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I-TASSER results for job id Rv0193c

[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 1 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 5 2ckjD FES Rep, Mult 181,182,184,185,186,187,189,210
20.07 4 2ckjA FES Rep, Mult 544,545,546,570,571,572,573
30.03 2 2rdqA FE Rep, Mult 207,209,311
40.03 2 3kxyJ III Rep, Mult 604,605
50.02 1 1xp3A ZN Rep, Mult 146,203,207
60.02 1 2j62A GSZ Rep, Mult 458,460
70.02 1 2ohjA FE Rep, Mult 206,207
80.02 1 2ckjD PO4 Rep, Mult 190,196,198,201,257
90.02 1 4dk4A CA Rep, Mult 469,472
100.02 1 2zt9G III Rep, Mult 506,514
110.02 1 2ckjC FES Rep, Mult 582,583,584,596,597,598,599
120.02 1 4bntD 36E Rep, Mult 511,515
130.02 1 1izlA CLA Rep, Mult 567,568
140.02 1 1fx9B SO4 Rep, Mult 471,475
150.02 1 3slrA MG Rep, Mult 203,209,334
160.02 1 2j62B GSZ Rep, Mult 453,460
170.02 1 3gjoB III Rep, Mult 575,578,579
180.02 1 3m4oA C7P Rep, Mult 113,114,117
190.02 1 5sy1A CLR Rep, Mult 518,521
200.02 1 3fg4C ACD Rep, Mult 575,605,606,609

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
10.0602vz8A0.2748.470.0320.4712.3.1.85NA
20.0603cmmC0.3107.580.0420.4886.3.2.19190,254
30.0603gqbA0.2987.190.0620.4473.6.3.14NA
40.0603b8eC0.3087.780.0460.4883.6.3.9179,255
50.0601eulA0.2708.150.0380.4553.6.3.8NA
60.0601itwB0.2797.210.0460.4191.1.1.42208,214
70.0602e1qA0.2997.430.0330.4631.17.3.2,1.17.1.4NA
80.0603ixzA0.2936.250.0410.4063.6.3.10NA
90.0601n1hA0.3297.590.0370.5222.7.7.48NA
100.0603b8eA0.3077.640.0210.4783.6.3.9NA
110.0602hg4C0.2897.810.0370.4632.3.1.94247
120.0603i4lA0.2787.270.0550.4243.6.3.14NA
130.0601w36C0.2767.830.0390.4523.1.11.5184,252
140.0601fo4A0.3027.440.0290.4681.17.1.4NA
150.0602b0tA0.2867.120.0240.4291.1.1.42180,575
160.0602np0A0.2597.710.0200.4113.4.24.69NA
170.0601ygpA0.2808.000.0680.4632.4.1.1NA
180.0603b8cB0.2837.810.0370.4543.6.3.6571
190.0602gv9B0.2877.790.0370.4632.7.7.7NA

(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
00.230.9252.720.100.993jd8A GO:0001618 GO:0004872 GO:0004888 GO:0005319 GO:0005576 GO:0005635 GO:0005764 GO:0005765 GO:0005768 GO:0005783 GO:0005794 GO:0005886 GO:0005887 GO:0006486 GO:0006629 GO:0006897 GO:0006914 GO:0007041 GO:0007165 GO:0007628 GO:0008202 GO:0008203 GO:0008206 GO:0015248 GO:0015485 GO:0016020 GO:0016021 GO:0016032 GO:0016242 GO:0030301 GO:0031579 GO:0031902 GO:0031982 GO:0033344 GO:0042493 GO:0042632 GO:0045121 GO:0046686 GO:0046718 GO:0048471 GO:0060548 GO:0070062 GO:0071383 GO:0071404 GO:0090150 GO:2000189
10.070.6105.670.070.793d9bA GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015307 GO:0016020 GO:0016021 GO:0042493 GO:0042802 GO:0046618
20.070.5935.560.060.763nogA GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015307 GO:0016020 GO:0016021 GO:0042493 GO:0042802 GO:0046618
30.070.6025.890.070.802v50D GO:0005215 GO:0005886 GO:0006810 GO:0006855 GO:0015238 GO:0016020 GO:0016021 GO:0046677
40.070.6115.750.050.794mt1A GO:0005215 GO:0006810 GO:0016020 GO:0016021
50.070.5915.920.070.783w9iF GO:0005215 GO:0005886 GO:0006810 GO:0006855 GO:0015238 GO:0016020 GO:0016021 GO:0046677
60.070.5756.340.060.784dnrA GO:0005215 GO:0005375 GO:0005507 GO:0005886 GO:0006810 GO:0006811 GO:0006812 GO:0006825 GO:0006878 GO:0008324 GO:0010272 GO:0010273 GO:0015080 GO:0015673 GO:0015679 GO:0016020 GO:0016021 GO:0046688 GO:0060003 GO:1902601
70.070.5586.180.060.754k0eA GO:0005215 GO:0006810 GO:0006812 GO:0008324 GO:0016020 GO:0016021 GO:0098655
80.070.5456.230.070.734k0eB GO:0005215 GO:0006810 GO:0006812 GO:0008324 GO:0016020 GO:0016021 GO:0098655
90.070.5466.140.070.734k0eC GO:0005215 GO:0006810 GO:0006812 GO:0008324 GO:0016020 GO:0016021 GO:0098655
100.060.2107.510.040.325en5C GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015307 GO:0016020 GO:0016021 GO:0042493 GO:0042802 GO:0046618
110.060.2094.950.070.264r86B GO:0005215 GO:0006810 GO:0016020 GO:0016021
120.060.1566.320.030.223qntA GO:0005886 GO:0006629 GO:0006695 GO:0008144 GO:0008202 GO:0008203 GO:0015918 GO:0016020 GO:0016021 GO:0016324 GO:0017137 GO:0030299 GO:0030301 GO:0030659 GO:0031410 GO:0031489 GO:0031526 GO:0042157 GO:0042493
130.060.1486.410.060.213f7jA GO:0016491 GO:0043892 GO:0055114
140.060.1586.580.040.234mkmA GO:0016020 GO:0016021 GO:0046872
150.060.1266.120.060.174l0jA GO:0000746 GO:0003677 GO:0003678 GO:0004386 GO:0005524 GO:0016818 GO:0032508
160.060.1406.600.050.204ni5B GO:0016491 GO:0055114
170.060.1135.610.060.154zbgA GO:0008080 GO:0016740
180.060.1256.840.060.193bwwA GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0099600 GO:0005319 GO:0038023 GO:0032934 GO:0043178 GO:0022857 GO:0090484
GO-Score 0.46 0.46 0.46 0.46 0.46 0.37 0.37
Biological Processes GO:0010941 GO:0010507 GO:0008344 GO:0045184 GO:0016241 GO:0016192 GO:0072657 GO:0032846 GO:0032787 GO:0055098 GO:0030301 GO:0009101 GO:2000188 GO:0071396 GO:0048545 GO:0016125 GO:0032870 GO:0071407 GO:0044700 GO:0030260 GO:0007154 GO:0043413 GO:0010038 GO:0006464 GO:0007034 GO:0071402 GO:0019058 GO:1902652 GO:0090659 GO:0015893 GO:0055085
GO-Score 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.37 0.37
Cellular Component GO:0098852 GO:0031967 GO:0044428 GO:0005770 GO:0010008 GO:0000323 GO:0031988 GO:1903561 GO:0098857 GO:0005887
GO-Score 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.33

(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.