[Home] [Server] [About] [Statistics] [Annotation]

I-TASSER results for job id Rv0388c

[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
10.24 7 3s90A III Rep, Mult 21,23,24,27,30,31,34,37,76,90
20.09 2 2g381 III Rep, Mult 3,14,15,17,18,19,20,23,24,27,30,31,33,34,37,38,40,41,44,45,48,52,57,65,72,75,83,86,90,97,154,155,158,164,165,167,168
30.05 1 2g38B MN Rep, Mult 149,152,153
40.04 1 1t01A III Rep, Mult 6,9,10,14,19,23,24,27,30,31,97
50.04 1 2vs0B ZN Rep, Mult 36,84
60.04 1 3mylX POP Rep, Mult 99,100,101,102,103,104,150
70.04 1 1zww0 III Rep, Mult 19,24,27,30,31,34,37,38,77,79,82,83,90,137,138,140,141,144,145,147,148,151,152,155,156,158,159,162,163

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
10.0603b8cB0.4694.910.0570.7283.6.3.6100,148
20.0603gtdA0.4964.040.0740.7114.2.1.246
30.0602o6yA0.4644.670.0870.7064.3.1.-NA
40.0603i9wA0.6043.700.0620.8392.7.13.338,40,84
50.0602pfdB0.4633.570.0600.6282.1.2.5,4.3.1.4NA
60.0601dcnB0.4953.460.0450.6564.3.2.1137
70.0601f1oA0.4813.730.0390.6444.3.2.2NA
80.0601ynnJ0.2395.480.0570.4282.7.7.6118,128
90.0601i0aA0.4933.740.0540.6834.3.2.1NA
100.0603e04D0.5044.230.0740.7284.2.1.2102
110.0602zr3B0.4733.650.0330.6506.1.1.11NA
120.0602iw5A0.4654.510.0230.6671.-.-.-NA
130.0601j3uA0.5114.080.0770.7174.3.1.1NA
140.0602np0A0.4525.030.0460.7503.4.24.69NA
150.0601qd1B0.2555.210.0600.4282.1.2.5,4.3.1.4NA
160.0601k7wD0.4923.850.0540.6894.3.2.1NA
170.0601w27A0.5124.200.0570.7394.3.1.24NA
180.0602vuaA0.2525.670.0180.4563.4.24.69137
190.0601sesA0.4283.720.0630.6116.1.1.1117,155

