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I-TASSER results for job id Rv1174c

[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 5 3qvdA FE Rep, Mult 12,15,49
20.08 4 2c0rA PLP Rep, Mult 36,37
30.06 3 4jolA III Rep, Mult 18,21
40.06 3 2c6pA UUU Rep, Mult 52,55,56,59,66
50.04 2 2z0aA GLY Rep, Mult 53,69,70,73
60.04 2 2fonA FAD Rep, Mult 52,59,68,69,72,103,105,106
70.04 2 2uuhA GSH Rep, Mult 18,22,25,26,41,45
80.02 1 3hdlA UUU Rep, Mult 40,43
90.02 1 5dwkA 78N Rep, Mult 20,43,46,47,50,55
100.02 1 2qtsC MAL Rep, Mult 13,17
110.02 1 4ismA ZN Rep, Mult 27,32
120.02 1 4l6v6 CLA Rep, Mult 4,8

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
10.0992h8aA0.5923.520.0610.8912.5.1.1834
20.0603fedA0.5893.750.0580.9463.4.17.21NA
30.0601fgjA0.5393.280.0410.7731.7.3.496
40.0603dwwA0.5374.230.0950.9365.3.99.398
50.0603czoB0.5663.520.0800.8464.3.1.3NA
60.0602fonB0.6073.400.0930.9181.3.3.6NA
70.0602pfmA0.5902.940.0280.8004.3.2.2NA
80.0602hroA0.5333.340.0760.7732.7.3.9NA
90.0603djlA0.5483.600.0450.8821.3.99.-NA
100.0602ix6E0.5383.080.0480.7731.3.3.669
110.0602ix6A0.5383.080.0480.7731.3.3.6NA
120.0602uxwA0.5713.570.0780.8641.3.99.-22
130.0602e9fB0.5682.830.1040.7824.3.2.1NA
140.0601l8aA0.5443.890.0710.8731.2.4.1NA
150.0603exeA0.5463.930.0730.8641.2.4.1NA
160.0602v8tA0.5584.220.0990.9181.11.1.642
170.0601z8lA0.5863.610.0670.9363.4.17.21NA
180.0601m56A0.5534.330.1120.9731.9.3.1NA
190.0602wqdA0.5433.850.0830.8462.7.3.9NA
200.0603i39X0.5423.230.0560.7911.2.99.276

