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I-TASSER results for job id Rv0366c

[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
10.61 87 3a4lA ANP Rep, Mult 11,12,14,15,16,17,112,116,159
20.03 5 4mdeA NUC Rep, Mult 11,15,35,36,39,47,48,51,55,59,77,80,83,122,127,128,132
30.02 4 1qf9A ALF Rep, Mult 11,12,15,79,116,121,128
40.02 5 1z83C AP5 Rep, Mult 11,12,14,15,16,17,35,36,39,40,76,77,79,112,116,121,128
50.01 1 4jstB NA Rep, Mult 17,18,21,159
60.01 1 1qhxA MG Rep, Mult 15,16,36,74
70.01 2 5cb6B MG Rep, Mult 16,34,116
80.00 1 1qhsA CLM Rep, Mult 22,23,71
90.00 1 3q8xD UD1 Rep, Mult 34,35,36,55,59,62,74,75,76,77,79,82,86

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
10.3192cdnA0.6543.120.1550.8172.7.4.315,116,123,132
20.3031tevA0.6413.480.1270.8382.7.4.1415,116,123,132
30.2793hjnA0.6363.030.1050.7772.7.4.916
40.2621kagA0.5833.310.1450.7362.7.1.7110,13,16,32
50.2131ki9B0.5983.860.1550.8172.7.4.39,12,14,34
60.2132pt5B0.5723.850.1230.7822.7.1.7114,17,37
70.2051viaA0.5793.130.1300.7362.7.1.7112,14,17
80.1962yvuA0.6563.000.1070.8072.7.1.2512,14,36,77
90.1931khtB0.6443.010.1300.8172.7.4.312,14,76
100.1892ax4C0.6543.150.1180.8072.7.1.25,2.7.7.412,14,36
110.1852pbrB0.6503.260.1380.8072.7.4.912,14
120.1831kofA0.6193.440.1090.7922.7.1.1212,14,16
130.1821rkbA0.6223.390.1140.7822.7.4.314,34
140.1811zuiA0.5962.750.1390.7312.7.1.7112,14,16
150.1492p0eA0.6023.140.1270.7512.7.1.2214
160.0873dkvA0.6822.890.1100.8272.7.4.3123,132
170.0841zinA0.6772.890.1170.8272.7.4.315,123,132
180.0763fb4A0.6732.950.0860.8222.7.4.315,123,132
190.0672ofxA0.6573.240.1240.8122.7.7.412,14,36,38
200.0601akeA0.6503.160.1380.8122.7.4.315,36,123,132
210.0603eplB0.6923.590.1360.9092.5.1.816,112
220.0602peyB0.6112.760.1300.7362.7.1.25,2.7.7.412,14
230.0602qajB0.6772.970.1100.8272.7.4.312,14,123
240.0601ukyA0.6723.010.1230.8272.7.4.-15,116,123,132
250.0601m7hC0.6513.330.1280.8172.7.1.2514,16
260.0602eu8A0.6792.810.1110.8222.7.4.315,123,132
270.0601nn5A0.6343.100.1040.7822.7.4.914,16,37
280.0603tmkA0.6523.140.1120.8172.7.4.914
290.0601k6mA0.6903.450.0820.8682.7.1.105,3.1.3.4614,154
300.0601xjqB0.6553.450.1020.8222.7.1.25,2.7.7.4NA
310.0602rgxA0.6542.980.1450.8072.7.4.315,116,123,132
320.0601bifA0.6943.290.0770.8633.1.3.46,2.7.1.105154
330.0601qf9A0.6743.060.1330.8382.7.4.1415,116,123,132
340.0601zakA0.6603.150.1130.8272.7.4.315,123,132
350.0601s3gA0.6773.140.0840.8432.7.4.315,123,130
360.0601zioA0.6772.900.1170.8272.7.4.312,14,36,39,116,123
370.0601z83A0.6712.960.0920.8272.7.4.3116,123
380.0601p60A0.6523.630.1120.8582.7.1.74NA

