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I-TASSER results for job id Rv1835c

[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
10.59 14 3i2gA DBC Rep, Mult 67,126,156,157,189,190,204,325,350
20.04 1 3puiA NA Rep, Mult 180,318,319,322,325,326,329
30.03 1 1mx1C THA Rep, Mult 156,324,325

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
10.4232b4kA0.7753.500.1990.8713.1.1.4367,156,157,322,350
20.1951l7qA0.8251.960.2320.8573.1.1.1NA
30.0601k8qA0.3754.680.1000.4483.1.1.3NA
40.0601mx9D0.4005.430.0860.5103.1.1.1NA
50.0603lxuX0.3686.990.0600.5433.4.14.10154,172
60.0602qr5A0.3803.340.1040.4273.4.19.1NA
70.0601e5tA0.3873.690.1080.4413.4.21.26NA
80.0603g0bB0.3833.300.0930.4283.4.14.5NA
90.0601ivyA0.3804.480.1120.4553.4.16.5194
100.0602pm8A0.3945.340.0650.4953.1.1.8NA
110.0603n2zB0.3604.970.0830.4413.4.16.2156
120.0601cleA0.3975.620.0990.5113.1.1.3NA
130.0602pl5A0.3654.760.0860.4432.3.1.31422
140.0601nx9A0.7763.440.1970.8693.1.1.43172
150.0601orvA0.2868.650.0270.4953.4.14.5NA
160.0601qo9A0.3945.150.0820.4863.1.1.7NA
170.0601b41A0.3955.490.0620.5023.1.1.7NA
180.0601lnsA0.6684.110.1330.7693.4.14.11NA
190.0601maaD0.3985.520.0520.5033.1.1.7NA
200.0601hlgA0.3714.570.0910.4413.1.1.3NA
210.0601r9mB0.3833.300.0970.4283.4.14.5NA

(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
00.340.8251.960.230.863i2gA GO:0005737 GO:0006508 GO:0008239 GO:0016787 GO:0050784 GO:0052689
10.150.7773.400.210.871mpxA GO:0006508 GO:0008239 GO:0016787 GO:0046872 GO:0047658
20.150.7783.400.220.874pf1A GO:0006508 GO:0008239 GO:0016787
30.150.7753.500.200.872b4kA GO:0006508 GO:0008239 GO:0016787 GO:0047658
40.110.6993.080.180.763iiiA GO:0006508 GO:0008239 GO:0016787
50.080.6684.110.130.771lnsA GO:0004177 GO:0005737 GO:0006508 GO:0008233 GO:0008236 GO:0008239 GO:0016787
60.060.3383.640.070.383aikA GO:0008152 GO:0016787 GO:0042802 GO:0052689
70.060.3364.020.090.392xmqA GO:0001818 GO:0005634 GO:0005654 GO:0005737 GO:0005794 GO:0005813 GO:0005815 GO:0005829 GO:0007165 GO:0007275 GO:0007399 GO:0010574 GO:0016055 GO:0021762 GO:0030154 GO:0030426 GO:0042995 GO:0048471 GO:0048662 GO:0070062 GO:0070373 GO:0090361
80.060.2992.880.120.332i3dB GO:0016787
90.060.2418.090.040.402panA GO:0000287 GO:0003824 GO:0009028 GO:0009436 GO:0016829 GO:0030976 GO:0042802 GO:0046296 GO:0071949
100.060.2307.460.030.364peeC GO:0004560 GO:0005975 GO:0006004
110.060.2056.430.060.293hurA GO:0003824 GO:0006522 GO:0008784 GO:0016853 GO:0030170 GO:0030632
120.060.2377.810.040.395hdrC GO:0004560 GO:0005975 GO:0006004
130.060.1805.360.050.233hheA GO:0004751 GO:0006098 GO:0009052 GO:0016853
140.060.1995.850.040.271dosA GO:0003824 GO:0004332 GO:0005618 GO:0005829 GO:0005886 GO:0005975 GO:0006094 GO:0006096 GO:0008270 GO:0016829 GO:0016832 GO:0046872
150.060.1846.270.050.261zcwA GO:0016740
160.060.1855.870.040.254pr3A GO:0003824 GO:0008152 GO:0008782 GO:0008930 GO:0009116 GO:0016787 GO:0016798
170.060.1706.340.080.244gquA GO:0000105 GO:0004424 GO:0005737 GO:0008652 GO:0016829 GO:0040007
180.060.1445.860.040.204mvnD GO:0004252 GO:0005576 GO:0006508 GO:0008233 GO:0008236 GO:0016787


Consensus prediction of GO terms
 
Molecular Function GO:0008239 GO:0052689 GO:0043169
GO-Score 0.64 0.34 0.31
Biological Processes GO:0006508 GO:0050784
GO-Score 0.64 0.34
Cellular Component GO:0005737
GO-Score 0.34

(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.