(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
00.200.6473.300.060.941fbvA GO:0001784 GO:0003700 GO:0004842 GO:0004871 GO:0005509 GO:0005634 GO:0005737 GO:0005829 GO:0005886 GO:0005913 GO:0006355 GO:0007166 GO:0007173 GO:0007179 GO:0008270 GO:0008543 GO:0014068 GO:0016020 GO:0016567 GO:0016600 GO:0016874 GO:0017124 GO:0019901 GO:0023051 GO:0042059 GO:0042787 GO:0043066 GO:0045742 GO:0046872 GO:0046875 GO:0048260 GO:0061630 GO:0098609 GO:0098641
10.110.6983.050.090.963op0A GO:0001784 GO:0004842 GO:0004871 GO:0005154 GO:0005509 GO:0005634 GO:0007166 GO:0007175 GO:0008270 GO:0016567 GO:0016874 GO:0017124 GO:0023051 GO:0042059 GO:0042787 GO:0043407 GO:0046872 GO:0061630 GO:0070062
20.080.6473.590.050.953zniA GO:0000209 GO:0001784 GO:0004842 GO:0004871 GO:0005509 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0005886 GO:0006607 GO:0007165 GO:0007166 GO:0008270 GO:0009629 GO:0009725 GO:0016567 GO:0016874 GO:0019901 GO:0023051 GO:0045121 GO:0046872
30.070.6473.620.040.953pfvB GO:0000209 GO:0001784 GO:0004842 GO:0004871 GO:0005509 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0005886 GO:0006607 GO:0007165 GO:0007166 GO:0008270 GO:0009629 GO:0009725 GO:0016567 GO:0016874 GO:0019901 GO:0023051 GO:0045121 GO:0046872
40.070.5793.280.050.833vrqA GO:0001784 GO:0004842 GO:0004871 GO:0005154 GO:0005509 GO:0005634 GO:0007166 GO:0007175 GO:0008270 GO:0016567 GO:0016874 GO:0017124 GO:0023051 GO:0042059 GO:0042787 GO:0043407 GO:0046872 GO:0061630 GO:0070062
50.060.3364.780.090.652ywcA GO:0000166 GO:0003922 GO:0005524 GO:0006164 GO:0006177 GO:0006541 GO:0016462 GO:0016874
60.060.3284.560.030.611ijxA GO:0004930 GO:0005576 GO:0005615 GO:0007186 GO:0007275 GO:0008285 GO:0010721 GO:0014033 GO:0016021 GO:0016055 GO:0017147 GO:0030154 GO:0030178 GO:0030308 GO:0035567 GO:0042472 GO:0042813 GO:0043065 GO:0045600 GO:0060029 GO:0061037 GO:0061053 GO:0070367 GO:0090090 GO:0090103
70.060.6383.310.050.923ay5A GO:0005634 GO:0005654 GO:0005737 GO:0007049 GO:0051726
80.060.3374.430.050.625ekqD GO:0009279 GO:0016020 GO:0043165 GO:0051205 GO:1990063
90.060.3204.750.050.583pcoB GO:0000049 GO:0000166 GO:0000287 GO:0003723 GO:0004812 GO:0004826 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006432 GO:0008033 GO:0009328 GO:0016020 GO:0016874 GO:0042802 GO:0046872
100.060.3084.140.010.513sipF GO:0000209 GO:0004842 GO:0004869 GO:0005634 GO:0005737 GO:0005876 GO:0006915 GO:0007275 GO:0007283 GO:0007289 GO:0007298 GO:0007423 GO:0008270 GO:0008354 GO:0008407 GO:0016055 GO:0016874 GO:0031398 GO:0031624 GO:0031625 GO:0042787 GO:0043027 GO:0043066 GO:0043154 GO:0044390 GO:0045035 GO:0045116 GO:0046673 GO:0046872 GO:0048800 GO:0051865 GO:0061630 GO:0061663 GO:0070936 GO:0089720 GO:0090263 GO:0090307 GO:0097340 GO:1990001 GO:1990381 GO:2001271
110.060.3284.520.050.575aitA GO:0003677 GO:0004842 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0006351 GO:0006355 GO:0007283 GO:0008270 GO:0008584 GO:0016567 GO:0016605 GO:0016874 GO:0017025 GO:0030331 GO:0031491 GO:0031624 GO:0032184 GO:0032355 GO:0033142 GO:0033234 GO:0033768 GO:0042803 GO:0043161 GO:0044752 GO:0045893 GO:0045944 GO:0046685 GO:0046872 GO:0050681 GO:0051865 GO:0060548 GO:0061630 GO:0070534 GO:0070936 GO:0070979 GO:0071243 GO:0071345 GO:0071394 GO:0071480 GO:0072711 GO:0085020 GO:0090169 GO:0090234
120.060.3054.980.020.542iosA GO:0003723 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0006915 GO:0007569 GO:0034393 GO:0043066 GO:0043508 GO:0045892 GO:0051246 GO:1904761
130.060.2704.190.080.443lrqD GO:0000122 GO:0003682 GO:0004842 GO:0005164 GO:0005622 GO:0005737 GO:0005777 GO:0005829 GO:0006351 GO:0008270 GO:0016235 GO:0016567 GO:0016874 GO:0031625 GO:0032088 GO:0035098 GO:0035518 GO:0036353 GO:0042803 GO:0046600 GO:0046872 GO:0048471 GO:0051091 GO:0051092 GO:0051865 GO:0061630 GO:0070842
140.060.2843.860.040.452l0bA GO:0005737 GO:0008270 GO:0016567 GO:0016874 GO:0030163 GO:0046872 GO:0061630
150.060.3104.370.050.533da7A GO:0003723 GO:0004518 GO:0004519 GO:0004521 GO:0004540 GO:0005576 GO:0016787 GO:0090305 GO:0090501 GO:0090502
160.060.3255.340.060.671q20A GO:0000103 GO:0004027 GO:0005634 GO:0005737 GO:0005783 GO:0005829 GO:0006629 GO:0008146 GO:0008202 GO:0016740 GO:0043231 GO:0050294 GO:0050427 GO:0070062
170.060.2524.780.060.453knvA GO:0000151 GO:0002726 GO:0004842 GO:0004871 GO:0005102 GO:0005164 GO:0005174 GO:0005737 GO:0005829 GO:0005938 GO:0006461 GO:0006915 GO:0006919 GO:0007165 GO:0007249 GO:0007250 GO:0008270 GO:0008289 GO:0009898 GO:0010803 GO:0010939 GO:0012506 GO:0016567 GO:0016874 GO:0019899 GO:0019901 GO:0019903 GO:0030163 GO:0031435 GO:0031625 GO:0031996 GO:0032403 GO:0032743 GO:0033209 GO:0034351 GO:0034976 GO:0035631 GO:0042802 GO:0042981 GO:0043123 GO:0043234 GO:0043507 GO:0043623 GO:0045121 GO:0046328 GO:0046625 GO:0046872 GO:0050870 GO:0051023 GO:0051091 GO:0051092 GO:0051291 GO:0051865 GO:0070059 GO:0070207 GO:0070534 GO:0071550 GO:0071732 GO:0090073 GO:0097057 GO:0097296 GO:0097300 GO:1901215 GO:1902041 GO:1902042 GO:1903265 GO:1903721 GO:1990597 GO:1990604 GO:2001238
180.060.2684.830.000.484rndB GO:0000221 GO:0000329 GO:0006810 GO:0006811 GO:0007035 GO:0015991 GO:0015992 GO:0033180 GO:0034220 GO:0046961


Consensus prediction of GO terms
 
Molecular Function GO:0004871 GO:0008270 GO:0001784 GO:0005509 GO:0016874 GO:0001071 GO:0098632 GO:0045296 GO:0017124 GO:0061630 GO:0070851 GO:0019901
GO-Score 0.43 0.43 0.43 0.43 0.43 0.41 0.41 0.41 0.34 0.34 0.34 0.32
Biological Processes GO:1903506 GO:0042981 GO:0006351 GO:1901186 GO:0007155 GO:0048259 GO:1902533 GO:0044344 GO:0045807 GO:0071560 GO:2000112 GO:0043069 GO:0014066 GO:0010468 GO:0007178 GO:0043405 GO:0042787 GO:0007176 GO:0061099 GO:0071901 GO:0042059 GO:2000272 GO:0043409
GO-Score 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.34 0.34 0.34 0.34 0.34 0.34 0.34 0.34
Cellular Component GO:0005634 GO:0005912 GO:0098797 GO:0005911 GO:0005901 GO:1903561 GO:0031988 GO:0005829
GO-Score 0.43 0.41 0.41 0.41 0.41 0.34 0.34 0.32

(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.