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I-TASSER results for job id Rv1628c

[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
10.66 19 1e31A ZN Rep, Mult 30,33,47,50

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
10.0601d8yA0.3785.860.0330.7492.7.7.725
20.0601e5mA0.3945.530.0480.7122.3.1.179NA
30.0602ckzB0.4133.910.0260.6072.7.7.667
40.0602uvnA0.3865.180.0860.6691.14.-.-NA
50.0602ecfA0.3975.370.0760.7363.4.14.568,115
60.0601kasA0.4005.670.0480.7242.3.1.179111
70.0601b3nA0.3895.330.0340.6812.3.1.179,2.3.1.41NA
80.0602r93G0.3853.980.0510.5712.7.7.6123
90.0601txgB0.3905.140.0410.6561.1.1.94139
100.0602zsgA0.4014.840.0280.6813.4.11.9NA
110.0603dfjA0.3205.550.0820.5953.4.21.-24,105
120.0603l24A0.3895.050.0790.6933.1.8.2,3.4.13.9,3.1.8.1NA
130.0601k9aB0.3884.070.0430.5832.7.10.2,2.7.1.112115
140.0602wk5A0.3824.980.0670.6562.4.2.4NA
150.0603d7uA0.2845.460.0400.5402.7.10.263
160.0603hkzQ0.4013.950.0390.5892.7.7.689
170.0601txgA0.3944.980.0480.6751.1.1.94NA
180.0601wqlA0.3964.570.0250.6381.14.12.-NA
190.0602c9hA0.3125.530.0520.5892.3.1.41NA

