0046729
190.070.5493.600.020.835a20A GO:0019012 GO:0019028 GO:0019076 GO:0046718 GO:0046729
200.060.3863.360.060.572eabA GO:0003824 GO:0016020 GO:0016021 GO:0046872
210.060.3533.640.020.504h1zB GO:0003824 GO:0008152 GO:0009063 GO:0046872
220.060.2973.970.020.474ic6A GO:0004252 GO:0006508 GO:0008233 GO:0008236 GO:0009507 GO:0009534 GO:0009536 GO:0009543 GO:0009579 GO:0010206 GO:0016787 GO:0031977
230.060.2585.400.080.592z9iA GO:0004252 GO:0005576 GO:0006508 GO:0006950 GO:0008233 GO:0008236 GO:0009405 GO:0016020 GO:0016021 GO:0030163
240.060.2773.210.010.402ogiB GO:0046872
250.060.3024.400.040.511j6uA GO:0000166 GO:0005524 GO:0005737 GO:0007049 GO:0008360 GO:0008763 GO:0009058 GO:0009252 GO:0016874 GO:0051301 GO:0071555


Consensus prediction of GO terms
 
Molecular Function GO:0019901 GO:0099600 GO:0043169 GO:0038023
GO-Score 0.41 0.41 0.41 0.41
Biological Processes GO:0010243 GO:0042330 GO:1901700 GO:0001101 GO:0051674 GO:0006928 GO:0007165 GO:0009405
GO-Score 0.41 0.41 0.41 0.41 0.41 0.41 0.40 0.36
Cellular Component GO:0031226 GO:0005576 GO:0036338
GO-Score 0.41 0.36 0.36

(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.