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I-TASSER results for job id Rv0250c

[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
10.22 19 3uoiQ HEM Rep, Mult 11,14,15,18,38,42,45,48,49
20.05 5 4hfdE MBR Rep, Mult 9,10,48,51
30.04 4 3atsA MG Rep, Mult 88,90
40.04 4 4rynA MPG Rep, Mult 18,21,22,25,42
50.04 4 2y00A 2CV Rep, Mult 17,20,37,44
60.03 3 2ia5C MG Rep, Mult 76,80
70.03 3 1mz9B VDY Rep, Mult 10,13,17
80.02 2 4l35A 22B Rep, Mult 2,3,10,44,51,55
90.02 2 5dwkA 78N Rep, Mult 21,38,41,42,45,50
100.02 2 2q7mA 2CS Rep, Mult 17,19,20,21,23,24
110.01 1 2q7mC 2CS Rep, Mult 8,10,11,12,14,48
120.01 1 3atsA MG Rep, Mult 76,78,81,88
130.01 1 2b0qA MG Rep, Mult 80,88
140.01 1 3iukA MG Rep, Mult 90,95
150.01 1 2ypaB NUC Rep, Mult 40,43

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
10.0801wu0A0.4512.590.0660.6293.6.3.14NA
20.0602pnoL0.6883.180.0990.9174.4.1.20NA
30.0601m56A0.5813.750.0530.9691.9.3.1NA
40.0603mddA0.5993.360.0430.8041.3.99.382
50.0602yyjA0.5833.310.0730.8351.14.13.3NA
60.0601ivhA0.5923.570.0430.8141.3.99.1041
70.0601fbvA0.6333.260.0320.9496.3.2.19NA
80.0602nyfA0.5923.170.0110.8144.3.1.5NA
90.0602h8aA0.6333.480.0670.9282.5.1.1845,48,72
100.0601jqiA0.5953.330.0430.7941.3.99.2NA
110.0602uxwA0.5873.730.0530.8351.3.99.-NA
120.0601bucB0.5973.390.0740.8141.3.99.292
130.0601w27A0.5933.790.0530.8974.3.1.24NA
140.0603czoB0.5613.580.0520.8764.3.1.383
150.0601i0aA0.4773.560.0920.7224.3.2.1NA
160.0603djlA0.6513.440.0530.9171.3.99.-NA
170.0602ebaA0.5913.460.0430.8041.3.99.7NA
180.0601j3uA0.5942.920.0630.8044.3.1.122
190.0601rx0A0.5913.460.1040.8251.3.99.-NA
200.0601k7wD0.5253.400.0440.7834.3.2.190

