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I-TASSER results for job id Rv0387c

[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
10.07 4 1izlA CLA Rep, Mult 221,222
20.05 3 3pfdD FDA Rep, Mult 204,205,224,225,228
30.05 3 3fbyC CA Rep, Mult 24,26,57,59,62,63,64,67
40.05 3 4v1fA BQ1 Rep, Mult 231,232,235
50.05 3 5d56A 78M Rep, Mult 226,227,230
60.03 2 2jifD FAD Rep, Mult 111,113,120,124,137,237
70.03 2 4wzsB NUC Rep, Mult 229,231,232
80.02 1 3pipA MG Rep, Mult 63,73
90.02 1 1u8vC FAD Rep, Mult 167,169,204,205,207,208
100.02 1 3kitP MG Rep, Mult 204,209
110.02 1 3pfdA FDA Rep, Mult 166,175,223,224,227
120.02 1 5tglA HEE Rep, Mult 104,154
130.02 1 2bhwA CLA Rep, Mult 151,153
140.02 1 1yklG DHB Rep, Mult 183,184
150.02 1 2ebaE FAD Rep, Mult 180,182,184,187,190,215,218
160.02 1 4durA UUU Rep, Mult 90,92,93
170.02 1 1jqiB FAD Rep, Mult 113,116,238

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
10.0603ii9C0.4065.890.0570.6931.3.99.7205
20.0602wbiB0.3936.440.0540.7131.3.99.-212
30.0601siqA0.4125.890.0530.6971.3.99.7154
40.0601pg3B0.3895.980.0610.6686.2.1.1221
50.0601rx0A0.4115.960.0670.6971.3.99.-212
60.0603d9dA0.4185.800.0670.6971.7.3.1NA
70.0601ukwA0.4085.820.0890.6891.3.99.3NA
80.0603gpbA0.3896.010.0800.6722.4.1.1NA
90.0601jqiA0.4135.960.0870.6971.3.99.2NA
100.0602yyjA0.3996.570.0430.7341.14.13.3NA
110.0601u8vA0.4146.490.0520.7465.3.3.3NA
120.0602pm8A0.3896.420.0770.7213.1.1.8NA
130.0602vdcA0.3916.410.0270.7051.4.1.13NA
140.0601e1yA0.3325.750.0320.5412.4.1.1NA
150.0601ivhA0.4115.710.0400.6761.3.99.10NA
160.0601b41A0.3986.320.1170.7253.1.1.7NA
170.0602c4mC0.4066.070.0470.7092.4.1.1NA
180.0601ygpA0.3985.770.0410.6722.4.1.1NA
190.0601k4yA0.3466.460.0380.6233.1.1.1NA

(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
00.230.9211.640.050.984nl6A GO:0000245 GO:0000387 GO:0003723 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0006353 GO:0006397 GO:0007399 GO:0008380 GO:0015030 GO:0030018 GO:0032797 GO:0034719 GO:0036464 GO:0042802 GO:0043005 GO:0043204 GO:0051170 GO:0097504
10.090.4075.820.060.692jbsC GO:0000166 GO:0004497 GO:0008152 GO:0016491 GO:0016627 GO:0019439 GO:0050660 GO:0052881 GO:0055114
20.070.4135.750.060.693pfdC GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
30.070.4115.850.060.702ebaA GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
40.070.3906.150.050.693oibA GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
50.060.3526.510.090.655iduC GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
60.060.4155.680.100.684m9aB GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
70.060.4095.860.080.684ktoA GO:0000166 GO:0003995 GO:0008152 GO:0008470 GO:0016491 GO:0016627 GO:0050660 GO:0055114
80.060.4125.790.060.693swoA GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
90.060.4165.790.060.694irnA GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
100.060.4235.790.070.702dvlA GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
110.060.4135.960.090.701jqiA GO:0000062 GO:0003995 GO:0004085 GO:0005739 GO:0005759 GO:0006629 GO:0006631 GO:0006635 GO:0008152 GO:0009055 GO:0016491 GO:0016627 GO:0031966 GO:0033539 GO:0042594 GO:0046359 GO:0050660 GO:0051289 GO:0051384 GO:0055088 GO:0055114
120.060.3235.480.090.514n5fA GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
130.060.4125.830.060.702r0mA GO:0000062 GO:0003995 GO:0004361 GO:0005739 GO:0005759 GO:0006554 GO:0006568 GO:0006637 GO:0008152 GO:0009055 GO:0016491 GO:0016627 GO:0019395 GO:0033539 GO:0046949 GO:0050660 GO:0052890 GO:0055088 GO:0055114
140.060.4095.790.080.682jifA GO:0000062 GO:0003995 GO:0005739 GO:0005759 GO:0006629 GO:0006631 GO:0008152 GO:0009055 GO:0009083 GO:0016491 GO:0016627 GO:0033539 GO:0050660 GO:0052890 GO:0055088 GO:0055114 GO:0070062
150.060.4035.870.070.692pg0A GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
160.060.4055.630.110.683r7kA GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
170.060.4125.760.070.684l1fA GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
180.060.4125.890.060.695af7B GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0000166 GO:0050662 GO:0005515 GO:0003676 GO:0003824
GO-Score 0.52 0.52 0.45 0.45 0.36
Biological Processes GO:0044710 GO:0048731 GO:0006351 GO:0000398 GO:0022618 GO:0006913
GO-Score 0.52 0.45 0.45 0.45 0.45 0.45
Cellular Component GO:0043234 GO:0042995 GO:0035770 GO:0043025 GO:0016604 GO:0031674
GO-Score 0.45 0.45 0.45 0.45 0.45 0.45

(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.