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I-TASSER results for job id Rv2175c

[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 10 1znnB SO4 Rep, Mult 136,139,140
20.07 3 2wieC CVM Rep, Mult 81,84,88
30.04 2 1c6dA KR Rep, Mult 88,98,101,126,129,140
40.02 1 4o6mA MPG Rep, Mult 88,101
50.02 1 2d2mD OXY Rep, Mult 133,137
60.02 1 1p8j0 III Rep, Mult 56,58,59,126
70.02 1 3o72C OXY Rep, Mult 90,139
80.02 1 3fcsC IMD Rep, Mult 103,133
90.02 1 1aorB SF4 Rep, Mult 69,71,99,103
100.02 1 2wpnB SF4 Rep, Mult 59,68
110.02 1 2yl8A MN Rep, Mult 31,77

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
10.0601euzF0.4325.200.0800.8151.4.1.395
20.0602aw5B0.4464.330.0470.7331.1.1.40NA
30.0601hrdA0.4395.070.1070.8081.4.1.279,84
40.0602ecfA0.4334.820.0750.7263.4.14.5NA
50.0602dvmA0.4724.780.0920.7941.1.1.38NA
60.0602hldK0.4124.750.0450.6783.6.3.14NA
70.0601gytJ0.4365.140.0450.8223.4.11.1128
80.0601thmA0.4504.310.0850.6643.4.21.66NA
90.0602gepA0.4254.290.0400.6641.8.1.2NA
100.0601ah2A0.3954.520.0320.6303.4.21.-NA
110.0603bx1B0.4324.380.0550.6573.4.21.6244
120.0602tohA0.4465.240.0500.8291.14.16.237
130.0601ltuA0.4275.270.0500.7881.14.16.1NA
140.0601dbiA0.4454.190.1090.6573.4.21.-NA
150.0601aupA0.4445.110.0730.8221.4.1.2NA
160.0603e2tA0.4495.000.0440.8011.14.16.4NA
170.0601gq2A0.4065.200.0290.7531.1.1.40NA
180.0601g72A0.4165.320.0380.7811.1.99.8NA
190.0601bvuA0.3915.020.0630.7061.4.1.3NA

(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
00.880.9850.751.001.002kfsA GO:0003677 GO:0018107 GO:0019217
10.110.4065.200.030.751gq2A GO:0004470 GO:0004471 GO:0004473 GO:0005737 GO:0006108 GO:0008948 GO:0016491 GO:0046872 GO:0051287 GO:0055114
20.070.4734.610.070.773qybA GO:0005096 GO:0005622 GO:0005737 GO:0006886 GO:0012505 GO:0016192 GO:0017137 GO:0030659 GO:0031338 GO:0031339 GO:0031988 GO:0032869 GO:0061024 GO:0070062 GO:0090630
30.070.4834.770.070.821b25A GO:0009055 GO:0016491 GO:0016625 GO:0046872 GO:0051536 GO:0051539 GO:0055114
40.070.4155.210.060.752qq8A GO:0005096 GO:0005776 GO:0005794 GO:0005829 GO:0006886 GO:0010507 GO:0017137 GO:0019901 GO:0031338 GO:0055037 GO:0071955 GO:0090630 GO:1902017 GO:2000785
50.070.4584.830.040.782g77A GO:0005096 GO:0005794 GO:0005795 GO:0006886 GO:0016192 GO:0017137 GO:0031338 GO:0090630
60.070.4255.450.100.793nv9A GO:0004470 GO:0004471 GO:0006108 GO:0051287 GO:0055114
70.070.4724.780.090.792dvmA GO:0000166 GO:0004470 GO:0004471 GO:0006108 GO:0051287 GO:0055114
80.070.4345.050.040.763dzxA GO:0005096 GO:0005622 GO:0006886 GO:0012505 GO:0017137 GO:0031338 GO:0071889 GO:0090630 GO:1902017
90.060.4375.040.060.791vl6B GO:0000166 GO:0004470 GO:0004471 GO:0006108 GO:0008948 GO:0016491 GO:0046872 GO:0051287 GO:0055114
100.060.4734.930.070.801vl6A GO:0000166 GO:0004470 GO:0004471 GO:0006108 GO:0008948 GO:0016491 GO:0046872 GO:0051287 GO:0055114
110.060.2725.690.020.534axsA GO:0006525 GO:0008804 GO:0016301 GO:0016310 GO:0016740
120.060.4454.440.040.722a9fA GO:0004470 GO:0004471 GO:0006108 GO:0016491 GO:0046872 GO:0051287 GO:0055114
130.060.4764.740.040.792qfzA GO:0005096 GO:0005622 GO:0006886 GO:0012505 GO:0017137 GO:0031338 GO:0042803 GO:0071889 GO:0090630 GO:1902017
140.060.4534.830.060.773hzjC GO:0005096 GO:0005634 GO:0005769 GO:0005794 GO:0006886 GO:0017137 GO:0031338 GO:0032880 GO:0090630
150.060.4544.740.050.764p17B GO:0005096 GO:0005622 GO:0006886 GO:0012505 GO:0017137 GO:0031338 GO:0090630
160.060.3975.220.060.723wjaB GO:0004470 GO:0004471 GO:0004473 GO:0005737 GO:0005739 GO:0005829 GO:0005975 GO:0006108 GO:0006741 GO:0008948 GO:0009055 GO:0009725 GO:0009743 GO:0016491 GO:0030145 GO:0043531 GO:0046872 GO:0050661 GO:0051262 GO:0051287 GO:0055114 GO:1902031
170.060.4725.130.070.833qyeA GO:0005096 GO:0005622 GO:0005634 GO:0005829 GO:0006886 GO:0012505 GO:0017137 GO:0031338 GO:0032880 GO:0061024 GO:0090630 GO:1902017
180.060.4684.760.080.821aorA GO:0009055 GO:0016491 GO:0016625 GO:0033726 GO:0046872 GO:0051536 GO:0051539 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0003677 GO:0043169
GO-Score 0.88 0.34
Biological Processes GO:0019217 GO:0018107
GO-Score 0.88 0.88
Cellular Component GO:0044424
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.