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I-TASSER results for job id Rv0441c

[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
10.21 14 2e83A FMN Rep, Mult 33,35,36,37,38,57,58,59,62,63,64
20.09 6 5jabB 6J4 Rep, Mult 83,85,87,114,116
30.05 3 2ou5A FMN Rep, Mult 77,89,91,116,118
40.04 3 2iab0 III Rep, Mult 20,22,24,25,26,27,29,30,31,32,33,34,36,71,73,75,76,77,87,89,118
50.03 2 1ty9A FMN Rep, Mult 24,75,91,114
60.01 1 3dr2B CA Rep, Mult 31,46
70.01 1 3t91A MN Rep, Mult 91,135
80.01 1 2x8fA CA Rep, Mult 19,134
90.01 1 3hy6A MG Rep, Mult 38,43,65
100.01 1 3gz8A APR Rep, Mult 18,20
110.01 1 2jcbB MG Rep, Mult 102,135

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
10.1571ty9B0.6313.790.1570.8591.4.-.-21,34,37,89
20.0661ci0A0.6203.760.0870.8521.4.3.5NA
30.0602w1kB0.4923.800.0920.7392.3.2.12NA
40.0601bbrH0.4263.970.0580.6343.4.21.5NA
50.0603h09B0.4764.140.0390.7113.4.21.7297
60.0601c5mD0.4763.710.0660.6763.4.21.6NA
70.0601bruP0.4703.990.0850.6833.4.21.71NA
80.0601wv4A0.6243.570.1360.8381.4.3.5NA
90.0602oq5A0.4744.150.0890.7043.4.21.-NA
100.0601fizA0.5024.000.0960.7323.4.21.10NA
110.0602iukA0.4764.540.0590.8031.13.11.12NA
120.0603a31A0.4714.850.0490.8106.1.1.3NA
130.0602iukB0.4824.280.0250.7751.13.11.12NA
140.0601mkwK0.4534.410.0780.7253.4.21.5NA
150.0603cb0A0.4923.110.0710.6621.14.13.3NA
160.0601ucyE0.3664.060.0510.5563.4.21.5NA
170.0601pytD0.4734.310.0780.7183.4.21.2NA
180.0601pfxC0.4773.630.0780.6763.4.21.22NA
190.0601kigH0.4734.140.0730.7043.4.21.6NA
200.0601autC0.4704.180.0520.7043.4.21.69NA
210.0601rfnA0.4753.720.0700.6763.4.21.22NA

(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
00.290.6452.590.190.774zkyA GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
10.250.6801.960.120.794qvbB GO:0004733 GO:0010181 GO:0016491 GO:0030170 GO:0042803 GO:0042816 GO:0042823 GO:0055114
20.240.6182.390.210.752asfA GO:0004733 GO:0005576 GO:0005618 GO:0010181 GO:0016491 GO:0042823 GO:0055114
30.230.6002.930.120.752htdB GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
40.220.6233.250.110.821rfeA GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
50.190.5942.530.130.735escA GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
60.190.5843.180.100.753fkhD GO:0010181 GO:0016491 GO:0055114
70.180.6122.400.130.733db0B GO:0010181 GO:0016491 GO:0055114
80.180.6433.010.110.812arzA GO:0010181 GO:0016491 GO:0055114
90.180.6203.750.090.851nrgA GO:0002230 GO:0004733 GO:0005654 GO:0005737 GO:0005829 GO:0008615 GO:0010181 GO:0016491 GO:0016638 GO:0042816 GO:0042823 GO:0055114 GO:0070062 GO:0098779 GO:0098792
100.170.5942.970.140.752htiA GO:0000166 GO:0010181 GO:0016491 GO:0055114
110.170.6172.650.100.752hq9B GO:0000166 GO:0010181 GO:0016491 GO:0055114
120.170.6132.720.110.753u5wA GO:0010181 GO:0016491 GO:0055114
130.160.6243.570.140.841wv4A GO:0004733 GO:0005829 GO:0008615 GO:0009443 GO:0010181 GO:0016491 GO:0016638 GO:0042816 GO:0055114
140.160.6293.850.130.861jnwA GO:0004733 GO:0005829 GO:0008615 GO:0009443 GO:0010181 GO:0016491 GO:0016638 GO:0042816 GO:0055114
150.160.6233.910.170.861t9mA GO:0000166 GO:0002047 GO:0004733 GO:0008615 GO:0010181 GO:0016491 GO:0016638 GO:0042823 GO:0055114
160.160.6132.890.100.773dnhA GO:0010181 GO:0016491 GO:0055114
170.150.6362.810.150.802iabA GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
180.150.6253.150.120.785bncA GO:0010181 GO:0016491 GO:0055114
190.140.6203.760.090.851ci0A GO:0004733 GO:0005758 GO:0008615 GO:0009443 GO:0010181 GO:0016491 GO:0016638 GO:0055114
200.140.6103.210.100.803dmbA GO:0010181 GO:0016491 GO:0055114
210.140.6533.220.070.832ou5A GO:0000166 GO:0010181 GO:0016491 GO:0055114
220.140.6242.320.130.753f7eA GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
230.130.6172.820.090.753ec6A GO:0000166 GO:0003677 GO:0010181 GO:0016491 GO:0055114
240.120.6233.070.090.782fg9A GO:0000166 GO:0010181 GO:0016491 GO:0055114
250.080.6243.930.130.864hmwB GO:0000166 GO:0004733 GO:0008615 GO:0010181 GO:0016491 GO:0016638 GO:0042823 GO:0055114
260.070.6323.660.080.852i51A GO:0000166 GO:0010181 GO:0016491 GO:0055114
270.070.6173.360.140.822a2jA GO:0004733 GO:0008615 GO:0010181 GO:0016491 GO:0016638 GO:0042816 GO:0042823 GO:0055114
280.070.6313.290.110.822i02A GO:0000166 GO:0010181 GO:0016491 GO:0055114
290.070.6323.770.160.864hmtB GO:0002047 GO:0004733 GO:0008615 GO:0009405 GO:0010181 GO:0016491 GO:0016638 GO:0017000 GO:0042823 GO:0055114
300.070.6213.040.090.812hq7B GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0004733 GO:0010181 GO:0042802 GO:0043168 GO:0046983
GO-Score 0.76 0.76 0.50 0.50 0.50
Biological Processes GO:0055114 GO:0042823 GO:0006767 GO:0044763 GO:0072524
GO-Score 0.76 0.76 0.50 0.50 0.50
Cellular Component GO:0030312
GO-Score 0.48

(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.