(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
00.160.6393.670.070.922q7mC GO:0004364 GO:0004464 GO:0004602 GO:0005634 GO:0005635 GO:0005783 GO:0005789 GO:0006691 GO:0008047 GO:0016020 GO:0016021 GO:0019370 GO:0019372 GO:0031965 GO:0043085 GO:0047485 GO:0050544 GO:0070207 GO:0071277 GO:2001300
10.120.6903.160.100.924jrzA GO:0004364 GO:0004464 GO:0004602 GO:0005634 GO:0005635 GO:0005640 GO:0005783 GO:0005789 GO:0006691 GO:0008047 GO:0008289 GO:0010035 GO:0016020 GO:0016021 GO:0016829 GO:0019370 GO:0019372 GO:0032496 GO:0042493 GO:0043085 GO:0043231 GO:0043295 GO:0046982 GO:0048678 GO:0071222 GO:0071299 GO:0098869 GO:2001300
20.110.6943.210.090.934ntaA GO:0004364 GO:0004464 GO:0004602 GO:0005634 GO:0005635 GO:0005640 GO:0005783 GO:0005789 GO:0006691 GO:0008047 GO:0008289 GO:0010035 GO:0016020 GO:0016021 GO:0016829 GO:0019370 GO:0032496 GO:0042493 GO:0043085 GO:0043231 GO:0043295 GO:0046982 GO:0048678 GO:0071222 GO:0071299 GO:0098869
30.110.6693.300.080.964wvmA GO:0005576 GO:0019835 GO:0044179
40.110.6383.580.100.954tweA GO:0003824 GO:0004180 GO:0005886 GO:0006508 GO:0008152 GO:0008233 GO:0008237 GO:0016020 GO:0016021 GO:0016324 GO:0016787 GO:0016805 GO:0046872
50.090.5012.020.050.613k9aA
60.090.6563.400.070.951cx8A GO:0001558 GO:0001618 GO:0001666 GO:0001948 GO:0003725 GO:0004998 GO:0005576 GO:0005615 GO:0005739 GO:0005768 GO:0005886 GO:0005887 GO:0005905 GO:0006879 GO:0006897 GO:0006898 GO:0006953 GO:0007568 GO:0007584 GO:0009897 GO:0009986 GO:0010033 GO:0010035 GO:0010039 GO:0010042 GO:0016020 GO:0016021 GO:0016023 GO:0016032 GO:0016323 GO:0030316 GO:0030544 GO:0032526 GO:0033570 GO:0033572 GO:0035690 GO:0042127 GO:0042470 GO:0042802 GO:0042803 GO:0043231 GO:0044822 GO:0045780 GO:0046688 GO:0046718 GO:0048471 GO:0051087 GO:0055037 GO:0055038 GO:0070062 GO:0072562 GO:0097286 GO:1903561 GO:1990712
70.090.6523.190.050.954wvmB GO:0005576 GO:0019835 GO:0044179
80.070.6063.720.040.955f09A GO:0003824 GO:0004180 GO:0004181 GO:0005737 GO:0005886 GO:0005887 GO:0006508 GO:0006760 GO:0008152 GO:0008233 GO:0008237 GO:0008652 GO:0009986 GO:0016020 GO:0016021 GO:0016787 GO:0016805 GO:0035609 GO:0046872 GO:0070062 GO:1904492 GO:1904493
90.070.6073.630.040.953fedA GO:0003824 GO:0004180 GO:0005886 GO:0006508 GO:0008152 GO:0008233 GO:0008236 GO:0008237 GO:0008239 GO:0008652 GO:0016020 GO:0016021 GO:0016787 GO:0016805 GO:0042135 GO:0046872 GO:0050129
100.070.6143.680.050.983ripA GO:0000226 GO:0000922 GO:0000923 GO:0000930 GO:0005200 GO:0005737 GO:0005813 GO:0005815 GO:0005816 GO:0005829 GO:0005856 GO:0005874 GO:0006461 GO:0007020 GO:0007126 GO:0008274 GO:0015630 GO:0016020 GO:0031122 GO:0043015 GO:0044732 GO:0051011 GO:0051298 GO:0051415 GO:0055037 GO:0090307
110.070.5224.270.020.985flzB GO:0000226 GO:0000922 GO:0000923 GO:0000928 GO:0005200 GO:0005634 GO:0005737 GO:0005813 GO:0005815 GO:0005816 GO:0005822 GO:0005824 GO:0005856 GO:0005874 GO:0007020 GO:0007126 GO:0030472 GO:0031122 GO:0043015 GO:0051011 GO:0051298 GO:0051415 GO:0090307
120.070.4274.700.060.821ampA GO:0004177 GO:0005576 GO:0006508 GO:0008233 GO:0016787 GO:0046872
130.070.4793.260.050.671zb1A GO:0005737 GO:0005768 GO:0006511 GO:0006810 GO:0007034 GO:0007584 GO:0010008 GO:0015031 GO:0016579 GO:0035800 GO:0036010 GO:0043328 GO:0070676 GO:2000158
140.060.4374.350.070.722ek8A GO:0004177 GO:0006508 GO:0046872
150.060.5782.990.090.793ay5A GO:0005634 GO:0005654 GO:0005737 GO:0007049 GO:0051726
160.060.3894.270.010.684nf2A GO:0004585 GO:0005737 GO:0006520 GO:0006526 GO:0006591 GO:0008652 GO:0016597 GO:0016740 GO:0016743
170.060.4084.380.070.733eifA GO:0004252 GO:0005618 GO:0006508 GO:0008233 GO:0008236 GO:0016020 GO:0016787
180.060.3912.570.120.522fztB GO:0046872
190.060.3774.500.050.711f2oA GO:0004177 GO:0004252 GO:0005576 GO:0006508 GO:0008233 GO:0016787 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:1900750 GO:1901681 GO:0046983 GO:0072341 GO:0008047 GO:0004602 GO:0004364 GO:0004464 GO:0050543 GO:0050542
GO-Score 0.44 0.44 0.44 0.44 0.35 0.35 0.35 0.35 0.33 0.33
Biological Processes GO:1901568 GO:0009611 GO:0071396 GO:1901701 GO:1990748 GO:0071219 GO:0032496 GO:0071295 GO:0033189 GO:0019370 GO:0043085 GO:0051260 GO:0070206 GO:0071248 GO:0051592
GO-Score 0.53 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.35 0.35 0.33 0.33 0.33 0.33
Cellular Component GO:0031965 GO:0031968 GO:0016021 GO:0005789
GO-Score 0.44 0.44 0.42 0.35

(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.