(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
00.450.6402.200.160.712ia5H GO:0000166 GO:0005524 GO:0006281 GO:0006974 GO:0016032 GO:0016301 GO:0016310 GO:0016311 GO:0016740 GO:0016787 GO:0046404 GO:0047846
10.440.7112.440.110.833addA GO:0000166 GO:0005524 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0097056
20.380.6023.500.140.781lvgA GO:0000166 GO:0004385 GO:0005524 GO:0006163 GO:0016301 GO:0016310 GO:0016740 GO:0046037 GO:0046710
30.330.7371.900.180.814gp6A GO:0000166 GO:0005524 GO:0005525 GO:0016787 GO:0046872
40.260.7303.140.150.892p5tD GO:0000166 GO:0005524 GO:0009405 GO:0016301 GO:0016310 GO:0016740
50.260.6503.130.180.811zp6A
60.240.7542.850.120.911gvnB GO:0000166 GO:0005524 GO:0016301 GO:0016310 GO:0016740
70.200.6782.160.150.754xrpA GO:0000166 GO:0005524 GO:0046872
80.200.5663.300.180.732if2C GO:0000166 GO:0004140 GO:0005524 GO:0005737 GO:0015937 GO:0016301 GO:0016310 GO:0016740
90.190.6062.480.180.711yj5B GO:0000166 GO:0003690 GO:0003824 GO:0005524 GO:0005634 GO:0005730 GO:0006281 GO:0006974 GO:0006979 GO:0008152 GO:0016020 GO:0016301 GO:0016310 GO:0016311 GO:0016740 GO:0016787 GO:0019201 GO:0032212 GO:0042769 GO:0046403 GO:0046404 GO:0046939 GO:0051973 GO:0098504 GO:0098506 GO:1904355
100.150.5702.240.150.644xruD GO:0000166 GO:0005524 GO:0046872
110.080.6303.650.110.853a8tA GO:0000166 GO:0005524 GO:0008033 GO:0009691 GO:0009824 GO:0016740 GO:0034265
120.070.5414.800.100.824q9nA GO:0004319 GO:0016491 GO:0055114
130.070.5384.150.110.765hoeA GO:0016787
140.070.4944.140.110.695l3rC GO:0000166 GO:0003723 GO:0003924 GO:0005525 GO:0005786 GO:0006614 GO:0008312 GO:0009507 GO:0009536 GO:0009570 GO:0030529 GO:0048500 GO:0080085
150.070.3445.350.070.592ghiA GO:0000166 GO:0005524 GO:0006810 GO:0016020 GO:0016021 GO:0016887 GO:0042626 GO:0055085
160.070.4614.550.070.675c1aK GO:0000166 GO:0000502 GO:0005102 GO:0005524 GO:0005634 GO:0005654 GO:0005737 GO:0005783 GO:0005789 GO:0005811 GO:0005829 GO:0006281 GO:0006302 GO:0006511 GO:0006734 GO:0006810 GO:0006888 GO:0006919 GO:0006974 GO:0008289 GO:0010918 GO:0016567 GO:0016787 GO:0016887 GO:0018279 GO:0019079 GO:0019903 GO:0019904 GO:0019985 GO:0030433 GO:0030968 GO:0030970 GO:0031334 GO:0031593 GO:0031625 GO:0032403 GO:0032436 GO:0034098 GO:0034214 GO:0035800 GO:0035861 GO:0036435 GO:0036503 GO:0036513 GO:0042288 GO:0042802 GO:0042981 GO:0043161 GO:0043209 GO:0043231 GO:0043234 GO:0043531 GO:0044389 GO:0044822 GO:0045184 GO:0045732 GO:0046034 GO:0048471 GO:0051260 GO:0070062 GO:0070842 GO:0070987 GO:0071712 GO:0072389 GO:1903006 GO:1903007 GO:1903715 GO:1903862 GO:1904288 GO:1990381 GO:1990730 GO:2001171
170.070.4564.590.100.674d80F GO:0005524
180.070.4664.220.120.685eumA GO:0000166 GO:0005319 GO:0005524 GO:0005886 GO:0006810 GO:0006869 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0034040 GO:0042626 GO:0043190 GO:0055085


Consensus prediction of GO terms
 
Molecular Function GO:0005524 GO:0046404 GO:0047846 GO:0004385 GO:0005525 GO:0046872
GO-Score 0.91 0.45 0.45 0.38 0.33 0.33
Biological Processes GO:0016310 GO:0016032 GO:0016311 GO:0006281 GO:0097056 GO:0046710 GO:0046037
GO-Score 0.86 0.45 0.45 0.45 0.44 0.38 0.38
Cellular Component
GO-Score

(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.