(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
00.520.8771.920.310.974kxrB GO:0005576 GO:0009405 GO:0009986
10.160.7462.330.160.873j83A GO:0005576 GO:0009405 GO:0044315
20.100.6773.670.040.952d4cB GO:0000139 GO:0002090 GO:0005737 GO:0005829 GO:0005886 GO:0006897 GO:0007018 GO:0007165 GO:0007417 GO:0008289 GO:0016020 GO:0019886 GO:0030669 GO:0042059 GO:0042802 GO:0048488 GO:0070062
30.080.6613.900.080.952rajA GO:0000281 GO:0001726 GO:0005545 GO:0005737 GO:0005768 GO:0005794 GO:0005802 GO:0005886 GO:0005913 GO:0006810 GO:0006886 GO:0006897 GO:0006898 GO:0007049 GO:0007067 GO:0008289 GO:0015031 GO:0016020 GO:0016023 GO:0016050 GO:0016197 GO:0030136 GO:0030659 GO:0031234 GO:0031410 GO:0031625 GO:0032461 GO:0035091 GO:0036089 GO:0042803 GO:0042995 GO:0043547 GO:0045860 GO:0051044 GO:0051301 GO:0060988 GO:0070062 GO:0071933 GO:0097320 GO:0098609 GO:0098641
40.070.7412.090.140.844xxxA GO:0005576 GO:0009405 GO:0044315
50.070.6584.080.070.984akvB GO:0000281 GO:0005737 GO:0005768 GO:0005829 GO:0006810 GO:0006886 GO:0006897 GO:0007032 GO:0007049 GO:0007067 GO:0015031 GO:0016020 GO:0016023 GO:0016050 GO:0016197 GO:0017038 GO:0019898 GO:0030659 GO:0031410 GO:0035091 GO:0036089 GO:0042802 GO:0044351 GO:0045806 GO:0051044 GO:0051301 GO:0097320 GO:2000009 GO:2000010
60.070.5375.120.030.922z0vA GO:0005737 GO:0005768 GO:0005769 GO:0006897 GO:0007165 GO:0007417 GO:0008289 GO:0016020 GO:0031901 GO:0042802 GO:0070062
70.060.3283.520.040.431ocuA GO:0000139 GO:0000407 GO:0005737 GO:0005768 GO:0005794 GO:0005829 GO:0006810 GO:0006897 GO:0006914 GO:0008104 GO:0008289 GO:0015031 GO:0016020 GO:0016050 GO:0019898 GO:0031902 GO:0032258 GO:0032266 GO:0034499 GO:0035091
80.060.2575.850.040.484dziC GO:0016787
90.060.2585.240.030.432zg6B GO:0008152 GO:0016787
100.060.2652.460.090.325fvlA GO:0000166 GO:0005524 GO:0005634 GO:0005768 GO:0006810 GO:0007033 GO:0008568 GO:0010008 GO:0015031 GO:0016020 GO:0016125 GO:0016236 GO:0016887 GO:0031122 GO:0032511 GO:0042802 GO:0042803 GO:0045053 GO:0045324 GO:0051260 GO:0070676 GO:1990621
110.060.2714.130.020.392j5bA GO:0000166 GO:0004812 GO:0004831 GO:0005524 GO:0006412 GO:0006418 GO:0016874 GO:0042802
120.060.2544.240.100.373luiC GO:0003279 GO:0005102 GO:0005737 GO:0005768 GO:0005769 GO:0005794 GO:0005829 GO:0006707 GO:0006810 GO:0006886 GO:0006898 GO:0007165 GO:0008022 GO:0008289 GO:0010008 GO:0015031 GO:0016020 GO:0016023 GO:0016197 GO:0030100 GO:0030659 GO:0031410 GO:0035091 GO:0035904 GO:0043231 GO:0043234 GO:0050750 GO:0060976 GO:1990126
130.060.2434.860.090.372mxcA GO:0005737 GO:0005768 GO:0005769 GO:0005829 GO:0006810 GO:0008289 GO:0009617 GO:0010008 GO:0010314 GO:0010324 GO:0010976 GO:0015031 GO:0016055 GO:0019898 GO:0019903 GO:0022615 GO:0030111 GO:0030136 GO:0030904 GO:0031410 GO:0031901 GO:0032009 GO:0032266 GO:0035091 GO:0042177 GO:0045335 GO:0046597 GO:0050765 GO:0051224 GO:0070062 GO:0070273 GO:0070676 GO:0080025 GO:2000642
140.060.3044.220.040.422cskA GO:0005769 GO:0006810 GO:0008289 GO:0010629 GO:0010955 GO:0015031 GO:0016020 GO:0016050 GO:0019898 GO:0019899 GO:0030100 GO:0035091 GO:0042177 GO:0051224 GO:0070062 GO:2000642
150.060.2773.470.030.361xteA GO:0000166 GO:0001558 GO:0004672 GO:0004674 GO:0005246 GO:0005524 GO:0005768 GO:0005769 GO:0006468 GO:0006883 GO:0010765 GO:0015459 GO:0016023 GO:0016301 GO:0016310 GO:0016740 GO:0017080 GO:0017081 GO:0018105 GO:0031410 GO:0032411 GO:0035091 GO:0035556 GO:0042127 GO:0055037 GO:2001240
160.060.2685.520.060.471gveA GO:0004032 GO:0004033 GO:0005737 GO:0009636 GO:0016491 GO:0046222 GO:0046223 GO:0055114
170.060.2735.650.020.501gveB GO:0004032 GO:0004033 GO:0005737 GO:0009636 GO:0016491 GO:0046222 GO:0046223 GO:0055114
180.060.2424.540.040.372i4kA GO:0005154 GO:0005158 GO:0005737 GO:0005768 GO:0005769 GO:0005794 GO:0005829 GO:0005913 GO:0006810 GO:0006886 GO:0008289 GO:0010008 GO:0015031 GO:0016020 GO:0016050 GO:0016197 GO:0019898 GO:0030027 GO:0030904 GO:0030905 GO:0031623 GO:0031901 GO:0031982 GO:0034498 GO:0035091 GO:0042147 GO:0042802 GO:0042803 GO:0042995 GO:0043231 GO:0043234 GO:0045732 GO:0046982 GO:0072673 GO:0098609 GO:0098641 GO:1990459 GO:1990460


Consensus prediction of GO terms
 
Molecular Function GO:0005545 GO:0031625 GO:0071933 GO:0098641 GO:0042803
GO-Score 0.08 0.08 0.08 0.08 0.08
Biological Processes GO:0009405 GO:0009306 GO:0071806 GO:0016192
GO-Score 0.62 0.44 0.44 0.35
Cellular Component GO:0009986 GO:1903561 GO:0071944 GO:0031988 GO:0044424
GO-Score 0.52 0.35 0.35 0.35 0.35

(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.