(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
00.360.6812.040.170.763irbA GO:0046872
10.060.4274.080.030.611l1oC GO:0000082 GO:0000722 GO:0000723 GO:0000724 GO:0000784 GO:0003676 GO:0003677 GO:0003684 GO:0003697 GO:0005634 GO:0005654 GO:0005662 GO:0006260 GO:0006261 GO:0006281 GO:0006283 GO:0006284 GO:0006289 GO:0006293 GO:0006294 GO:0006295 GO:0006296 GO:0006297 GO:0006298 GO:0006310 GO:0006974 GO:0016605 GO:0016925 GO:0019985 GO:0033683 GO:0036297 GO:0042276 GO:0042769 GO:0046872 GO:0070987 GO:1900034 GO:1901796
20.060.4295.230.040.774ifdJ GO:0000049 GO:0000175 GO:0000176 GO:0000177 GO:0000178 GO:0000467 GO:0003676 GO:0003723 GO:0004518 GO:0004519 GO:0004521 GO:0004527 GO:0005634 GO:0005730 GO:0005737 GO:0005739 GO:0006364 GO:0016075 GO:0016787 GO:0043628 GO:0070478 GO:0070481 GO:0070651 GO:0071028 GO:0071035 GO:0071038 GO:0071039 GO:0071042 GO:0071051 GO:0090502
30.060.4015.230.050.724pmwA GO:0000175 GO:0000176 GO:0000177 GO:0000287 GO:0000291 GO:0000932 GO:0003723 GO:0004518 GO:0004527 GO:0004540 GO:0005737 GO:0006364 GO:0006402 GO:0007049 GO:0007067 GO:0008266 GO:0008285 GO:0010587 GO:0016075 GO:0016787 GO:0019827 GO:0034427 GO:0046872 GO:0051301 GO:0051306 GO:0090501 GO:0090503 GO:1990074
40.060.3934.340.040.591fguA GO:0000082 GO:0000722 GO:0000723 GO:0000724 GO:0000784 GO:0003676 GO:0003677 GO:0003684 GO:0003697 GO:0005634 GO:0005654 GO:0005662 GO:0006260 GO:0006261 GO:0006281 GO:0006283 GO:0006284 GO:0006289 GO:0006293 GO:0006294 GO:0006295 GO:0006296 GO:0006297 GO:0006298 GO:0006310 GO:0006974 GO:0016605 GO:0016925 GO:0019985 GO:0033683 GO:0036297 GO:0042276 GO:0042769 GO:0046872 GO:0070987 GO:1900034 GO:1901796
50.060.3724.940.020.612ix1A GO:0000175 GO:0000178 GO:0003676 GO:0003723 GO:0004518 GO:0004527 GO:0004540 GO:0005737 GO:0005829 GO:0006364 GO:0006401 GO:0006402 GO:0008859 GO:0016070 GO:0016787 GO:0090305 GO:0090501 GO:0090503
60.060.4004.270.070.583u50C GO:0003676 GO:0046872
70.060.3623.930.030.522k5vA GO:0003676
80.060.3754.300.080.562k50A GO:0003676 GO:0003677 GO:0006260 GO:0006281 GO:0006974 GO:0046872
90.060.3275.550.020.602iqtA GO:0003824 GO:0004332 GO:0006096 GO:0016829
100.060.3654.260.040.551ynxA GO:0000722 GO:0000724 GO:0000781 GO:0000794 GO:0003676 GO:0003677 GO:0003690 GO:0003697 GO:0005634 GO:0005662 GO:0005737 GO:0005829 GO:0006260 GO:0006265 GO:0006268 GO:0006281 GO:0006289 GO:0006310 GO:0006312 GO:0007004 GO:0007131 GO:0010833 GO:0016567 GO:0030491 GO:0043565 GO:0043934 GO:0045184 GO:0046872
110.060.3245.510.030.614ro1B GO:0000175 GO:0000176 GO:0000177 GO:0000291 GO:0000932 GO:0003723 GO:0004518 GO:0004527 GO:0005737 GO:0005829 GO:0006364 GO:0008266 GO:0010587 GO:0016075 GO:0016787 GO:0034427 GO:0046872 GO:0090305 GO:0090503 GO:1990074
120.060.3235.350.060.583jbwB GO:0003677 GO:0003682 GO:0005546 GO:0005547 GO:0005634 GO:0006310 GO:0008270 GO:0016568 GO:0030098 GO:0030183 GO:0033077 GO:0033151 GO:0035064 GO:0035091 GO:0043325 GO:0046872 GO:0048534 GO:0048538 GO:0080025
130.060.3125.480.060.601frvB GO:0008901 GO:0016151 GO:0016491 GO:0042597 GO:0046872 GO:0047806 GO:0055114
140.060.3055.310.050.564iedC GO:0008658
150.060.3085.160.060.523libA GO:0000155 GO:0000160 GO:0004871 GO:0005622 GO:0007165 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0023014
160.060.3005.640.050.594v6wAg GO:0000398 GO:0005080 GO:0005737 GO:0005776 GO:0005829 GO:0005875 GO:0007626 GO:0009267 GO:0016243 GO:0018991 GO:0035220 GO:0042335 GO:0044829 GO:0045725 GO:0046716 GO:0048477 GO:0071011 GO:0071013 GO:0075522
170.060.3135.750.050.623ii0C GO:0003824 GO:0004069 GO:0004609 GO:0005634 GO:0005737 GO:0005739 GO:0005764 GO:0005829 GO:0006094 GO:0006103 GO:0006107 GO:0006114 GO:0006520 GO:0006531 GO:0006532 GO:0006533 GO:0006536 GO:0007219 GO:0008483 GO:0008652 GO:0009058 GO:0016740 GO:0019550 GO:0019551 GO:0030170 GO:0031406 GO:0032869 GO:0042802 GO:0043648 GO:0043679 GO:0047801 GO:0051384 GO:0055089 GO:0070062 GO:0080130
180.060.3075.280.040.553li8A GO:0000155 GO:0000160 GO:0004871 GO:0005622 GO:0007165 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0023014


Consensus prediction of GO terms
 
Molecular Function GO:0046872 GO:0097159 GO:1901363
GO-Score 0.48 0.35 0.35
Biological Processes GO:0006283 GO:0000082 GO:0006298 GO:1900034 GO:0006293 GO:0006297 GO:0016925 GO:0000724 GO:0006296 GO:0036297 GO:0070987 GO:0000722 GO:1901796 GO:0006284 GO:0006294 GO:0042276 GO:0006261 GO:0006295 GO:0042769 GO:0071042 GO:0071038 GO:0071051 GO:0090502 GO:0000467 GO:0070481 GO:0071035 GO:0071028 GO:0071039 GO:0070651 GO:0070478 GO:1990074 GO:0008285 GO:0051301 GO:0019827 GO:0051306 GO:0010587
GO-Score 0.12 0.12 0.12 0.12 0.12 0.12 0.12 0.12 0.12 0.12 0.12 0.12 0.12 0.12 0.12 0.12 0.12 0.12 0.12 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.06 0.06 0.06 0.06 0.06 0.06
Cellular Component GO:0043231
GO-Score 0.36

(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.