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I-TASSER results for job id Rv2704

[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
10.63 26 1oniC BEZ Rep, Mult 20,34,36,107,114
20.14 6 2uynA 2KT Rep, Mult 34,36,114
30.12 8 3du7C HOS Rep, Mult 80,83,84,98,100
40.10 6 3i3fC BUA Rep, Mult 15,20,34,108
50.04 4 3d01H PG5 Rep, Mult 110
60.01 1 3d01A PG5 Rep, Mult 79,81
70.01 1 3i3fA LEA Rep, Mult 98,99,100
80.01 1 2b33B CA Rep, Mult 39
90.01 1 1oniB BEZ Rep, Mult 74,77,80,100
100.01 1 2uyjA EDO Rep, Mult 20,34
110.01 1 3vczB MG Rep, Mult 76,78

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
10.0671ufyA0.4753.400.1080.6625.4.99.5NA
20.0601cpyA0.4274.950.0960.7393.4.16.5NA
30.0603kizB0.5542.950.0810.7256.3.3.111,106
40.0601w0iA0.4994.240.0940.7682.3.1.41NA
50.0603a31A0.4973.940.0700.7686.1.1.354
60.0602pffD0.4994.810.1060.8102.3.1.8653
70.0601qf6A0.4974.640.0500.8176.1.1.3NA
80.0601ivyA0.4984.340.0370.7823.4.16.5NA
90.0601t3tA0.5783.670.0630.8106.3.5.3NA
100.0602zodB0.5672.740.0750.7182.7.9.323
110.0603h8eA0.5023.870.0680.7113.4.11.1NA
120.0601hp4A0.4934.030.0530.7533.2.1.52NA
130.0601kogH0.4354.610.0490.7396.1.1.347,114
140.0601yhtA0.4934.220.0500.7683.2.1.52NA
150.0602veoB0.5024.370.0660.7683.1.1.337,42
160.0601ac5A0.4964.360.0580.7893.4.16.6NA
170.0601h7rA0.4974.370.0640.7894.2.1.24NA
180.0602vhhC0.4934.270.0840.7753.5.1.6NA
190.0603fd5B0.5593.220.0950.7612.7.9.3NA
200.0602btuA0.5012.840.0580.6486.3.3.1NA

(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
00.640.7791.320.990.833i7tA GO:0005886
10.480.7451.490.260.811qu9A GO:0005737 GO:0005829 GO:0008652 GO:0009082 GO:0009097 GO:0009636 GO:0016020 GO:0016787 GO:0019239 GO:0042802 GO:0051082
20.420.8291.440.270.891oniA GO:0001822 GO:0004518 GO:0004519 GO:0005634 GO:0005737 GO:0005739 GO:0005777 GO:0005829 GO:0006449 GO:0007420 GO:0016787 GO:0016892 GO:0017148 GO:0030324 GO:0033993 GO:0036041 GO:0042803 GO:0043167 GO:0044822 GO:0046914 GO:0050680 GO:0070062 GO:0070314 GO:0090502 GO:1902074 GO:1904012 GO:1904013
30.420.8021.350.280.861qahA GO:0001822 GO:0004518 GO:0004519 GO:0005634 GO:0005737 GO:0005739 GO:0005777 GO:0005829 GO:0007420 GO:0016787 GO:0016892 GO:0017148 GO:0030324 GO:0033993 GO:0036041 GO:0042803 GO:0043167 GO:0044822 GO:0046914 GO:0050680 GO:0070062 GO:0070314 GO:0090305 GO:0090502 GO:1902074 GO:1904012 GO:1904013
40.380.8071.440.280.871nq3A GO:0004518 GO:0004519 GO:0009986 GO:0016787 GO:0090305
50.340.6931.490.300.762cwjA GO:0016787
60.340.7581.370.290.821qd9A GO:0005737 GO:0008652 GO:0009082 GO:0009097 GO:0009636 GO:0016787 GO:0019239 GO:0046360
70.340.7631.510.270.831jd1A GO:0005634 GO:0005737 GO:0005739 GO:0005758 GO:0005829
80.330.7431.820.280.841pf5A
90.300.7781.510.280.853v4dF GO:0006212 GO:0016491 GO:0019740 GO:0055114
100.140.7581.480.240.822uyjA GO:0006566 GO:0016787 GO:0042802 GO:0070689
110.140.7571.490.230.823quwA GO:0005739 GO:0005759 GO:0009097 GO:0032543
120.100.6821.170.220.733lybB
130.060.3945.200.050.753ozqA GO:0005615
140.060.4084.710.040.663dwcB GO:0004180 GO:0004181 GO:0006508 GO:0016787
150.060.2765.490.050.533tswB GO:0001825 GO:0005516 GO:0005634 GO:0005737 GO:0005829 GO:0005886 GO:0005911 GO:0005912 GO:0005913 GO:0005921 GO:0005923 GO:0007043 GO:0007605 GO:0014704 GO:0016020 GO:0016323 GO:0016324 GO:0016327 GO:0019904 GO:0030054 GO:0035329 GO:0043296 GO:0045177 GO:0046581 GO:0090557 GO:0098609 GO:0098641 GO:1901350
160.060.4405.200.050.821flgA GO:0005509 GO:0006069 GO:0016020 GO:0016491 GO:0016614 GO:0018468 GO:0030288 GO:0042597 GO:0046872 GO:0052934 GO:0052935 GO:0052936 GO:0055114
170.060.2883.920.040.424lowA GO:0006729 GO:0008124
180.060.2713.660.100.374q2qA GO:0001825 GO:0005516 GO:0005634 GO:0005737 GO:0005829 GO:0005886 GO:0005911 GO:0005912 GO:0005913 GO:0005921 GO:0005923 GO:0007043 GO:0007605 GO:0014704 GO:0016020 GO:0016323 GO:0016324 GO:0016327 GO:0019904 GO:0030054 GO:0035329 GO:0043296 GO:0045177 GO:0046581 GO:0090557 GO:0098609 GO:0098641 GO:1901350


Consensus prediction of GO terms
 
Molecular Function GO:0044822 GO:0042803 GO:0016892 GO:1904012 GO:0036041 GO:0046914 GO:1904013 GO:0051082 GO:0019239
GO-Score 0.66 0.66 0.66 0.66 0.66 0.66 0.66 0.48 0.48
Biological Processes GO:0050680 GO:0007420 GO:0030324 GO:0090502 GO:1902074 GO:0033993 GO:0017148 GO:0001822 GO:0070314 GO:0008652 GO:0009097 GO:0009636 GO:0006449
GO-Score 0.66 0.66 0.66 0.66 0.66 0.66 0.66 0.66 0.66 0.48 0.48 0.48 0.42
Cellular Component GO:0005829 GO:0005777 GO:0070062 GO:0005634 GO:0005739 GO:0005886 GO:0009986
GO-Score 0.82 0.66 0.66 0.66 0.66 0.64 0.38

(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.