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I-TASSER results for job id Rv1214c

[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
10.14 12 4mbeE III Rep, Mult 43,46,47,50,51,53,54,57
20.07 8 1a02F NUC Rep, Mult 39,40,43,44,46,47,50,51
30.06 7 4qidB MPG Rep, Mult 51,54,55,58,59,62,107
40.05 6 1dh3C NUC Rep, Mult 38,39,42,43,46
50.04 5 2i0mA ZN Rep, Mult 17,21,54,58
60.04 5 3u90A SDS Rep, Mult 20,54,58,62
70.04 5 4mbeB III Rep, Mult 47,50,51,53,54,57
80.02 2 2np5A NDS Rep, Mult 103,104,105,106,107
90.02 2 3q0vA LL4 Rep, Mult 16,26,27,30,31,34,64,70,71,74,98,101
100.02 2 4j4qA BOG Rep, Mult 75,93,96
110.02 2 2lfdA ZN Rep, Mult 9,64,67,96,101
120.02 2 1zv8C III Rep, Mult 46,47,50,54,57,58,61,64,65,68,71,72,75,78,79,82
130.01 1 2q0yA MG Rep, Mult 34,36
140.01 1 1i4d1 III Rep, Mult 7,10,13,14,17,18,20,21,22,24,25,58,61,65,68,69

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
10.1121cxzB0.4872.220.0300.6002.7.11.1329
20.1031urfA0.4583.370.0410.6642.7.11.1351
30.1031a91A0.4972.440.1000.6363.6.3.14NA
40.0661wu0A0.4762.440.0740.6183.6.3.14NA
50.0662w5jA0.4652.680.1160.6273.6.3.14NA
60.0601qd1B0.3644.910.0320.7002.1.2.5,4.3.1.4NA
70.0601mhyD0.6142.600.0820.7821.14.13.25NA
80.0601y2mB0.6243.730.1200.9644.3.1.24NA
90.0602hvgA0.6373.110.0940.8734.3.2.2NA
100.0603a68R0.6262.350.1130.7821.16.3.117
110.0603gzhA0.6052.650.0340.7914.3.2.2NA
120.0601cc1L0.6502.920.0910.8911.12.99.6NA
130.0601i0aA0.6592.840.0790.9094.3.2.1NA
140.0601j3uA0.6832.440.0610.8824.3.1.1NA
150.0601occA0.6063.300.0800.8911.9.3.1NA
160.0601vdkA0.6372.700.0790.8554.2.1.2NA
170.0601yfmA0.6332.760.1090.8554.2.1.2NA
180.0602b5uA0.6102.500.0550.7643.1.-.-NA
190.0601c3cA0.6173.010.0930.8824.3.2.2NA
200.0602occN0.6063.360.0790.9001.9.3.131,46,49
210.0603e04D0.6143.030.0790.8554.2.1.270
220.0601yfeA0.6293.280.0890.8824.2.1.2NA
230.0603czoB0.6163.130.0630.8644.3.1.3NA
240.0602fonB0.6603.890.1020.9821.3.3.6NA

(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
00.270.7110.920.320.754kxrA GO:0005576 GO:0009405
10.250.4992.720.050.643k9aA
20.240.7822.270.090.994wpcB GO:0005096 GO:0005546 GO:0005737 GO:0005933 GO:0007165 GO:0007231 GO:0010314 GO:0010447 GO:0030479 GO:0032266 GO:0043547 GO:0070273 GO:0080025
30.230.8022.050.100.993pltA GO:0005737 GO:0005938 GO:0006469 GO:0006897 GO:0008289 GO:0009408 GO:0032126
40.230.7852.330.061.005c1fA GO:0001786 GO:0005547 GO:0005737 GO:0005826 GO:0005829 GO:0005856 GO:0007049 GO:0007067 GO:0051301 GO:0070273 GO:1903475
50.230.7892.370.060.992v0oA GO:0001786 GO:0005546 GO:0005886 GO:0005905 GO:0006897 GO:0010324 GO:0016020 GO:0030136 GO:0035091 GO:0048268 GO:0072583 GO:0072659
60.220.7142.510.130.954nqiD 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
70.190.4692.580.030.653p30A
80.160.5522.150.070.693wfvA 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
90.150.7372.660.110.992d1lA 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
100.140.4822.470.120.623cp1A GO:0005198 GO:0019031
110.140.6512.890.060.914h8sC GO:0005634 GO:0005737 GO:0005768 GO:0007049 GO:0007165 GO:0008283 GO:0010008 GO:0016020 GO:0016581 GO:0031901 GO:0070062
120.140.7312.660.121.001y2oA 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
130.110.5362.700.060.731qbzA 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
140.100.5964.050.080.972q13A 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
150.090.7932.220.101.004ckgA GO:0005096 GO:0005768 GO:0006810 GO:0015031 GO:0016020 GO:0043547 GO:0046872 GO:0055038
160.070.4373.870.110.701zl9A GO:0004364 GO:0016740 GO:0045087
170.070.4263.450.020.651i1iP GO:0004222 GO:0005737 GO:0005739 GO:0005758 GO:0005829 GO:0006508 GO:0006518 GO:0008233 GO:0008237 GO:0016787 GO:0046872 GO:0070012
180.070.7652.360.110.981i49A 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
190.070.4484.420.130.742h1yB GO:0003824 GO:0004314 GO:0008152 GO:0016740 GO:0016746
200.060.5013.600.120.733w8sA GO:0016740
210.060.4473.970.040.712o36A GO:0004222 GO:0005737 GO:0005758 GO:0006508 GO:0006518 GO:0008233 GO:0008237 GO:0016787 GO:0042277 GO:0046872
220.060.4402.640.050.523oa7A 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
230.060.3124.340.090.474h6dE GO:0009228 GO:0009229
240.060.4033.800.090.632frhA GO:0003677 GO:0005737 GO:0006351 GO:0006355 GO:0009405 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0043168 GO:1902936 GO:0030695 GO:0008047 GO:0072341 GO:0070273
GO-Score 0.48 0.48 0.48 0.48 0.46 0.42
Biological Processes GO:0051704 GO:0044700 GO:0051345 GO:0043087 GO:0007154 GO:0071470 GO:0009268 GO:0045859 GO:0033673 GO:0016192 GO:0009266 GO:0001933 GO:1902407 GO:0000280 GO:0000915
GO-Score 0.54 0.48 0.48 0.48 0.48 0.48 0.48 0.47 0.47 0.47 0.47 0.47 0.46 0.46 0.46
Cellular Component GO:0030864 GO:0061645 GO:0070938 GO:0032155
GO-Score 0.48 0.48 0.46 0.46

(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.