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I-TASSER results for job id S775877

(Click on S775877_results.tar.bz2 to download the tarball file including all modeling results listed on this page. Click on Annotation of I-TASSER Output to read the instructions for how to interpret the results on this page. Model results are kept on the server for 60 days, there is no way to retrieve the modeling data older than 2 months)

  Submitted Sequence in FASTA format

>protein
VLLSDSNLDGTYWNYRSNNNNIGTPYKE

  Predicted Secondary Structure

Sequence                  20
                   |        
VLLSDSNLDGTYWNYRSNNNNIGTPYKE
PredictionCCCCCCCCCHHHHCCCCCCCCCCCCCCC
Conf.Score9144565563130000357866774769
H:Helix; S:Strand; C:Coil

  Predicted Solvent Accessibility

Sequence                  20
                   |        
VLLSDSNLDGTYWNYRSNNNNIGTPYKE
Prediction6324466244431423466643444368
Values range from 0 (buried residue) to 9 (highly exposed residue)

   Predicted normalized B-factor

(B-factor is a value to indicate the extent of the inherent thermal mobility of residues/atoms in proteins. In I-TASSER, this value is deduced from threading template proteins from the PDB in combination with the sequence profiles derived from sequence databases. The reported B-factor profile in the figure below corresponds to the normalized B-factor of the target protein, defined by B=(B'-u)/s, where B' is the raw B-factor value, u and s are respectively the mean and standard deviation of the raw B-factors along the sequence. Click here to read more about predicted normalized B-factor)


  Top 10 threading templates used by I-TASSER

(I-TASSER modeling starts from the structure templates identified by LOMETS from the PDB library. LOMETS is a meta-server threading approach containing multiple threading programs, where each threading program can generate tens of thousands of template alignments. I-TASSER only uses the templates of the highest significance in the threading alignments, the significance of which are measured by the Z-score, i.e. the difference between the raw and average scores in the unit of standard deviation. The templates in this section are the 10 best templates selected from the LOMETS threading programs. Usually, one template of the highest Z-score is selected from each threading program, where the threading programs are sorted by the average performance in the large-scale benchmark test experiments.)

Rank PDB
Hit		Iden1Iden2CovNorm.
Z-score		Download
Align.		                   20
                   |        
Sec.Str
Seq		CCCCCCCCCHHHHCCCCCCCCCCCCCCC
VLLSDSNLDGTYWNYRSNNNNIGTPYKE
16fjqA 0.70 0.71 0.96 0.32Download -LLKDSSLDKEYWNYRSNNNNVGSAYEE
28ofsA 0.50 0.50 1.00 1.21Download KLLTGSSLDGNYWNYKNKDSVIGSPYEN
36fjq 0.71 0.71 1.00 2.14Download VLLKDSSLDKEYWNYRSNNNNVGSAYEE
46fjq 0.71 0.71 1.00 1.49Download VLLKDSSLDKEYWNYRSNNNNVGSAYEE
52fmlA 0.12 0.14 0.93 1.24Download --FASKAEEKNYYERQASLAEFLTWYHQ
66fjq 0.70 0.71 0.96 2.32Download VLLKDSSLDKEYWNYRSNNNNVGSAYE-
76fjqA 0.71 0.71 1.00 0.68Download VLLKDSSLDKEYWNYRSNNNNVGSAYEE
81cl4A 0.26 0.25 0.96 1.07Download GLCPRCK-RGKHWECKSKTDNQGNPIPP
98ajyB 0.21 0.21 1.00 0.41Download DVNKDNMIDATYYAISSTRDDITLHQPL
106qpnA 0.50 0.54 1.00 1.63Download KLLTGSSLDGNYWNYKNKDSVIGSPYEN
(a)All the residues are colored in black; however, those residues in template which are identical to the residue in the query sequence are highlighted in color. Coloring scheme is based on the property of amino acids, where polar are brightly coloured while non-polar residues are colored in dark shade. (more about the colors used)
(b)Rank of templates represents the top ten threading templates used by I-TASSER.
(c)Ident1 is the percentage sequence identity of the templates in the threading aligned region with the query sequence.
(d)Ident2 is the percentage sequence identity of the whole template chains with query sequence.
(e)Cov represents the coverage of the threading alignment and is equal to the number of aligned residues divided by the length of query protein.
(f)Norm. Z-score is the normalized Z-score of the threading alignments. Alignment with a Normalized Z-score >1 mean a good alignment and vice versa.
(g)Download Align. provides the 3D structure of the aligned regions of the threading templates.
(h)The top 10 alignments reported above (in order of their ranking) are from the following threading programs:
       1: FFAS-3D   2: SPARKS-X   3: HHSEARCH2   4: HHSEARCH I   5: Neff-PPAS   6: HHSEARCH   7: pGenTHREADER   8: wdPPAS   9: PROSPECT2   10: SP3   

   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 a higher value signifies a model with a higher 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.)
    (By right-click on the images, you can export image file or change the configurations, e.g. modifying the background color or stopping the spin of your models)
  • Download Model 1
  • C-score=-1.17 (Read more about C-score)
  • Estimated TM-score = 0.57±0.15
  • Estimated RMSD = 3.7±2.6Å

  • Download Model 2
  • C-score = -1.75

  • Download Model 3
  • C-score = -2.88

  • Download Model 4
  • C-score = -3.40

  • Download Model 5
  • C-score = -1.82


  Proteins structurally close to the target in the 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.)


