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I-TASSER results for job id Rv0372c

[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
10.06 3 3ze6A SBY Rep, Mult 114,116,137,154,181,226,230,233
20.04 2 1gzmA C8E Rep, Mult 230,233
30.04 2 5d51S KR Rep, Mult 116,118,128,137,229
40.04 2 2a68P MG Rep, Mult 224,227
50.04 2 1jb0M CLA Rep, Mult 222,226
60.04 2 1w5cD CLA Rep, Mult 218,221,222,229
70.04 2 5ezmA MPG Rep, Mult 219,222
80.04 2 1xzqA FON Rep, Mult 3,19,38,46,48
90.02 1 1bdiA QNA Rep, Mult 37,52,55
100.02 1 1ibvA UUU Rep, Mult 183,184
110.02 1 3p27A GDP Rep, Mult 122,123,124,125,127,128,129,130,224
120.02 1 2wtfA CA Rep, Mult 193,196
130.02 1 1vpwA QNA Rep, Mult 21,22,47,55,58
140.02 1 1k4pA ZN Rep, Mult 35,228
150.02 1 1c9uA CA Rep, Mult 166,178,186
160.02 1 3q9cH Q9C Rep, Mult 178,201
170.02 1 2fkaA CXS Rep, Mult 135,223,226

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
10.0603mtjA0.4233.430.1070.5181.1.1.3139,227
20.0601b8pA0.4203.380.0990.5181.1.1.37NA
30.0602jfdA0.3116.020.0970.5262.3.1.85NA
40.0602ldxA0.4223.970.1220.5421.1.1.2714
50.0601p1jA0.4324.320.0660.5785.5.1.4NA
60.0602vz8B0.4445.610.0790.7212.3.1.85NA
70.0602f7kA0.4244.040.0720.5582.7.1.35NA
80.0605ldhA0.4123.840.1210.5301.1.1.27NA
90.0605r1rA0.4365.490.0730.6891.17.4.1NA
100.0601cqzB0.4355.380.0520.6973.3.2.10,3.3.2.3NA
110.0601sy7A0.5145.660.0640.8291.11.1.6NA
120.0602h31A0.4624.680.0830.6694.1.1.21,6.3.2.666
130.0601ldxA0.4114.040.1150.5341.1.1.27156,190,221,224
140.0601sy7B0.4915.140.0530.7251.11.1.6224,230,233
150.0603ej6D0.4905.840.0710.8091.11.1.6229
160.0602iufA0.4955.960.0830.8411.11.1.6NA
170.0601cf9A0.4995.820.0870.8171.11.1.6NA
180.0603ej6A0.4895.900.0700.8211.11.1.6NA
190.0602ejwA0.4222.770.1450.4941.1.1.3NA

(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
00.070.5145.660.060.831sy7A GO:0004096 GO:0004601 GO:0005576 GO:0005618 GO:0005619 GO:0005829 GO:0006979 GO:0016491 GO:0020037 GO:0042542 GO:0042744 GO:0046872 GO:0048315 GO:0055114 GO:0098869
10.070.4356.030.070.764b2yA GO:0004096 GO:0004601 GO:0006979 GO:0016491 GO:0020037 GO:0042744 GO:0046872 GO:0055114 GO:0098869
20.070.4885.830.090.802xf2A GO:0004096 GO:0004601 GO:0006979 GO:0016491 GO:0020037 GO:0042744 GO:0046872 GO:0055114 GO:0098869
30.060.3694.160.090.492vrnA GO:0006508 GO:0008233 GO:0016798 GO:0019172 GO:0019243 GO:0019249 GO:0046872
40.060.3563.650.080.454y0nB GO:0016798
50.060.3503.640.090.451g2iA GO:0005737 GO:0006508 GO:0008233 GO:0016787 GO:0016798
60.060.3543.820.070.463l18A GO:0006508 GO:0008233 GO:0016798
70.060.5015.840.090.825bv2P GO:0004096 GO:0004601 GO:0005506 GO:0005737 GO:0005829 GO:0006972 GO:0006974 GO:0006979 GO:0016491 GO:0020037 GO:0042542 GO:0042744 GO:0042802 GO:0046872 GO:0055114 GO:0098869
80.060.2956.540.020.531si8A GO:0004096 GO:0004601 GO:0006979 GO:0016491 GO:0020037 GO:0042744 GO:0046872 GO:0055114 GO:0098869
90.060.3543.540.070.451ba2A GO:0005886 GO:0006810 GO:0006935 GO:0008643 GO:0015145 GO:0015749 GO:0016020 GO:0016021 GO:0030288 GO:0042597
100.060.3096.710.040.574cabA GO:0004096 GO:0004601 GO:0005737 GO:0006979 GO:0016491 GO:0020037 GO:0042542 GO:0042744 GO:0046872 GO:0055114 GO:0098869
110.060.2955.420.030.473ozcA GO:0003824 GO:0004645 GO:0005634 GO:0005737 GO:0005829 GO:0006139 GO:0006166 GO:0006738 GO:0009116 GO:0016740 GO:0016757 GO:0016763 GO:0017061 GO:0019509 GO:0032259 GO:0033574 GO:0043101 GO:0070062
120.060.3066.650.010.571a4eA GO:0000302 GO:0001315 GO:0004096 GO:0004601 GO:0005759 GO:0005777 GO:0005782 GO:0006979 GO:0016491 GO:0020037 GO:0042542 GO:0042744 GO:0046872 GO:0055114 GO:0098869
130.060.2706.260.040.481h99A GO:0003723 GO:0006351 GO:0006355 GO:0045893
140.060.2776.870.060.535akrA GO:0005507 GO:0006807 GO:0016491 GO:0019333 GO:0042128 GO:0042597 GO:0046872 GO:0050421 GO:0055114
150.060.2905.560.030.471u0bB GO:0000166 GO:0004812 GO:0004817 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006423 GO:0008270 GO:0016874 GO:0046872
160.060.2816.610.030.524qoqA GO:0004096 GO:0004601 GO:0006979 GO:0016491 GO:0020037 GO:0042744 GO:0046872 GO:0055114 GO:0098869
170.060.3096.720.040.581qwlA GO:0004096 GO:0004601 GO:0005737 GO:0006979 GO:0016491 GO:0020037 GO:0042744 GO:0046872 GO:0055114 GO:0098869
180.060.3096.700.030.572isaA GO:0004096 GO:0004601 GO:0006979 GO:0016491 GO:0020037 GO:0042744 GO:0046872 GO:0055114 GO:0098869


Consensus prediction of GO terms
 
Molecular Function GO:0043169 GO:0016684 GO:0016209 GO:0046906
GO-Score 0.47 0.37 0.37 0.37
Biological Processes GO:0044248 GO:0006950 GO:0044710 GO:1990748 GO:0042743
GO-Score 0.37 0.37 0.37 0.37 0.37
Cellular Component GO:0005829 GO:0005619 GO:0005576
GO-Score 0.07 0.07 0.07

(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.