Top 10 Identified stuctural analogs in PDB

Click
to view		RankPDB HitTM-scoreRMSDaIDENaCovAlignment
11qiuA0.495 1.470.3931.000Download
26hcnA0.494 1.750.3931.000Download
31uxbA0.489 1.520.5711.000Download
46stuA0.483 1.580.5001.000Download
57op2A0.481 1.730.3211.000Download
62wstA0.476 1.660.2960.964Download
76fjnA0.460 1.470.3700.964Download
81p69A0.423 2.370.1791.000Download
96fjqA0.409 2.230.5560.929Download
107tbvA20.402 3.030.0361.000Download

(a)Query structure is shown in cartoon, while the structural analog is displayed using backbone trace.
(b)Ranking of proteins is based on TM-score of the structural alignment between the query structure and known structures in the PDB library.
(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 the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.


  Predicted function using COFACTOR and COACH

(This section reports biological annotations of the target protein by COFACTOR and COACH based on the I-TASSER structure prediction. While COFACTOR deduces protein functions (ligand-binding sites, EC and GO) using structure comparison and protein-protein networks, COACH is a meta-server approach that combines multiple function annotation results (on ligand-binding sites) from the COFACTOR, TM-SITE and S-SITE programs.)

  Ligand binding sites


Click
to view		RankC-scoreCluster
size		 PDB
Hit		 Lig
Name		 Download
Complex		 Ligand Binding Site Residues
10.19 6 1lwuC CA Rep, Mult 4,6,8,9,10
20.15 5 3wufA ZN Rep, Mult 9,11
30.06 2 2wguB 42D Rep, Mult 15,17,21
40.03 1 2bn0B BGC Rep, Mult 23,24
50.03 1 2hdqA C21 Rep, Mult 25,26,27


Download the residue-specific ligand binding probability, which is estimated by SVM.
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


Click
to view		RankCscoreECPDB
Hit		TM-scoreRMSDaIDENaCovEC NumberActive Site Residues
10.0992vavB0.329 3.000.0000.821 2.3.1.175  NA
20.0947mdhB0.357 3.200.1070.929 1.1.1.82  NA
30.0914mdhA0.353 3.450.1430.964 1.1.1.37  NA
40.0892mdhB0.323 3.120.0360.893 1.1.1.37  NA
50.0891civA0.247 2.930.0000.821 1.1.1.82  NA

 Click on the radio buttons to visualize predicted active site residues.
(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
Top 10 homologous GO templates in PDB 
RankCscoreGOTM-scoreRMSDaIDENaCovPDB HitAssociated GO Terms
1 0.190.4951 1.47 0.39 1.001qiuA GO:0007155 GO:0008037 GO:0019058 GO:0009405
2 0.160.4775 1.70 0.39 1.001knbA GO:0007155 GO:0008037 GO:0019058
3 0.150.3611 2.05 0.26 0.962wbvB GO:0007155 GO:0008037 GO:0019058
4 0.150.4557 1.55 0.57 1.001uxaA GO:0007155 GO:0008037 GO:0019058
5 0.150.4760 1.66 0.30 0.962wstA GO:0007155 GO:0008037 GO:0019058
6 0.110.2404 3.07 0.10 0.642fmlA GO:0016787
7 0.110.3774 2.14 0.23 0.933f0yG GO:0007155 GO:0008037 GO:0019058
8 0.100.3480 3.18 0.04 0.751z2cB GO:0003779 GO:0005488 GO:0016043 GO:0017048 GO:0030036
9 0.100.4235 2.37 0.18 1.001kacA GO:0007155 GO:0008037 GO:0019058
10 0.090.3571 3.20 0.11 0.937mdhB GO:0003824 GO:0005488 GO:0005975 GO:0006108 GO:0016491 GO:0016615 GO:0016616 GO:0044262 GO:0046554 GO:0055114


Consensus prediction of GO terms		 
Molecular Function None was predicted
Biological Process GO:0019058 GO:0007155 GO:0008037 GO:0051704
GO-Score 0.58 0.58 0.58 0.38
Cellular Component None was predicted

(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 S775877_results.tar.bz2 to download the tarball file including all modeling results listed on this page]


Please cite the following articles when you use the I-TASSER server:
  • Wei Zheng, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. Cell Reports Methods, 1: 100014 (2021).
  • Chengxin Zhang, Peter L. Freddolino, and Yang Zhang. COFACTOR: improved protein function prediction by combining structure, sequence and protein-protein interaction information. Nucleic Acids Research, 45: W291-299 (2017).
  • Jianyi Yang, Yang Zhang. I-TASSER server: new development for protein structure and function predictions, Nucleic Acids Research, 43: W174-W181, 2015.